WorldWideScience

Sample records for patent sequence databases

  1. The role of patent and non-patent databases in patent research in universities

    Science.gov (United States)

    Tolstaya, A. M.; Suslina, I. V.; Tolstaya, P. M.

    2017-01-01

    This studies deal with the description and systematization of the popular patent retrieval resources. The importance of the non-patent information when conducting patent research for the intellectual property created in educational and scientific activity of the university is highlighted. The differences in the patent and non-patent information are found out. Based on the databases` analysis the authors conducted the patent research on "Wireless endoscopic capsules" (development of the NRNU MEPhI). This study can be used to facilitate the university work on the new product development in order to improve the efficiency of the process of the commercialization of the intellectual activity results, including the entering the international market.

  2. A Database of EPO-Patenting Firms in Denmark

    DEFF Research Database (Denmark)

    Nielsen, Anders Østergaard

    1998-01-01

    The first section gives a brief introduction of the basic stages to be observed by the patent applicant from idea to the patent is granted. Section two presents three examples of how patents are registered in the online patent database INPADOC. Section three accounts for the initial analysis...... of the existing patent stock issued to firms with domicile in Denmark. Sections four and five report the basic characteristics of the EPO-patent sample and the procedures for linking the patent statistics to accounting data at the firm level, and finally they present the basic properties of the resulting database...

  3. Analysis of Patent Databases Using VxInsight

    Energy Technology Data Exchange (ETDEWEB)

    BOYACK,KEVIN W.; WYLIE,BRIAN N.; DAVIDSON,GEORGE S.; JOHNSON,DAVID K.

    2000-12-12

    We present the application of a new knowledge visualization tool, VxInsight, to the mapping and analysis of patent databases. Patent data are mined and placed in a database, relationships between the patents are identified, primarily using the citation and classification structures, then the patents are clustered using a proprietary force-directed placement algorithm. Related patents cluster together to produce a 3-D landscape view of the tens of thousands of patents. The user can navigate the landscape by zooming into or out of regions of interest. Querying the underlying database places a colored marker on each patent matching the query. Automatically generated labels, showing landscape content, update continually upon zooming. Optionally, citation links between patents may be shown on the landscape. The combination of these features enables powerful analyses of patent databases.

  4. Teaching Chemistry Students How To Use Patent Databases and Glean Patent Information

    Science.gov (United States)

    MacMillan, Margy; Shaw, Lawton

    2008-07-01

    Patent literature is an important source of chemical information that is often neglected by chemical educators. This paper describes an effort to teach chemistry students how to use patent databases to search for information on applied chemical technology related to the manufacture of industrial and specialty chemicals. Students in a second-year-level organic chemistry class were shown how to search patent literature as part of a group research paper assignment that involved determining the feasibility of starting an industrial chemical operation to manufacture a given industrial chemical. Students who were assigned high value or specialty chemicals were most likely to cite patent literature in their final papers. Students who were assigned plastics or bulk commodity chemicals were less likely to cite patents. It is suggested that students made choices about the usefulness of patent literature and that patents were most useful when current patents existed and provided the patent owner a competitive advantage. For plastics or commodity chemicals, manufacturing technologies tend to be mature and are well described by more accessible information sources. Suggestions are made for effective introduction of patent literature instruction into upper-level chemistry courses.

  5. Cleaning of scientific references in large patent databases using rule-based scoring and clustering

    NARCIS (Netherlands)

    Caron, Emiel

    2017-01-01

    Patent databases contain patent related data, organized in a relational data model, and are used to produce various patent statistics. These databases store raw data about scientific references cited by patents. For example, Patstat holds references to tens of millions of scientific journal

  6. Using Patent Classification to Discover Chemical Information in a Free Patent Database: Challenges and Opportunities

    Science.gov (United States)

    Ha¨rtinger, Stefan; Clarke, Nigel

    2016-01-01

    Developing skills for searching the patent literature is an essential element of chemical information literacy programs at the university level. The present article creates awareness of patents as a rich source of chemical information. Patent classification is introduced as a key-component in comprehensive search strategies. The free Espacenet…

  7. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  8. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  9. Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

    Science.gov (United States)

    Senger, Stefan; Bartek, Luca; Papadatos, George; Gaulton, Anna

    2015-12-01

    First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large corpus of documents is the automated extraction of chemical structures. A number of patent chemistry databases generated by using the latter approach are now available but little is known that can help to manage expectations when using them. This study aims to address this by comparing two such freely available sources, SureChEMBL and IBM SIIP (IBM Strategic Intellectual Property Insight Platform), with manually curated commercial databases. When looking at the percentage of chemical structures successfully extracted from a set of patents, using SciFinder as our reference, 59 and 51 % were also found in our comparison in SureChEMBL and IBM SIIP, respectively. When performing this comparison with compounds as starting point, i.e. establishing if for a list of compounds the databases provide the links between chemical structures and patents they appear in, we obtained similar results. SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys. In our comparison of automatically generated vs. manually curated patent chemistry databases, the former successfully provided approximately 60 % of links between chemical structure and patents. It needs to be stressed that only a very limited number of patents and compound-patent pairs were used for our comparison. Nevertheless, our results will hopefully help to manage expectations of users of patent chemistry databases of this type and provide a useful framework for more studies like ours as well as guide future developments of the workflows used for the automated extraction of chemical structures from patents. The challenges we have encountered

  10. International patent analysis of water source heat pump based on orbit database

    Science.gov (United States)

    Li, Na

    2018-02-01

    Using orbit database, this paper analysed the international patents of water source heat pump (WSHP) industry with patent analysis methods such as analysis of publication tendency, geographical distribution, technology leaders and top assignees. It is found that the beginning of the 21st century is a period of rapid growth of the patent application of WSHP. Germany and the United States had done researches and development of WSHP in an early time, but now Japan and China have become important countries of patent applications. China has been developing faster and faster in recent years, but the patents are concentrated in universities and urgent to be transferred. Through an objective analysis, this paper aims to provide appropriate decision references for the development of domestic WSHP industry.

  11. The International Nucleotide Sequence Database Collaboration.

    Science.gov (United States)

    Cochrane, Guy; Karsch-Mizrachi, Ilene; Nakamura, Yasukazu

    2011-01-01

    Under the International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org), globally comprehensive public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data formats and conventions that enable consistent data submission to their databases and support regular data exchange around the globe. Clearly defined policy and governance in relation to free access to data and relationships with journal publishers have positioned INSDC databases as a key provider of the scientific record and a core foundation for the global bioinformatics data infrastructure. While growth in sequence data volumes comes no longer as a surprise to INSDC partners, the uptake of next-generation sequencing technology by mainstream science that we have witnessed in recent years brings a step-change to growth, necessarily making a clear mark on INSDC strategy. In this article, we introduce the INSDC, outline data growth patterns and comment on the challenges of increased growth.

  12. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  13. Winnowing sequences from a database search.

    Science.gov (United States)

    Berman, P; Zhang, Z; Wolf, Y I; Koonin, E V; Miller, W

    2000-01-01

    In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy." An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

  14. Quality Control of the Traditional Patent Medicine Yimu Wan Based on SMRT Sequencing and DNA Barcoding

    Science.gov (United States)

    Jia, Jing; Xu, Zhichao; Xin, Tianyi; Shi, Linchun; Song, Jingyuan

    2017-01-01

    Substandard traditional patent medicines may lead to global safety-related issues. Protecting consumers from the health risks associated with the integrity and authenticity of herbal preparations is of great concern. Of particular concern is quality control for traditional patent medicines. Here, we establish an effective approach for verifying the biological composition of traditional patent medicines based on single-molecule real-time (SMRT) sequencing and DNA barcoding. Yimu Wan (YMW), a classical herbal prescription recorded in the Chinese Pharmacopoeia, was chosen to test the method. Two reference YMW samples were used to establish a standard method for analysis, which was then applied to three different batches of commercial YMW samples. A total of 3703 and 4810 circular-consensus sequencing (CCS) reads from two reference and three commercial YMW samples were mapped to the ITS2 and psbA-trnH regions, respectively. Moreover, comparison of intraspecific genetic distances based on SMRT sequencing data with reference data from Sanger sequencing revealed an ITS2 and psbA-trnH intergenic spacer that exhibited high intraspecific divergence, with the sites of variation showing significant differences within species. Using the CCS strategy for SMRT sequencing analysis was adequate to guarantee the accuracy of identification. This study demonstrates the application of SMRT sequencing to detect the biological ingredients of herbal preparations. SMRT sequencing provides an affordable way to monitor the legality and safety of traditional patent medicines. PMID:28620408

  15. MIPS: a database for protein sequences and complete genomes.

    Science.gov (United States)

    Mewes, H W; Hani, J; Pfeiffer, F; Frishman, D

    1998-01-01

    The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). Through its WWW server (http://www.mips.biochem.mpg.de ) MIPS provides access to a variety of generic databases, including a database of protein families as well as automatically generated data by the systematic application of sequence analysis algorithms. The yeast genome sequence and its related information was also compiled on CD-ROM to provide dynamic interactive access to the 16 chromosomes of the first eukaryotic genome unraveled. PMID:9399795

  16. Study of event sequence database for a nuclear power domain

    International Nuclear Information System (INIS)

    Kusumi, Yoshiaki

    1998-01-01

    A retrieval engine developed to extract event sequences from an accident information database using a time series retrieval formula expressed with ordered retrieval terms is explored. This engine outputs not only a sequence which completely matches with a time series retrieval formula, but also sequence which approximately matches the formula (fuzzy retrieval). An event sequence database in which records consist of three ordered parameters, namely the causal event, the process and result. Then the database is used to assess the feasibility of this engine and favorable results were obtained. (author)

  17. ZINClick: a database of 16 million novel, patentable, and readily synthesizable 1,4-disubstituted triazoles.

    Science.gov (United States)

    Massarotti, Alberto; Brunco, Angelo; Sorba, Giovanni; Tron, Gian Cesare

    2014-02-24

    Since Professors Sharpless, Finn, and Kolb first introduced the concept of "click reactions" in 2001 as powerful tools in drug discovery, 1,4-disubstituted-1,2,3-triazoles have become important in medicinal chemistry due to the simultaneous discovery by Sharpless, Fokin, and Meldal of a perfect click 1,3-dipolar cycloaddition reaction between azides and alkynes catalyzed by copper salts. Because of their chemical features, these triazoles are proposed to be aggressive pharmacophores that participate in drug-receptor interactions while maintaining an excellent chemical and metabolic profile. Surprisingly, no virtual libraries of 1,4-disubstituted-1,2,3-triazoles have been generated for the systematic investigation of the click-chemical space. In this manuscript, a database of triazoles called ZINClick is generated from literature-reported alkynes and azides that can be synthesized within three steps from commercially available products. This combinatorial database contains over 16 million 1,4-disubstituted-1,2,3-triazoles that are easily synthesizable, new, and patentable! The structural diversity of ZINClick ( http://www.symech.it/ZINClick ) will be explored. ZINClick will also be compared to other available databases, and its application during the design of novel bioactive molecules containing triazole nuclei will be discussed.

  18. MIPS: a database for genomes and protein sequences.

    Science.gov (United States)

    Mewes, H W; Frishman, D; Güldener, U; Mannhaupt, G; Mayer, K; Mokrejs, M; Morgenstern, B; Münsterkötter, M; Rudd, S; Weil, B

    2002-01-01

    The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

  19. International patent applications for non-injectable naloxone for opioid overdose reversal: Exploratory search and retrieve analysis of the PatentScope database.

    Science.gov (United States)

    McDonald, Rebecca; Danielsson Glende, Øyvind; Dale, Ola; Strang, John

    2018-02-01

    Non-injectable naloxone formulations are being developed for opioid overdose reversal, but only limited data have been published in the peer-reviewed domain. Through examination of a hitherto-unsearched database, we expand public knowledge of non-injectable formulations, tracing their development and novelty, with the aim to describe and compare their pharmacokinetic properties. (i) The PatentScope database of the World Intellectual Property Organization was searched for relevant English-language patent applications; (ii) Pharmacokinetic data were extracted, collated and analysed; (iii) PubMed was searched using Boolean search query '(nasal OR intranasal OR nose OR buccal OR sublingual) AND naloxone AND pharmacokinetics'. Five hundred and twenty-two PatentScope and 56 PubMed records were identified: three published international patent applications and five peer-reviewed papers were eligible. Pharmacokinetic data were available for intranasal, sublingual, and reference routes. Highly concentrated formulations (10-40 mg mL -1 ) had been developed and tested. Sublingual bioavailability was very low (1%; relative to intravenous). Non-concentrated intranasal spray (1 mg mL -1 ; 1 mL per nostril) had low bioavailability (11%). Concentrated intranasal formulations (≥10 mg mL -1 ) had bioavailability of 21-42% (relative to intravenous) and 26-57% (relative to intramuscular), with peak concentrations (dose-adjusted C max  = 0.8-1.7 ng mL -1 ) reached in 19-30 min (t max ). Exploratory analysis identified intranasal bioavailability as associated positively with dose and negatively with volume. We find consistent direction of development of intranasal sprays to high-concentration, low-volume formulations with bioavailability in the 20-60% range. These have potential to deliver a therapeutic dose in 0.1 mL volume. [McDonald R, Danielsson Glende Ø, Dale O, Strang J. International patent applications for non-injectable naloxone for opioid overdose reversal

  20. Polymorphism Sequence - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us JSNP Polymorphism Sequence Data detail Data name Polymorphism Sequence DOI 10.18908/lsdba.nb...dc00114-001 Description of data contents Information on polymorphisms (SNPs and insertions/deletions) and th...se Name database name JSNP_SNP: single nucleotide polymorphism JSNP_InsDel_IND: insertion/deletion JSNP_InsD...ved allele observed 3' Flanking Sequence 3' flanking sequence Offset in Flanking Sequence position of the polymorphism...uence Accession No. accession No. of the sequence for polymorphism screening Offset in Record position of the polymorphism

  1. Using SQL Databases for Sequence Similarity Searching and Analysis.

    Science.gov (United States)

    Pearson, William R; Mackey, Aaron J

    2017-09-13

    Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  2. Specialized microbial databases for inductive exploration of microbial genome sequences

    Directory of Open Access Journals (Sweden)

    Cabau Cédric

    2005-02-01

    Full Text Available Abstract Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore http://bioinfo.hku.hk/genochore.html, a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis associated to related organisms for comparison.

  3. Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

    Directory of Open Access Journals (Sweden)

    Qingyu Chen

    Full Text Available First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases.We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material.

  4. Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

    Science.gov (United States)

    Chen, Qingyu; Zobel, Justin; Zhang, Xiuzhen; Verspoor, Karin

    2016-01-01

    First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases. We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material.

  5. Sequence modelling and an extensible data model for genomic database

    Energy Technology Data Exchange (ETDEWEB)

    Li, Peter Wei-Der [California Univ., San Francisco, CA (United States); Univ. of California, Berkeley, CA (United States)

    1992-01-01

    The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS`s do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the ``Extensible Object Model``, to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

  6. Sequence modelling and an extensible data model for genomic database

    Energy Technology Data Exchange (ETDEWEB)

    Li, Peter Wei-Der (California Univ., San Francisco, CA (United States) Lawrence Berkeley Lab., CA (United States))

    1992-01-01

    The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS's do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data model that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the Extensible Object Model'', to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.

  7. International nanotechnology development in 2003: Country, institution, and technology field analysis based on USPTO patent database

    International Nuclear Information System (INIS)

    Huang Zan; Chen Hsinchun; Chen Zhikai; Roco, Mihail C.

    2004-01-01

    Nanoscale science and engineering (NSE) have seen rapid growth and expansion in new areas in recent years. This paper provides an international patent analysis using the U.S. Patent and Trademark Office (USPTO) data searched by keywords of the entire text: title, abstract, claims, and specifications. A fraction of these patents fully satisfy the National Nanotechnology Initiative definition of nanotechnology (which requires exploiting specific phenomena and direct manipulation at the nanoscale), while others only make use of NSE tools and methods of investigation. In previous work we proposed an integrated patent analysis and visualization framework of patent content mapping for the NSE field and of knowledge flow pattern identification until 2002. In this paper, the results are updated for 2003, and the new trends are presented

  8. International nanotechnology development in 2003: Country, institution, and technology field analysis based on USPTO patent database

    Science.gov (United States)

    Huang, Zan; Chen, Hsinchun; Chen, Zhi-kai; Roco, Mihail C.

    2004-08-01

    Nanoscale science and engineering (NSE) have seen rapid growth and expansion in new areas in recent years. This paper provides an international patent analysis using the U.S. Patent and Trademark Office (USPTO) data searched by keywords of the entire text: title, abstract, claims, and specifications. A fraction of these patents fully satisfy the National Nanotechnology Initiative definition of nanotechnology (which requires exploiting specific phenomena and direct manipulation at the nanoscale), while others only make use of NSE tools and methods of investigation. In previous work we proposed an integrated patent analysis and visualization framework of patent content mapping for the NSE field and of knowledge flow pattern identification until 2002. In this paper, the results are updated for 2003, and the new trends are presented.

  9. [Method of traditional Chinese medicine formula design based on 3D-database pharmacophore search and patent retrieval].

    Science.gov (United States)

    He, Yu-su; Sun, Zhi-yi; Zhang, Yan-ling

    2014-11-01

    By using the pharmacophore model of mineralocorticoid receptor antagonists as a starting point, the experiment stud- ies the method of traditional Chinese medicine formula design for anti-hypertensive. Pharmacophore models were generated by 3D-QSAR pharmacophore (Hypogen) program of the DS3.5, based on the training set composed of 33 mineralocorticoid receptor antagonists. The best pharmacophore model consisted of two Hydrogen-bond acceptors, three Hydrophobic and four excluded volumes. Its correlation coefficient of training set and test set, N, and CAI value were 0.9534, 0.6748, 2.878, and 1.119. According to the database screening, 1700 active compounds from 86 source plant were obtained. Because of lacking of available anti-hypertensive medi cation strategy in traditional theory, this article takes advantage of patent retrieval in world traditional medicine patent database, in order to design drug formula. Finally, two formulae was obtained for antihypertensive.

  10. Construction of an integrated database to support genomic sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, W.; Overbeek, R.

    1994-11-01

    The central goal of this project is to develop an integrated database to support comparative analysis of genomes including DNA sequence data, protein sequence data, gene expression data and metabolism data. In developing the logic-based system GenoBase, a broader integration of available data was achieved due to assistance from collaborators. Current goals are to easily include new forms of data as they become available and to easily navigate through the ensemble of objects described within the database. This report comments on progress made in these areas.

  11. BIOPEP database and other programs for processing bioactive peptide sequences.

    Science.gov (United States)

    Minkiewicz, Piotr; Dziuba, Jerzy; Iwaniak, Anna; Dziuba, Marta; Darewicz, Małgorzata

    2008-01-01

    This review presents the potential for application of computational tools in peptide science based on a sample BIOPEP database and program as well as other programs and databases available via the World Wide Web. The BIOPEP application contains a database of biologically active peptide sequences and a program enabling construction of profiles of the potential biological activity of protein fragments, calculation of quantitative descriptors as measures of the value of proteins as potential precursors of bioactive peptides, and prediction of bonds susceptible to hydrolysis by endopeptidases in a protein chain. Other bioactive and allergenic peptide sequence databases are also presented. Programs enabling the construction of binary and multiple alignments between peptide sequences, the construction of sequence motifs attributed to a given type of bioactivity, searching for potential precursors of bioactive peptides, and the prediction of sites susceptible to proteolytic cleavage in protein chains are available via the Internet as are other approaches concerning secondary structure prediction and calculation of physicochemical features based on amino acid sequence. Programs for prediction of allergenic and toxic properties have also been developed. This review explores the possibilities of cooperation between various programs.

  12. The development and application of a Mycoplasma gallisepticum sequence database.

    Science.gov (United States)

    Armour, Natalie K; Laibinis, Victoria A; Collett, Stephen R; Ferguson-Noel, Naola

    2013-01-01

    Molecular analysis was conducted on 36 Mycoplasma gallisepticum DNA extracts from tracheal swab samples of commercial poultry in seven South African provinces between 2009 and 2012. Twelve unique M. gallisepticum genotypes were identified by polymerase chain reaction and sequence analysis of the 16S-23S rRNA intergenic spacer region (IGSR), M. gallisepticum cytadhesin 2 (mgc2), MGA_0319 and gapA genetic regions. The DNA sequences of these genotypes were distinct from those of M. gallisepticum isolates in a database composed of sequences from other countries, vaccine and reference strains. The most prevalent genotype (SA-WT#7) was detected in samples from commercial broilers, broiler breeders and layers in five provinces. South African M. gallisepticum sequences were more similar to those of the live vaccines commercially available in South Africa, but were distinct from that of F strain vaccine, which is not registered for use in South Africa. The IGSR, mgc2 or MGA_0319 sequences of three South African genotypes were identical to those of the ts-11 vaccine strain, necessitating a combination of mgc2 and IGSR targeted sequencing to differentiate South African wild-type genotypes from ts-11 vaccine. To identify and differentiate all 12 wild-types, mgc2, IGSR and MGA_0319 sequencing was required. Sequencing of gapA was least effective at strain differentiation. This research serves as a model for the development of an M. gallisepticum sequence database, and illustrates its application to characterize M. gallisepticum genotypes, select diagnostic tests and better understand the epidemiology of M. gallisepticum.

  13. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Science.gov (United States)

    Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

    2011-01-01

    Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  14. Comprehensive Genetic Database of Expressed Sequence Tags for Coccolithophorids

    Science.gov (United States)

    Ranji, Mohammad; Hadaegh, Ahmad R.

    Coccolithophorids are unicellular, marine, golden-brown, single-celled algae (Haptophyta) commonly found in near-surface waters in patchy distributions. They belong to the Phytoplankton family that is known to be responsible for much of the earth reproduction. Phytoplankton, just like plants live based on the energy obtained by Photosynthesis which produces oxygen. Substantial amount of oxygen in the earth's atmosphere is produced by Phytoplankton through Photosynthesis. The single-celled Emiliana Huxleyi is the most commonly known specie of Coccolithophorids and is known for extracting bicarbonate (HCO3) from its environment and producing calcium carbonate to form Coccoliths. Coccolithophorids are one of the world's primary producers, contributing about 15% of the average oceanic phytoplankton biomass to the oceans. They produce elaborate, minute calcite platelets (Coccoliths), covering the cell to form a Coccosphere and supplying up to 60% of the bulk pelagic calcite deposited on the sea floors. In order to understand the genetics of Coccolithophorid and the complexities of their biochemical reactions, we decided to build a database to store a complete profile of these organisms' genomes. Although a variety of such databases currently exist, (http://www.geneservice.co.uk/home/) none have yet been developed to comprehensively address the sequencing efforts underway by the Coccolithophorid research community. This database is called CocooExpress and is available to public (http://bioinfo.csusm.edu) for both data queries and sequence contribution.

  15. MSDB: A Comprehensive Database of Simple Sequence Repeats.

    Science.gov (United States)

    Avvaru, Akshay Kumar; Saxena, Saketh; Sowpati, Divya Tej; Mishra, Rakesh Kumar

    2017-06-01

    Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

    Science.gov (United States)

    Mackey, Aaron J; Pearson, William R

    2004-10-01

    Relational databases are designed to integrate diverse types of information and manage large sets of search results, greatly simplifying genome-scale analyses. Relational databases are essential for management and analysis of large-scale sequence analyses, and can also be used to improve the statistical significance of similarity searches by focusing on subsets of sequence libraries most likely to contain homologs. This unit describes using relational databases to improve the efficiency of sequence similarity searching and to demonstrate various large-scale genomic analyses of homology-related data. This unit describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. These include basic use of the database to generate a novel sequence library subset, how to extend and use seqdb_demo for the storage of sequence similarity search results and making use of various kinds of stored search results to address aspects of comparative genomic analysis.

  17. cDNA sequence quality data - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Budding yeast cDNA sequencing project cDNA sequence quality data Data detail Data name cDNA sequence quality... data DOI 10.18908/lsdba.nbdc00838-003 Description of data contents Phred's quality score. P...tion Download License Update History of This Database Site Policy | Contact Us cDNA sequence quality

  18. MIPS: a database for protein sequences, homology data and yeast genome information.

    Science.gov (United States)

    Mewes, H W; Albermann, K; Heumann, K; Liebl, S; Pfeiffer, F

    1997-01-01

    The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request. PMID:9016498

  19. Searching bioremediation patents through Cooperative Patent Classification (CPC).

    Science.gov (United States)

    Prasad, Rajendra

    2016-03-01

    Patent classification systems have traditionally evolved independently at each patent jurisdiction to classify patents handled by their examiners to be able to search previous patents while dealing with new patent applications. As patent databases maintained by them went online for free access to public as also for global search of prior art by examiners, the need arose for a common platform and uniform structure of patent databases. The diversity of different classification, however, posed problems of integrating and searching relevant patents across patent jurisdictions. To address this problem of comparability of data from different sources and searching patents, WIPO in the recent past developed what is known as International Patent Classification (IPC) system which most countries readily adopted to code their patents with IPC codes along with their own codes. The Cooperative Patent Classification (CPC) is the latest patent classification system based on IPC/European Classification (ECLA) system, developed by the European Patent Office (EPO) and the United States Patent and Trademark Office (USPTO) which is likely to become a global standard. This paper discusses this new classification system with reference to patents on bioremediation.

  20. Database-driven primary analysis of raw sequencing data

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to methods for identifying the source of a biological sequence containing sample from raw sequencing reads. The method may be used to identify the source of unknown DNA and can be used for diagnostic, biodefense, food safety and quality, and hygiene applications...

  1. AgdbNet – antigen sequence database software for bacterial typing

    Directory of Open Access Journals (Sweden)

    Maiden Martin CJ

    2006-06-01

    Full Text Available Abstract Background Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. Results Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. Conclusion The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated.

  2. Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.

    Science.gov (United States)

    Bousfield, David; McEntyre, Johanna; Velankar, Sameer; Papadatos, George; Bateman, Alex; Cochrane, Guy; Kim, Jee-Hyub; Graef, Florian; Vartak, Vid; Alako, Blaise; Blomberg, Niklas

    2016-01-01

    Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method development and to derive new scientific insights. Indicators that estimate the extent and utility of such secondary use of research data need to reflect this complex and highly variable data usage. By linking open access scientific literature, via Europe PubMedCentral, to the metadata in biological data resources we separate data citations associated with a deposition statement from citations that capture the subsequent, long-term, reuse of data in academia and industry.  We extend this analysis to begin to investigate citations of biomolecular resources in patent documents. We find citations in more than 8,000 patents from 2014, demonstrating substantial use and an important role for data resources in defining biological concepts in granted patents to both academic and industrial innovators. Combined together our results indicate that the citation patterns in biomedical literature and patents vary, not only due to citation practice but also according to the data resource cited. The results guard against the use of simple metrics such as citation counts and show that indicators of data use must not only take into account citations within the biomedical literature but also include reuse of data in industry and other parts of society by including patents and other scientific and technical documents such as guidelines, reports and grant applications.

  3. Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources

    Science.gov (United States)

    Bousfield, David; McEntyre, Johanna; Velankar, Sameer; Papadatos, George; Bateman, Alex; Cochrane, Guy; Kim, Jee-Hyub; Graef, Florian; Vartak, Vid; Alako, Blaise; Blomberg, Niklas

    2016-01-01

    Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method development and to derive new scientific insights. Indicators that estimate the extent and utility of such secondary use of research data need to reflect this complex and highly variable data usage. By linking open access scientific literature, via Europe PubMedCentral, to the metadata in biological data resources we separate data citations associated with a deposition statement from citations that capture the subsequent, long-term, reuse of data in academia and industry.  We extend this analysis to begin to investigate citations of biomolecular resources in patent documents. We find citations in more than 8,000 patents from 2014, demonstrating substantial use and an important role for data resources in defining biological concepts in granted patents to both academic and industrial innovators. Combined together our results indicate that the citation patterns in biomedical literature and patents vary, not only due to citation practice but also according to the data resource cited. The results guard against the use of simple metrics such as citation counts and show that indicators of data use must not only take into account citations within the biomedical literature but also include reuse of data in industry and other parts of society by including patents and other scientific and technical documents such as guidelines, reports and grant applications. PMID:27092246

  4. Taxonomic evaluation of selected Ganoderma species and database sequence validation

    Directory of Open Access Journals (Sweden)

    Suldbold Jargalmaa

    2017-07-01

    Full Text Available Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily on DNA sequencing using BLAST searches, which are only reliable if the GenBank submissions are accurately labeled. In this study, we examined 113 specimens collected from 1969 to 2016 from various regions in Korea using morphological features and multigene analysis (internal transcribed spacer, translation elongation factor 1-α, and the second largest subunit of RNA polymerase II. These specimens were identified as four Ganoderma species: G. sichuanense, G. cf. adspersum, G. cf. applanatum, and G. cf. gibbosum. With the exception of G. sichuanense, these species were difficult to distinguish based solely on morphological features. However, phylogenetic analysis at three different loci yielded concordant phylogenetic information, and supported the four species distinctions with high bootstrap support. A survey of over 600 Ganoderma sequences available on GenBank revealed that 65% of sequences were either misidentified or ambiguously labeled. Here, we suggest corrected annotations for GenBank sequences based on our phylogenetic validation and provide updated global distribution patterns for these Ganoderma species.

  5. Taxonomic evaluation of selected Ganoderma species and database sequence validation

    Science.gov (United States)

    Jargalmaa, Suldbold; Eimes, John A.; Park, Myung Soo; Park, Jae Young; Oh, Seung-Yoon

    2017-01-01

    Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily on DNA sequencing using BLAST searches, which are only reliable if the GenBank submissions are accurately labeled. In this study, we examined 113 specimens collected from 1969 to 2016 from various regions in Korea using morphological features and multigene analysis (internal transcribed spacer, translation elongation factor 1-α, and the second largest subunit of RNA polymerase II). These specimens were identified as four Ganoderma species: G. sichuanense, G. cf. adspersum, G. cf. applanatum, and G. cf. gibbosum. With the exception of G. sichuanense, these species were difficult to distinguish based solely on morphological features. However, phylogenetic analysis at three different loci yielded concordant phylogenetic information, and supported the four species distinctions with high bootstrap support. A survey of over 600 Ganoderma sequences available on GenBank revealed that 65% of sequences were either misidentified or ambiguously labeled. Here, we suggest corrected annotations for GenBank sequences based on our phylogenetic validation and provide updated global distribution patterns for these Ganoderma species. PMID:28761785

  6. License - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Budding yeast cDNA sequencing project License to Use This Database Last updated : 2010/02/15 You may use this databas...ional License described below. The Standard License specifies the license terms regarding the use of this database... and the requirements you must follow in using this database. The Additiona...n the Standard License. Standard License The Standard License for this database is the license specified in ...the Creative Commons Attribution-Share Alike 2.1 Japan . If you use data from this database

  7. The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences

    Directory of Open Access Journals (Sweden)

    Gibbs Mark J

    2008-02-01

    Full Text Available Abstract Background Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. Results The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. Conclusion VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

  8. The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.

    Science.gov (United States)

    Fourment, Mathieu; Gibbs, Mark J

    2008-02-05

    Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

  9. PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species

    Directory of Open Access Journals (Sweden)

    Lalucat Jorge

    2010-04-01

    Full Text Available Abstract Background The genus Pseudomonas comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution; the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects. Description The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of Pseudomonas species. The core of the database is composed of selected gene sequences from all Pseudomonas type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA procedures, for the identification and characterisation of any Pseudomonas bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI. Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results. Conclusions The PseudoMLSA database amasses strains and sequence information of validly described Pseudomonas species, and allows free querying of the database via a user-friendly, web-based interface available at http://www.uib.es/microbiologiaBD/Welcome.html. The web-based platform enables easy retrieval at strain or gene sequence information level; including references to published peer

  10. Quality standards for DNA sequence variation databases to improve clinical management under development in Australia

    Directory of Open Access Journals (Sweden)

    B. Bennetts

    2014-09-01

    Full Text Available Despite the routine nature of comparing sequence variations identified during clinical testing to database records, few databases meet quality requirements for clinical diagnostics. To address this issue, The Royal College of Pathologists of Australasia (RCPA in collaboration with the Human Genetics Society of Australasia (HGSA, and the Human Variome Project (HVP is developing standards for DNA sequence variation databases intended for use in the Australian clinical environment. The outputs of this project will be promoted to other health systems and accreditation bodies by the Human Variome Project to support the development of similar frameworks in other jurisdictions.

  11. The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

    Energy Technology Data Exchange (ETDEWEB)

    Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi; Wong, Mike; Stillman, Jonathon H.

    2010-01-27

    Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in

  12. Organizing, exploring, and analyzing antibody sequence data: the case for relational-database managers.

    Science.gov (United States)

    Owens, John

    2009-01-01

    Technological advances in the acquisition of DNA and protein sequence information and the resulting onrush of data can quickly overwhelm the scientist unprepared for the volume of information that must be evaluated and carefully dissected to discover its significance. Few laboratories have the luxury of dedicated personnel to organize, analyze, or consistently record a mix of arriving sequence data. A methodology based on a modern relational-database manager is presented that is both a natural storage vessel for antibody sequence information and a conduit for organizing and exploring sequence data and accompanying annotation text. The expertise necessary to implement such a plan is equal to that required by electronic word processors or spreadsheet applications. Antibody sequence projects maintained as independent databases are selectively unified by the relational-database manager into larger database families that contribute to local analyses, reports, interactive HTML pages, or exported to facilities dedicated to sophisticated sequence analysis techniques. Database files are transposable among current versions of Microsoft, Macintosh, and UNIX operating systems.

  13. Combining next-generation sequencing and online databases for microsatellite development in non-model organisms.

    Science.gov (United States)

    Rico, Ciro; Normandeau, Eric; Dion-Côté, Anne-Marie; Rico, María Inés; Côté, Guillaume; Bernatchez, Louis

    2013-12-03

    Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes.

  14. Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

    Science.gov (United States)

    Truong, Kevin; Ikura, Mitsuhiko

    2003-05-06

    Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

  15. muBLASTP: database-indexed protein sequence search on multicore CPUs.

    Science.gov (United States)

    Zhang, Jing; Misra, Sanchit; Wang, Hao; Feng, Wu-Chun

    2016-11-04

    The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e.g., MegaBLAST. Due to different challenges and characteristics between query indexing and database indexing, the existing techniques for query-indexed search cannot be used into database indexed search. muBLASTP, a novel database-indexed BLAST for protein sequence search, delivers identical hits returned to NCBI BLAST. On Intel Haswell multicore CPUs, for a single query, the single-threaded muBLASTP achieves up to a 4.41-fold speedup for alignment stages, and up to a 1.75-fold end-to-end speedup over single-threaded NCBI BLAST. For a batch of queries, the multithreaded muBLASTP achieves up to a 5.7-fold speedups for alignment stages, and up to a 4.56-fold end-to-end speedup over multithreaded NCBI BLAST. With a newly designed index structure for protein database and associated optimizations in BLASTP algorithm, we re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory footprint for the database index.

  16. SinEx DB: a database for single exon coding sequences in mammalian genomes.

    Science.gov (United States)

    Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

    2016-01-01

    Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl. © The Author(s) 2016. Published by Oxford University Press.

  17. Intelligent Access to Sequence and Structure Databases (IASSD) - an interface for accessing information from major web databases.

    Science.gov (United States)

    Ganguli, Sayak; Gupta, Manoj Kumar; Basu, Protip; Banik, Rahul; Singh, Pankaj Kumar; Vishal, Vineet; Bera, Abhisek Ranjan; Chakraborty, Hirak Jyoti; Das, Sasti Gopal

    2014-01-01

    With the advent of age of big data and advances in high throughput technology accessing data has become one of the most important step in the entire knowledge discovery process. Most users are not able to decipher the query result that is obtained when non specific keywords or a combination of keywords are used. Intelligent access to sequence and structure databases (IASSD) is a desktop application for windows operating system. It is written in Java and utilizes the web service description language (wsdl) files and Jar files of E-utilities of various databases such as National Centre for Biotechnology Information (NCBI) and Protein Data Bank (PDB). Apart from that IASSD allows the user to view protein structure using a JMOL application which supports conditional editing. The Jar file is freely available through e-mail from the corresponding author.

  18. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

    Science.gov (United States)

    Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

    2011-01-01

    PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

  19. Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

    Science.gov (United States)

    Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

    2016-01-01

    Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

  20. EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes

    Directory of Open Access Journals (Sweden)

    Grover Atul

    2007-07-01

    Full Text Available Abstract Background Microsatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology. Existing microsatellite databases are of limited utility for experimental and computational biologists with regard to their content and information output. EuMicroSatdb (Eukaryotic MicroSatellite database http://ipu.ac.in/usbt/EuMicroSatdb.htm is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes. Description A user friendly web interface has been developed for microsatellite data retrieval using Active Server Pages (ASP. The backend database codes for data extraction and assembly have been written using Perl based scripts and C++. Precise need based microsatellites data retrieval is possible using different input parameters like microsatellite type (simple perfect or compound perfect, repeat unit length (mono- to hexa-nucleotide, repeat number, microsatellite length and chromosomal location in the genome. Furthermore, information about clustering of different microsatellites in the genome can also be retrieved. Finally, to facilitate primer designing for PCR amplification of any desired microsatellite locus, 200 bp upstream and downstream sequences are provided. Conclusion The database allows easy systematic retrieval of comprehensive information about simple and compound microsatellites, microsatellite clusters and their locus coordinates in 31 sequenced eukaryotic genomes. The information content of the database is useful in different areas of research like gene tagging, genome mapping, population genetics, germplasm characterization and in understanding microsatellite dynamics in eukaryotic genomes.

  1. Developing a Systematic Patent Search Training Program

    Science.gov (United States)

    Zhang, Li

    2009-01-01

    This study aims to develop a systematic patent training program using patent analysis and citation analysis techniques applied to patents held by the University of Saskatchewan. The results indicate that the target audience will be researchers in life sciences, and aggregated patent database searching and advanced search techniques should be…

  2. Estimating the annotation error rate of curated GO database sequence annotations

    Directory of Open Access Journals (Sweden)

    Brown Alfred L

    2007-05-01

    Full Text Available Abstract Background Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO sequence database (GOSeqLite. This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences. Results We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006 at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS had an estimated error rate of 49%. Conclusion While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.

  3. Online Patent Searching: The Realities.

    Science.gov (United States)

    Kaback, Stuart M.

    1983-01-01

    Considers patent subject searching capabilities of major online databases, noting patent claims, "deep-indexed" files, test searches, retrieval of related references, multi-database searching, improvements needed in indexing of chemical structures, full text searching, improvements needed in handling numerical data, and augmenting a…

  4. mESAdb: microRNA expression and sequence analysis database.

    Science.gov (United States)

    Kaya, Koray D; Karakülah, Gökhan; Yakicier, Cengiz M; Acar, Aybar C; Konu, Ozlen

    2011-01-01

    microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.

  5. An Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

    Science.gov (United States)

    Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated wi...

  6. PATACSDB—the database of polyA translational attenuators in coding sequences

    Directory of Open Access Journals (Sweden)

    Malgorzata Habich

    2016-02-01

    Full Text Available Recent additions to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA tracks encoding for poly-lysine runs in protein sequences. Such tracks stall the translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such, they substantially influence the stability of mRNA and the amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance; this makes each of these sequences a potentially interesting case study for the effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present PATACSDB, a resource that contain a comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on the Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A’s allowing for one mismatched base. The PATACSDB database is accessible at: http://sysbio.ibb.waw.pl/patacsdb. The source code is available at http://github.com/habich/PATACSDB, and it includes the scripts with which the database can be recreated.

  7. CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

    Directory of Open Access Journals (Sweden)

    Maskell Douglas L

    2009-05-01

    Full Text Available Abstract Background The Smith-Waterman algorithm is one of the most widely used tools for searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith-Waterman algorithm is computationally demanding, which is further compounded by the exponential growth of sequence databases. The recent emergence of many-core architectures, and their associated programming interfaces, provides an opportunity to accelerate sequence database searches using commonly available and inexpensive hardware. Findings Our CUDASW++ implementation (benchmarked on a single-GPU NVIDIA GeForce GTX 280 graphics card and a dual-GPU GeForce GTX 295 graphics card provides a significant performance improvement compared to other publicly available implementations, such as SWPS3, CBESW, SW-CUDA, and NCBI-BLAST. CUDASW++ supports query sequences of length up to 59K and for query sequences ranging in length from 144 to 5,478 in Swiss-Prot release 56.6, the single-GPU version achieves an average performance of 9.509 GCUPS with a lowest performance of 9.039 GCUPS and a highest performance of 9.660 GCUPS, and the dual-GPU version achieves an average performance of 14.484 GCUPS with a lowest performance of 10.660 GCUPS and a highest performance of 16.087 GCUPS. Conclusion CUDASW++ is publicly available open-source software. It provides a significant performance improvement for Smith-Waterman-based protein sequence database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs.

  8. Data anonymization patent landscape

    Directory of Open Access Journals (Sweden)

    Mirjana Pejić Bach

    2017-01-01

    Full Text Available The omnipresent, unstoppable increase in digital data has led to a greater understanding of the importance of data privacy. Different approaches are used to implement data privacy. The goal of this paper is to develop a data anonymization patent landscape, by determining the following: (i the trend in data anonymization patenting, (ii the type of technical content protected in data anonymization, (iii the organizations and countries most active in patenting data anonymization know-how; and (iv the topics emerging most often in patent titles. Patents from the PatSeer database relating to data anonymization from 2001 to 2015 were analyzed. We used the longitudinal approach in combination with text mining techniques to develop a data anonymization patent landscape. The results indicated the following. The number of single patent families is growing with a high increase after 2010, thus indicating a positive trend in the area of patenting data anonymization solutions. The majority of patenting activities relate to the G Physics section. Organizations from the USA and Japan assigned the majority of patents related to data anonymization. The results of text mining indicate that the most often used word in titles of data anonymization patents are “anonym*, “method”, “data” and “system”. Several additional words that indicated the most frequent topics related to data anonymization were: “equipment”, “software”, “protection”, “identification”, or “encryption”, and specific topics such as “community”, “medical”, or “service”.

  9. PrionHome: a database of prions and other sequences relevant to prion phenomena.

    Directory of Open Access Journals (Sweden)

    Djamel Harbi

    Full Text Available Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions, prionoids (i.e., proteins that propagate like prions between individual cells, and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant, and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments. We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic

  10. PrionHome: a database of prions and other sequences relevant to prion phenomena.

    Science.gov (United States)

    Harbi, Djamel; Parthiban, Marimuthu; Gendoo, Deena M A; Ehsani, Sepehr; Kumar, Manish; Schmitt-Ulms, Gerold; Sowdhamini, Ramanathan; Harrison, Paul M

    2012-01-01

    Prions are units of propagation of an altered state of a protein or proteins; prions can propagate from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We report the bioinformatic construction of the PrionHome, a database of >2000 prion-related sequences. The data was collated from various public and private resources and filtered for redundancy. The data was then processed according to a transparent classification system of prionogenic sequences (i.e., sequences that can make prions), prionoids (i.e., proteins that propagate like prions between individual cells), and other prion-related phenomena. There are eight PrionHome classifications for sequences. The first four classifications are derived from experimental observations: prionogenic sequences, prionoids, other prion-related phenomena, and prion interactors. The second four classifications are derived from sequence analysis: orthologs, paralogs, pseudogenes, and candidate-prionogenic sequences. Database entries list: supporting information for PrionHome classifications, prion-determinant areas (where relevant), and disordered and compositionally-biased regions. Also included are literature references for the PrionHome classifications, transcripts and genomic coordinates, and structural data (including comparative models made for the PrionHome from manually curated alignments). We provide database usage examples for both vertebrate and fungal prion contexts. Using the database data, we have performed a detailed analysis of the compositional biases in known budding-yeast prionogenic sequences, showing

  11. Patenting Human Genes in Europe

    DEFF Research Database (Denmark)

    Minssen, Timo

    2017-01-01

    In accordance with the concept of the book and the assigned scope of the contribution, this chapter describes the European law with respect to the patent-eligibility of isolated DNA sequences. This chapter will further include a brief comparison with recent developments from the US and Australia....... It will, however, not focus on the important debates regarding the patent-eligibility of other biological material, diagnostic methods patents (as data aggregators) or abstract ideas which will be addressed by other contributions. Moreover, the analysis will merely concentrate on patent-eligibility. Other...... patentability requirement will only be briefly touched upon in the discussion part. The paper starts out in section 1.5.2 by discussing the patent-eligibility of isolated human DNA sequences on the European national level and under the Biotechnology Directive. Then the patent-eligibility of isolated human DNA...

  12. Protein backbone angle restraints from searching a database for chemical shift and sequence homology

    Energy Technology Data Exchange (ETDEWEB)

    Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    1999-03-15

    Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

  13. GarlicESTdb: an online database and mining tool for garlic EST sequences

    Directory of Open Access Journals (Sweden)

    Choi Sang-Haeng

    2009-05-01

    Full Text Available Abstract Background Allium sativum., commonly known as garlic, is a species in the onion genus (Allium, which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. Description GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition software technology (JSP/EJB/JavaServlet for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation

  14. GarlicESTdb: an online database and mining tool for garlic EST sequences.

    Science.gov (United States)

    Kim, Dae-Won; Jung, Tae-Sung; Nam, Seong-Hyeuk; Kwon, Hyuk-Ryul; Kim, Aeri; Chae, Sung-Hwa; Choi, Sang-Haeng; Kim, Dong-Wook; Kim, Ryong Nam; Park, Hong-Seog

    2009-05-18

    Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The Garlic

  15. Sequence protein identification by randomized sequence database and transcriptome mass spectrometry (SPIDER-TMS): from manual to automatic application of a 'de novo sequencing' approach.

    Science.gov (United States)

    Pascale, Raffaella; Grossi, Gerarda; Cruciani, Gabriele; Mecca, Giansalvatore; Santoro, Donatello; Sarli Calace, Renzo; Falabella, Patrizia; Bianco, Giuliana

    Sequence protein identification by a randomized sequence database and transcriptome mass spectrometry software package has been developed at the University of Basilicata in Potenza (Italy) and designed to facilitate the determination of the amino acid sequence of a peptide as well as an unequivocal identification of proteins in a high-throughput manner with enormous advantages of time, economical resource and expertise. The software package is a valid tool for the automation of a de novo sequencing approach, overcoming the main limits and a versatile platform useful in the proteomic field for an unequivocal identification of proteins, starting from tandem mass spectrometry data. The strength of this software is that it is a user-friendly and non-statistical approach, so protein identification can be considered unambiguous.

  16. Google Patents: The global patent search engine

    OpenAIRE

    Noruzi, Alireza; Abdekhoda, Mohammadhiwa

    2014-01-01

    Google Patents (www.google.com/patents) includes over 8 million full-text patents. Google Patents works in the same way as the Google search engine. Google Patents is the global patent search engine that lets users search through patents from the USPTO (United States Patent and Trademark Office), EPO (European Patent Office), etc. This study begins with an overview of how to use Google Patent and identifies advanced search techniques not well-documented by Google Patent. It makes several sug...

  17. SeqHound: biological sequence and structure database as a platform for bioinformatics research

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2002-10-01

    Full Text Available Abstract Background SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. Results SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. Conclusions The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.

  18. Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches.

    Science.gov (United States)

    Tran, Trung T; Bollineni, Ravi C; Strozynski, Margarita; Koehler, Christian J; Thiede, Bernd

    2017-07-07

    Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Using this database allows an easy access to splice variant-specific peptide sequences that match to MS data. Furthermore, we combined this database without alternative splice variant-1-specific peptides with human Swiss-Prot. This combined database can be used as a general database for searching of LC-MS data. LC-MS data derived from in-solution digests of two different cell lines (LNCaP, HeLa) and phosphoproteomics studies were analyzed using these two databases. Several nonalternative splice variant-1-specific peptides were found in both cell lines, and some of them seemed to be cell-line-specific. Control and apoptotic phosphoproteomes from Jurkat T cells revealed several nonalternative splice variant-1-specific peptides, and some of them showed clear quantitative differences between the two states.

  19. A Public Database of Memory and Naive B-Cell Receptor Sequences.

    Directory of Open Access Journals (Sweden)

    William S DeWitt

    Full Text Available The vast diversity of B-cell receptors (BCR and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics.

  20. High Performance Protein Sequence Database Scanning on the Cell Broadband Engine

    Directory of Open Access Journals (Sweden)

    Adrianto Wirawan

    2009-01-01

    Full Text Available The enormous growth of biological sequence databases has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the computational power needed by bioinformatics applications is growing rapidly as well. The recent emergence of low cost parallel multicore accelerator technologies has made it possible to reduce execution times of many bioinformatics applications. In this paper, we demonstrate how the Cell Broadband Engine can be used as a computational platform to accelerate two approaches for protein sequence database scanning: exhaustive and heuristic. We present efficient parallelization techniques for two representative algorithms: the dynamic programming based Smith–Waterman algorithm and the popular BLASTP heuristic. Their implementation on a Playstation®3 leads to significant runtime savings compared to corresponding sequential implementations.

  1. A Public Database of Memory and Naive B-Cell Receptor Sequences.

    Science.gov (United States)

    DeWitt, William S; Lindau, Paul; Snyder, Thomas M; Sherwood, Anna M; Vignali, Marissa; Carlson, Christopher S; Greenberg, Philip D; Duerkopp, Natalie; Emerson, Ryan O; Robins, Harlan S

    2016-01-01

    The vast diversity of B-cell receptors (BCR) and secreted antibodies enables the recognition of, and response to, a wide range of epitopes, but this diversity has also limited our understanding of humoral immunity. We present a public database of more than 37 million unique BCR sequences from three healthy adult donors that is many fold deeper than any existing resource, together with a set of online tools designed to facilitate the visualization and analysis of the annotated data. We estimate the clonal diversity of the naive and memory B-cell repertoires of healthy individuals, and provide a set of examples that illustrate the utility of the database, including several views of the basic properties of immunoglobulin heavy chain sequences, such as rearrangement length, subunit usage, and somatic hypermutation positions and dynamics.

  2. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.

    Science.gov (United States)

    Carver, Tim; Berriman, Matthew; Tivey, Adrian; Patel, Chinmay; Böhme, Ulrike; Barrell, Barclay G; Parkhill, Julian; Rajandream, Marie-Adèle

    2008-12-01

    Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/

  3. Alignment of high-throughput sequencing data inside in-memory databases.

    Science.gov (United States)

    Firnkorn, Daniel; Knaup-Gregori, Petra; Lorenzo Bermejo, Justo; Ganzinger, Matthias

    2014-01-01

    In times of high-throughput DNA sequencing techniques, performance-capable analysis of DNA sequences is of high importance. Computer supported DNA analysis is still an intensive time-consuming task. In this paper we explore the potential of a new In-Memory database technology by using SAP's High Performance Analytic Appliance (HANA). We focus on read alignment as one of the first steps in DNA sequence analysis. In particular, we examined the widely used Burrows-Wheeler Aligner (BWA) and implemented stored procedures in both, HANA and the free database system MySQL, to compare execution time and memory management. To ensure that the results are comparable, MySQL has been running in memory as well, utilizing its integrated memory engine for database table creation. We implemented stored procedures, containing exact and inexact searching of DNA reads within the reference genome GRCh37. Due to technical restrictions in SAP HANA concerning recursion, the inexact matching problem could not be implemented on this platform. Hence, performance analysis between HANA and MySQL was made by comparing the execution time of the exact search procedures. Here, HANA was approximately 27 times faster than MySQL which means, that there is a high potential within the new In-Memory concepts, leading to further developments of DNA analysis procedures in the future.

  4. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

    Science.gov (United States)

    Carver, Tim; Berriman, Matthew; Tivey, Adrian; Patel, Chinmay; Böhme, Ulrike; Barrell, Barclay G.; Parkhill, Julian; Rajandream, Marie-Adèle

    2008-01-01

    Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18845581

  5. The need for high-quality whole-genome sequence databases in microbial forensics.

    Science.gov (United States)

    Sjödin, Andreas; Broman, Tina; Melefors, Öjar; Andersson, Gunnar; Rasmusson, Birgitta; Knutsson, Rickard; Forsman, Mats

    2013-09-01

    Microbial forensics is an important part of a strengthened capability to respond to biocrime and bioterrorism incidents to aid in the complex task of distinguishing between natural outbreaks and deliberate acts. The goal of a microbial forensic investigation is to identify and criminally prosecute those responsible for a biological attack, and it involves a detailed analysis of the weapon--that is, the pathogen. The recent development of next-generation sequencing (NGS) technologies has greatly increased the resolution that can be achieved in microbial forensic analyses. It is now possible to identify, quickly and in an unbiased manner, previously undetectable genome differences between closely related isolates. This development is particularly relevant for the most deadly bacterial diseases that are caused by bacterial lineages with extremely low levels of genetic diversity. Whole-genome analysis of pathogens is envisaged to be increasingly essential for this purpose. In a microbial forensic context, whole-genome sequence analysis is the ultimate method for strain comparisons as it is informative during identification, characterization, and attribution--all 3 major stages of the investigation--and at all levels of microbial strain identity resolution (ie, it resolves the full spectrum from family to isolate). Given these capabilities, one bottleneck in microbial forensics investigations is the availability of high-quality reference databases of bacterial whole-genome sequences. To be of high quality, databases need to be curated and accurate in terms of sequences, metadata, and genetic diversity coverage. The development of whole-genome sequence databases will be instrumental in successfully tracing pathogens in the future.

  6. Decoding Patent Information Using Patent Maps

    OpenAIRE

    Liu, Chen-Yuan; Yang, James Chingyu

    2008-01-01

    Patent information is a derivative product from the legal patent system. This information, which includes patent applications, patent descriptions, patent gazettes, patent abstracts, and patent data, is prepared in exact compliance with the regulations and specifications of the patent acts. Patent information, different from other published circulating information, is legally well protected. For convenience, this study classifies patent information into bibliographic and numeric data to creat...

  7. Databases

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.

    Information on bibliographic as well as numeric/textual databases relevant to coastal geomorphology has been included in a tabular form. Databases cover a broad spectrum of related subjects like coastal environment and population aspects, coastline...

  8. A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.

    Science.gov (United States)

    Goodacre, Norman; Aljanahi, Aisha; Nandakumar, Subhiksha; Mikailov, Mike; Khan, Arifa S

    2018-01-01

    Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank. IMPORTANCE To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have

  9. TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.

    Science.gov (United States)

    Liu, Wanting; Xiang, Lunping; Zheng, Tingkai; Jin, Jingjie; Zhang, Gong

    2018-01-04

    Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translatomedb.net/) which provides collection and integrated analysis of published and user-generated translatome sequencing data. The current version includes 2453 Ribo-seq, 10 RNC-seq and their 1394 corresponding mRNA-seq datasets in 13 species. The database emphasizes the analysis functions in addition to the dataset collections. Differential gene expression (DGE) analysis can be performed between any two datasets of same species and type, both on transcriptome and translatome levels. The translation indices translation ratios, elongation velocity index and translational efficiency can be calculated to quantitatively evaluate translational initiation efficiency and elongation velocity, respectively. All datasets were analyzed using a unified, robust, accurate and experimentally-verifiable pipeline based on the FANSe3 mapping algorithm and edgeR for DGE analyzes. TranslatomeDB also allows users to upload their own datasets and utilize the identical unified pipeline to analyze their data. We believe that our TranslatomeDB is a comprehensive platform and knowledgebase on translatome and proteome research, releasing the biologists from complex searching, analyzing and comparing huge sequencing data without needing local computational power. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  11. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

    Directory of Open Access Journals (Sweden)

    Rognes Torbjørn

    2011-06-01

    Full Text Available Abstract Background The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. Results A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Conclusions Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.

  12. Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

    Science.gov (United States)

    Bailey, Sarah F; Scheible, Melissa K; Williams, Christopher; Silva, Deborah S B S; Hoggan, Marina; Eichman, Christopher; Faith, Seth A

    2017-11-01

    Next-generation Sequencing (NGS) is a rapidly evolving technology with demonstrated benefits for forensic genetic applications, and the strategies to analyze and manage the massive NGS datasets are currently in development. Here, the computing, data storage, connectivity, and security resources of the Cloud were evaluated as a model for forensic laboratory systems that produce NGS data. A complete front-to-end Cloud system was developed to upload, process, and interpret raw NGS data using a web browser dashboard. The system was extensible, demonstrating analysis capabilities of autosomal and Y-STRs from a variety of NGS instrumentation (Illumina MiniSeq and MiSeq, and Oxford Nanopore MinION). NGS data for STRs were concordant with standard reference materials previously characterized with capillary electrophoresis and Sanger sequencing. The computing power of the Cloud was implemented with on-demand auto-scaling to allow multiple file analysis in tandem. The system was designed to store resulting data in a relational database, amenable to downstream sample interpretations and databasing applications following the most recent guidelines in nomenclature for sequenced alleles. Lastly, a multi-layered Cloud security architecture was tested and showed that industry standards for securing data and computing resources were readily applied to the NGS system without disadvantageous effects for bioinformatic analysis, connectivity or data storage/retrieval. The results of this study demonstrate the feasibility of using Cloud-based systems for secured NGS data analysis, storage, databasing, and multi-user distributed connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.

    Science.gov (United States)

    Rognes, Torbjørn

    2011-06-01

    The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.

  14. Genome cluster database. A sequence family analysis platform for Arabidopsis and rice.

    Science.gov (United States)

    Horan, Kevin; Lauricha, Josh; Bailey-Serres, Julia; Raikhel, Natasha; Girke, Thomas

    2005-05-01

    The genome-wide protein sequences from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) spp. japonica were clustered into families using sequence similarity and domain-based clustering. The two fundamentally different methods resulted in separate cluster sets with complementary properties to compensate the limitations for accurate family analysis. Functional names for the identified families were assigned with an efficient computational approach that uses the description of the most common molecular function gene ontology node within each cluster. Subsequently, multiple alignments and phylogenetic trees were calculated for the assembled families. All clustering results and their underlying sequences were organized in the Web-accessible Genome Cluster Database (http://bioinfo.ucr.edu/projects/GCD) with rich interactive and user-friendly sequence family mining tools to facilitate the analysis of any given family of interest for the plant science community. An automated clustering pipeline ensures current information for future updates in the annotations of the two genomes and clustering improvements. The analysis allowed the first systematic identification of family and singlet proteins present in both organisms as well as those restricted to one of them. In addition, the established Web resources for mining these data provide a road map for future studies of the composition and structure of protein families between the two species.

  15. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2007-01-01

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ 1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

  16. Spreadsheet Patents

    DEFF Research Database (Denmark)

    Borum, Holger Stadel; Kirkbro, Malthe Ettrup; Sestoft, Peter

    2018-01-01

    This technical report gives a list of US patents and patent applications related to spreadsheet implementation technology. It is intended as a companion to the monograph Spreadsheet Implementation Technology (Peter Sestoft, MIT Press 2014), and substantially extends and updates an appendix from...

  17. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

    NARCIS (Netherlands)

    Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; Vos, de Willem M.

    2015-01-01

    Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to

  18. Monitoring innovation in electrochemical energy storage technologies: A patent-based approach

    International Nuclear Information System (INIS)

    Mueller, Simon C.; Sandner, Philipp G.; Welpe, Isabell M.

    2015-01-01

    Highlights: • Grid effects of intermittent sources show increasing need for decentralized storage. • Novel patent classification is applied to monitor competing technologies. • Up-to-date geographical, organizational, and qualitative insight is given. • Redox flow patenting shows strong growth, lithium also strong absolute numbers. • Revealed patents allow the expectation of improved modules in the future. - Abstract: Due to the suitability to balance the intermittency in decentralized systems with renewable sources, electrochemical energy storage possibilities have been analyzed in several studies, all highlighting the need for improvements in relevant techno-economic parameters. Particularly a reduction in the costs per cycle is much needed, which could either come from innovation in more cost-efficient manufacturing methods, a higher endurance of charge/discharge sequences or higher capacities. Looking at patent applications as a metric allows us to determine whether the necessary technological progress is indeed occurring, as the mandatory publication of the underlying inventions provides access to otherwise hidden R and D activities. Our paper contributes to the literature with a compilation of technological classes related to important battery types in the novel Cooperative Patent Classification (CPC), which can be used to identify relevant patent applications of the competing technologies. Using the worldwide patent statistical database (PATSTAT), we find that promising technologies have been showing increasing patent counts in recent years. For example, the number of patent applications related to regenerative fuel cells (e.g. redox flow batteries) doubled from 2009 to 2011. Nevertheless, the volume of patent filings in technologies related to lithium remains unchallenged. Patent applications in this area are still growing, which indicates that the introduction of improved modules will continue. Using citation analysis, we have identified

  19. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex

    DEFF Research Database (Denmark)

    O'Donnell, Kerry; Gueidan, C; Sink, S

    2009-01-01

    We constructed a two-locus database, comprising partial translation elongation factor (EF-1alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species compl...... of the IGS rDNA sequences may be non-orthologous. We also evaluated enniatin, fumonisin and moniliformin mycotoxin production in vitro within a phylogenetic framework....

  20. Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database.

    Science.gov (United States)

    Holcomb, C L; Rastrou, M; Williams, T C; Goodridge, D; Lazaro, A M; Tilanus, M; Erlich, H A

    2014-01-01

    The high-resolution human leukocyte antigen (HLA) genotyping assay that we developed using 454 sequencing and Conexio software uses generic polymerase chain reaction (PCR) primers for DRB exon 2. Occasionally, we observed low abundance DRB amplicon sequences that resulted from in vitro PCR 'crossing over' between DRB1 and DRB3/4/5. These hybrid sequences, revealed by the clonal sequencing property of the 454 system, were generally observed at a read depth of 5%-10% of the true alleles. They usually contained at least one mismatch with the IMGT/HLA database, and consequently, were easily recognizable and did not cause a problem for HLA genotyping. Sometimes, however, these artifactual sequences matched a rare allele and the automatic genotype assignment was incorrect. These observations raised two issues: (1) could PCR conditions be modified to reduce such artifacts? and (2) could some of the rare alleles listed in the IMGT/HLA database be artifacts rather than true alleles? Because PCR crossing over occurs during late cycles of PCR, we compared DRB genotypes resulting from 28 and (our standard) 35 cycles of PCR. For all 21 cell line DNAs amplified for 35 cycles, crossover products were detected. In 33% of the cases, these hybrid sequences corresponded to named alleles. With amplification for only 28 cycles, these artifactual sequences were not detectable. To investigate whether some rare alleles in the IMGT/HLA database might be due to PCR artifacts, we analyzed four samples obtained from the investigators who submitted the sequences. In three cases, the sequences were generated from true alleles. In one case, our 454 sequencing revealed an error in the previously submitted sequence. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. Interactive overlay maps for US Patent (USPTO) data based on International Patent Classifications (IPC)

    NARCIS (Netherlands)

    Leydesdorff, L.; Kushnir, D.; Rafols, I.

    2014-01-01

    We report on the development of an interface to the US Patent and Trademark Office (USPTO) that allows for the mapping of patent portfolios as overlays to basemaps constructed from citation relations among all patents contained in this database during the period 1976-2011. Both the interface and the

  2. Are biosimilars patentable?

    Science.gov (United States)

    Rolfe, Damian; Parker, Jayson; Morgan, Max

    2016-08-01

    This paper explores whether, and under what circumstances, a biosimilar approved in the United States under the Biologics Price Competition and Innovation Act (hereafter 'BPCIA') can be patented. The possibility that a biosimilar product could have meaningful patent protection arises from specific requirements for biosimilarity under the BPCIA, which account for the fact that manufacturing processes of biologics are inherently imprecise. The requirements for biosimilar approval may provide sufficient leeway to a biosimilar applicant to patent structural or formulation differences that provide non-clinical but business-relevant advantages over the reference molecule, such as improved shelf-life or ease of manufacture, without compromising clinical biosimilarity. Examination of the BPCIA and related Acts, Food and Drug Administration (FDA) guidance papers, case law, patent database searching, and relevant scholarly articles. Legislative and regulatory requirements for the approval of a biosimilar under the BPCIA are focused on clinical results and allow a degree of leeway for differences to exist between a biosimilar's structure and non-clinical components and those of the biosimilar's reference molecule. This leeway can be exploited to provide the biosimilar with potentially patentable business-relevant advantages over its reference product while maintaining clinical biosimilarity to the reference product.

  3. Genomics dataset on unclassified published organism (patent US 7547531

    Directory of Open Access Journals (Sweden)

    Mohammad Mahfuz Ali Khan Shawan

    2016-12-01

    Full Text Available Nucleotide (DNA sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531 is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database. Quick response (QR code of those DNA sequences was constructed by DNA BarID tool. QR code is useful for the identification and comparison of isolates with other organisms. AT/GC content of the DNA sequences was determined using ENDMEMO GC Content Calculator, which indicates their stability at different temperature. The highest GC content was observed in GP445188 (62.5% which was followed by GP445198 (61.8% and GP445189 (59.44%, while lowest was in GP445178 (24.39%. In addition, New England BioLabs (NEB database was used to identify cleavage code indicating the 5, 3 and blunt end and enzyme code indicating the methylation site of the DNA sequences was also shown. These data will be helpful for the construction of the organisms’ hierarchical classification, determination of their phylogenetic and taxonomic position and revelation of their molecular characteristics.

  4. Reticulamoeba Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases

    Science.gov (United States)

    Bass, David; Yabuki, Akinori; Santini, Sébastien; Romac, Sarah; Berney, Cédric

    2012-01-01

    We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate Reticulamoeba Grell, which resolved into four genetically distinct Reticulamoeba lineages, two of which correspond to R. gemmipara Grell and R. minor Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both R. minor and R. gemmipara but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus Mesofila. The basic morphology of Reticulamoeba is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. Reticulamoeba is frequently observed in coastal marine environmental samples. PCR primers specific to the Reticulamoeba clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. Therefore, although such datasets are very powerful tools in microbial ecology, they may, for several methodological reasons, fail to detect ecologically and evolutionary key lineages. PMID:23226495

  5. Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database.

    Science.gov (United States)

    Billoud, B; Kontic, M; Viari, A

    1996-01-01

    At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usually dedicated to particular structures and are written using general purpose programming languages through a complex and time consuming process where the biological problem of defining the structure and the computer engineering problem of looking for it are intimately intertwined. In this paper, we describe a general representation of structures, suitable for database scanning, together with a programming language, Palingol, designed to manipulate it. Palingol has specific data types, corresponding to structural elements-basically helices-that can be arranged in any way to form a complex structure. As a consequence of the declarative approach used in Palingol, the user should only focus on 'what to search for' while the language engine takes care of 'how to look for it'. Therefore, it becomes simpler to write a scanning program and the structural constraints that define the required structure are more clearly identified. PMID:8628670

  6. Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    David Bousfield

    2016-02-01

    Full Text Available Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method development and to derive new scientific insights. Indicators that estimate the extent and utility of such secondary use of research data need to reflect this complex and highly variable data usage. By linking open access scientific literature, via Europe PubMedCentral, to the metadata in biological data resources we separate data citations associated with a deposition statement from citations that capture the subsequent, long-term, reuse of data in academia and industry.  We extend this analysis to begin to investigate citations of biomolecular resources in patent documents. We find citations in more than 8,000 patents from 2014, demonstrating substantial use and an important role for data resources in defining biological concepts in granted patents to both academic and industrial innovators. Combined together our results indicate that the citation patterns in biomedical literature and patents vary, not only due to citation practice but also according to the data resource cited. The results guard against the use of simple metrics such as citation counts and show that indicators of data use must not only take into account citations within the biomedical literature but also include reuse of data in industry and other parts of society by including patents and other scientific and technical documents such as guidelines, reports and grant applications.

  7. Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases.

    Science.gov (United States)

    Muñoz, Marina; Ríos-Chaparro, Dora Inés; Patarroyo, Manuel Alfonso; Ramírez, Juan David

    2017-03-14

    Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7%), followed by C2 (29.1%). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0%). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes' contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity.

  8. Patent office governance and patent system quality

    OpenAIRE

    PICARD, Pierre M.; VAN POTTELSBERGHE DE LA POTTERIE, Bruno

    2011-01-01

    The present paper discusses the role of quality in patent systems from the perspective of patent offices' behavior and organization. After documenting original stylized facts, the paper presents a model in which patent offices set patent fees and the quality level of their examination processes. Various objectives of patent offices' governors are considered. We show that the quality of the patent system is maximal for the patent offices that maximises either the social welfare or its own prof...

  9. HIVBrainSeqDB: a database of annotated HIV envelope sequences from brain and other anatomical sites

    Directory of Open Access Journals (Sweden)

    O'Connor Niall

    2010-12-01

    Full Text Available Abstract Background The population of HIV replicating within a host consists of independently evolving and interacting sub-populations that can be genetically distinct within anatomical compartments. HIV replicating within the brain causes neurocognitive disorders in up to 20-30% of infected individuals and is a viral sanctuary site for the development of drug resistance. The primary determinant of HIV neurotropism is macrophage tropism, which is primarily determined by the viral envelope (env gene. However, studies of genetic aspects of HIV replicating in the brain are hindered because existing repositories of HIV sequences are not focused on neurotropic virus nor annotated with neurocognitive and neuropathological status. To address this need, we constructed the HIV Brain Sequence Database. Results The HIV Brain Sequence Database is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i brain, brainstem, and spinal cord; (ii meninges, choroid plexus, and CSF; (iii blood and lymphoid; and (iv other (bone marrow, colon, lung, liver, etc. Patient coding is correlated across studies, allowing sequences from the same patient to be grouped to increase statistical power. Using Cytoscape, we visualized relationships between studies, patients and sequences, illustrating interconnections between studies and the varying depth of sequencing, patient number, and tissue representation across studies

  10. Current Energy Patents

    International Nuclear Information System (INIS)

    Kelly, R.C.

    1982-01-01

    Current Energy Patents (CEP) provides abstracting and indexing coverage of the international patent literature, including patent applications, that concerns any aspect of energy production, conservation, and utilization

  11. Trends in worldwide nanotechnology patent applications: 1991 to 2008

    OpenAIRE

    Dang, Yan; Zhang, Yulei; Fan, Li; Chen, Hsinchun; Roco, Mihail C.

    2009-01-01

    Nanotechnology patent applications published during 1991?2008 have been examined using the ?title?abstract? keyword search on esp@cenet ?worldwide? database. The longitudinal evolution of the number of patent applications, their topics, and their respective patent families have been evaluated for 15 national patent offices covering 98% of the total global activity. The patent offices of the United States (USA), People?s Republic of China (PRC), Japan, and South Korea have published the larges...

  12. Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies.

    NARCIS (Netherlands)

    G.P. Patrinos (George); B. Giardine (Belinda); C. Riemer (Cathy); W. Miller (Webb); D.H. Chui (David); N.P. Anagnou (Nicholas); H. Wajcman (Henri); R.C. Hardison (Ross)

    2004-01-01

    textabstractHbVar (http://globin.cse.psu.edu/globin/hbvar/) is a relational database developed by a multi-center academic effort to provide up-to-date and high quality information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and

  13. US photovoltaic patents: 1991--1993

    Energy Technology Data Exchange (ETDEWEB)

    Pohle, L

    1995-03-01

    This document contains US patents on terrestrial photovoltaic (PV) power applications, including systems, components, and materials as well as manufacturing and support functions. The patent entries in this document were issued from 1991 to 1993. The entries were located by searching USPA, the database of the US Patent Office. The final search retrieved all patents under the class ``Batteries, Thermoelectric and Photoelectric`` and the subclasses ``Photoelectric,`` ``Testing,`` and ``Applications.`` The search also located patents that contained the words ``photovoltaic(s)`` or ``solar cell(s)`` and their derivatives. After the initial list was compiled, most of the patents on the following subjects were excluded: space photovoltaic technology, use of the photovoltaic effect for detectors, and subjects only peripherally concerned with photovoltaic. Some patents on these three subjects were included when ft appeared that those inventions might be of use in terrestrial PV power technologies.

  14. An Efficient Approach to Mining Maximal Contiguous Frequent Patterns from Large DNA Sequence Databases

    Directory of Open Access Journals (Sweden)

    Md. Rezaul Karim

    2012-03-01

    Full Text Available Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.

  15. UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

    Science.gov (United States)

    Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

    2016-01-04

    The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. FishPathogens.eu/vhsv: a user-friendly viral haemorrhagic septicaemia virus isolate and sequence database

    DEFF Research Database (Denmark)

    Jonstrup, Søren Peter; Gray, Tanya; Kahns, Søren

    2009-01-01

    A database has been created, http://www.Fish Pathogens.eu, with the aim of providing a single repository for collating important information on significant pathogens of aquaculture, relevant to their control and management. This database will be developed, maintained and managed as part of the Eu......A database has been created, http://www.Fish Pathogens.eu, with the aim of providing a single repository for collating important information on significant pathogens of aquaculture, relevant to their control and management. This database will be developed, maintained and managed as part...... of the European Community Reference Laboratory for Fish Diseases function. This concept has been initially developed for viral haemorrhagic septicaemia virus and will be extended in future to include information on other significant aquaculture pathogens. Information included for each isolate comprises sequence...... to obtain data from any selected part of the genome of interest. The output of the sequence search can be readily retrieved as a FASTA file ready to be imported into a sequence alignment tool of choice, facilitating further molecular epidemiological study....

  17. Analysis of US patents on spacer grids

    International Nuclear Information System (INIS)

    Kim, Hyung Kyu; Song, Kee Nam; Yoon, Kyung Ho; Kang, Hong Seok; Kim, Hyung Kyu; Jeon, Tae Hyun; Oh, Dong Seok; In, Wang Ki; Bang, Jae Keun; Oh, Seung Eun; Seo, Jeong Min; Lee, Jin Seok; Park, Seong Keun

    1997-06-01

    The total of 137 US patents on spacer grids patented from 1968 through 1993 are analyzed and summarized. Database is constituted with designing the appropriate fields by which each patent can be identified. The fields consist of patent number, inventor, assignee, date of patent, title and major foci of the patent. The major foci are again classified by detailed subjects such as the fretting failure and fuel rod support-related, the strength-related, the fabrication-related as for mechanical subjects, while the cooling performance-related and the pressure drop-related as for thermal-hydraulic one. The 92% of the patents analyzed were issued form nuclear companies of USA, France and Germany. Among the patents dealing with mechanical subjects, the fretting failure and fuel rod support-related is more than the pressure drop-related among the patents of thermal-hydraulic subjects. The number of patents issued from Japan ranks just after Germany i.e., the 4th country. It is thought that much concern as well as investment should be increased in this field, the patent of nuclear components. (author). 2 tabs., 5 figs

  18. Analysis of US patents on spacer grids

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyung Kyu; Song, Kee Nam; Yoon, Kyung Ho; Kang, Hong Seok; Kim, Hyung Kyu; Jeon, Tae Hyun; Oh, Dong Seok; In, Wang Ki; Bang, Jae Keun [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of); Oh, Seung Eun; Seo, Jeong Min; Lee, Jin Seok; Park, Seong Keun [Korea Nuclear Fuel Company, Taejon (Korea, Republic of)

    1997-06-01

    The total of 137 US patents on spacer grids patented from 1968 through 1993 are analyzed and summarized. Database is constituted with designing the appropriate fields by which each patent can be identified. The fields consist of patent number, inventor, assignee, date of patent, title and major foci of the patent. The major foci are again classified by detailed subjects such as the fretting failure and fuel rod support-related, the strength-related, the fabrication-related as for mechanical subjects, while the cooling performance-related and the pressure drop-related as for thermal-hydraulic one. The 92% of the patents analyzed were issued form nuclear companies of USA, France and Germany. Among the patents dealing with mechanical subjects, the fretting failure and fuel rod support-related is more than the pressure drop-related among the patents of thermal-hydraulic subjects. The number of patents issued from Japan ranks just after Germany i.e., the 4th country. It is thought that much concern as well as investment should be increased in this field, the patent of nuclear components. (author). 2 tabs., 5 figs.

  19. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Ussery, David

    2004-01-01

    , these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web...... and frequent addition of new models are factors that require a dynamic database layout. Using basic tools like the GNU Make system, csh, Perl and MySQL, we have created a flexible database environment for storing and maintaining such results for a collection of complete microbial genomes. Currently...... content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues....

  20. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  1. Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences.

    Science.gov (United States)

    Mi, Tian; Merlin, Jerlin Camilus; Deverasetty, Sandeep; Gryk, Michael R; Bill, Travis J; Brooks, Andrew W; Lee, Logan Y; Rathnayake, Viraj; Ross, Christian A; Sargeant, David P; Strong, Christy L; Watts, Paula; Rajasekaran, Sanguthevar; Schiller, Martin R

    2012-01-01

    Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins and causes of disease.

  2. Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

    Science.gov (United States)

    Li, Li; Brunk, Brian P.; Kissinger, Jessica C.; Pape, Deana; Tang, Keliang; Cole, Robert H.; Martin, John; Wylie, Todd; Dante, Mike; Fogarty, Steven J.; Howe, Daniel K.; Liberator, Paul; Diaz, Carmen; Anderson, Jennifer; White, Michael; Jerome, Maria E.; Johnson, Emily A.; Radke, Jay A.; Stoeckert, Christian J.; Waterston, Robert H.; Clifton, Sandra W.; Roos, David S.; Sibley, L. David

    2003-01-01

    Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55,192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, ∼15%–20% represent putative homologs with a conservative cutoff of p neurona: , , , , , , , , , , , , , –, –, –, –, –. Eimeria tenella: –, –, –, –, –, –, –, –, – , –, –, –, –, –, –, –, –, –, –, –. Neospora caninum: –, –, , – , –, –.] PMID:12618375

  3. Patents - Overlooked Source of Information

    Czech Academy of Sciences Publication Activity Database

    Matějíček, Jiří; Ilavský, J.

    2004-01-01

    Roč. 13, č. 4 (2004), s. 473-476 ISSN 1059-9630 Institutional research plan: CEZ:AV0Z2043910 Keywords : patent * database * thermal spraying Subject RIV: JK - Corrosion ; Surface Treatment of Materials Impact factor: 1.068, year: 2004

  4. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

    Directory of Open Access Journals (Sweden)

    Marais Gabriel AB

    2011-07-01

    Full Text Available Abstract Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO terms, and thousands of single-nucleotide polymorphisms (SNPs were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49% that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to

  5. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

    Science.gov (United States)

    2011-01-01

    Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a

  6. Cluster based on sequence comparison of homologous proteins of 95 organism species - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Gclust Server Cluster based on sequence comparison of homologous proteins of 95 organism spe...cies Data detail Data name Cluster based on sequence comparison of homologous proteins of 95 organism specie...istory of This Database Site Policy | Contact Us Cluster based on sequence compariso

  7. MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

    Directory of Open Access Journals (Sweden)

    Kuczmarski Thomas A

    2006-10-01

    Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

  8. ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

    Science.gov (United States)

    Büssow, Konrad; Hoffmann, Steve; Sievert, Volker

    2002-12-19

    Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format. Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence. The program has a graphical user interface, although it can be used in a non-interactive mode. For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes. Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format. The ORFer program is freely available at http://www.proteinstrukturfabrik.de/orfer. The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank. Furthermore, storage of sequences and features in a relational database is supported. Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information.

  9. Patenting of university and non-university public research organisations in Germany: evidence from patent applications for medical research results.

    Directory of Open Access Journals (Sweden)

    Peter Tinnemann

    Full Text Available BACKGROUND: Patents are one of the most important forms of intellectual property. They grant a time-limited exclusivity on the use of an invention allowing the recuperation of research costs. The use of patents is fiercely debated for medical innovation and especially controversial for publicly funded research, where the patent holder is an institution accountable to public interest. Despite this controversy, for the situation in Germany almost no empirical information exists. The purpose of this study is to examine the amount, types and trends of patent applications for health products submitted by German public research organisations. METHODS/PRINCIPAL FINDINGS: We conducted a systematic search for patent documents using the publicly accessible database search interface of the German Patent and Trademark Office. We defined keywords and search criteria and developed search patterns for the database request. We retrieved documents with application date between 1988 and 2006 and processed the collected data stepwise to compile the most relevant documents in patent families for further analysis. We developed a rationale and present individual steps of a systematic method to request and process patent data from a publicly accessible database. We retrieved and processed 10194 patent documents. Out of these, we identified 1772 relevant patent families, applied for by 193 different universities and non-university public research organisations. 827 (47% of these patent families contained granted patents. The number of patent applications submitted by universities and university-affiliated institutions more than tripled since the introduction of legal reforms in 2002, constituting almost half of all patent applications and accounting for most of the post-reform increase. Patenting of most non-university public research organisations remained stable. CONCLUSIONS: We search, process and analyse patent applications from publicly accessible databases

  10. How patent experts create patent breadth

    DEFF Research Database (Denmark)

    Beukel, Karin

    2014-01-01

    Science as an input to patented inventions is a fundamental of economic growth. However, our understanding of how science is transformed into patents is limited. In the present paper I seek to fill this gap by examining the micro-foundations of science-patent transformations. Using an inductive......, grounded theory approach to study the transformation of 12 scientific discoveries into patents I recast the relationship between science and patents: I show it as a particular process that affects patent breadth. Exploiting surplus patent breadth depends on the processes of abstraction and cognitive...... variety, which can be mobilized by patenting experts. The theory is tested using a recently published algebraic interpretive method for examining causal relationships in small-N studies....

  11. How patent experts create patent breadth

    DEFF Research Database (Denmark)

    Beukel, Karin

    2018-01-01

    Science as an input to patented inventions is a fundamental of economic growth. However, our understanding of how science is transformed into patents is limited. In the present paper I seek to fill this gap by examining the micro-foundations of science-patent transformations. Using an inductive......, grounded theory approach to study the transformation of 12 scientific discoveries into patents I recast the relationship between science and patents: I show it as a particular process that affects patent breadth. Exploiting surplus patent breadth depends on the processes of abstraction and cognitive...... variety, which can be mobilized by patenting experts. The theory is tested using a recently published algebraic interpretive method for examining causal relationships in small-N studies....

  12. TMC-SNPdb: an Indian germline variant database derived from whole exome sequences.

    Science.gov (United States)

    Upadhyay, Pawan; Gardi, Nilesh; Desai, Sanket; Sahoo, Bikram; Singh, Ankita; Togar, Trupti; Iyer, Prajish; Prasad, Ratnam; Chandrani, Pratik; Gupta, Sudeep; Dutt, Amit

    2016-01-01

    Cancer is predominantly a somatic disease. A mutant allele present in a cancer cell genome is considered somatic when it's absent in the paired normal genome along with public SNP databases. The current build of dbSNP, the most comprehensive public SNP database, however inadequately represents several non-European Caucasian populations, posing a limitation in cancer genomic analyses of data from these populations. We present the T: ata M: emorial C: entre-SNP D: ata B: ase (TMC-SNPdb), as the first open source, flexible, upgradable, and freely available SNP database (accessible through dbSNP build 149 and ANNOVAR)-representing 114 309 unique germline variants-generated from whole exome data of 62 normal samples derived from cancer patients of Indian origin. The TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or using an easy-to-use graphical user interface with the ability to deplete additional Indian population specific SNPs over and above dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb could deplete 42, 33 and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of the TMC-SNPdb in several Mendelian germline diseases. In addition to dbSNP build 149 and ANNOVAR, the TMC-SNPdb along with the subtraction tool is available for download in the public domain at the following:Database URL: http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNP/TMCSNPdp.html. © The Author(s) 2016. Published by Oxford University Press.

  13. Polymorphisms and resistance mutations of hepatitis C virus on sequences in the European hepatitis C virus database

    Science.gov (United States)

    Kliemann, Dimas Alexandre; Tovo, Cristiane Valle; da Veiga, Ana Beatriz Gorini; de Mattos, Angelo Alves; Wood, Charles

    2016-01-01

    AIM To evaluate the occurrence of resistant mutations in treatment-naïve hepatitis C virus (HCV) sequences deposited in the European hepatitis C virus database (euHCVdb). METHODS The sequences were downloaded from the euHCVdb (https://euhcvdb.ibcp.fr/euHCVdb/). The search was performed for full-length NS3 protease, NS5A and NS5B polymerase sequences of HCV, separated by genotypes 1a, 1b, 2a, 2b and 3a, and resulted in 798 NS3, 708 NS5A and 535 NS5B sequences from HCV genotypes 1a, 1b, 2a, 2b and 3a, after the exclusion of sequences containing errors and/or gaps or incomplete sequences, and sequences from patients previously treated with direct antiviral agents (DAA). The sequence alignment was performed with MEGA 6.06 MAC and the resulting protein sequences were then analyzed using the BioEdit 7.2.5. for mutations associated with resistance. Only positions that have been described as being associated with failure in treatment in in vivo studies, and/or as conferring a more than 2-fold change in replication in comparison to the wildtype reference strain in in vitro phenotypic assays were included in the analysis. RESULTS The Q80K variant in the NS3 gene was the most prevalent mutation, being found in 44.66% of subtype 1a and 0.25% of subtype 1b. Other frequent mutations observed in more than 2% of the NS3 sequences were: I170V (3.21%) in genotype 1a, and Y56F (15.93%), V132I (23.28%) and I170V (65.20%) in genotype 1b. For the NS5A, 2.21% of the genotype 1a sequences have the P58S mutation, 5.95% of genotype 1b sequences have the R30Q mutation, 15.79% of subtypes 2a sequences have the Q30R mutation, 23.08% of subtype 2b sequences have a L31M mutation, and in subtype 3a sequences, 23.08% have the M31L resistant variants. For the NS5B, the V321L RAV was identified in 0.60% of genotype 1a and in 0.32% of genotype 1b sequences, and the N142T variant was observed in 0.32% of subtype 1b sequences. The C316Y, S556G, D559N RAV were identified in 0.33%, 7.82% and 0.32% of

  14. Polymorphisms and resistance mutations of hepatitis C virus on sequences in the European hepatitis C virus database.

    Science.gov (United States)

    Kliemann, Dimas Alexandre; Tovo, Cristiane Valle; da Veiga, Ana Beatriz Gorini; de Mattos, Angelo Alves; Wood, Charles

    2016-10-28

    To evaluate the occurrence of resistant mutations in treatment-naïve hepatitis C virus (HCV) sequences deposited in the European hepatitis C virus database (euHCVdb). The sequences were downloaded from the euHCVdb (https://euhcvdb.ibcp.fr/euHCVdb/). The search was performed for full-length NS3 protease, NS5A and NS5B polymerase sequences of HCV, separated by genotypes 1a, 1b, 2a, 2b and 3a, and resulted in 798 NS3, 708 NS5A and 535 NS5B sequences from HCV genotypes 1a, 1b, 2a, 2b and 3a, after the exclusion of sequences containing errors and/or gaps or incomplete sequences, and sequences from patients previously treated with direct antiviral agents (DAA). The sequence alignment was performed with MEGA 6.06 MAC and the resulting protein sequences were then analyzed using the BioEdit 7.2.5. for mutations associated with resistance. Only positions that have been described as being associated with failure in treatment in in vivo studies, and/or as conferring a more than 2-fold change in replication in comparison to the wildtype reference strain in in vitro phenotypic assays were included in the analysis. The Q80K variant in the NS3 gene was the most prevalent mutation, being found in 44.66% of subtype 1a and 0.25% of subtype 1b. Other frequent mutations observed in more than 2% of the NS3 sequences were: I170V (3.21%) in genotype 1a, and Y56F (15.93%), V132I (23.28%) and I170V (65.20%) in genotype 1b. For the NS5A, 2.21% of the genotype 1a sequences have the P58S mutation, 5.95% of genotype 1b sequences have the R30Q mutation, 15.79% of subtypes 2a sequences have the Q30R mutation, 23.08% of subtype 2b sequences have a L31M mutation, and in subtype 3a sequences, 23.08% have the M31L resistant variants. For the NS5B, the V321L RAV was identified in 0.60% of genotype 1a and in 0.32% of genotype 1b sequences, and the N142T variant was observed in 0.32% of subtype 1b sequences. The C316Y, S556G, D559N RAV were identified in 0.33%, 7.82% and 0.32% of genotype 1b sequences

  15. ChickVD: a sequence variation database for the chicken genome

    DEFF Research Database (Denmark)

    Wang, Jing; He, Ximiao; Ruan, Jue

    2005-01-01

    Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DN...... on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics.org.cn. Udgivelsesdato: 2005-Jan-1...

  16. Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999

    Energy Technology Data Exchange (ETDEWEB)

    Harger, Carol A.

    1999-10-28

    Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence. [The annual report for June 1996 to August 1997 is included as an attachment to this final report.

  17. Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999; FINAL

    International Nuclear Information System (INIS)

    Harger, Carol A.

    1999-01-01

    Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence.[The annual report for June 1996 to August 1997 is included as an attachment to this final report.

  18. Performance of Correspondence Algorithms in Vision-Based Driver Assistance Using an Online Image Sequence Database

    DEFF Research Database (Denmark)

    Klette, Reinhard; Krüger, Norbert; Vaudrey, Tobi

    2011-01-01

    the classification of recorded video data into situations defined by a cooccurrence of some events in recorded traffic scenes. About 100-400 stereo frames (or 4-16 s of recording) are considered a basic sequence, which will be identified with one particular situation. Future testing is expected to be on data...

  19. Patents as instruments for exploring innovation dynamics: geographic and technological perspectives on “photovoltaic cells”

    NARCIS (Netherlands)

    Leydesdorff, L.; Alkemade, F.; Heimeriks, G.; Hoekstra, R.J.

    2015-01-01

    The recently developed Cooperative Patent Classifications of the U.S. Patent and Trade Office (USPTO) and the European Patent Office (EPO) provide new options for an informed delineation of samples in both USPTO data and the Worldwide Patent Statistical Database (PatStat) of EPO. Among the

  20. Trends in worldwide nanotechnology patent applications: 1991 to 2008

    International Nuclear Information System (INIS)

    Dang Yan; Zhang Yulei; Fan Li; Chen Hsinchun; Roco, Mihail C.

    2010-01-01

    Nanotechnology patent applications published during 1991-2008 have been examined using the 'title-abstract' keyword search on esp-cenet 'worldwide' database. The longitudinal evolution of the number of patent applications, their topics, and their respective patent families have been evaluated for 15 national patent offices covering 98% of the total global activity. The patent offices of the United States (USA), People's Republic of China (PRC), Japan, and South Korea have published the largest number of nanotechnology patent applications, and experienced significant but different growth rates after 2000. In most repositories, the largest numbers of nanotechnology patent applications originated from their own countries/regions, indicating a significant 'home advantage.' The top applicant institutions are from different sectors in different countries (e.g., from industry in the US and Canada patent offices, and from academe or government agencies at the PRC office). As compared to 2000, the year before the establishment of the US National Nanotechnology Initiative (NNI), numerous new invention topics appeared in 2008, in all 15 patent repositories. This is more pronounced in the USA and PRC. Patent families have increased among the 15 patent offices, particularly after 2005. Overlapping patent applications increased from none in 1991 to about 4% in 2000 and to about 27% in 2008. The largest share of equivalent nanotechnology patent applications (1,258) between two repositories was identified between the US and Japan patent offices.

  1. Trends in worldwide nanotechnology patent applications: 1991 to 2008

    Science.gov (United States)

    Dang, Yan; Zhang, Yulei; Fan, Li; Chen, Hsinchun; Roco, Mihail C.

    2010-03-01

    Nanotechnology patent applications published during 1991-2008 have been examined using the "title-abstract" keyword search on esp@cenet "worldwide" database. The longitudinal evolution of the number of patent applications, their topics, and their respective patent families have been evaluated for 15 national patent offices covering 98% of the total global activity. The patent offices of the United States (USA), People's Republic of China (PRC), Japan, and South Korea have published the largest number of nanotechnology patent applications, and experienced significant but different growth rates after 2000. In most repositories, the largest numbers of nanotechnology patent applications originated from their own countries/regions, indicating a significant "home advantage." The top applicant institutions are from different sectors in different countries (e.g., from industry in the US and Canada patent offices, and from academe or government agencies at the PRC office). As compared to 2000, the year before the establishment of the US National Nanotechnology Initiative (NNI), numerous new invention topics appeared in 2008, in all 15 patent repositories. This is more pronounced in the USA and PRC. Patent families have increased among the 15 patent offices, particularly after 2005. Overlapping patent applications increased from none in 1991 to about 4% in 2000 and to about 27% in 2008. The largest share of equivalent nanotechnology patent applications (1,258) between two repositories was identified between the US and Japan patent offices.

  2. Trends in worldwide nanotechnology patent applications: 1991 to 2008

    Energy Technology Data Exchange (ETDEWEB)

    Dang Yan, E-mail: ydang@email.arizona.edu; Zhang Yulei, E-mail: ylzhang@email.arizona.edu; Fan Li, E-mail: fanli@email.arizona.edu; Chen Hsinchun, E-mail: hchen@eller.arizona.ed [University of Arizona, Department of Management Information Systems, Eller College of Management (United States); Roco, Mihail C., E-mail: mroco@nsf.go [National Science Foundation (United States)

    2010-03-15

    Nanotechnology patent applications published during 1991-2008 have been examined using the 'title-abstract' keyword search on esp-cenet 'worldwide' database. The longitudinal evolution of the number of patent applications, their topics, and their respective patent families have been evaluated for 15 national patent offices covering 98% of the total global activity. The patent offices of the United States (USA), People's Republic of China (PRC), Japan, and South Korea have published the largest number of nanotechnology patent applications, and experienced significant but different growth rates after 2000. In most repositories, the largest numbers of nanotechnology patent applications originated from their own countries/regions, indicating a significant 'home advantage.' The top applicant institutions are from different sectors in different countries (e.g., from industry in the US and Canada patent offices, and from academe or government agencies at the PRC office). As compared to 2000, the year before the establishment of the US National Nanotechnology Initiative (NNI), numerous new invention topics appeared in 2008, in all 15 patent repositories. This is more pronounced in the USA and PRC. Patent families have increased among the 15 patent offices, particularly after 2005. Overlapping patent applications increased from none in 1991 to about 4% in 2000 and to about 27% in 2008. The largest share of equivalent nanotechnology patent applications (1,258) between two repositories was identified between the US and Japan patent offices.

  3. Amino acid sequences of predicted proteins and their annotation for 95 organism species. - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Gclust Server Amino acid sequences of predicted proteins and their annotation for 95 organis...m species. Data detail Data name Amino acid sequences of predicted proteins and their annotation for 95 orga...nism species. DOI 10.18908/lsdba.nbdc00464-001 Description of data contents Amino acid sequences of predicted proteins...Database Description Download License Update History of This Database Site Policy | Contact Us Amino acid sequences of predicted prot...eins and their annotation for 95 organism species. - Gclust Server | LSDB Archive ...

  4. Digital pathology: A systematic evaluation of the patent landscape

    Directory of Open Access Journals (Sweden)

    Ioan C. Cucoranu

    2014-01-01

    Full Text Available Introduction: Digital pathology is a relatively new field. Inventors of technology in this field typically file for patents to protect their intellectual property. An understanding of the patent landscape is crucial for companies wishing to secure patent protection and market dominance for their products. To our knowledge, there has been no prior systematic review of patents related to digital pathology. Therefore, the aim of this study was to systematically identify and evaluate United States patents and patent applications related to digital pathology. Materials and Methods: Issued patents and patent applications related to digital pathology published in the United States Patent and Trademark Office (USPTO database (www.uspto.gov (through January 2014 were searched using the Google Patents search engine (Google Inc., Mountain View, California, USA. Keywords and phrases related to digital pathology, whole-slide imaging (WSI, image analysis, and telepathology were used to query the USPTO database. Data were downloaded and analyzed using the Papers application (Mekentosj BV, Aalsmeer, Netherlands. Results: A total of 588 United States patents that pertain to digital pathology were identified. In addition, 228 patent applications were identified, including 155 that were pending, 65 abandoned, and eight rejected. Of the 588 patents granted, 348 (59.18% were specific to pathology, while 240 (40.82% included more general patents also usable outside of pathology. There were 70 (21.12% patents specific to pathology and 57 (23.75% more general patents that had expired. Over 120 unique entities (individual inventors, academic institutions, and private companies applied for pathology specific patents. Patents dealt largely with telepathology and image analysis. WSI related patents addressed image acquisition (scanning and focus, quality (z-stacks, management (storage, retrieval, and transmission of WSI files, and viewing (graphical user interface (GUI

  5. Digital pathology: A systematic evaluation of the patent landscape.

    Science.gov (United States)

    Cucoranu, Ioan C; Parwani, Anil V; Vepa, Suryanarayana; Weinstein, Ronald S; Pantanowitz, Liron

    2014-01-01

    Digital pathology is a relatively new field. Inventors of technology in this field typically file for patents to protect their intellectual property. An understanding of the patent landscape is crucial for companies wishing to secure patent protection and market dominance for their products. To our knowledge, there has been no prior systematic review of patents related to digital pathology. Therefore, the aim of this study was to systematically identify and evaluate United States patents and patent applications related to digital pathology. Issued patents and patent applications related to digital pathology published in the United States Patent and Trademark Office (USPTO) database (www.uspto.gov) (through January 2014) were searched using the Google Patents search engine (Google Inc., Mountain View, California, USA). Keywords and phrases related to digital pathology, whole-slide imaging (WSI), image analysis, and telepathology were used to query the USPTO database. Data were downloaded and analyzed using the Papers application (Mekentosj BV, Aalsmeer, Netherlands). A total of 588 United States patents that pertain to digital pathology were identified. In addition, 228 patent applications were identified, including 155 that were pending, 65 abandoned, and eight rejected. Of the 588 patents granted, 348 (59.18%) were specific to pathology, while 240 (40.82%) included more general patents also usable outside of pathology. There were 70 (21.12%) patents specific to pathology and 57 (23.75%) more general patents that had expired. Over 120 unique entities (individual inventors, academic institutions, and private companies) applied for pathology specific patents. Patents dealt largely with telepathology and image analysis. WSI related patents addressed image acquisition (scanning and focus), quality (z-stacks), management (storage, retrieval, and transmission of WSI files), and viewing (graphical user interface (GUI), workflow, slide navigation and remote control). An

  6. Sequence Classification - TMBETA-GENOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ansmembrane helical proteins by applying statistical and machine learning methods to each amino acid sequenc.... Amino Acid Result of predicting β-barrel membrane protein with a statistical method using amino acid compo...sition. ( TMBETADISC-COMP ) Dipeptide Result of predicting β-barrel membrane protein with a statistic...ting β-barrel membrane protein with a statistical method using motifs. ( TMBETADISC-MOTIF ) SVM Result of pr

  7. Patent Assessment Quality

    DEFF Research Database (Denmark)

    Burke, Paul F.; Reitzig, Markus

    2006-01-01

    The increasing number of patent applications worldwide and the extension of patenting to the areas of software and business methods have triggered a debate on "patent quality". While patent quality may have various dimensions, this paper argues that consistency in the decision making on the side...... of the patent office is one important dimension, particularly in new patenting areas (emerging technologies). In order to understand whether patent offices appear capable of providing consistent assessments of a patent's technological quality in such novel industries from the beginning, we study the concordance...... of the European Patent Office's (EPO's) granting and opoposition decisions for individual patents. We use the historical example of biotech patens filed between 1978 until 1986, the early stage of the industry. Our results indicate that the EPO shows systematically different assessments of technological quality...

  8. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

    OpenAIRE

    Lescot, Magali; Déhais, Patrice; Thijs, Gert; Marchal, Kathleen; Moreau, Yves; Van de Peer, Yves; Rouzé, Pierre; Rombauts, Stephane

    2002-01-01

    PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific t...

  9. Identification of Anhydrobiosis-related Genes from an Expressed Sequence Tag Database in the Cryptobiotic Midge Polypedilum vanderplanki (Diptera; Chironomidae)*

    Science.gov (United States)

    Cornette, Richard; Kanamori, Yasushi; Watanabe, Masahiko; Nakahara, Yuichi; Gusev, Oleg; Mitsumasu, Kanako; Kadono-Okuda, Keiko; Shimomura, Michihiko; Mita, Kazuei; Kikawada, Takahiro; Okuda, Takashi

    2010-01-01

    Some organisms are able to survive the loss of almost all their body water content, entering a latent state known as anhydrobiosis. The sleeping chironomid (Polypedilum vanderplanki) lives in the semi-arid regions of Africa, and its larvae can survive desiccation in an anhydrobiotic form during the dry season. To unveil the molecular mechanisms of this resistance to desiccation, an anhydrobiosis-related Expressed Sequence Tag (EST) database was obtained from the sequences of three cDNA libraries constructed from P. vanderplanki larvae after 0, 12, and 36 h of desiccation. The database contained 15,056 ESTs distributed into 4,807 UniGene clusters. ESTs were classified according to gene ontology categories, and putative expression patterns were deduced for all clusters on the basis of the number of clones in each library; expression patterns were confirmed by real-time PCR for selected genes. Among up-regulated genes, antioxidants, late embryogenesis abundant (LEA) proteins, and heat shock proteins (Hsps) were identified as important groups for anhydrobiosis. Genes related to trehalose metabolism and various transporters were also strongly induced by desiccation. Those results suggest that the oxidative stress response plays a central role in successful anhydrobiosis. Similarly, protein denaturation and aggregation may be prevented by marked up-regulation of Hsps and the anhydrobiosis-specific LEA proteins. A third major feature is the predicted increase in trehalose synthesis and in the expression of various transporter proteins allowing the distribution of trehalose and other solutes to all tissues. PMID:20833722

  10. The History of Patenting Genetic Material.

    Science.gov (United States)

    Sherkow, Jacob S; Greely, Henry T

    2015-01-01

    The US Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics, Inc. declared, for the first time, that isolated human genes cannot be patented. Many have wondered how genes were ever the subjects of patents. The answer lies in a nuanced understanding of both legal and scientific history. Since the early twentieth century, "products of nature" were not eligible to be patented unless they were "isolated and purified" from their surrounding environment. As molecular biology advanced, and the capability to isolate genes both physically and by sequence came to fruition, researchers (and patent offices) began to apply patent-law logic to genes themselves. These patents, along with other biological patents, generated substantial social and political criticism. Myriad Genetics, a company with patents on BRCA1 and BRCA2, two genes critical to assessing early-onset breast and ovarian cancer risk, and with a particularly controversial business approach, became the antagonist in an ultimately successful campaign to overturn gene patents in court. Despite Myriad's defeat, some questions concerning the rights to monopolize genetic information remain. The history leading to that defeat may be relevant to these future issues.

  11. Patents in INIS

    International Nuclear Information System (INIS)

    Scheel, H.; Breitfeld, B.

    1983-01-01

    Proceeding from the INIS rules for collecting, characterizing, and making available patent documents, results of an analysis are presented, which concern timeliness, origin, and classification of patents according to the INIS subject categories and the International Patent Classification. GDR's capabilities for SDI services and retrospective searches are outlined taking into account patents. For a selected subject area (IPC G21) the coverage of patents announced by INIS was found to be about 30%

  12. PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools

    Directory of Open Access Journals (Sweden)

    Adeel Malik

    2010-01-01

    Full Text Available Understanding of the three-dimensional structures of proteins that interact with carbohydrates covalently (glycoproteins as well as noncovalently (protein-carbohydrate complexes is essential to many biological processes and plays a significant role in normal and disease-associated functions. It is important to have a central repository of knowledge available about these protein-carbohydrate complexes as well as preprocessed data of predicted structures. This can be significantly enhanced by tools de novo which can predict carbohydrate-binding sites for proteins in the absence of structure of experimentally known binding site. PROCARB is an open-access database comprising three independently working components, namely, (i Core PROCARB module, consisting of three-dimensional structures of protein-carbohydrate complexes taken from Protein Data Bank (PDB, (ii Homology Models module, consisting of manually developed three-dimensional models of N-linked and O-linked glycoproteins of unknown three-dimensional structure, and (iii CBS-Pred prediction module, consisting of web servers to predict carbohydrate-binding sites using single sequence or server-generated PSSM. Several precomputed structural and functional properties of complexes are also included in the database for quick analysis. In particular, information about function, secondary structure, solvent accessibility, hydrogen bonds and literature reference, and so forth, is included. In addition, each protein in the database is mapped to Uniprot, Pfam, PDB, and so forth.

  13. The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit.

    Science.gov (United States)

    Hussing, C; Bytyci, R; Huber, C; Morling, N; Børsting, C

    2018-05-24

    Some STR loci have internal sequence variations, which are not revealed by the standard STR typing methods used in forensic genetics (PCR and fragment length analysis by capillary electrophoresis (CE)). Typing of STRs with next-generation sequencing (NGS) uncovers the sequence variation in the repeat region and in the flanking regions. In this study, 363 Danish individuals were typed for 56 STRs (26 autosomal STRs, 24 Y-STRs, and 6 X-STRs) using the ForenSeq™ DNA Signature Prep Kit to establish a Danish STR sequence database. Increased allelic diversity was observed in 34 STRs by the PCR-NGS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were around four times larger than the numbers of alleles determined by repeat length alone. Thirteen SNPs and one InDel were identified in the flanking regions of 12 STRs. Furthermore, 36 single positions and five longer stretches in the STR flanking regions were found to have dubious genotyping quality. The combined match probability of the 26 autosomal STRs was 10,000 times larger using the PCR-NGS assay than by using PCR-CE. The typical paternity indices for trios and duos were 500 and 100 times larger, respectively, than those obtained with PCR-CE. The assay also amplified 94 SNPs selected for human identification. Eleven of these loci were not in Hardy-Weinberg equilibrium in the Danish population, most likely because the minimum threshold for allele calling (30 reads) in the ForenSeq™ Universal Analysis Software was too low and frequent allele dropouts were not detected.

  14. Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.

    Directory of Open Access Journals (Sweden)

    Patrik L Ståhl

    Full Text Available Biomarker identification is of utmost importance for the development of novel diagnostics and therapeutics. Here we make use of a translational database selection strategy, utilizing data from the Human Protein Atlas (HPA on differentially expressed protein patterns in healthy and breast cancer tissues as a means to filter out potential biomarkers for underlying genetic causatives of the disease. DNA was isolated from ten breast cancer biopsies, and the protein coding and flanking non-coding genomic regions corresponding to the selected proteins were extracted in a multiplexed format from the samples using a single DNA sequence capture array. Deep sequencing revealed an even enrichment of the multiplexed samples and a great variation of genetic alterations in the tumors of the sampled individuals. Benefiting from the upstream filtering method, the final set of biomarker candidates could be completely verified through bidirectional Sanger sequencing, revealing a 40 percent false positive rate despite high read coverage. Of the variants encountered in translated regions, nine novel non-synonymous variations were identified and verified, two of which were present in more than one of the ten tumor samples.

  15. Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.

    Science.gov (United States)

    Allard, Marc W; Strain, Errol; Melka, David; Bunning, Kelly; Musser, Steven M; Brown, Eric W; Timme, Ruth

    2016-08-01

    The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  16. Patent analysis for competitive technical intelligence and innovative thinking

    Directory of Open Access Journals (Sweden)

    H Dou

    2006-01-01

    Full Text Available Patents are a very useful source of technical information. The public availability of patents over the Internet, with for some databases (eg. Espacenet the assurance of a constant format, allows the development of high value added products using this information source and provides an easy way to analyze patent information. This simple and powerful tool facilitates the use of patents in academic research, in SMEs and in developing countries providing a way to use patents as a ideas resource thus improving technological innovation.

  17. To succeed using patent and invention which are brillant idea

    International Nuclear Information System (INIS)

    Yu, Jae Bok

    1999-07-01

    This book deals with what invention is, how we can be a inventor, how we apply inventions to intellectual property office, and other useful advice and lesson on patent. These are the titles of each part : trouble stories on success to invent, everybody can be a inventor, this is a invention. There is a problem when the idea is same or similar, preceding patent, where does it hide? database on patent, patent information, Let's go to Korean intellectual property office, patient application which we misses in our dream, and instructions of patent including various sides.

  18. CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.

    Science.gov (United States)

    Park, Byung H; Karpinets, Tatiana V; Syed, Mustafa H; Leuze, Michael R; Uberbacher, Edward C

    2010-12-01

    The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich and invaluable information stored in the database, software tools utilizing this information for annotation of newly sequenced genomes by CAZy families are limited. We have employed two annotation approaches to fill the gap between manually curated high-quality protein sequences collected in the CAZy database and the growing number of other protein sequences produced by genome or metagenome sequencing projects. The first approach is based on a similarity search against the entire nonredundant sequences of the CAZy database. The second approach performs annotation using links or correspondences between the CAZy families and protein family domains. The links were discovered using the association rule learning algorithm applied to sequences from the CAZy database. The approaches complement each other and in combination achieved high specificity and sensitivity when cross-evaluated with the manually curated genomes of Clostridium thermocellum ATCC 27405 and Saccharophagus degradans 2-40. The capability of the proposed framework to predict the function of unknown protein domains and of hypothetical proteins in the genome of Neurospora crassa is demonstrated. The framework is implemented as a Web service, the CAZymes Analysis Toolkit, and is available at http://cricket.ornl.gov/cgi-bin/cat.cgi.

  19. Characterization and compilation of polymorphic simple sequence repeat (SSR markers of peanut from public database

    Directory of Open Access Journals (Sweden)

    Zhao Yongli

    2012-07-01

    Full Text Available Abstract Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L. genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5% within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5% was the most abundant followed by AAG (12.1%, AAT (10.9%, and AT (10.3%.The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.

  20. Patentability of inventions under the Nigeria's patents and designs act

    African Journals Online (AJOL)

    Patentability of inventions under the Nigeria's patents and designs act: an examination. ... AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search · USING ... The Nigerian Patent Registry refuses patent applications for Software or ...

  1. Litigation-proof patents: avoiding the most common patent mistakes

    National Research Council Canada - National Science Library

    Goldstein, Larry M

    2014-01-01

    "Litigation-Proof Patents: Avoiding the Most Common Patent Mistakes explains the principles of excellent patents, presents the ten most common errors in patents, and details a step-by-step method for avoiding these common errors...

  2. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

    Science.gov (United States)

    Portales-Casamar, Elodie; Arenillas, David; Lim, Jonathan; Swanson, Magdalena I.; Jiang, Steven; McCallum, Anthony; Kirov, Stefan; Wasserman, Wyeth W.

    2009-01-01

    The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein–DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ‘boutiques’ within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation. Since its initial release, PAZAR has grown in terms of data, features and through the addition of an associated package of software tools called the ORCA toolkit (ORCAtk). ORCAtk allows users to rapidly develop analyses based on the information stored in the PAZAR system. PAZAR is available at http://www.pazar.info. ORCAtk can be accessed through convenient buttons located in the PAZAR pages or via our website at http://www.cisreg.ca/ORCAtk. PMID:18971253

  3. Modern evaluation of patents

    Science.gov (United States)

    Ignat, V.

    2016-08-01

    The number of patents is not so important as the market value. The market value is especially important for licensing of patents, make-or-buy decisions for technology procurement, corporate finance. Patents can be used as collateral for financing. Patents and credit approvals: without patents only 46% and with patents 54%. The value share of knowledge-based components to industrial products already reached 50% and it is still rising. OECD called these developments under the slogan "knowledge economy”. German Norm-DIN 77100 provides a working method for monetary evaluation of a patent. The value of a patent arises from its use. A patent can be used to protect or to earn licensing revenues. An evaluation expertise is required in areas, such as marketing, finance, R & D and strategic planning. As an indicator of the value of a patent is often used the number of citations. The number of a patent citation refers to its meaning and value. Other indicators would be: size of the patent family, validity of the patent, result of objections against patent application, number and quality of claims. The analysis of 9.000 patents resulted that only 7.2% worth over 10 million euro and 68% below 1 million euro. The cost method: it is considered the cost that would be incurred for the development and patenting of a similar invention. The market method: are used the prices that have been achieved in comparable with recently transactions. The Income method: the potential reward is measured, which can arise from a patent. The evaluation will be in the following areas: legal status, technology, market conditions, finance and strategy. Each question relates to a different parameter of a value.

  4. Functional role of bacteriophage transfer RNAs: codon usage analysis of genomic sequences stored in the GENBANK/EMBL/DDBJ databases

    Directory of Open Access Journals (Sweden)

    T Kunisawa

    2006-01-01

    Full Text Available Complete genomic sequence data are stored in the public GenBank/EMBL/DDBJ databases so that any investigator can make use of the data. This report describes a comparative analysis of codon usage that is impossible without such a public and open data system. A limited number of bacteriophages harbor their own transfer RNAs. Based on a comparison between T4 phage-encoded tRNA species and the relative cellular amounts of host Escherichia coli tRNAs, it is hypothesized that T4 tRNAs could serve to supplement host isoacceptor tRNA species that are present in minor amounts and thus enhance the translational efficiency of phage proteins. When compared to their respective host bacteria, the codon usage data of bacteriophages D3, φC31, HP1, D29 and 933W all show an increased frequency of synonymous codons or amino acids that correspond to phage tRNA species, suggesting their supplemental role in the efficient production of phage proteins. The data-analysis presents an example in which the availability of an open and fully accessible database system would allow one to obtain comprehensive insights into a fundamental problem in molecular biology.

  5. Biotechnological Patents Applications of the Deuterium Oxide in Human Health.

    Science.gov (United States)

    da S Mariano, Reysla M; Bila, Wendell C; Trindade, Maria Jaciara F; Lamounier, Joel A; Galdino, Alexsandro S

    2017-01-01

    Deuterium oxide is a molecule that has been used for decades in several studies related to human health. Currently, studies on D2O have mobilized a "Race for Patenting" worldwide. Several patents have been registered from biomedical and technological studies of D2O showing the potential of this stable isotope in industry and health care ecosystems. Most of the patents related to the applications of the deuterium oxide in human health have been summarized in this review. The following patents databases were consulted: European Patent Office (Espacenet), the United States Patent and Trademark Office (USPTO), the United States Latin America Patents (LATIPAT), Patent scope -Search International and National Patent Collections (WIPO), Google Patents and Free Patents Online. With this review, the information was collected on recent publications including 22 patents related to deuterium oxide and its applications in different areas. This review showed that deuterium oxide is a promising component in different areas, including biotechnology, chemistry and medicine. In addition, the knowledge of this compound was covered, reinforcing its importance in the field of biotechnology and human health. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  6. A guide of patent map

    International Nuclear Information System (INIS)

    1999-12-01

    This book introduces application and characteristic of patent information, types of patent information data and research of patent information, arrangement of patent information and patent map, analysis of patent information, necessity, writing period arrangement way of patent map, cases of patent map on selection of task of research and development, system of research and development and application, examples of PM such as MAP by year, application, technique, Inventor, and claim point map and computerization like data arrangement of PM patent, collection of analysis range and item analysis of patent, cases and written reports on patent analysis.

  7. Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

    Science.gov (United States)

    Sheik, Cody S; Reese, Brandi Kiel; Twing, Katrina I; Sylvan, Jason B; Grim, Sharon L; Schrenk, Matthew O; Sogin, Mitchell L; Colwell, Frederick S

    2018-01-01

    Earth's subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface environments has been compiled. However, due to low quantities of biomass in the deep subsurface, the potential for incorporation of contaminants from reagents used during sample collection, processing, and/or sequencing is high. Thus, to understand the ecology of subsurface microorganisms (i.e., the distribution, richness, or survival), it is necessary to minimize, identify, and remove contaminant sequences that will skew the relative abundances of all taxa in the sample. In this meta-analysis, we identify putative contaminants associated with the CoDL dataset, recommend best practices for removing contaminants from samples, and propose a series of best practices for subsurface microbiology sampling. The most abundant putative contaminant genera observed, independent of evenness across samples, were Propionibacterium , Aquabacterium , Ralstonia , and Acinetobacter . While the top five most frequently observed genera were Pseudomonas , Propionibacterium , Acinetobacter , Ralstonia , and Sphingomonas . The majority of the most frequently observed genera (high evenness) were associated with reagent or potential human contamination. Additionally, in DNA extraction blanks, we observed potential archaeal contaminants, including methanogens, which have not been discussed in previous contamination studies. Such contaminants would directly affect the interpretation of subsurface molecular studies, as methanogenesis is an important subsurface biogeochemical process. Utilizing previously identified contaminant genera, we found that ∼27% of the total dataset were identified as contaminant sequences that likely originate from DNA

  8. Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

    Directory of Open Access Journals (Sweden)

    Arun Prabhu Dhanapal

    2015-01-01

    Full Text Available The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.

  9. Patents for Soldiers

    Science.gov (United States)

    2016-06-10

    PATENTS FOR SOLDIERS A thesis presented to the Faculty of the U.S. Army Command and General Staff College in partial fulfillment...COVERED (From - To) AUG 2015 – JUNE 2016 4. TITLE AND SUBTITLE Patents for Soldiers 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...protection of an innovative idea; that is, a patent . A Soldier’s pursuit of patents provides the Army with tangible and intangible benefits. There are on

  10. MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard A.; Panyala, Ajay R.; Glass, Kevin A.; Colby, Sean M.; Glaesemann, Kurt R.; Jansson, Georg C.; Jansson, Janet K.

    2017-02-21

    MerCat is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. MerCat inputs include assembled contigs and raw sequence reads from any platform resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST and/or DIAMOND for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and metatranscriptomes).

  11. Herbal drug patenting in India: IP potential.

    Science.gov (United States)

    Sahoo, Niharika; Manchikanti, Padmavati; Dey, Satya Hari

    2011-09-01

    Herbal drugs are gaining worldwide prominence due to their distinct advantages. Developing countries have started exploring the ethnopharmacological approach of drug discovery and have begun to file patents on herbal drugs. The expansion of R&D in Indian herbal research organizations and presence of manufacturing units at non-Indian sites is an indication of the capability to develop new products and processes. The present study attempts to identify innovations in the Indian herbal drug sector by analyzing the patenting trends in India, US and EU. Based on key word and IPC based search at the IPO, USPTO, Esp@cenet and WIPO databases, patent applications and grant in herbal drugs by Indian applicants/assignees was collected for the last ten years (from 1st January 2001 to 31st October 2010). From this collection patents related to human therapeutic use only were selected. Analysis was performed to identify filing trends, major applicants/assignees, disease area and major plant species used for various treatments. There is a gradual increase in patent filing through the years. In India, individual inventors have maximum applications and grants. CSIR, among research organizations and Hindustan Unilever, Avesthagen, Piramal Life Science, Sahajanand Biotech and Indus Biotech among the companies have the maximum granted patents in India, US and EU respectively. Diabetes, cancer and inflammatory disorders are the major areas for patenting in India and abroad. Recent patents are on new herbal formulations for treatment of AIDS, hepatitis, skin disorders and gastrointestinal disorders. A majority of the herbal patents applications and grants in India are with individual inventors. Claim analysis indicates that these patents include novel multi-herb compositions with synergistic action. Indian research organizations are more active than companies in filing for patents. CSIR has maximum numbers of applications not only in India but also in the US and EU. Patents by research

  12. PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill).

    Science.gov (United States)

    Chaudhary, Sakshi; Mishra, Bharat Kumar; Vivek, Thiruvettai; Magadum, Santoshkumar; Yasin, Jeshima Khan

    2016-01-01

    Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting.

  13. MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures.

    Science.gov (United States)

    Khan, Javed Mohammed; Cheruku, Harish Reddy; Tong, Joo Chuan; Ranganathan, Shoba

    2011-04-15

    Sequence-structure-function information is critical in understanding the mechanism of pMHC and TR/pMHC binding and recognition. A database for sequence-structure-function information on pMHC and TR/pMHC interactions, MHC-Peptide Interaction Database-TR version 2 (MPID-T2), is now available augmented with the latest PDB and IMGT/3Dstructure-DB data, advanced features and new parameters for the analysis of pMHC and TR/pMHC structures. http://biolinfo.org/mpid-t2. shoba.ranganathan@mq.edu.au Supplementary data are available at Bioinformatics online.

  14. Patenting Nanomedicine in Europe:

    DEFF Research Database (Denmark)

    Nordberg, Ana

    Patenting Nanomedicine in Europe: Applying the ‘medical methods exception’ to emerging technologies is based on the authors PhD dissertation, defended in March 2014, at the University of Copenhagen. The book debates restrictions on the patentability of medical methods in European Patent Law....... The main question addressed is whether it is viable and advisable the reinterpretation, reformulation or replacement of Article 53 (c) EPC – a provision restricting the patenting of medical methods. The subject is approached by reference to emerging technologies, and using nanomedicine innovation...... as example and point of departure. Nanotechnology inventions blur the lines between patentable subject matter and what may fall under the exception from patentability. It is a good example of how in recent years, emerging technologies have been challenging the patent system and exposing the need for re...

  15. Worldwide nanotechnology development: a comparative study of USPTO, EPO, and JPO patents (1976-2004)

    International Nuclear Information System (INIS)

    Li Xin; Lin Yiling; Chen Hsinchun; Roco, Mihail C.

    2007-01-01

    To assess worldwide development of nanotechnology, this paper compares the numbers and contents of nanotechnology patents in the United States Patent and Trademark Office (USPTO), European Patent Office (EPO), and Japan Patent Office (JPO). It uses the patent databases as indicators of nanotechnology trends via bibliographic analysis, content map analysis, and citation network analysis on nanotechnology patents per country, institution, and technology field. The numbers of nanotechnology patents published in USPTO and EPO have continued to increase quasi-exponentially since 1980, while those published in JPO stabilized after 1993. Institutions and individuals located in the same region as a repository's patent office have a higher contribution to the nanotechnology patent publication in that repository ('home advantage' effect). The USPTO and EPO databases had similar high-productivity contributing countries and technology fields with large number of patents, but quite different high-impact countries and technology fields after the average number of received cites. Bibliographic analysis on USPTO and EPO patents shows that researchers in the United States and Japan published larger numbers of patents than other countries, and that their patents were more frequently cited by other patents. Nanotechnology patents covered physics research topics in all three repositories. In addition, USPTO showed the broadest representation in coverage in biomedical and electronics areas. The analysis of citations by technology field indicates that USPTO had a clear pattern of knowledge diffusion from highly cited fields to less cited fields, while EPO showed knowledge exchange mainly occurred among highly cited fields

  16. The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

    DEFF Research Database (Denmark)

    Celis, J E; Leffers, H; Rasmussen, H H

    1991-01-01

    autoantigens" and "cDNAs". For convenience we have included an alphabetical list of all known proteins recorded in this database. In the long run, the main goal of this database is to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture......The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus...

  17. gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes.

    Science.gov (United States)

    Nakagawa, So; Takahashi, Mahoko Ueda

    2016-01-01

    In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species.Database URL: http://geve.med.u-tokai.ac.jp. © The Author(s) 2016. Published by Oxford University Press.

  18. Invention note and patent note

    International Nuclear Information System (INIS)

    Chang, Sung Su

    1997-09-01

    This book deals with origin of invention and term related patent and invention, making idea, brain storming, 10 laws of invention skill, attitude of inventors, invention order, making good inventions, patent system, preparation of application, procedure and method of patent, management of patent, patent and trademark office, patent lawyer, copyright, new intellectual property right, industrial property right, trademark, invasion of industrial property right, patent, Judgment, preparation of items, application of industrial property right and effect of inventor and related people.

  19. AcEST(EST sequences of Adiantum capillus-veneris and their annotation) - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us AcEST AcEST(EST sequences of Adiantum capillus-veneris and their annotation) Data detail Dat...a name AcEST(EST sequences of Adiantum capillus-veneris and their annotation) DOI 10.18908/lsdba.nbdc00839-0...01 Description of data contents EST sequence of Adiantum capillus-veneris and its annotation (clone ID, libr...le search URL http://togodb.biosciencedbc.jp/togodb/view/archive_acest#en Data acquisition method Capillary ...ainst UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases) Number of data entries Adiantum capillus-veneris

  20. Nano/micro-electro mechanical systems: a patent view

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Guangyuan, E-mail: hu.guangyuan@mail.shufe.edu.cn, E-mail: hu.guangyuan@shufe.edu.cn [Shanghai University of Finance and Economics, School of Public Economics and Administration (China); Liu, Weishu [Shanghai Jiao Tong University, Antai College of Economics and Management (China)

    2015-12-15

    Combining both bibliometrics and citation network analysis, this research evaluates the global development of micro-electro mechanical systems (MEMS) research based on the Derwent Innovations Index database. We found that worldwide, the growth trajectory of MEMS patents demonstrates an approximate S shape, with United States, Japan, China, and Korea leading the global MEMS race. Evidenced by Derwent class codes, the technology structure of global MEMS patents remains steady over time. Yet there does exist a national competitiveness component among the top country players. The latecomer China has become the second most prolific country filing MEMS patents, but its patent quality still lags behind the global average.

  1. Nano/micro-electro mechanical systems: a patent view

    International Nuclear Information System (INIS)

    Hu, Guangyuan; Liu, Weishu

    2015-01-01

    Combining both bibliometrics and citation network analysis, this research evaluates the global development of micro-electro mechanical systems (MEMS) research based on the Derwent Innovations Index database. We found that worldwide, the growth trajectory of MEMS patents demonstrates an approximate S shape, with United States, Japan, China, and Korea leading the global MEMS race. Evidenced by Derwent class codes, the technology structure of global MEMS patents remains steady over time. Yet there does exist a national competitiveness component among the top country players. The latecomer China has become the second most prolific country filing MEMS patents, but its patent quality still lags behind the global average

  2. Advances in CO2 capture technology: A patent review

    International Nuclear Information System (INIS)

    Li, Bingyun; Duan, Yuhua; Luebke, David; Morreale, Bryan

    2013-01-01

    Highlights: ► Timely updates on carbon capture technologies: More than 1000 patents on solvent, sorbent, and membrane. ► More patents on solvent and sorbent compared to membrane. ► Environmental and health concerns exist regarding carbon capture technologies. -- Abstract: Carbon dioxide (CO 2 ) emissions are believed to be a major contributor to global warming. As a consequence, large anthropogenic CO 2 sources worldwide will eventually be required to implement CO 2 capture and storage technologies to control CO 2 emissions. In order to guide the establishment of policies for CO 2 removal, we reviewed the current status of CO 2 capture patents and technologies based on the Espacenet patent database and found that more than 1000 patents have been published on sorbent, solvent, and membrane. More than 60% of these patents were published since the year 2000, and a sharp increase in patent numbers was seen in the last several years; ∼25% patents were published in the last 2 years. Substantially more patents on CO 2 removal and separation technologies are expected in the coming years. Meanwhile, the top four major types of patents, which consist of more than 2/3 of these patents, were patents granted by Japan (JP), United States (US), World Intellectual Property Organization (WO), and China (CN), and approximately half of the patents were JP and US patents. Unfortunately, no current technologies for removing CO 2 from large sources like coal-based power plants exist which satisfy the needs of safety, efficiency, and economy; further enhancement and innovation are much needed.

  3. Patents and nanomedicine.

    Science.gov (United States)

    Bawa, Raj

    2007-06-01

    Big pharma's business model, which relies on a few blockbusters to generate profits, is clearly broken. Patent expiration on numerous blockbusters in recent years is already altering the drug landscape. Drug companies are also facing other challenges that necessitate development and implementation of novel R&D strategies, including those that focus on nanotechnology and miniaturization. Clearly, there is enormous excitement and expectation regarding nanomedicine's potential impact. However, securing valid and defensible patent protection will be critical. Although early forecasts for nanomedicine commercialization are encouraging, there are numerous bottlenecks as well. One of the major hurdles is an emerging thicket of patent claims, resulting primarily from patent proliferation as well as continued issuance of surprisingly broad patents by the US Patent and Trademark Office (PTO). Adding to this confusion is the fact that the US National Nanotechnology Initiative's widely cited definition of nanotechnology is inaccurate and irrelevant from a nanomedicine perspective. It is also the cause of the inadequate patent classification system that was recently unveiled by the PTO. All of this is creating a chaotic, tangled patent landscape in various sectors of nanomedicine where the competing players are unsure of the validity and enforceability of numerous issued patents. If this trend continues, it could stifle competition and limit access to some inventions. Therefore, reforms are urgently needed at the PTO to address problems ranging from poor patent quality and questionable examination practices to inadequate search capabilities, rising attrition, poor employee morale and a skyrocketing patent application backlog. Only a robust patent system will stimulate the development of commercially viable nanomedicine products that can drastically improve a patient's quality of life and reduce healthcare costs.

  4. Performance of Patenting Firms

    DEFF Research Database (Denmark)

    Madsen, Erik Strøjer; Smith, Valdemar; Nielsen, Anders Østergaard

    2000-01-01

    Most countries focus on industries with high technology and the governments grant subsidies to innovating firms. However, there has been remarkable few studies of the performance of innovative firms or industries. This study examines the performance of patent active firms compared to the non-patenting...... firms within the manufacturing sector in Denmark. Performance is measured both by growth in employment as well as in the return on equity and profit share in turnover. The results suggest that differences in performance of patenting and non-patenting firms are very small, which questions the political...

  5. A curated gluten protein sequence database to support development of proteomics methods for determination of gluten in gluten-free foods.

    Science.gov (United States)

    Bromilow, Sophie; Gethings, Lee A; Buckley, Mike; Bromley, Mike; Shewry, Peter R; Langridge, James I; Clare Mills, E N

    2017-06-23

    The unique physiochemical properties of wheat gluten enable a diverse range of food products to be manufactured. However, gluten triggers coeliac disease, a condition which is treated using a gluten-free diet. Analytical methods are required to confirm if foods are gluten-free, but current immunoassay-based methods can unreliable and proteomic methods offer an alternative but require comprehensive and well annotated sequence databases which are lacking for gluten. A manually a curated database (GluPro V1.0) of gluten proteins, comprising 630 discrete unique full length protein sequences has been compiled. It is representative of the different types of gliadin and glutenin components found in gluten. An in silico comparison of their coeliac toxicity was undertaken by analysing the distribution of coeliac toxic motifs. This demonstrated that whilst the α-gliadin proteins contained more toxic motifs, these were distributed across all gluten protein sub-types. Comparison of annotations observed using a discovery proteomics dataset acquired using ion mobility MS/MS showed that more reliable identifications were obtained using the GluPro V1.0 database compared to the complete reviewed Viridiplantae database. This highlights the value of a curated sequence database specifically designed to support the proteomic workflows and the development of methods to detect and quantify gluten. We have constructed the first manually curated open-source wheat gluten protein sequence database (GluPro V1.0) in a FASTA format to support the application of proteomic methods for gluten protein detection and quantification. We have also analysed the manually verified sequences to give the first comprehensive overview of the distribution of sequences able to elicit a reaction in coeliac disease, the prevalent form of gluten intolerance. Provision of this database will improve the reliability of gluten protein identification by proteomic analysis, and aid the development of targeted mass

  6. Patent landscape of neglected tropical diseases: an analysis of worldwide patent families.

    Science.gov (United States)

    Akinsolu, Folahanmi Tomiwa; de Paiva, Vitor Nobre; Souza, Samuel Santos; Varga, Orsolya

    2017-11-14

    "Neglected Tropical Diseases" (NTDs) affect millions of people in Africa, Asia and South America. The two primary ways of strategic interventions are "preventive chemotherapy and transmission control" (PCT), and "innovative and intensified disease management" (IDM). In the last 5 years, phenomenal progress has been achieved. However, it is crucial to intensify research effort into NTDs, because of the emerging drug resistance. According to the World Health Organization (WHO), the term NTDs covers 17 diseases, namely buruli ulcer, Chagas disease, dengue, dracunculiasis, echinococcosis, trematodiasis, human African trypanosomiasis, leishmaniasis, leprosy, lymphatic filariasis, onchocerciasis, rabies, schistosomiasis, soil-transmitted helminthes, taeniasis, trachoma, and yaws. The aim of this study is to map out research and development (R&D) landscape through patent analysis of these identified NTDs. To achieve this, analysis and evaluation have been conducted on patenting trends, current legal status of patent families, priority countries by earliest priority years and their assignee types, technological fields of patent families over time, and original and current patent assignees. Patent families were extracted from Patseer, an international database of patents from over 100 patent issuing authorities worldwide. Evaluation of the patents was carried out using the combination of different search terms related to each identified NTD. In this paper, a total number of 12,350 patent families were analyzed. The main countries with sources of inventions were identified to be the United States (US) and China. The main technological fields covered by NTDs patent landscape are pharmaceuticals, biotechnology, organic fine chemistry, analysis of biological materials, basic materials chemistry, and medical technology. Governmental institutions and universities are the primary original assignees. Among the NTDs, leishmaniasis, dengue, and rabies received the highest number of

  7. Trends in genetic patent applications: the commercialization of academic intellectual property.

    Science.gov (United States)

    Kers, Jannigje G; Van Burg, Elco; Stoop, Tom; Cornel, Martina C

    2014-10-01

    We studied trends in genetic patent applications in order to identify the trends in the commercialization of research findings in genetics. To define genetic patent applications, the European version (ECLA) of the International Patent Classification (IPC) codes was used. Genetic patent applications data from the PATSTAT database from 1990 until 2009 were analyzed for time trends and regional distribution. Overall, the number of patent applications has been growing. In 2009, 152 000 patent applications were submitted under the Patent Cooperation Treaty (PCT) and within the EP (European Patent) system of the European Patent Office (EPO). The number of genetic patent applications increased until a peak was reached in the year 2000, with >8000 applications, after which it declined by almost 50%. Continents show different patterns over time, with the global peak in 2000 mainly explained by the USA and Europe, while Asia shows a stable number of >1000 per year. Nine countries together account for 98.9% of the total number of genetic patent applications. In The Netherlands, 26.7% of the genetic patent applications originate from public research institutions. After the year 2000, the number of genetic patent applications dropped significantly. Academic leadership and policy as well as patent regulations seem to have an important role in the trend differences. The ongoing investment in genetic research in the past decade is not reflected by an increase of patent applications.

  8. Environmentally conscious patent histories

    Science.gov (United States)

    Crouch, Dennis D.; Crouch, Henry L.

    2004-02-01

    There is a need for investigators, legislators, and business leaders to understand the magnitude of innovation and discovery in the field of environmentally conscious technologies (ECTs). Knowledge of the "big picture" is important to providing a national and global account of actual environmental stewardship over the last twenty-five years. A recitation of the Environmental Protection Agency (EPA) supported Acts which have been enacted into law reveals one facet of the multifaceted dynamic of environmental consciousness. The popular discussion and debate, as well as partisan lobbying, which created the political forces leading to environmentally conscious legislation is another facet. A third facet is the corporate response to the threats and opportunities predicted by CEO"s and others through environmental scanning. This paper examines changes in environmentally conscious inventive effort by comparing data from United States Patents issued from 1976 through 2003. Patents are useful tool for measuring technological innovation because they are publicly available records of innovative activity. Although not all inventions result in patent applications, the monopoly rights granted on the invention give the inventor a strong incentive to obtain patents on any viable product or process. Among the results, we found a significant increase in patents relating to environmentally conscious products and processes during the period in question. Specifically, a dramatic increase in patent activity was seen for the decade of the 1990"s. Surprisingly, the patenting rate from 2000 to 2003 seems to have stabilized. Additionally public discussion of ECTs appears to have a positive impact on patent filings.

  9. Truth and falsity of patent

    International Nuclear Information System (INIS)

    Park, Gum Jin

    2006-10-01

    This book describes the process of the effect to build the business of patent strongly in difficult situation. The titles of this contents are finally, lawsuit if formed, the task of patent application introduction of tasks of patent negotiation, negotiation with Fujitsu, Mitsubishi, Oki and NEC, amalgamation between LG semiconductor and Hyundai Electronic Industry, life in incorporated company, current condition of application for a patent, the method to process strategy patent, how to make strong patent and effective negotiation strategy for a patent and strategy of patent application.

  10. FishPathogens.eu/vhsv: A user-friendly Viral Haemorrhagic Septicaemia Virus (VHSV) isolate and sequence database

    DEFF Research Database (Denmark)

    Jonstrup, Søren Peter; Gray, Tanya; Kahns, Søren

    A database has been created, www.FishPathogens.eu, with the aim of providing a single repository for collating important information on significant pathogens of aquaculture, relevant to their control and management. This database will be developed, maintained and managed as part of the European...

  11. Analysing patent landscapes in plant biotechnology and new plant breeding techniques.

    Science.gov (United States)

    Parisi, Claudia; Rodríguez-Cerezo, Emilio; Thangaraj, Harry

    2013-02-01

    This article aims to inform the reader of the importance of searching patent landscapes in plant biotechnology and the use of basic tools to perform a patent search. The recommendations for a patent search strategy are illustrated with the specific example of zinc finger nuclease technology for genetic engineering in plants. Within this scope, we provide a general introduction to searching using two online and free-access patent databases esp@cenet and PatentScope. The essential features of the two databases, and their functionality is described, together with short descriptions to enable the reader to understand patents, searching, their content, patent families, and their territorial scope. We mostly stress the value of patent searching for mining scientific, rather than legal information. Search methods through the use of keywords and patent codes are elucidated together with suggestions about how to search with or combine codes with keywords and we also comment on limitations of each method. We stress the importance of patent literature to complement more mainstream scientific literature, and the relative complexities and difficulties in searching patents compared to the latter. A parallel online resource where we describe detailed search exercises is available through reference for those intending further exploration. In essence this is aimed at a novice patent searcher who may want to examine accessory patent literature to complement knowledge gained from mainstream journal resources.

  12. Construction of an Ostrea edulis database from genomic and expressed sequence tags (ESTs) obtained from Bonamia ostreae infected haemocytes: Development of an immune-enriched oligo-microarray.

    Science.gov (United States)

    Pardo, Belén G; Álvarez-Dios, José Antonio; Cao, Asunción; Ramilo, Andrea; Gómez-Tato, Antonio; Planas, Josep V; Villalba, Antonio; Martínez, Paulino

    2016-12-01

    The flat oyster, Ostrea edulis, is one of the main farmed oysters, not only in Europe but also in the United States and Canada. Bonamiosis due to the parasite Bonamia ostreae has been associated with high mortality episodes in this species. This parasite is an intracellular protozoan that infects haemocytes, the main cells involved in oyster defence. Due to the economical and ecological importance of flat oyster, genomic data are badly needed for genetic improvement of the species, but they are still very scarce. The objective of this study is to develop a sequence database, OedulisDB, with new genomic and transcriptomic resources, providing new data and convenient tools to improve our knowledge of the oyster's immune mechanisms. Transcriptomic and genomic sequences were obtained using 454 pyrosequencing and compiled into an O. edulis database, OedulisDB, consisting of two sets of 10,318 and 7159 unique sequences that represent the oyster's genome (WG) and de novo haemocyte transcriptome (HT), respectively. The flat oyster transcriptome was obtained from two strains (naïve and tolerant) challenged with B. ostreae, and from their corresponding non-challenged controls. Approximately 78.5% of 5619 HT unique sequences were successfully annotated by Blast search using public databases. A total of 984 sequences were identified as being related to immune response and several key immune genes were identified for the first time in flat oyster. Additionally, transcriptome information was used to design and validate the first oligo-microarray in flat oyster enriched with immune sequences from haemocytes. Our transcriptomic and genomic sequencing and subsequent annotation have largely increased the scarce resources available for this economically important species and have enabled us to develop an OedulisDB database and accompanying tools for gene expression analysis. This study represents the first attempt to characterize in depth the O. edulis haemocyte transcriptome in

  13. Evaluation of Brazilian biotechnology patent activity from 1975 to 2010.

    Science.gov (United States)

    Dias, F; Delfim, F; Drummond, I; Carmo, A O; Barroca, T M; Horta, C C; Kalapothakis, E

    2012-08-01

    The analysis of patent activity is one methodology used for technological monitoring. In this paper, the activity of biotechnology-related patents in Brazil were analyzed through 30 International Patent Classification (IPC) codes published by the Organization for Economic Cooperation and Development (OECD). We developed a program to analyse the dynamics of the major patent applicants, countries and IPC codes extracted from the Brazilian Patent Office (INPI) database. We also identified Brazilian patent applicants who tried to expand protection abroad via the Patent Cooperation Treaty (PCT). We had access to all patents published online at the INPI from 1975 to July 2010, including 9,791 biotechnology patent applications in Brazil, and 163 PCTs published online at World Intellectual Property Organization (WIPO) from 1997 to December 2010. To our knowledge, there are no other online reports of biotechnology patents previous to the years analyzed here. Most of the biotechnology patents filed in the INPI (10.9%) concerned measuring or testing processes involving nucleic acids. The second and third places belonged to patents involving agro-technologies (recombinant DNA technology for plant cells and new flowering plants, i.e. angiosperms, or processes for obtaining them, and reproduction of flowering plants by tissue culture techniques). The majority of patents (87.2%) were filed by nonresidents, with USA being responsible for 51.7% of all biotechnology patents deposited in Brazil. Analyzing the resident applicants per region, we found a hub in the southeast region of Brazil. Among the resident applicants for biotechnology patents filed in the INPI, 43.5% were from São Paulo, 18.3% were from Rio de Janeiro, and 9.7% were from Minas Gerais. Pfizer, Novartis, and Sanofi were the largest applicants in Brazil, with 339, 288, and 245 biotechnology patents filed, respectively. For residents, the largest applicant was the governmental institution FIOCRUZ (Oswaldo Cruz

  14. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    Science.gov (United States)

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-08

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. How Important are Noncorporate Patents?

    DEFF Research Database (Denmark)

    Schneider, Cédric

    2011-01-01

    This article analyses the innovative performances of noncorporate inventors using patent citations data from the European Patent Office. The results show that inventions patented outside an established corporate framework are on average less ‘important’ than corporate patents, but with large...... variations across technology classes. Patents applied for by independent inventors, start-ups and corporate firms are of comparable ‘quality’ in emerging technologies. The results also highlight that in these fields noncorporate patents are more ‘radical’ than corporate patents....

  16. Used, Blocking and Sleeping Patents

    DEFF Research Database (Denmark)

    Torrisi, Salvatore; Gambardella, Alfonso; Giuri, Paola

    2016-01-01

    This paper employs data from a large-scale survey (InnoS&T) of inventors in Europe, the USA, and Japan who were listed in patent applications filed at the European Patent Office with priority years between 2003 and 2005. We provide evidence regarding the reasons for patenting and the ways in which...... patents are being utilized. A substantial share of patents is neither used internally nor for market transactions, which confirms the importance of strategic patenting and inefficiency in the management of intellectual property. We investigate different types of unused patents—unused blocking patents...... and sleeping patents. We also examine the association between used and unused patents and their characteristics such as family size, scope, generality and overlapping claims, technology area, type of applicant, and the competitive environment from where these patents originate. We discuss our results...

  17. Patent Ductus Arteriosus

    Science.gov (United States)

    ... With Patent Ductus Arteriosus Figure A shows the interior of a normal heart and normal blood flow. ... PDA may shrink and go away. However, some children need treatment to close their PDAs. Some children ...

  18. DOE Patents Available for Licensing

    International Nuclear Information System (INIS)

    Stuber, C.

    1981-01-01

    DOE Patents Available for Licensing (DOE PAL) provides abstracting and indexing coverage of the DOE patent literature, including patent applications, that concerns any apsect of energy production, conservation, and utilization. The citations are arranged by subject category. DOE is prepared to grant exclusive or nonexclusive, revocable licenses under DOE-owned US patents and patent applications in accordance with the provisions of 10CFR781

  19. Technological Monitoring Study Based on Invention Patents of Omeprazoleand Derivatives with Pharmaceutical Applications

    Directory of Open Access Journals (Sweden)

    Leandra Guimarães de Oliveira

    2010-11-01

    Full Text Available The current study intends to present the relevance of omeprazole, esomeprazole, rabeprazole, pantoprazole and lansoprazole by means of the technological foresight study, through invention patent documents from Brazilian applicants as indicators of innovation. The European database of patents (Espacenet, Word Patent Index (DERWENT and the Brazilian Patent Base of INPI were used, combining keywords and International Patent Classifications. The major applicants, countries of publication and claims categories were mapped. The 212 patent requests collected are mainly distributed in Chemistry, Pharmacy and Pharmacology areas. The results obtained revealed that the US was the main country with studies directed to this technological area (59 patent applications and the major applicant was the company Astrazeneca AB. Therefore, we can understand that this is a promising technology that may reflect in an increase of R&D activities and patent applications in this area.

  20. Patent protection strategies

    Directory of Open Access Journals (Sweden)

    Himanshu Gupta

    2010-01-01

    Full Text Available It is widely recognized that the pharmaceutical industry faces serious financial challenges. Large numbers of blockbuster drugs are losing patent protection and going generic. The pipeline of new drugs is too sparse to fill the gap and generate a platform for future growth. Moreover, many of the new products are biologics with much narrower target patient populations and comparatively higher prices relative to traditional pharmaceuticals. So now the time has come for pharmaceutical scientists to have a better understanding of patent fundamentals. This need is illustrated by analyses of key scientific and legal issues that arose during recent patent infringement cases involving Prozac, Prilosec, and Buspar. Facing this scenario, the pharmaceutical industry has moved to accelerate drug development process and to adopt at the same time different strategies to extend the life time of the patent monopoly to provide the economic incentives and utilizing it for drug discovery and development. This review covers the need of patent protection and various strategies to extend the patent.

  1. Patenting Nanomedicine in Europe

    DEFF Research Database (Denmark)

    Nordberg, Ana

    This work addresses the question of determining whether reinterpretation, reformulation or replacement of article 53 (c) of the European Patent Convention is viable and advisable. It does so by reference to novel or resurfacing interpretative concerns connected with emerging technologies exemplif......This work addresses the question of determining whether reinterpretation, reformulation or replacement of article 53 (c) of the European Patent Convention is viable and advisable. It does so by reference to novel or resurfacing interpretative concerns connected with emerging technologies...... exemplified by nanomedicine, while considering known interpretative issues and traditional objections to this provision. The debate concerning the patentability of ‘medical methods’ is multi-layered and complex. The ‘medical methods exception’ is a public policy mechanism, intended to introduce flexibility...... in the patent system in order to allow for the protection of core ethical values of society. Nanotechnology inventions blur the lines between patentable subject matter and what may fall under the exception from patentability. It is a good example of how in recent years, emerging technologies have been...

  2. 37 CFR 1.5 - Identification of patent, patent application, or patent-related proceeding.

    Science.gov (United States)

    2010-07-01

    ... UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES General Provisions General Information and Correspondence § 1.5 Identification of patent, patent... benefit of the date of deposit with the United States Postal Service. If the returned correspondence is...

  3. The SDH mutation database: an online resource for succinate dehydrogenase sequence variants involved in pheochromocytoma, paraganglioma and mitochondrial complex II deficiency

    Directory of Open Access Journals (Sweden)

    Devilee Peter

    2005-11-01

    Full Text Available Abstract Background The SDHA, SDHB, SDHC and SDHD genes encode the subunits of succinate dehydrogenase (succinate: ubiquinone oxidoreductase, a component of both the Krebs cycle and the mitochondrial respiratory chain. SDHA, a flavoprotein and SDHB, an iron-sulfur protein together constitute the catalytic domain, while SDHC and SDHD encode membrane anchors that allow the complex to participate in the respiratory chain as complex II. Germline mutations of SDHD and SDHB are a major cause of the hereditary forms of the tumors paraganglioma and pheochromocytoma. The largest subunit, SDHA, is mutated in patients with Leigh syndrome and late-onset optic atrophy, but has not as yet been identified as a factor in hereditary cancer. Description The SDH mutation database is based on the recently described Leiden Open (source Variation Database (LOVD system. The variants currently described in the database were extracted from the published literature and in some cases annotated to conform to current mutation nomenclature. Researchers can also directly submit new sequence variants online. Since the identification of SDHD, SDHC, and SDHB as classic tumor suppressor genes in 2000 and 2001, studies from research groups around the world have identified a total of 120 variants. Here we introduce all reported paraganglioma and pheochromocytoma related sequence variations in these genes, in addition to all reported mutations of SDHA. The database is now accessible online. Conclusion The SDH mutation database offers a valuable tool and resource for clinicians involved in the treatment of patients with paraganglioma-pheochromocytoma, clinical geneticists needing an overview of current knowledge, and geneticists and other researchers needing a solid foundation for further exploration of both these tumor syndromes and SDHA-related phenotypes.

  4. The lifespan of semiconductor patents by assignee and patent characteristics

    Directory of Open Access Journals (Sweden)

    Chang Shu-Hao

    2017-01-01

    Full Text Available Evaluating the values of patents is critical for both managers and investors. Patent maintenance time is an ideal proxy indicator for evaluating commercial patent value. This study investigated the survival rates of patents in the semiconductor industry by using a survival analysis and incorporated a predictive model for patent maintenance times. The technical characteristics of the patents, the assignee factors, and the statuses of the patents were used as the predictive factors for patent maintenance time. The results revealed a small entity size and the number of assignees are the risk factors that increase the likelihood of the maintenance time of a patent decreasing. The litigation status of a patent and the number of its international patent classifications, claims, forward citations, and assignments were determined to be the protection factors that raise the likelihood of its maintenance time extending. Additionally, substantial differences were noted between small entities and nonsmall entities and between being litigated and not in their effects on the survival rates of patents. This study examined the factors that affect the survival rates of patents and provides a reference for the managers and investors of intellectual property rights to use when assessing technical and commercial patent values.

  5. Test Collections for Patent-to-Patent Retrieval and Patent Map Generation in NTCIR-4 Workshop

    OpenAIRE

    Fujii, Atsushi; Iwayama, Makoto; Kando, Noriko

    2004-01-01

    This paper describes the Patent Retrieval Task in the Fourth NTCIR Workshop, and the test collections produced in this task. We perform the invalidity search task, in which each participant group searches a patent collection for the patents that can invalidate the demand in an existing claim. We also perform the automatic patent map generation task, in which the patents associated with a specific topic are organized in a multi-dimensional matrix.

  6. Strategic management and utilization of patents

    International Nuclear Information System (INIS)

    Kim, Gyeong Go; Yun, Gwon Jun

    1993-11-01

    This book deals with why does management of patents need?, system of management of patents with function and site of management of patents and system and composition, what does management of patents department do?, task like technical development, management regulation, patent information, management of patents in small business with technical development of small business, how does business manage the patents in real, introduction of management of patents in the U.S, Europe, Japan, and Korea, and management of patents as strategic management.

  7. Como pesquisar o perfil patentário de um fármaco: o caso Efavirenz How to determine the patent profile of a drug: a case study of Efavirenz

    Directory of Open Access Journals (Sweden)

    Jaqueline Mendes Soares

    2010-01-01

    Full Text Available The importance of the patent system for researchers, especially in chemistry and related areas, is undeniable. In this context, this work aims at guiding the search in major search engines of patents, in order to map the patents related to a specific chemical compound and identify the material that each patent document protects. In this case study, it was performed a search for the drug efavirenz to demonstrate how to conduct a literature search in patents databases and to map patent applications at national and international levels.

  8. Comprehension and application of patent information

    International Nuclear Information System (INIS)

    Lee, Sang Nam

    2004-05-01

    This book gives descriptions of conception of patent information such as the meaning, characteristic, function, investigation and map of patent information, pro-patent period and patent strategy of the business. It also deals with comprehension of patent information like publication of nations, patent document, patent procedure in Korea, patent procedure in Japan, the U.S, and Europe, article and function of patent document, patent information survey such as writing of search keyword, procedure of the survey and search site of other countries, patent analysis and patent map.

  9. Effect of the economic crisis on the production of immunology patents managed through the Patent Cooperation Treaty agreement from 2004-2011.

    Science.gov (United States)

    Campos, Elena; Campos, Adolfo

    2015-07-01

    To determine the evolution of patents in immunology, as a result of research and innovation in the years 2004-2011. The search for patents published internationally in immunology was made by using the SCOPUSTM database. SCOPUS gives information about over 23 million patents. The extracted data from patents were: inventors and applicants; their nationalities; sections, classes and subclasses of the International Patent Classification. 89 countries. Data have been obtained from the database SCOPUS. It has been used for the international patent classification. Patents by country, Productive sectors, Productive areas. A total of 17,281 patents were applied for immunology during 2004-2011 of which 16,811 were from 30 Organisation for Economic Cooperation and Development countries, and 5326 from 28 countries in the European Union. These patents were granted in 89 countries and 13,699 of them were submitted by researchers from only one country. Private entities applied for 62.45% of all patents, universities 17.48%, hospitals 3.40% and public research organisations and private applicants applied for the rest. The university that made more applications was the University of California with 315 and the company was Genentech Inc. (US) with 302. The reduction in the number of applications of international patents in all disciplines of science also affected the area of immunology. Collaboration in immunology between universities, companies and hospitals is hard because their interests are different. It is shown in patent applications that the majority of patents in immunology are applied for by only one entity. Patents in immunology are developed, mainly, in aspects such as medical preparations, peptides, mutation or genetic engineering, therapeutic activity of chemical compounds and analysing materials by determining their chemical or physical properties.

  10. A Selection Model of Patenting Firms in Demark

    DEFF Research Database (Denmark)

    Nielsen, Anders Østergaard

    1999-01-01

    on how market structure relate to innovative activity in small open economies. The paper explores the relation between patenting activity and market structure in the Danish manufacturing industries using data from a recently developed database containing accounting information on a sample of patenting...... firms in Denmark. Market structure by concentration and firm size in manufacturing industries was found to be of opposite effects on firms patent activity. Studies on the relation between industrial innovation and market structure in the Danish manufacturing industries are few. Also, since the majority...

  11. Patenting human genes: Chinese academic articles' portrayal of gene patents.

    Science.gov (United States)

    Du, Li

    2018-04-24

    The patenting of human genes has been the subject of debate for decades. While China has gradually come to play an important role in the global genomics-based testing and treatment market, little is known about Chinese scholars' perspectives on patent protection for human genes. A content analysis of academic literature was conducted to identify Chinese scholars' concerns regarding gene patents, including benefits and risks of patenting human genes, attitudes that researchers hold towards gene patenting, and any legal and policy recommendations offered for the gene patent regime in China. 57.2% of articles were written by law professors, but scholars from health sciences, liberal arts, and ethics also participated in discussions on gene patent issues. While discussions of benefits and risks were relatively balanced in the articles, 63.5% of the articles favored gene patenting in general and, of the articles (n = 41) that explored gene patents in the Chinese context, 90.2% supported patent protections for human genes in China. The patentability of human genes was discussed in 33 articles, and 75.8% of these articles reached the conclusion that human genes are patentable. Chinese scholars view the patent regime as an important legal tool to protect the interests of inventors and inventions as well as the genetic resources of China. As such, many scholars support a gene patent system in China. These attitudes towards gene patents remain unchanged following the court ruling in the Myriad case in 2013, but arguments have been raised about the scope of gene patents, in particular that the increasing numbers of gene patents may negatively impact public health in China.

  12. Expedited patent examination for green inventions: Developing countries' policy choices

    International Nuclear Information System (INIS)

    Lu, Bingbin

    2013-01-01

    Innovation in green technology is important. Patent rights can provide incentives for green technology research and development. Expedited patent examination for green inventions has emerged as a policy instrument to provide such incentives. Developing countries were never opposed to patents for green technologies. China and Brazil have led the way by offering expedited examinations for green patent applications. More developing countries are expected to follow. Expedited examination for green technologies is consistent with the intellectual property system objectives and is justified by the clear social benefit from green technologies. Introducing such expedited programs in developing countries has sufficient advantages. Existing models of expedited programs for green technologies are analyzed to generalize key issues and to discern suitable policy choices for developing countries. When introducing such programs, a balanced definition for green technology is preferred; a special classification requirement is premature and is not recommended; a pre-examination search requirement is generally recommended to balance patent office workloads, and a green patent database is recommended. - Highlights: • There is no north–south divide in promoting green technologies. • Earlier issuance of green patents has its great social benefit. • Green patent application should receive expedited examination. • Developing countries should introduce such expedited programs. • A suitable approach for developing countries is searched and recommended

  13. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.

    Science.gov (United States)

    Shen, Li; Shao, Ningyi; Liu, Xiaochuan; Nestler, Eric

    2014-04-15

    Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. We have developed ngs.plot - a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.

  14. Structural and sequence variants in patients with Silver-Russell syndrome or similar features-Curation of a disease database

    DEFF Research Database (Denmark)

    Tümer, Zeynep; López-Hernández, Julia Angélica; Netchine, Irène

    2018-01-01

    data of these patients. The clinical features are scored according to the Netchine-Harbison clinical scoring system (NH-CSS), which has recently been accepted as standard by consensus. The structural and sequence variations are reviewed and where necessary redescribed according to recent...

  15. A search for pre-main-sequence stars in high-latitude molecular clouds. 3: A survey of the Einstein database

    Science.gov (United States)

    Caillault, Jean-Pierre; Magnani, Loris; Fryer, Chris

    1995-01-01

    In order to discern whether the high-latitude molecular clouds are regions of ongoing star formation, we have used X-ray emission as a tracer of youthful stars. The entire Einstein database yields 18 images which overlap 10 of the clouds mapped partially or completely in the CO (1-0) transition, providing a total of approximately 6 deg squared of overlap. Five previously unidentified X-ray sources were detected: one has an optical counterpart which is a pre-main-sequence (PMS) star, and two have normal main-sequence stellar counterparts, while the other two are probably extragalactic sources. The PMS star is located in a high Galactic latitude Lynds dark cloud, so this result is not too suprising. The translucent clouds, though, have yet to reveal any evidence of star formation.

  16. Patent Races and Market Value

    DEFF Research Database (Denmark)

    Czarnitzki, Dirk; Hussinger, Katrin; Leten, Bart

    Patent races are models of strategic interactions between firms competing to develop an invention. The winning firm secures a patent, protecting the invention from imitation. This paper tests the assumption made about the reward structure in patent races, both in discrete and complex industries. We...... identify patent race winners using detailed information from the patent examination reports at the European Patent Office (EPO). Estimates of a market value equation featuring large, R&D-intensive U.S., European and Japanese firms, show that if firms win patent races, their market value increases...... significantly. We further show that the gain in market value is significantly larger for patent race winners in discrete industries than for firms in complex industries....

  17. Ethics in scientific results application: Gene and life forms patenting

    Directory of Open Access Journals (Sweden)

    Konstantinov Kosana

    2010-01-01

    Full Text Available The remarkable development and application of new genetic technologies over the past decades has been accompanied by profound changes in the way in which research is commercialized in the life sciences. As results, new varieties of commercially grown crops with improved or new traits are developed. Many thousands of patents which assert rights over DNA sequences have been granted to researchers across the public and private sector. The effects of many of these patents are extensive, because inventors who assert rights over DNA sequences obtain protection on all uses of the sequences. Extremely valuable to breeders in the national agricultural research system is the ability to genotype their collections to get a clear picture of their diversity and how diversity could be enhanced through sharing and access to global collections. The issue of the eligibility for patenting of DNA sequences needs to be reopened. Patents that assert rights over DNA sequences and their uses are, in some cases, supportable, but in others, should be treated with great caution. Rights over DNA sequences as research tools should be discouraged. That the best way to discourage the award of such patents is by stringent application of the criteria for patenting, particularly utility. A more equitable, ethically - based food and agricultural system must incorporate concern for three accepted global goals: improved well being, protection of the environment and improved public health (particular point food from GMO. To mitigate conflict one of the approach to solve problem is ethical and truthful label of GM food, because consumers have a right to choose whether to eat genetically modified foods or not. Interesting examples and risks as consequences of free availability of genetic resources utilization, its transformation, patenting of 'new' organism and selling it back to the genetic resource owner are presented. Society has obligations to raise levels of nutrition and

  18. (reprocessed)HeliscopeCAGE sequencing, Delve mapping and CAGE TSS aggregation - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM...ntified by CAGE tag analysis (BED format) *.rdna.fa.gz: rDNA sequences (FASTA format) Data file File name: fantom...5_rp_exp_details.zip File URL: ftp://ftp.biosciencedbc.jp/archive/fantom5/20161221/fantom5_rp_exp_detai...tp://ftp.biosciencedbc.jp/archive/fantom5/datafiles/reprocessed/hg38_latest/basic/ File size: 1.4 TB File na...me: (reprocessed)basic (Mus musculus) File URL: ftp://ftp.biosciencedbc.jp/archive/fantom5/datafiles/reproce

  19. The fallacy of Software Patents

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    Software patents are usually used as argument for innovation but do they really promote innovation? Who really benefits from software patents? This talk attempts to show the problems with software patents and how they can actually harm innovation having little value for software users and our society in general.

  20. Patent Applications on Representative Sectors of Biotechnology in Brazil: an Analysis of the Last Decade

    Directory of Open Access Journals (Sweden)

    Liliana Machado Mendes

    2013-12-01

    The website of European Patent Office (EPO patent database - Espacenet was used to conduct the survey, and the search strategy fields selected for the patent applications were: (i Priority Number: BR (Brazil, and (ii the International Patent Classification (IPC - C12N, C07K14, and C07H21/04. The patent applications by Brazilian residents, from 2000 to 2010 in the Espacenet for the classifications adopted indicates a total of 396 patent applications in the most representative sectors in biotechnology over the past 10 years. After the Brazilian Innovation Law there is a growth trend line particularly in the years 2007 and 2008. The universities hold 48% of the patent applications in biotechnology, following by Individuals/ Researchers with 20%, Public Research Centers and Private Firms with 15%, and 11% of the total, respectively.

  1. Patent Searching for Librarians and Inventors.

    Science.gov (United States)

    Wherry, Timothy Lee

    Information on patents is provided for librarians and laypersons requiring an understanding of the system and the processes involved. Chapter 1 discusses successful patents; terms and concepts; patent types; copyright; trademark; requirements; patent examiners; patent pending; expiration; patentee and assignee; and reissued patents. Chapter 2…

  2. Patent pools: Intellectual property rights and competition.

    NARCIS (Netherlands)

    Rodriguez, V.F.

    2010-01-01

    Patent pools do not correct all problems associated with patent thickets. In this respect, patent pools might not stop the outsider problem from striking pools. Moreover, patent pools can be expensive to negotiate, can exclude patent holders with smaller numbers of patents or enable a group of major

  3. Patent urachus repair - slideshow

    Science.gov (United States)

    ... Drugs & Supplements Videos & Tools About MedlinePlus Show Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Patent urachus repair - series—Normal anatomy URL of this ...

  4. Patent ductus arteriosus

    Science.gov (United States)

    ... Drugs & Supplements Videos & Tools About MedlinePlus Show Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Patent ductus arteriosus URL of this page: //medlineplus.gov/ ...

  5. Patent urachus repair

    Science.gov (United States)

    ... Drugs & Supplements Videos & Tools About MedlinePlus Show Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Medical Encyclopedia → Patent urachus repair URL of this page: //medlineplus.gov/ ...

  6. METRICS DEVELOPMENT FOR PATENTS.

    Science.gov (United States)

    Veiga, Daniela Francescato; Ferreira, Lydia Masako

    2015-01-01

    To develop a proposal for metrics for patents to be applied in assessing the postgraduate programs of Medicine III - Capes. From the reading and analysis of the 2013 area documents of all the 48 areas of Capes, a proposal for metrics for patents was developed to be applied in Medicine III programs. Except for the areas Biotechnology, Food Science, Biological Sciences III, Physical Education, Engineering I, III and IV and Interdisciplinary, most areas do not adopt a scoring system for patents. The proposal developed was based on the criteria of Biotechnology, with adaptations. In general, it will be valued, in ascending order, the deposit, the granting and licensing/production. It will also be assigned higher scores to patents registered abroad and whenever there is a participation of students. This proposal can be applied to the item Intellectual Production of the evaluation form, in subsection Technical Production/Patents. The percentage of 10% for academic programs and 40% for Masters Professionals should be maintained. The program will be scored as Very Good when it reaches 400 points or over; Good, between 200 and 399 points; Regular, between 71 and 199 points; Weak up to 70 points; Insufficient, no punctuation. Desenvolver uma proposta de métricas para patentes a serem aplicadas na avaliação dos Programas de Pós-Graduação da Área Medicina III - Capes. A partir da leitura e análise dos documentos de área de 2013 de todas as 48 Áreas da Capes, desenvolveu-se uma proposta de métricas para patentes, a ser aplicada na avaliação dos programas da área. Constatou-se que, com exceção das áreas Biotecnologia, Ciência de Alimentos, Ciências Biológicas III, Educação Física, Engenharias I, III e IV e Interdisciplinar, a maioria não adota sistema de pontuação para patentes. A proposta desenvolvida baseou-se nos critérios da Biotecnologia, com adaptações. De uma forma geral, foi valorizado, em ordem crescente, o depósito, a concessão e o

  7. Database Description - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name ASTRA Alternative n...tics Journal Search: Contact address Database classification Nucleotide Sequence Databases - Gene structure,...3702 Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The database represents classified p...(10):1211-6. External Links: Original website information Database maintenance site National Institute of Ad... for user registration Not available About This Database Database Description Dow

  8. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L..

    Directory of Open Access Journals (Sweden)

    Bin Han

    Full Text Available Microsatellites or simple sequence repeats (SSRs are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR; 70,564 (23.9% were found to be monomorphic and 224,703 (76.1% were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3% amplified one locus, 8 (17.8% amplified multiple identical loci, and 13 (28.9% did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising

  9. Patent Documents as a Resource for Studies and Education in Geophysics - An Approach.

    Science.gov (United States)

    Wollny, K. G.

    2016-12-01

    Patents are a highly neglected source of information in geophysics, although they supply a wealth of technical and historically relevant data and might be an important asset for researchers and students. The technical drawings and descriptions in patent documents provide insight into the personal work of a researcher or a scientific group and give detailed technical background information, show interdisciplinary solutions for similar problems, help to learn about inventions too advanced for their time but maybe useful now, and to explore the historical background and timelines of inventions and their inventors. It will be shown how to get access to patent documents and how to use them for research and education purposes. Exemplary inventions by well-known geoscientists or scientists in related fields will be presented to illustrate the usefulness of patent documents. The data pool used is the International Patent Classification (IPC) class G01V that the United Nations' World Intellectual Property Organisation (WIPO) has set up mainly for inventions with key aspects in geophysics. This class contains approximately 235,000 patent documents (July 2016) for methods, apparatuses or scientific instruments developed during scientific projects or by geophysical companies. The patent documents can be accessed via patent databases. The most important patent databases are for free, search functionality is self-explanatory and the amount of information to be extracted is enormous. For example, more than 90 million multilingual patent documents are currently available online (July 2016) in DEPATIS database of the German Patent and Trade Mark Office or ESPACENET of the European Patent Office. To summarize, patent documents are a highly useful tool for educational and research purposes to strengthen students' and scientists' knowledge in a practically orientated geophysical field and to widen the horizon to adjacent technical areas. Last but not least, they also provide insight

  10. Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed.

    Science.gov (United States)

    Eisinger, Daniel; Tsatsaronis, George; Bundschus, Markus; Wieneke, Ulrich; Schroeder, Michael

    2013-04-15

    Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms.Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources.

  11. Decoding gene patents in Australia.

    Science.gov (United States)

    Denley, Adam; Cherry, James

    2014-10-03

    Patents directed to naturally occurring genetic material, such as DNA, RNA, chromosomes, and genes, in an isolated or purified form have been granted in Australia for many years. This review provides scientists with a summary of the gene patent debate from an Australian perspective and specifically reviews how the various levels of the legal system as they apply to patents-the Australian Patent Office, Australian courts, and Australian government-have dealt with the issue of whether genetic material is proper subject matter for a patent. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

  12. RegTransBase - A Database Of Regulatory Sequences and Interactionsin a Wide Range of Prokaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kazakov, Alexei E.; Cipriano, Michael J.; Novichkov, Pavel S.; Minovitsky, Simon; Vinogradov, Dmitry V.; Arkin, Adam; Mironov, AndreyA.; Gelfand, Mikhail S.; Dubchak, Inna

    2006-07-01

    RegTransBase, a manually curated database of regulatoryinteractions in prokaryotes, captures the knowledge in publishedscientific literature using a controlled vocabulary. Although a number ofdatabases describing interactions between regulatory proteins and theirbinding sites are currently being maintained, they focus mostly on themodel organisms Escherichia coli and Bacillus subtilis, or are entirelycomputationally derived. RegTransBase describes a large number ofregulatory interactions reported in many organisms and contains varioustypes of experimental data, in particular: the activation or repressionof transcription by an identified direct regulator; determining thetranscriptional regulatory function of a protein (or RNA) directlybinding to DNA (RNA); mapping or prediction of binding site for aregulatory protein; characterization of regulatory mutations. Currently,the RegTransBase content is derived from about 3000 relevant articlesdescribing over 7000 experiments in relation to 128 microbes. It containsdata on the regulation of about 7500 genes and evidence for 6500interactions with 650 regulators. RegTransBase also contains manuallycreated position weight matrices (PWM) that can be used to identifycandidate regulatory sites in over 60 species. RegTransBase is availableat http://regtransbase.lbl.gov.

  13. Optimal patent policies: A survey

    DEFF Research Database (Denmark)

    Poulsen, Odile

    2002-01-01

    This paper surveys some of the patent literature, in particular, it focuses on optimal patent policies. We compare two situations. The first where the government only has a single policy tool to design the optimal patent policy, namely the optimal patent length. In the second situation......, the government uses two policy tools, the optimal breadth and length. We show that theoretical models give very different answers to what is the optimal patent policy. In particular, we show that the optimal patent policy depends among othet things on the price elasticity of demand, the intersectoral elasticity...... of research outputs as well as the degree of compettition in the R&D sector. The actual law on intellectual property, which advocates a unique patent length of 20 years is in general not supported by theoretical models....

  14. Labor Mobility and Patenting Activity

    DEFF Research Database (Denmark)

    Kaiser, Ulrich; Kongsted, Hans Christian; Rønde, Thomas

    We measure the quantitative importance of labor mobility as a vehicle for the transmission of knowledge and skills across firms. For this purpose we create a unique data set that matches all applications of Danish firms at the European Patent Office to linked employer-employee register data...... for the years 1999-2002. The Danish workforce is split into "R&D workers", who hold a bachelor's or a master's degree in a technical field, and "non{R&D workers". We find that mobile R&D workers ("R&D joiners"') contribute more to patenting activity than immobile R&D workers. Furthermore, R&D workers who have...... previously been employed by a patenting firm ("patent exposed workers") have a larger effect on patenting activity than R&D workers without this experience. Patent exposed R&D joiners constitute the most productive group of workers: for firms that patented prior to 1999, one additional worker of this type...

  15. Lovely but dangerous: The impact of patent citations on patent duration

    OpenAIRE

    Maurseth, Per Botolf

    2001-01-01

    - What is the impact of patent citations on patent renewal behaviour? Patent citations are commonly used as an indicator of technology spillovers. For cited patents therefore, patent citations have a potentially ambiguous impact. On the one hand, patent citations may indicate a scientific breakthrough, a high value of the cited patent and therefore a long survival period. On the other hand, patent citations may indicate competing innovations that render the cited patent obsolete. By discri...

  16. Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases.

    Science.gov (United States)

    Le Vu, Stéphane; Ratmann, Oliver; Delpech, Valerie; Brown, Alison E; Gill, O Noel; Tostevin, Anna; Fraser, Christophe; Volz, Erik M

    2018-06-01

    Phylogenetic clustering of HIV sequences from a random sample of patients can reveal epidemiological transmission patterns, but interpretation is hampered by limited theoretical support and statistical properties of clustering analysis remain poorly understood. Alternatively, source attribution methods allow fitting of HIV transmission models and thereby quantify aspects of disease transmission. A simulation study was conducted to assess error rates of clustering methods for detecting transmission risk factors. We modeled HIV epidemics among men having sex with men and generated phylogenies comparable to those that can be obtained from HIV surveillance data in the UK. Clustering and source attribution approaches were applied to evaluate their ability to identify patient attributes as transmission risk factors. We find that commonly used methods show a misleading association between cluster size or odds of clustering and covariates that are correlated with time since infection, regardless of their influence on transmission. Clustering methods usually have higher error rates and lower sensitivity than source attribution method for identifying transmission risk factors. But neither methods provide robust estimates of transmission risk ratios. Source attribution method can alleviate drawbacks from phylogenetic clustering but formal population genetic modeling may be required to estimate quantitative transmission risk factors. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  17. Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

    Science.gov (United States)

    Pujar, Shashikant; O'Leary, Nuala A; Farrell, Catherine M; Loveland, Jane E; Mudge, Jonathan M; Wallin, Craig; Girón, Carlos G; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew E; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Gonzalez, Jose M; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike P; Kodali, Vamsi K; Martin, Fergal J; McAndrews, Monica; McGarvey, Kelly M; Murphy, Michael; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Seal, Ruth L; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen L; Bruford, Elspeth A; Bult, Carol J; Frankish, Adam; Murphy, Terence; Pruitt, Kim D

    2018-01-04

    The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

  18. PATENT ANALYSIS: A LOOK AT THE INNOVATIVE NATURE OF PLANT-BASED COSMETICS

    Directory of Open Access Journals (Sweden)

    Francine C. S. César

    Full Text Available The use of plants have become a important trend in cosmetic market, with a crescent number of patent applications. Despite various herbal-based ingredients have been described in scientific literature, most of them are restricted to patent databases. In this work we analyze the innovative use of plants and its derivatives in cosmetic technologies, based on patent analysis. The investigation was conducted using Derwent World Patents Index (Thomson Reuters Scientific, USA from 1995 to 2015. The search was carried out to evaluate the number of patent deposits, the patent depositors profiles, the countries with most patent applications, the International Patent Classification (IPC and the main plant families using in cosmetics. Patent analysis revealed an increase number of applications involving cosmetic containing plants components, with a higher number of deposits related to anti-ageing and whitening skin treatment. Fabaceae, Asteraceae, Rosaceae, Lamiaceae, Poaceae, Rutaceae, Lilliacae and Apiaceae were the key plant families used in cosmetic formulations for skin care treatment. Comparison between scientific and technological data pointed out divergences between patents deposits and aid-based scientific reports. The use of patent analysis in combination with scientific data opens up wider aspects of knowledge and enables a better rationalization of innovative works.

  19. Recent patents on flavonoids.

    Science.gov (United States)

    Mamta, Gokhale; Bansal, Y K; Sandhu, S S

    2013-12-01

    Flavonoids are substances which are widely distributed in the plant kingdom. They occur in considerable quantities in common food products, spices and beverages. Interest of researchers has been greatly enhanced towards therapeutic potential of flavonoids in last some years. This review summarizes important patents pertaining to recent biotechnological techniques applied for the production, analysis of biosynthetic pathways, effects and applications of different flavonoids. For systematic studies investigations which have been published in the form of patents, are classified in different sectors like biosynthesis, medical application, antimicrobial activity, alteration of flower color, industrial application, cosmetics, food and plant tissue culture. A number of activities have been observed in each sector with vast area of research on flavonoids.

  20. End-User Searching in a Large Library Network: A Case Study of Patent Attorneys.

    Science.gov (United States)

    Vollaro, Alice J.; Hawkins, Donald T.

    1986-01-01

    Reports results of study of a group of end users (patent attorneys) doing their own online searching at AT&T Bell Laboratories. Highlights include DIALOG databases used by the attorneys, locations and searching modes, characteristics of patent attorney searchers, and problem areas. Questionnaire is appended. (5 references) (EJS)

  1. How Patent Function Integration with R&D Influence the Value of Patents

    DEFF Research Database (Denmark)

    Beukel, Karin; Valentin, Finn

    Patent strategies are endogenous to firm appropriability. However, to what extent does firm’s R&D teams’ engagement with patent experts influence the value of patents? We estimate the relationship between firm’s R&D use of patent functions on patent value in Biotech firms. Controlling...... for characteristics of scientific team, firm effects, and other patent value indicators, we find that having a firm specific (in-house) internal patent function is a driver of patent value. In addition, we find that the way in which patent functions create patent value differs dependent on whether the firm has...... internal patent function or not. In-house patent functions create value through narrow patents, whereas, firms with no in-house patent function create valuable patents by the use of broader scoped patents. Our results point to a strong effect of firm specific patent functions, but also explain how firms...

  2. Science of invention patent

    International Nuclear Information System (INIS)

    Park, Yeong Taek; Park, Su Dong

    1999-02-01

    This book tells science of invention patent about new way of invention and creative solution for problems, basic conception of TRIZ, resolution of physical contradictory and technical contradictory, development of system and types of evolution, change of thinking for solving the problems, analysis of structure for problem solution, problem solution using scientific phenomenon and effect, use of standard solution and algorithm of creative problem solution.

  3. Do Military Personnel Patent

    Science.gov (United States)

    2016-12-01

    following questions: In what fields are military personnel most likely to patent, and how do demographics, such as age, race, and gender , along with...technologies, which have transformed how the United States wages war. DARPA continues to develop new technologies and capabilities for the U.S. military today...build the European navies so it instead decided to utilize an innovative ship design to exploit a gap specific to the British Royal Navy. The six

  4. Database Description - TMFunction | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available sidue (or mutant) in a protein. The experimental data are collected from the literature both by searching th...the sequence database, UniProt, structural database, PDB, and literature database

  5. Database Description - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ase Description General information of database Database name RMG Alternative name ...raki 305-8602, Japan National Institute of Agrobiological Sciences E-mail : Database... classification Nucleotide Sequence Databases Organism Taxonomy Name: Oryza sativa Japonica Group Taxonomy ID: 39947 Database...rnal: Mol Genet Genomics (2002) 268: 434–445 External Links: Original website information Database...available URL of Web services - Need for user registration Not available About This Database Database Descri

  6. HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

    Directory of Open Access Journals (Sweden)

    Charles Richard Bradshaw

    Full Text Available Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10, a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in

  7. Decoding Gene Patents in Australia

    OpenAIRE

    Denley, Adam; Cherry, James

    2015-01-01

    Patents directed to naturally occurring genetic material, such as DNA, RNA, chromosomes, and genes, in an isolated or purified form have been granted in Australia for many years. This review provides scientists with a summary of the gene patent debate from an Australian perspective and specifically reviews how the various levels of the legal system as they apply to patents—the Australian Patent Office, Australian courts, and Australian government—have dealt with the issue of whether genetic m...

  8. Patents: Recent Trends and Puzzles

    OpenAIRE

    Zvi Griliches

    1989-01-01

    This paper reviews the historical data on patenting in the United States with special reference to the last 20 years and their potential relation, if any, to the recent productivity slowdown. Two Points are made: Patents are not a "constant-yardstick" indicator of either inventive input or output. Moreover, they are "produced" by a governmental agency which goes through its own budgetary and inefficiency cycles. The paper shows that the appearance of an absolute decline in patenting in the 19...

  9. Assessment of analytical techniques for characterization of crystalline clopidogrel forms in patent applications

    Directory of Open Access Journals (Sweden)

    Luiz Marcelo Lira

    2014-04-01

    Full Text Available The aim of this study was to evaluate two important aspects of patent applications of crystalline forms of drugs: (i the physicochemical characterization of the crystalline forms; and (ii the procedure for preparing crystals of the blockbuster drug clopidogrel. To this end, searches were conducted using online patent databases. The results showed that: (i the majority of patent applications for clopidogrel crystalline forms failed to comply with proposed Brazilian Patent Office guidelines. This was primarily due to insufficient number of analytical techniques evaluating the crystalline phase. In addition, some patent applications lacked assessment of chemical/crystallography purity; (ii use of more than two analytical techniques is important; and (iii the crystallization procedure for clopidogrel bisulfate form II were irreproducible based on the procedure given in the patent application.

  10. Collaborative networks and patent production in Andean Community of Nations universities (UCANS, 2005-2015

    Directory of Open Access Journals (Sweden)

    Carlos Enrique Agüero Aguilar

    2017-06-01

    Full Text Available The competitiveness and technological development of a region are measured by the degree of innovation supporting them. The quantity and quality of patents generated and applied in production dynamics serve as an element for evaluation. In this sense, universities play a role as generators and transmitters of knowledge. So it is important to identify the level of their collaboration and the trends in terms of technology application in order to establish future policies for development in this sector. This article identifies the degree of collaboration, types of patents, actors (primary and secondary and dynamics of patents produced at the Andean Community of Nations universities during the period 2005-2015 and present in the European Patent Office database. In conclusion, there is a great disparity between CAN universities regarding patent production, so it is necessary to strengthen the collaborative level among universities in this community. Nevertheless, an increase is seen in the production of patents.

  11. Patent Administration by Office Computer - A Case at Mazda Motor Corporation

    Science.gov (United States)

    Kimura, Ikuo; Nakamura, Shinji

    The needs of patent administration have been diversified reflecting R&D activities under the severe competition of technical development, and business has been increased in quantity year after year as seen in patent application. Under these circumstances it is necessary to develop business mechanization which assists manual operation as much as possible to enforce the patent administration. Introducing office computer (CPU 512 KB, external memory 128 MB) for exclusive use in this purpose, Patent Department of Mazda Motor Corporation has been constructing database of patent administration centered around patent application by their own company, and utilizes it for automatic preparation of business forms, preparation of various statistical materials, and real-time reference to the application procedures.

  12. International patenting in ophthalmology: An analysis of its structure and relevance for the development of drugs and diagnostics

    Directory of Open Access Journals (Sweden)

    Hermann AM Mucke

    2008-10-01

    Full Text Available Hermann AM Mucke, Peter Mucke, Eva MuckeHM Pharma Consultancy, Vienna, AustriaAbstract: While investigative ophthalmologists access peer-reviewed journals as part of their daily routine, and while they regularly visit scientific congresses, they rarely peruse patent documents as an information source. Among the reasons for this negligence are the incompatibility of patent search algorithms with those known from journal databases, a legalistic and frequently redundant language, and misconceptions about the nature of the patenting system. Here we present key data and analyses from the ophthalmology module of a patent database system that we are developing to address some of these problems. We show that international patent applications consistently reflect developer interest in the ocular drug and diagnostics field; that they are technically focused lead indicators of developments that frequently feature in peer-reviewed patenting only much later; and that patenting targets are well aligned with the unmet therapeutic needs of populations in industrialized countries. Most applications (74%–78% in years since 2006 are supported with experimental data, and most (on average, 80%–90% faced at least one objection to patentability during their initial stage of examination. In contrast to the peer-reviewed scenery that is highly diverse, the corresponding patenting arena shows a pronounced focus on the United States.Keywords: ophthalmology, eye diseases, iontophoresis, intellectual property, patents as topic, bibliographic databases

  13. JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

    Science.gov (United States)

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/. © The Author(s) 2015. Published by Oxford University Press.

  14. Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening

    Directory of Open Access Journals (Sweden)

    Richardson Annette C

    2008-07-01

    Full Text Available Abstract Background Kiwifruit (Actinidia spp. are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs. Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons. Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases and pathways (terpenoid biosynthesis is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.

  15. The Academic Advantage: Gender Disparities in Patenting

    OpenAIRE

    Sugimoto, Cassidy R.; Ni, Chaoqun; West, Jevin D.; Larivi?re, Vincent

    2015-01-01

    We analyzed gender disparities in patenting by country, technological area, and type of assignee using the 4.6 million utility patents issued between 1976 and 2013 by the United States Patent and Trade Office (USPTO). Our analyses of fractionalized inventorships demonstrate that women's rate of patenting has increased from 2.7% of total patenting activity to 10.8% over the nearly 40-year period. Our results show that, in every technological area, female patenting is proportionally more likely...

  16. Wacky Patents Meet Economic Indicators

    DEFF Research Database (Denmark)

    Czarnitzki, Dirk; Hussinger, Katrin; Schneider, Cédric

    2011-01-01

    We investigate whether standard indicators can distinguish between “wacky” patents and a control group. Forward citations are good predictors of importance. However, “wacky” patents have higher originality, generality and citation lags, suggesting that these indicators should be interpreted...

  17. Pesticides and the Patent Bargain

    NARCIS (Netherlands)

    Timmermann, C.A.

    2015-01-01

    In order to enlarge the pool of knowledge available in the public domain, temporary exclusive rights (i.e. patents) are granted to innovators who are willing to fully disclose the information needed to reproduce their invention. After the 20-year patent protection period elapses, society should be

  18. Patent arterial duct

    Directory of Open Access Journals (Sweden)

    Martin Robin P

    2009-07-01

    Full Text Available Abstract Patent arterial duct (PAD is a congenital heart abnormality defined as persistent patency in term infants older than three months. Isolated PAD is found in around 1 in 2000 full term infants. A higher prevalence is found in preterm infants, especially those with low birth weight. The female to male ratio is 2:1. Most patients are asymptomatic when the duct is small. With a moderate-to-large duct, a characteristic continuous heart murmur (loudest in the left upper chest or infraclavicular area is typical. The precordium may be hyperactive and peripheral pulses are bounding with a wide pulse pressure. Tachycardia, exertional dyspnoea, laboured breathing, fatigue or poor growth are common. Large shunts may lead to failure to thrive, recurrent infection of the upper respiratory tract and congestive heart failure. In the majority of cases of PAD there is no identifiable cause. Persistence of the duct is associated with chromosomal aberrations, asphyxia at birth, birth at high altitude and congenital rubella. Occasional cases are associated with specific genetic defects (trisomy 21 and 18, and the Rubinstein-Taybi and CHARGE syndromes. Familial occurrence of PAD is uncommon and the usual mechanism of inheritance is considered to be polygenic with a recurrence risk of 3%. Rare families with isolated PAD have been described in which the mode of inheritance appears to be dominant or recessive. Familial incidence of PAD has also been linked to Char syndrome, familial thoracic aortic aneurysm/dissection associated with patent arterial duct, and familial patent arterial duct and bicuspid aortic valve associated with hand abnormalities. Diagnosis is based on clinical examination and confirmed with transthoracic echocardiography. Assessment of ductal blood flow can be made using colour flow mapping and pulsed wave Doppler. Antenatal diagnosis is not possible, as PAD is a normal structure during antenatal life. Conditions with signs and symptoms of

  19. 77 FR 48755 - Office Patent Trial Practice Guide

    Science.gov (United States)

    2012-08-14

    ... in a sequenced fashion. For example, the patent owner may begin deposing the petitioner's declarants... approach is consistent with the legislative history of the AIA, which indicates that Congress included... legislative history endorsed the expression of ``privy'' as follows: The word ``privy'' has acquired an...

  20. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  1. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  2. Comparative analysis between academic and patent publications based on Fenton Technologies among China, Brazil, and the rest of the world.

    Science.gov (United States)

    de Luna, Airton José; Santos, Douglas Alves

    2017-03-01

    Worldwide, year by year, Fenton's Technologies have been highlighted in both academic and patent scopes, in part due to their proven efficiency as environment-friendly technologies destined to the abatement of organic pollutants, and also by their growing interest to produce industrial applications. Thus, aiming to understand the effective dynamic between two worlds, academy vs patents, the present study performs a comparative analysis about publications on Fenton-based Technologies (FbT). Therefore, in this work, technological foresight techniques were adopted focusing on patent and non-patent databases, employing for this, the Web of Science (WoS) database as a prospecting tool. The main results for the last decade point out to a strong increment of the Fenton's Technologies, as much in R&D as in patent applications in the world. Chinese Universities and firms command the scenario. There is an expressive gap between the academic and patent issues.

  3. 75 FR 65611 - Native American Tribal Insignia Database

    Science.gov (United States)

    2010-10-26

    ... DEPARTMENT OF COMMERCE Patent and Trademark Office Native American Tribal Insignia Database ACTION... comprehensive database containing the official insignia of all federally- and State- recognized Native American... to create this database. The USPTO database of official tribal insignias assists trademark attorneys...

  4. Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case

    Science.gov (United States)

    Strope, Pooja K; Chaverri, Priscila; Gazis, Romina; Ciufo, Stacy; Domrachev, Michael; Schoch, Conrad L

    2017-01-01

    Abstract The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353 PMID:29220466

  5. Brazilian university patents: profile of inventors and production per knowledge area

    Directory of Open Access Journals (Sweden)

    Adriana Stefani Cativelli

    2016-09-01

    Full Text Available http://dx.doi.org/10.5007/1518-2924.2016v21n47p67 The study characterizes the inventions of patents of Brazilian universities concerning authorship and subject area to identify the institutions’ possible departments and areas that concentrate efforts on or are more easily able to produce and achieve the patent grants in Brazil. For the data collection of the universities, we used the E-mec platform; the database of the National Institute of Industrial Property (INPI for the collection of information concerning patents; and the International Patent Classification (IPC to determine the covered knowledge areas. Thus, we analyzed the production of patents by Brazilian region; the universities with patents granted; the number of inventors per patent; the profile of the main inventors; and the patents granted according to the IPC. The results indicate that the characteristics of the patents granted to Brazilian Public Universities belong predominantly to the areas of Chemistry and Metallurgy. They are developed by professors with graduation in Chemistry or Mechanical Engineering and most of them belong to the State University of Campinas.

  6. Economic Justification of Patents and Exceptions to Patentability

    DEFF Research Database (Denmark)

    Nordberg, Ana

    2012-01-01

    The present article is the conclusion of a review of economic justifications for patent rights conducted with the objective of determining whether such arguments are per se capable of sustaining the existence of a different patentability regime for inventions of methods for treatment and diagnostic...... methods (art.53 (c) European Patent Convention). It starts by exploring the normative background and summarily describes the different types of claims allowed under the current legal framework and their differences. The following sections will describe and apply the main economic arguments sustaining...... patent rights inventions of methods for treatment and diagnostic methods. These reasoning will be later confronted with contra-arguments. This piece will finalize with the formulation of conclusions extracted from the previous debate, inter-alia that economic reasoning does not per se sustain...

  7. Technology Clusters Exploration for Patent Portfolio through Patent Abstract Analysis

    Directory of Open Access Journals (Sweden)

    Gabjo Kim

    2016-12-01

    Full Text Available This study explores technology clusters through patent analysis. The aim of exploring technology clusters is to grasp competitors’ levels of sustainable research and development (R&D and establish a sustainable strategy for entering an industry. To achieve this, we first grouped the patent documents with similar technologies by applying affinity propagation (AP clustering, which is effective while grouping large amounts of data. Next, in order to define the technology clusters, we adopted the term frequency-inverse document frequency (TF-IDF weight, which lists the terms in order of importance. We collected the patent data of Korean electric car companies from the United States Patent and Trademark Office (USPTO to verify our proposed methodology. As a result, our proposed methodology presents more detailed information on the Korean electric car industry than previous studies.

  8. Patent protection for microbial technologies.

    Science.gov (United States)

    Sherkow, Jacob S

    2017-11-01

    Microbial technologies often serve as the basis of fundamental research tools in molecular biology. These present a variety of ethical, legal and social issues concerning their patenting. This commentary presents several case studies of these issues across three major microbiological tools: CRISPR, viral vectors and antimicrobial resistance drugs. It concludes that the development of these technologies-both scientifically and commercially-depend, in part, on the patent regime available for each, and researchers' willingness to enforce those patents against others. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Patenting Biotechnological Inventions in Europe

    Directory of Open Access Journals (Sweden)

    Peter Raspor

    2002-01-01

    Full Text Available The patent system has been able to provide the protection for the achievements of different technologies and in that way it has supported further development and growth of the industry where those achievements were implemented. Modern technologies like information technology and biotechnology with genetic engineering that appeared in the 70s have overgrown the frames of the existing patent system because of their exponential development during the last thirty years. Industry that invests a huge amount of money in these technologies, especially in the field of biotechnology, where the results are very uncertain, has started to claim changes in the patent system.

  10. THE USE OF THE PATENT ANALYSIS METHOD FOR FINDING ANALOGUES AND PROTOTYPES OF RECEIVED TECHNICAL SOLUTIONS

    Directory of Open Access Journals (Sweden)

    Irina Petrova

    2016-03-01

    Full Text Available The research deals with the issue of the patent analysis efficiency, which is a necessary stage of seaching analogues and prototypes to obtain technical solutions. The article presents the results of analyzing the present automation systems for finding necessary information in the patent databases and identifies their advantages and disadvantages. It gives a description of the “Intellect” system, which is an example of software systems for the conceptual design stage support. Materials and Methods The article presents some of the possible ways to organize the patents-analogues search process and specific features of searching analogues and prototypes for the generated parametric structure scheme of the technical solution, which is the result of the synthesis of a new information-measuring and control system element in the “Intellect” system. The description of the proposed search query forming method is given. The article gives the structure of the patent passport, which must be stored in a database to organize the process of searcing analogues and prototypes. There given a description of algorithms for automatic adding a patent to the database, recalculating the weights while adding a patent by experts, identifying the fact of using different physical and technical effects in a patent. Results The final part of the article contains an example of the results of testing the developed subsystem implementing the proposed method. According to the test results it is concluded that the selected software and algorithmic solutions are effective.

  11. 78 FR 31885 - Patent Term Extension

    Science.gov (United States)

    2013-05-28

    ... DEPARTMENT OF COMMERCE Patent and Trademark Office Patent Term Extension ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of its... States Patent and Trademark Office, P.O. Box 1450, Alexandria, VA 22313-1450. Federal Rulemaking Portal...

  12. 78 FR 7759 - Patent Cooperation Treaty

    Science.gov (United States)

    2013-02-04

    ... DEPARTMENT OF COMMERCE Patent and Trademark Office Patent Cooperation Treaty ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of its... States Patent and Trademark Office, P.O. Box 1450, Alexandria, VA 22313-1450. Federal Rulemaking Portal...

  13. 75 FR 20561 - Patent Term Extension

    Science.gov (United States)

    2010-04-20

    ... DEPARTMENT OF COMMERCE Patent and Trademark Office Patent Term Extension ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office (USPTO), as part of its... Officer, Office of the Chief Information Officer, United States Patent and Trademark Office, P.O. Box 1450...

  14. 76 FR 72000 - Patent, Trademark & Copyright Acts

    Science.gov (United States)

    2011-11-21

    ... DEPARTMENT OF THE INTERIOR Geological Survey Patent, Trademark & Copyright Acts AGENCY: U.S... Consultants, 1255 Roberts Boulevard NW., Suite 200, Kennesaw, GA 30144, on U.S. Patent Application Serial No. 12/133,666, and a divisional patent application to be filed shortly at the Patent and Trademark...

  15. Identification of the Key Fields and Their Key Technical Points of Oncology by Patent Analysis.

    Science.gov (United States)

    Zhang, Ting; Chen, Juan; Jia, Xiaofeng

    2015-01-01

    This paper aims to identify the key fields and their key technical points of oncology by patent analysis. Patents of oncology applied from 2006 to 2012 were searched in the Thomson Innovation database. The key fields and their key technical points were determined by analyzing the Derwent Classification (DC) and the International Patent Classification (IPC), respectively. Patent applications in the top ten DC occupied 80% of all the patent applications of oncology, which were the ten fields of oncology to be analyzed. The number of patent applications in these ten fields of oncology was standardized based on patent applications of oncology from 2006 to 2012. For each field, standardization was conducted separately for each of the seven years (2006-2012) and the mean of the seven standardized values was calculated to reflect the relative amount of patent applications in that field; meanwhile, regression analysis using time (year) and the standardized values of patent applications in seven years (2006-2012) was conducted so as to evaluate the trend of patent applications in each field. Two-dimensional quadrant analysis, together with the professional knowledge of oncology, was taken into consideration in determining the key fields of oncology. The fields located in the quadrant with high relative amount or increasing trend of patent applications are identified as key ones. By using the same method, the key technical points in each key field were identified. Altogether 116,820 patents of oncology applied from 2006 to 2012 were retrieved, and four key fields with twenty-nine key technical points were identified, including "natural products and polymers" with nine key technical points, "fermentation industry" with twelve ones, "electrical medical equipment" with four ones, and "diagnosis, surgery" with four ones. The results of this study could provide guidance on the development direction of oncology, and also help researchers broaden innovative ideas and discover new

  16. Research method of nuclear patent information

    International Nuclear Information System (INIS)

    Mo Dan; Gao An'na; Sun Chenglin; Wang Lei; You Xinfeng

    2010-01-01

    When faced with a huge amount of nuclear patent information, the key to effective research include: (1) Choose convenient way to search, quick access to nuclear technology related patents; (2) To overcome the language barrier, analysis the technical content of patent information; (3) Organize the publication date of retrieved patent documents, analysis the status and trends of nuclear technology development; (4) Research the patented technology of main applicants; (5) Always pay attention to the legal status of patent information, free use the invalid patents, at the same time avoid the patent infringement. Summary, patent information is important to obtain the latest technical information source, and the research work of patent information is a comprehensive understanding and mastery way for advanced nuclear technology. (authors)

  17. The academic advantage: gender disparities in patenting.

    Science.gov (United States)

    Sugimoto, Cassidy R; Ni, Chaoqun; West, Jevin D; Larivière, Vincent

    2015-01-01

    We analyzed gender disparities in patenting by country, technological area, and type of assignee using the 4.6 million utility patents issued between 1976 and 2013 by the United States Patent and Trade Office (USPTO). Our analyses of fractionalized inventorships demonstrate that women's rate of patenting has increased from 2.7% of total patenting activity to 10.8% over the nearly 40-year period. Our results show that, in every technological area, female patenting is proportionally more likely to occur in academic institutions than in corporate or government environments. However, women's patents have a lower technological impact than that of men, and that gap is wider in the case of academic patents. We also provide evidence that patents to which women--and in particular academic women--contributed are associated with a higher number of International Patent Classification (IPC) codes and co-inventors than men. The policy implications of these disparities and academic setting advantages are discussed.

  18. Religious coalition opposes gene patents.

    Science.gov (United States)

    James, J S

    1995-05-19

    The biotechnology industry is concerned about a coalition of mainstream religious leaders, working with Jeremy Rifkin of the Foundation of Economic Trends, who oppose the patenting of human and animal life forms, body parts, and genes. The coalition called a press conference on May 18 to ask the government to prohibit the current patenting practices for genetic engineering. The biotechnology industry argues that patents indicate that a company's research tool has significant value, and encourages capitalists to invest their dollars in the development of new treatments for diseases. They also argue that the 29 biotech drugs that are on the market have been developed as a result of patents on genes. Although most business leaders are united in opposing restrictions, many scientists are divided, citing both religious and scientific reasons.

  19. Exploration of Global Trend on Biomedical Application of Polyhydroxyalkanoate (PHA): A Patent Survey.

    Science.gov (United States)

    Ponnaiah, Paulraj; Vnoothenei, Nagiah; Chandramohan, Muruganandham; Thevarkattil, Mohamed Javad Pazhayakath

    2018-01-30

    Polyhydroxyalkanoates are bio-based, biodegradable naturally occurring polymers produced by a wide range of organisms, from bacteria to higher mammals. The properties and biocompatibility of PHA make it possible for a wide spectrum of applications. In this context, we analyze the potential applications of PHA in biomedical science by exploring the global trend through the patent survey. The survey suggests that PHA is an attractive candidate in such a way that their applications are widely distributed in the medical industry, drug delivery system, dental material, tissue engineering, packaging material as well as other useful products. In our present study, we explored patents associated with various biomedical applications of polyhydroxyalkanoates. Patent databases of European Patent Office, United States Patent and Trademark Office and World Intellectual Property Organization were mined. We developed an intensive exploration approach to eliminate overlapping patents and sort out significant patents. We demarcated the keywords and search criterions and established search patterns for the database request. We retrieved documents within the recent 6 years, 2010 to 2016 and sort out the collected data stepwise to gather the most appropriate documents in patent families for further scrutiny. By this approach, we retrieved 23,368 patent documents from all the three databases and the patent titles were further analyzed for the relevance of polyhydroxyalkanoates in biomedical applications. This ensued in the documentation of approximately 226 significant patents associated with biomedical applications of polyhydroxyalkanoates and the information was classified into six major groups. Polyhydroxyalkanoates has been patented in such a way that their applications are widely distributed in the medical industry, drug delivery system, dental material, tissue engineering, packaging material as well as other useful products. There are many avenues through which PHA & PHB could be

  20. A Review on Recent Patents and Applications of Inorganic Material Binding Peptides.

    Science.gov (United States)

    Thota, Veeranjaneyulu; Perry, Carole C

    2017-01-01

    Although the popularity of using combinatorial display techniques for recognising unique peptides having high affinity for inorganic (nano) particles has grown rapidly, there are no systematic reviews showcasing current developments or patents on binding peptides specific to these materials. In this review, we summarize and discuss recent progress in patents on material binding peptides specifically exploring inorganic nano surfaces such as metals, metal oxides, minerals, carbonbased materials, polymer based materials, magnetic materials and semiconductors. We consider both the peptide display strategies used and the exploitation of the identified peptides in the generation of advanced nanomaterials. In order to get a clear picture on the number of patents and literature present to date relevant to inorganic material binding biomolecules and their applications, a thorough online search was conducted using national and worldwide databases. The literature search include standard bibliographic databases while patents included EPO Espacenet, WIPO patent scope, USPTO, Google patent search, Patent lens, etc. along with commercial databases such as Derwent and Patbase. Both English and American spellings were included in the searches. The initial number of patents found related to material binders were 981. After reading and excluding irrelevant patents such as organic binding peptides, works published before 2001, repeated patents, documents not in English etc., 51 highly relevant patents published from 2001 onwards were selected and analysed. These patents were further separated into six categories based on their target inorganic material and combinatorial library used. They include relevant patents on metal, metal oxide or combination binding peptides (19), magnetic and semiconductor binding peptides (8), carbon based (3), mineral (5), polymer (8) and other binders (9). Further, how these material specific binders have been used to synthesize simple to complex bio- or

  1. Patent Law for Computer Scientists

    Science.gov (United States)

    Closa, Daniel; Gardiner, Alex; Giemsa, Falk; Machek, Jörg

    More than five centuries ago the first patent statute was passed by the Venetian senate. It already had most of the features of modern patent law, recognizing the public interest in innovation and granting exclusive right in exchange for a full disclosure. Some 350 years later the industrial revolution led to globalisation. The wish to protect intellectual property on a more international level evolved and supranational treaties were negotiated. Patent laws are still different in many countries, however, and inventors are sometimes at a loss to understand which basic requirements should be satisfied if an invention is to be granted a patent. This is particularly true for inventions implemented on a computer. While roughly a third of all applications (and granted patents) relate, in one way or another, to a computer, applications where the innovation mainly resides in software or in a business method are treated differently by the major patent offices. The procedures at the USPTO, JPO and EPO and, in particular, the differences in the treatment of applications centring on software are briefly explained. In later sections of this book, a wealth of examples will be presented. The methodology behind the treatment of these examples is explained.

  2. Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.

    Science.gov (United States)

    Ikeda, Shun; Abe, Takashi; Nakamura, Yukiko; Kibinge, Nelson; Hirai Morita, Aki; Nakatani, Atsushi; Ono, Naoaki; Ikemura, Toshimichi; Nakamura, Kensuke; Altaf-Ul-Amin, Md; Kanaya, Shigehiko

    2013-05-01

    Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.

  3. Technological Foresight Based on Citing and Cited Patents of Cellulose with Pharmaceutical Aplications.

    Directory of Open Access Journals (Sweden)

    Deysimar de Souza Carvalho

    2009-12-01

    Full Text Available The present study intends to present the relevance of cellulose by means of the technological foresight study through citing and cited documents from a patent application (WO 9745131 A1 as indicators of innovation. The European database of patents (espacenet was used, combining keywords and IPC. The major applicants, countries of publication and uses were mapped. The patent requests collected are mainly distributed in the area of polymers to medical devices and therapeutic methods that utilize cellulose. The results obtained revealed that the US were the main country with studies directed to this technological area (18 patent applications and the major applicant was the company Micro Therapeutics Inc. Therefore, we can understand that this is a promising technology that may reflect in an increase of R&D activities and in the patent deposits in this area.

  4. Constructing an Intelligent Patent Network Analysis Method

    Directory of Open Access Journals (Sweden)

    Chao-Chan Wu

    2012-11-01

    Full Text Available Patent network analysis, an advanced method of patent analysis, is a useful tool for technology management. This method visually displays all the relationships among the patents and enables the analysts to intuitively comprehend the overview of a set of patents in the field of the technology being studied. Although patent network analysis possesses relative advantages different from traditional methods of patent analysis, it is subject to several crucial limitations. To overcome the drawbacks of the current method, this study proposes a novel patent analysis method, called the intelligent patent network analysis method, to make a visual network with great precision. Based on artificial intelligence techniques, the proposed method provides an automated procedure for searching patent documents, extracting patent keywords, and determining the weight of each patent keyword in order to generate a sophisticated visualization of the patent network. This study proposes a detailed procedure for generating an intelligent patent network that is helpful for improving the efficiency and quality of patent analysis. Furthermore, patents in the field of Carbon Nanotube Backlight Unit (CNT-BLU were analyzed to verify the utility of the proposed method.

  5. 37 CFR 1.710 - Patents subject to extension of the patent term.

    Science.gov (United States)

    2010-07-01

    ... of Patent Term Extension of Patent Term Due to Regulatory Review § 1.710 Patents subject to extension... primarily manufactured using recombinant DNA, recombinant RNA, hybridoma technology, or other processes...

  6. Generation and analysis of a large-scale expressed sequence Tag database from a full-length enriched cDNA library of developing leaves of Gossypium hirsutum L.

    Directory of Open Access Journals (Sweden)

    Min Lin

    Full Text Available BACKGROUND: Cotton (Gossypium hirsutum L. is one of the world's most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence. METHODOLOGY/PRINCIPAL FINDINGS: In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR, which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves. CONCLUSIONS/SIGNIFICANCE: These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence

  7. The Pisa pre-main sequence tracks and isochrones. A database covering a wide range of Z, Y, mass, and age values

    Science.gov (United States)

    Tognelli, E.; Prada Moroni, P. G.; Degl'Innocenti, S.

    2011-09-01

    Context. In recent years new observations of pre-main sequence stars (pre-MS) with Z ≤ Z⊙ have been made available. To take full advantage of the continuously growing amount of data of pre-MS stars in different environments, we need to develop updated pre-MS models for a wide range of metallicity to assign reliable ages and masses to the observed stars. Aims: We present updated evolutionary pre-MS models and isochrones for a fine grid of mass, age, metallicity, and helium values. Methods: We use a standard and well-tested stellar evolutionary code (i.e. FRANEC), that adopts outer boundary conditions from detailed and realistic atmosphere models. In this code, we incorporate additional improvements to the physical inputs related to the equation of state and the low temperature radiative opacities essential to computing low-mass stellar models. Results: We make available via internet a large database of pre-MS tracks and isochrones for a wide range of chemical compositions (Z = 0.0002-0.03), masses (M = 0.2-7.0 M⊙), and ages (1-100 Myr) for a solar-calibrated mixing length parameter α (i.e. 1.68). For each chemical composition, additional models were computed with two different mixing length values, namely α = 1.2 and 1.9. Moreover, for Z ≥ 0.008, we also provided models with two different initial deuterium abundances. The characteristics of the models have been discussed in detail and compared with other work in the literature. The main uncertainties affecting theoretical predictions have been critically discussed. Comparisons with selected data indicate that there is close agreement between theory and observation. Tracks and isochrones are available on the web at the http://astro.df.unipi.it/stellar-models/Tracks and isochrones are also available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/533/A109

  8. Patents, Inducement Prizes, and Contestant Strategy

    DEFF Research Database (Denmark)

    Davis, Jerome; Davis, Lee N.

    2006-01-01

    Debate over the merits of patents versus inducement prizes has tended to ignore the signaling roles of patents, and totally ignores the impact of patent signaling on prize contests. This paper asks: How does patent signaling affect the strategic choices of firms considering entering prize contests......? First, we consider contests that do not allow patenting, then contests that do. If patenting is not allowed, we argue, patent-holders, both internal and external to the contest, can adversely impact prize contests by claiming prize winner violation of their patents, and suing for damages. The likelihood...... of such challenges being made can deter entry, particularly in contests requiring large sunk costs. Furthermore, the firm's decisionmaking process will discriminate against entering prize contests and favor R&D projects with patentable outcomes. Together, these problems may circumscribe any future wider role...

  9. Comprehensive two-dimensional gel protein databases offer a global approach to the analysis of human cells: the transformed amnion cells (AMA) master database and its link to genome DNA sequence data

    DEFF Research Database (Denmark)

    Celis, J E; Gesser, B; Rasmussen, H H

    1990-01-01

    , mitochondria, Golgi, ribosomes, intermediate filaments, microfilaments and microtubules), levels in fetal human tissues, partial protein sequences (containing information on 48 human proteins microsequenced so far), cell cycle-regulated proteins, proteins sensitive to interferons alpha, beta, and gamma, heat...

  10. The NBER Patent Citation Data File: Lessons, Insights and Methodological Tools

    OpenAIRE

    Bronwyn H. Hall; Adam B. Jaffe; Manuel Trajtenberg

    2001-01-01

    This paper describes the database on U.S. patents that we have developed over the past decade, with the goal of making it widely accessible for research. We present main trends in U. S. patenting over the last 30 years, including a variety of original measures constructed with citation data, such as backward and forward citation lags, indices of 'originality' and 'generality', self-citations, etc. Many of these measures exhibit interesting differences across the six main technological categor...

  11. Dictionary as Database.

    Science.gov (United States)

    Painter, Derrick

    1996-01-01

    Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

  12. A review of the health and economic implications of patent protection, with a specific focus on Thailand.

    Science.gov (United States)

    Yamabhai, Inthira; Smith, Richard D

    2012-08-01

    Although it has been two decades since the Thai Patent Act was amended to comply with the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS), there has been little emphasis given to assessing the implications of this amendment. The purpose of this review is to summarize the health and economic impact of patent protection, with a focus on the experience of Thailand. A review of national and international empirical evidence on the health and economic implications of patents from 1980 to 2009 was undertaken. The findings illustrate the role of patent protection in four areas: price, present access, future access, and international trade and investment. Forty-three empirical studies were found, three of which were from Thai databases. Patenting does increase price, although the size of effect differs according to the methodology and country. Although weakening patent rights could increase present access, evidence suggests that strengthening patenting may benefit future access; although this is based on complex assumptions and estimations. Moreover, while patent protection appears to have a positive impact on trade flow, the implication for foreign direct investment (FDI) is equivocal. Empirical studies in Thailand, and other similar countries, are rare, compromising the robustness and generalizability of conclusions. However, evidence does suggest that patenting presents a significant inter-temporal challenge in balancing aspects of current versus future access to technologies. This underlines the urgent need to prioritize health research resources to assess the wider implications of patent protection.

  13. Evolution of Industry Knowledge in the Public Domain: Prior Art Searching for Software Patents

    Directory of Open Access Journals (Sweden)

    Jinseok Park

    2005-03-01

    Full Text Available Searching prior art is a key part of the patent application and examination processes. A comprehensive prior art search gives the inventor ideas as to how he can improve or circumvent existing technology by providing up to date knowledge on the state of the art. It also enables the patent applicant to minimise the likelihood of an objection from the patent office. This article explores the characteristics of prior art associated with software patents, dealing with difficulties in searching prior art due to the lack of resources, and considers public contribution to the formation of prior art databases. It addresses the evolution of electronic prior art in line with technological development, and discusses laws and practices in the EPO, USPTO, and the JPO in relation to the validity of prior art resources on the Internet. This article also investigates the main features of searching sources and tools in the three patent offices as well as non-patent literature databases. Based on the analysis of various searching databases, it provides some strategies of efficient prior art searching that should be considered for software-related inventions.

  14. 78 FR 60861 - Native American Tribal Insignia Database

    Science.gov (United States)

    2013-10-02

    ... Database ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark... the report was that the USPTO create and maintain an accurate and comprehensive database containing... this recommendation, the Senate Committee on Appropriations directed the USPTO to create this database...

  15. Argonne National Laboratory patent portfolio

    International Nuclear Information System (INIS)

    Huguelet, B.C.

    1976-01-01

    This booklet contains the abstracts of all active U. S. patents on technology items that originated at ANL, the applicability of which is not limited to nuclear reactors. Also listed are the titles of all ANL-originated nuclear-related U. S. patents that are still in force. Selected technology items for which patent applications have been filed and are available for licensing are included in several categories. Categories included in this booklet are as follows: atmospheric and earth sciences; biological and medical sciences; chemistry and chemical engineering; cryogenics and superconductivity; electronics and electrical engineering; energy conversion; measurements and controls; methods and devices; materials and fabrication; physics, accelerators and fusion; and selected nuclear-related technology

  16. Patent quality and incentives at the patent office

    NARCIS (Netherlands)

    Schuett, F.

    2013-01-01

    Patent examination is a problem of moral hazard followed by adverse selection: examiners must have incentives to exert effort, but also to truthfully reveal the evidence they find. I develop a theoretical model to study the design of incentives for examiners. The model can explain the puzzling

  17. 48 CFR 1427.201 - Patent and copyright infringement liability.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Patent and copyright... INTERIOR GENERAL CONTRACTING REQUIREMENTS PATENTS, DATA, AND COPYRIGHTS Patents and Copyrights 1427.201 Patent and copyright infringement liability. ...

  18. 48 CFR 27.201 - Patent and copyright infringement liability.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Patent and copyright... REGULATION GENERAL CONTRACTING REQUIREMENTS PATENTS, DATA, AND COPYRIGHTS Patents and Copyrights 27.201 Patent and copyright infringement liability. ...

  19. Fundamentals of patenting and licensing for scientists and engineers

    National Research Council Canada - National Science Library

    Ma, M. Y. (Matthew Y.)

    2009-01-01

    ... ...28 3.2 Types of Patents...28 3.3 Patent Dates ...29 viiviii Fundamentals of Patenting and Licensing for Scientists and Engineers 3.4 Eligibility of Priority Date ...30 3.5 Patentability ...32...

  20. Foreign patent documentation and information research

    International Nuclear Information System (INIS)

    Wang Tongsheng; Wu Xianfeng; Liu Jia; Cao Jifen; Song Tianbao; Feng Beiyuan; Zhang Baozhu

    2014-01-01

    Patent documentations are important scientific and technical documentations, which gather legal information, technical information and economic information together. According to WIPO forecasts, making full use of patent documentation can save 40% of research funding and 60% of the study period. Foreign patent documentations are the world's most valuable patent documentations, and many original technologies that have significant influence are first disclosed in foreign patent documentation. Studying and making use of foreign patent documentations can improve our starting point of scientific and technological innovation, and reduce the research investment. This paper analyzes foreign patent documentation and, combining with the actual development of nuclear technology in our country, makes specific recommendations for patent documentation research. (authors)

  1. Effect of firm variables on patent price

    Directory of Open Access Journals (Sweden)

    Shyam Sreekumaran Nair

    2012-03-01

    Full Text Available In this study, using singleton patent auction price data from Ocean Tomo, LLC, we analyse the effect of firm variables on patent price. Patents owned by small firms attract higher price than patents owned by large firms, if they engage in multi-country filings. The patents owned by small firms get cited more than the patents owned by large firms. The patents owned by individual inventors attract a higher price than the patents owned by organisations when multi-country filings are not included. We believe that the lack of resources is preventing individual inventors from engaging in multi-country filings and maximising the revenue from their invention. A larger representative data should be used to replicate the results before generalising it.

  2. Can this kind of idea be a patent?

    International Nuclear Information System (INIS)

    Yu, Jae Bok

    2004-08-01

    This book mentions patent such as application, what is patents, patent law, procedure and patent attorney, which includes business idea is patent. Is internet domain name or name-brand? We can make a big money with others idea, the difference among patent, trademark, utility model rights and registration of design, priority system, new weapon in digital period, patent is a knife and a shield, the cost from application to registration, what is hunting of patent information, writing document for patent, patent examination and patent lawyer.

  3. Can this kind of idea be a patent?

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Jae Bok

    2004-08-15

    This book mentions patent such as application, what is patents, patent law, procedure and patent attorney, which includes business idea is patent. Is internet domain name or name-brand? We can make a big money with others idea, the difference among patent, trademark, utility model rights and registration of design, priority system, new weapon in digital period, patent is a knife and a shield, the cost from application to registration, what is hunting of patent information, writing document for patent, patent examination and patent lawyer.

  4. Increasing the Discovery and Use of Non-Patent Literature (NPL): Scientific Publications in Patent Examination

    OpenAIRE

    F. Loizides; B. Diallo; A. Pollard; A. Mavri

    2017-01-01

    In this work we present findings on non-patent literature use, and specifically scientific publications such as academic articles. We interview patent examiners and observe their prior art searching in order to provide insights into the perceived usage of non-patent literature and produce high level requirements for advancing non-patent literature search tools.

  5. 77 FR 4509 - Patent Public Advisory Committee Public Hearings on the Proposed Patent Fee Schedule

    Science.gov (United States)

    2012-01-30

    ... patent fees. The publication of that Notice will open a comment window through which the public may...-P-2012-0002] Patent Public Advisory Committee Public Hearings on the Proposed Patent Fee Schedule... Trademark Office (USPTO) may set or adjust by rule any patent or trademark fee established, authorized, or...

  6. Natural compounds for solar photoprotection: a patent review.

    Science.gov (United States)

    Serafini, Mairim R; Guimarães, Adriana G; Quintans, Jullyana S S; Araújo, Adriano A S; Nunes, Paula S; Quintans-Júnior, Lucindo J

    2015-04-01

    Ultraviolet irradiation has deleterious effects on human skin, including tanning, sunburn, cancer and connective tissue degradation (photoaging). Botanical antioxidants have been shown to be associated with reduced incidence of photocarcinogenesis and photoaging through their photoprotective profile. Here, the authors summarized therapeutic patent applications concerning the employment of medicinal plants on the technological development of a formulation with photoprotective or photoaging application. So, the patent search was conducted in the databases WIPO, Espacenet, USPTO and Derwent, using the keywords - photoaging, photoprotection and the IPC A61K 8/97 (cosmetics or similar cleaning supplies obtained from vegetable origin, for example, plant extracts) and A61K 36/00 (medicinal preparations of undetermined constitution containing material from algae, lichens, fungi or plants, or derivatives thereof, for example, traditional herbal medicines). We found 180 patents, out of which 25 were evaluated using inclusion criteria as application of natural products with photoprotective or photoaging application. We found that some patents related to the cosmetic compositions for improving skin wrinkle and either preventing or reducing the signs of photoaging and sunburn. The cosmetic compositions are manufactured in the form of a lotion, gel, soluble liquid, cream, essence, oil-in-water-type or water-in-oil-type formulation, containing the vegetal extracts as an active ingredient.

  7. Text mining factor analysis (TFA) in green tea patent data

    Science.gov (United States)

    Rahmawati, Sela; Suprijadi, Jadi; Zulhanif

    2017-03-01

    Factor analysis has become one of the most widely used multivariate statistical procedures in applied research endeavors across a multitude of domains. There are two main types of analyses based on factor analysis: Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA). Both EFA and CFA aim to observed relationships among a group of indicators with a latent variable, but they differ fundamentally, a priori and restrictions made to the factor model. This method will be applied to patent data technology sector green tea to determine the development technology of green tea in the world. Patent analysis is useful in identifying the future technological trends in a specific field of technology. Database patent are obtained from agency European Patent Organization (EPO). In this paper, CFA model will be applied to the nominal data, which obtain from the presence absence matrix. While doing processing, analysis CFA for nominal data analysis was based on Tetrachoric matrix. Meanwhile, EFA model will be applied on a title from sector technology dominant. Title will be pre-processing first using text mining analysis.

  8. Exploring gender differences in patenting in Spain

    OpenAIRE

    Elba Mauleón; Cinzia Daraio; Maria Bordons

    2013-01-01

    The under-representation of women in science and technology is a matter of current great concern. Obtaining patent-based indicators by gender is crucial to analyse the situation of women in innovation, identify potential cases of gender inequalities, and support policy measures to promote gender balance. In this article we analyse men and women involvement in Spanish patents applied to the European Patent Office during 1990--2004. At least one female inventor is present in 18% of the patents;...

  9. Beyond Invention: Patent as Knowledge Law

    OpenAIRE

    Madison, Michael

    2017-01-01

    The decision of the Supreme Court of the United States in Bilski v. Kappos, concerning the legal standard for determining patentable subject matter under the American Patent Act, is used as a starting point for a brief review of historical, philosophical, and cultural influences on subject matter questions in both patent and copyright law. The article suggests that patent and copyright law jurisprudence was constructed initially by the Court with explicit attention to the relationship between...

  10. 14 CFR 1260.28 - Patent rights.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Patent rights. 1260.28 Section 1260.28... Provisions § 1260.28 Patent rights. Patent Rights May 2006 As stated at § 1260.136, this award is subject to... “Patent Rights (Small Business Firms and Nonprofit Organizations)” and the following: (a) Where the term...

  11. Nanotechnology patenting trends through an environmental lens: analysis of materials and applications

    International Nuclear Information System (INIS)

    Leitch, Megan E.; Casman, Elizabeth; Lowry, Gregory V.

    2012-01-01

    Many international groups study environmental health and safety (EHS) concerns surrounding the use of engineered nanomaterials (ENMs). These researchers frequently use the “Project on Emerging Nanotechnologies” (PEN) inventory of nano-enabled consumer products to prioritize types of ENMs to study because estimates of life-cycle ENM releases to the environment can be extrapolated from the database. An alternative “snapshot” of nanomaterials likely to enter commerce can be determined from the patent literature. The goal of this research was to provide an overview of nanotechnology intellectual property trends, complementary to the PEN consumer product database, to help identify potentially “risky” nanomaterials for study by the nano-EHS community. Ten years of nanotechnology patents were examined to determine the types of nano-functional materials being patented, the chemical compositions of the ENMs, and the products in which they are likely to appear. Patenting trends indicated different distributions of nano-enabled products and materials compared to the PEN database. Recent nanotechnology patenting is dominated by electrical and information technology applications rather than the hygienic and anti-fouling applications shown by PEN. There is an increasing emphasis on patenting of nano-scale layers, coatings, and other surface modifications rather than traditional nanoparticles, and there is widespread use of nano-functional semiconductor, ceramic, magnetic, and biological materials that are currently less studied by EHS professionals. These commonly patented products and the nano-functional materials they contain may warrant life-cycle evaluations to determine the potential for environmental exposure and toxicity. The patent and consumer product lists contribute different and complementary insights into the emerging nanotechnology industry and its potential for introducing nanomaterials into the environment.

  12. Nanotechnology patenting trends through an environmental lens: analysis of materials and applications

    Energy Technology Data Exchange (ETDEWEB)

    Leitch, Megan E. [Carnegie Mellon University, Department of Civil and Environmental Engineering, Center for the Environmental Implications of NanoTechnology (CEINT) (United States); Casman, Elizabeth [Carnegie Mellon University, Department of Engineering and Public Policy, Center for the Environmental Implications of NanoTechnology (CEINT) (United States); Lowry, Gregory V., E-mail: glowry@cmu.edu [Carnegie Mellon University, Department of Civil and Environmental Engineering, Center for the Environmental Implications of NanoTechnology (CEINT) (United States)

    2012-12-15

    Many international groups study environmental health and safety (EHS) concerns surrounding the use of engineered nanomaterials (ENMs). These researchers frequently use the 'Project on Emerging Nanotechnologies' (PEN) inventory of nano-enabled consumer products to prioritize types of ENMs to study because estimates of life-cycle ENM releases to the environment can be extrapolated from the database. An alternative 'snapshot' of nanomaterials likely to enter commerce can be determined from the patent literature. The goal of this research was to provide an overview of nanotechnology intellectual property trends, complementary to the PEN consumer product database, to help identify potentially 'risky' nanomaterials for study by the nano-EHS community. Ten years of nanotechnology patents were examined to determine the types of nano-functional materials being patented, the chemical compositions of the ENMs, and the products in which they are likely to appear. Patenting trends indicated different distributions of nano-enabled products and materials compared to the PEN database. Recent nanotechnology patenting is dominated by electrical and information technology applications rather than the hygienic and anti-fouling applications shown by PEN. There is an increasing emphasis on patenting of nano-scale layers, coatings, and other surface modifications rather than traditional nanoparticles, and there is widespread use of nano-functional semiconductor, ceramic, magnetic, and biological materials that are currently less studied by EHS professionals. These commonly patented products and the nano-functional materials they contain may warrant life-cycle evaluations to determine the potential for environmental exposure and toxicity. The patent and consumer product lists contribute different and complementary insights into the emerging nanotechnology industry and its potential for introducing nanomaterials into the environment.

  13. tRNA sequence data, annotation data and curation data - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us tRNAD... tRNA sequence data, annotation data and curation data - tRNADB-CE | LSDB Archive ...

  14. Patentability aspects of computational cancer models

    Science.gov (United States)

    Lishchuk, Iryna

    2017-07-01

    Multiscale cancer models, implemented in silico, simulate tumor progression at various spatial and temporal scales. Having the innovative substance and possessing the potential of being applied as decision support tools in clinical practice, patenting and obtaining patent rights in cancer models seems prima facie possible. What legal hurdles the cancer models need to overcome for being patented we inquire from this paper.

  15. 43 CFR 402.10 - Patent.

    Science.gov (United States)

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Patent. 402.10 Section 402.10 Public Lands... LANDS IN FEDERAL RECLAMATION PROJECTS Public Lands § 402.10 Patent. When a purchaser has complied fully... and patent and shall state the statutory authority for such liens. The receipt shall be submitted to...

  16. 48 CFR 970.2703 - Patent rights.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Patent rights. 970.2703 Section 970.2703 Federal Acquisition Regulations System DEPARTMENT OF ENERGY AGENCY SUPPLEMENTARY REGULATIONS DOE MANAGEMENT AND OPERATING CONTRACTS Patents, Data, and Copyrights 970.2703 Patent rights. ...

  17. 48 CFR 35.012 - Patent rights.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Patent rights. 35.012 Section 35.012 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION SPECIAL CATEGORIES OF CONTRACTING RESEARCH AND DEVELOPMENT CONTRACTING 35.012 Patent rights. For a discussion of patent rights, see...

  18. A contribuição de patentes para a inovação sustentável: o caso de um trocador de calor

    Directory of Open Access Journals (Sweden)

    Carlos Mamori Kono

    2014-01-01

    Full Text Available Patents are useful indicators of innovation, although still of a very limited use. In patenting, the need for the precise registration of a method, process, or system facilitates understanding it and eventually motivates the scientific community to carry out research in a given area, thus accelerating technological progress. Patent data are not static; patents cite other connected patents, providing a dynamic view of technological antecedents and descendants leading to state-of-the-art knowledge. This article is an exercise on the usefulness of patents as a source of technological innovation. To do this, we searched patent databases considered as sources of technological innovation in order to introduce improvements in a heat-exchanging device coupled to an electric shower. The results enabled finding the state-of-the-art of the technology and led to suggestions of possible innovations for the product. This allowed us to improve the sustainability potential of this technology.

  19. 37 CFR 1.705 - Patent term adjustment determination.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Patent term adjustment determination. 1.705 Section 1.705 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES Adjustment and Extension of Patent Term...

  20. Imitation, patent protection and welfare

    NARCIS (Netherlands)

    Mukherjee, A.; Pennings, H.P.G.

    2000-01-01

    Once a new technology has been invented it is shown that the innovator has an incentive to postpone technology adoption when the cost of imitation is high and patent protection is strong. With the possibility of licensing it is shown that licensing oftechnology instead of delaying technology

  1. CLASSICS UNITED STATES PATENT OFFICE

    Indian Academy of Sciences (India)

    IAS Admin

    From the profits, he became a very rich man and was able ... The Schedule referred to in these Letters Patent and making part of the same. TO ALL ... This is the real character and purpose of my invention; and in order to enable others ... kneading, it is rubbed through a hair, silk, or brass-wire sieve, (iron corrodes) and any.

  2. Database Description - KAIKOcDNA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us KAIKOcDNA Database Description General information of database Database name KAIKOcDNA Alter...National Institute of Agrobiological Sciences Akiya Jouraku E-mail : Database cla...ssification Nucleotide Sequence Databases Organism Taxonomy Name: Bombyx mori Taxonomy ID: 7091 Database des...rnal: G3 (Bethesda) / 2013, Sep / vol.9 External Links: Original website information Database maintenance si...available URL of Web services - Need for user registration Not available About This Database Database

  3. In which developing countries are patents on essential medicines being filed?

    Science.gov (United States)

    Beall, Reed F; Blanchet, Rosanne; Attaran, Amir

    2017-06-26

    This article is based upon data gathered during a study conducted in partnership with the World Intellectual Property Organization on the patent status of products appearing on the World Health Organization's 2013 Model List of Essential Medicines (MLEM). It is a statistical analysis aimed at answering: in which developing countries are patents on essential medicines being filed? Patent data were collected by linking those listed in the United States and Canada's medicine patent registers to corresponding patents in developing countries using two international patent databases (INPADOC and Derwent) via a commerical-grade patent search platform (Thomson Innovation). The respective supplier companies were then contacted to correct and verify our data. We next tallied the number of MLEM patents per developing country. Spearman correlations were done to assess bivariate relationships between variables, and a multivariate regression model was developed to explain the number of MLEM patents in each country using SPSS 23.0. A subset of 20 of the 375 (5%) products on the 2013 MLEM fit our inclusion criteria. The patent estate reports (i.e., the global list of patents for a given drug) varied greatly in their number with a median of 48 patents (interquartile range [IQR]: 26-76). Their geographic reach had a median of 15% of the developing countries sampled (IQR: 8-28%). The number of developing countries covered appeared to increase with the age of the patent estate (r = .433, p = 0.028). The number of MLEM patents per country was significantly positively associated with human development index (HDI), gross domestic income (GDI) per capita, total healthcare expenditure per capita, population size, the Rule of Law Index, and average education level. Population size, GDI per capita, and healthcare expenditure (in % of national expenditure) were predictors of the number of MLEM patents in countries (p = 0.001, p = 0.001, p = 0.009, respectively). Population

  4. THPdb: Database of FDA-approved peptide and protein therapeutics.

    Directory of Open Access Journals (Sweden)

    Salman Sadullah Usmani

    Full Text Available THPdb (http://crdd.osdd.net/raghava/thpdb/ is a manually curated repository of Food and Drug Administration (FDA approved therapeutic peptides and proteins. The information in THPdb has been compiled from 985 research publications, 70 patents and other resources like DrugBank. The current version of the database holds a total of 852 entries, providing comprehensive information on 239 US-FDA approved therapeutic peptides and proteins and their 380 drug variants. The information on each peptide and protein includes their sequences, chemical properties, composition, disease area, mode of activity, physical appearance, category or pharmacological class, pharmacodynamics, route of administration, toxicity, target of activity, etc. In addition, we have annotated the structure of most of the protein and peptides. A number of user-friendly tools have been integrated to facilitate easy browsing and data analysis. To assist scientific community, a web interface and mobile App have also been developed.

  5. Cross-Border Patent Disputes: Unified Patent Court or International Commercial Arbitration?

    OpenAIRE

    Alba Betancourt, Ana

    2016-01-01

    Currently, the enforcement of a patent that is registered in several countries involves the risk of getting different and conflicting decisions from the national courts. In 2013, 25 European countries entered in an agreement that aims to homogenise the patent system by creating the European patent with unitary effect and a Unified Patent Court (UPC). This article focuses on the UPC, which aims to have a single court proceeding for cross-border patent conflicts. Does the UPC system represent a...

  6. Entrepreneurial patent management in pharmaceutical startups.

    Science.gov (United States)

    Holgersson, Marcus; Phan, Tai; Hedner, Thomas

    2016-07-01

    Startups fill an increasingly important role as innovators in the pharmaceutical industry, and patenting is typically central to their success. This article aims to explore patent management in pharmaceutical startups. The results show that startups need to deal with several challenges related to patenting and an 'entrepreneurial' approach to patent management is called for. Resource constraints, venture capital provision, exits and other conditions and events must be readily considered in the patent management process to build a successful pharmaceutical venture, something that could benefit the pharmaceutical industry as a whole. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Patent data mining method and apparatus

    Science.gov (United States)

    Boyack, Kevin W.; Grafe, V. Gerald; Johnson, David K.; Wylie, Brian N.

    2002-01-01

    A method of data mining represents related patents in a multidimensional space. Distance between patents in the multidimensional space corresponds to the extent of relationship between the patents. The relationship between pairings of patents can be expressed based on weighted combinations of several predicates. The user can select portions of the space to perceive. The user also can interact with and control the communication of the space, focusing attention on aspects of the space of most interest. The multidimensional spatial representation allows more ready comprehension of the structure of the relationships among the patents.

  8. The Patentability of Stem Cells in Australia.

    Science.gov (United States)

    Petering, Jenny; Cowin, Prue

    2015-07-01

    The potential therapeutic applications of stem cells are unlimited. However, the ongoing political and social debate surrounding the intellectual property and patenting considerations of stem cell research has led to the implementation of strict legislative regulations. In Australia the patent landscape surrounding stem cells has evolved considerably over the past 20 years. The Australian Patents Act 1990 includes a specific exclusion to the patentability of human beings and of biological processes for their generation. However, this exclusion has received no judicial consideration to date, and so its scope and potential impact on stem cell patents is unclear. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

  9. Idea on patent ; It is high time to stress quality

    International Nuclear Information System (INIS)

    2012-03-01

    This book deals with patent stressing on the quality, which includes from idea to technical business, It's simple to register the computer program, why do patent lawyer appoint the patent attorney's office? construction of patent right range, a good patent and a bad patent, strong patent and weak patent. It doesn't allow for Dus to use as we like, each patent has different value, Let's write technical specifications, advice on talking for invention with a patent attorney's office and what kind of task do intellectual property division do?

  10. DEVELOPING TECHNOLOGICAL INNOVATIONS ON THE BASES OF THE WORLD PATENT INFORMATION

    Directory of Open Access Journals (Sweden)

    N. A. KAMENEVA

    2015-04-01

    Full Text Available To ensure the innovative growth and progressive economic performance in high-technology industries, or at least to keep them at a fixed level it is necessary for the industrial enterprises to conduct scientific research and inventive activities through developing technological innovations and also through supporting, completing, replenishing, updating one of the most important intangible components of the business – patent resources: protective documents on inventions, industrial designs, utility models, trademarks etc. Scientific-and-engineering information, contained in international patent funds, allows determining the world state of the art, registering and securing the company’s exclusive patent rights to the innovations. This work presents the method of obtaining patent information in Russia by means of using various Russian and international databases and abstract journals that can help to investigate the world state of art in a given technological field.

  11. Information Extraction From Chemical Patents

    Directory of Open Access Journals (Sweden)

    Sandra Bergmann

    2012-01-01

    Full Text Available The development of new chemicals or pharmaceuticals is preceded by an indepth analysis of published patents in this field. This information retrieval is a costly and time inefficient step when done by a human reader, yet it is mandatory for potential success of an investment. The goal of the research project UIMA-HPC is to automate and hence speed-up the process of knowledge mining about patents. Multi-threaded analysis engines, developed according to UIMA (Unstructured Information Management Architecture standards, process texts and images in thousands of documents in parallel. UNICORE (UNiform Interface to COmputing Resources workflow control structures make it possible to dynamically allocate resources for every given task to gain best cpu-time/realtime ratios in an HPC environment.

  12. GOBASE: an organelle genome database

    OpenAIRE

    O?Brien, Emmet A.; Zhang, Yue; Wang, Eric; Marie, Veronique; Badejoko, Wole; Lang, B. Franz; Burger, Gertraud

    2008-01-01

    The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (?913 000) and chloroplast-encoded sequences (?250 000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing...

  13. A search for pre-main sequence stars in the high-latitude molecular clouds. II - A survey of the Einstein database

    Science.gov (United States)

    Caillault, Jean-Pierre; Magnani, Loris

    1990-01-01

    The preliminary results are reported of a survey of every EINSTEIN image which overlaps any high-latitude molecular cloud in a search for X-ray emitting pre-main sequence stars. This survey, together with complementary KPNO and IRAS data, will allow the determination of how prevalent low mass star formation is in these clouds in general and, particularly, in the translucent molecular clouds.

  14. The Coordination of Independently-Owned Vacuum Tube Patents in the Alleged Early Radio Patent Thicket

    DEFF Research Database (Denmark)

    Howells, John; Ron D, Katznelson

    -examines the legal trajectories and entrepreneurial exploitation of these patents with a focus on vacuum tube technology where Fleming’s diode patent ‘overlapped’ with earlier prior art and, dependent on court decisions, with later commercial implementations of De Forest’s triode patents. We show, by means...... of the relevant historical record, patent claims, litigation records and other relevant law, how the ‘overlapping’ patent rights were resolved by the courts and by the immunity of suppliers to the Government from patent infringement liability. We trace the cross-licensing agreements between the different radio...

  15. Patent first, ask questions later: morality and biotechnology in patent law.

    Science.gov (United States)

    Bagley, Margo A

    2003-12-01

    This Article explores the U.S. "patent first, ask questions later" approach to determining what subject matter should receive patent protection. Under this approach, the U.S. Patent and Trademark Office (USPTO or the Agency) issues patents on "anything under the sun made by man," and to the extent a patent's subject matter is sufficiently controversial, Congress acts retrospectively in assessing whether patents should issue on such interventions. This practice has important ramifications for morally controversial biotechnology patents specifically, and for American society generally. For many years a judicially created "moral utility" doctrine served as a type of gatekeeper of patent subject matter eligibility. The doctrine allowed both the USTPO and courts to deny patents on morally controversial subject matter under the fiction that such inventions were not "useful." The gate, however, is currently untended. A combination of the demise of the moral utility doctrine, along with expansive judicial interpretations of the scope of patent-eligible subject matter, has resulted in virtually no basis on which the USTPO or courts can deny patent protection to morally controversial, but otherwise patentable, subject matter. This is so despite position statements by the Agency to the contrary. Biotechnology is an area in which many morally controversial inventions are generated. Congress has been in react-mode following the issuance of a stream of morally controversial biotech patents, including patents on transgenic animals, surgical methods, and methods of cloning humans. With no statutory limits on patent eligibility, and with myriad concerns complicating congressional action following a patent's issuance, it is not Congress, the representative of the people, determining patent eligibility. Instead, it is patent applicants, scientific inventors, who are deciding matters of high public policy through the contents of the applications they file with the USTPO. This Article

  16. [Systematic review on methodology of randomized controlled trials of post-marketing Chinese patent drugs for treatment of type 2 diabetes].

    Science.gov (United States)

    Ma, Li-xin; Wang, Yu-yi; Li, Xin-xue; Liu, Jian-ping

    2012-03-01

    Randomized controlled trial (RCT) is considered as the gold standard for the efficacy assessment of medicines. With the increasing number of Chinese patent drugs for treatment of type 2 diabetes, the methodology of post-marketing RCTs evaluating the efficacy and specific effect has become more important. To investigate post-marketing Chinese patent drugs for treatment of type 2 diabetes, as well as the methodological quality of post-marketing RCTs. Literature was searched from the books of Newly Compiled Traditional Chinese Patent Medicine and Chinese Pharmacopeia, the websites of the State Food and Drug Administration and the Ministry of Human Resources and Social Security of the People's Republic of China, China National Knowledge Infrastructure Database, Chongqing VIP Chinese Science and Technology Periodical Database, Chinese Biomedical Database (SinoMed) and Wanfang Data. The time period for searching ran from the commencement of each database to August 2011. RCTs of post-marketing Chinese patent drugs for treatment of type 2 diabetes with intervention course no less than 3 months. Two authors independently evaluated the research quality of the RCTs by the checklist of risk bias assessment and the data collection forms based on the CONSORT Statement. Independent double data-extraction was performed. The authors identified a total of 149 Chinese patent drugs for treatment of type 2 diabetes. According to different indicative syndromes, the Chinese patent drugs can be divided into the following types, namely, yin deficiency and interior heat (n=48, 32%), dual deficiency of qi and yin (n=58, 39%) and dual deficiency of qi and yin combined with blood stasis (n=22, 15%). A total of 41 RCTs meeting the inclusion criteria were included. Neither multicenter RCTs nor endpoint outcome reports were found. Risk bias analysis showed that 81% of the included studies reported randomization for grouping without sequence generation, 98% of these studies did not report

  17. The Academic Advantage: Gender Disparities in Patenting

    Science.gov (United States)

    Sugimoto, Cassidy R.; Ni, Chaoqun; West, Jevin D.; Larivière, Vincent

    2015-01-01

    We analyzed gender disparities in patenting by country, technological area, and type of assignee using the 4.6 million utility patents issued between 1976 and 2013 by the United States Patent and Trade Office (USPTO). Our analyses of fractionalized inventorships demonstrate that women’s rate of patenting has increased from 2.7% of total patenting activity to 10.8% over the nearly 40-year period. Our results show that, in every technological area, female patenting is proportionally more likely to occur in academic institutions than in corporate or government environments. However, women’s patents have a lower technological impact than that of men, and that gap is wider in the case of academic patents. We also provide evidence that patents to which women—and in particular academic women—contributed are associated with a higher number of International Patent Classification (IPC) codes and co-inventors than men. The policy implications of these disparities and academic setting advantages are discussed. PMID:26017626

  18. The academic advantage: gender disparities in patenting.

    Directory of Open Access Journals (Sweden)

    Cassidy R Sugimoto

    Full Text Available We analyzed gender disparities in patenting by country, technological area, and type of assignee using the 4.6 million utility patents issued between 1976 and 2013 by the United States Patent and Trade Office (USPTO. Our analyses of fractionalized inventorships demonstrate that women's rate of patenting has increased from 2.7% of total patenting activity to 10.8% over the nearly 40-year period. Our results show that, in every technological area, female patenting is proportionally more likely to occur in academic institutions than in corporate or government environments. However, women's patents have a lower technological impact than that of men, and that gap is wider in the case of academic patents. We also provide evidence that patents to which women--and in particular academic women--contributed are associated with a higher number of International Patent Classification (IPC codes and co-inventors than men. The policy implications of these disparities and academic setting advantages are discussed.

  19. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  20. TECHNOLOGICAL INFORMATION REGARDING PREBIOTICS AND PROBIOTICS NUTRITION VERSUS THE PATENT REGISTERS: WHAT IS NEW?

    Science.gov (United States)

    Reis, José Maciel Caldas Dos; Pinheiro, Maurício Fortuna; Oti, André Takashi; Feitosa-Junior, Denilson José Silva; Pantoja, Mauro de Souza; Barros, Rui Sérgio Monteiro

    2016-01-01

    Food is a key factor both in prevention and in promoting human health. Among the functional food are highlighted probiotics and prebiotics. Patent databases are the main source of technological information about innovation worldwide, providing extensive library for research sector. Perform mapping in the main patent databases about pre and probiotics, seeking relevant information regarding the use of biotechnology, nanotechnology and genetic engineering in the production of these foods. Electronic consultation was conducted (online) in the main public databases of patents in Brazil (INPI), United States (USPTO) and the European Patent Bank (EPO). The research involved the period from January 2014 to July 2015, being used in the title fields and summary of patents, the following descriptors in INPI "prebiotic", "prebiotic" "probiotics", "probiotic" and the USPTO and EPO: "prebiotic", "prebiotics", "probiotic", "probiotics". This search haven't found any deposit at the brazilian patents website (INPI) in this period; US Patent &Trademark Office had registered 60 titles in patents and the European Patent Office (EPO) showed 10 documents on the issue. Information technology offered by genetic engineering, biotechnology and nanotechnology deposited in the form of titles and abstracts of patents in relation to early nutritional intervention as functional foods, has increasingly required to decrease the risks and control the progression of health problems. But, the existing summaries, although attractive and promising in this sense, are still incipient to recommend them safely as a therapeutic tool. Therefore, they should be seen more as diet elements and healthy lifestyles. A alimentação é fator primordial tanto na prevenção quanto na promoção para a saúde humana. Dentre os alimentos funcionais destacam-se os probióticos e prebióticos. Os bancos de dados de patentes representam a maior fonte de informação tecnológica acerca de inovação em nível mundial

  1. Biofuel Database

    Science.gov (United States)

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  2. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases such...

  3. Mycobacteriophage genome database.

    Science.gov (United States)

    Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

    2011-01-01

    Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

  4. Tank waste processing analysis: Database development, tank-by-tank processing requirements, and examples of pretreatment sequences and schedules as applied to Hanford Double-Shell Tank Supernatant Waste - FY 1993

    International Nuclear Information System (INIS)

    Colton, N.G.; Orth, R.J.; Aitken, E.A.

    1994-09-01

    This report gives the results of work conducted in FY 1993 by the Tank Waste Processing Analysis Task for the Underground Storage Tank Integrated Demonstration. The main purpose of this task, led by Pacific Northwest Laboratory, is to demonstrate a methodology to identify processing sequences, i.e., the order in which a tank should be processed. In turn, these sequences may be used to assist in the development of time-phased deployment schedules. Time-phased deployment is implementation of pretreatment technologies over a period of time as technologies are required and/or developed. The work discussed here illustrates how tank-by-tank databases and processing requirements have been used to generate processing sequences and time-phased deployment schedules. The processing sequences take into account requirements such as the amount and types of data available for the tanks, tank waste form and composition, required decontamination factors, and types of compact processing units (CPUS) required and technology availability. These sequences were developed from processing requirements for the tanks, which were determined from spreadsheet analyses. The spreadsheet analysis program was generated by this task in FY 1993. Efforts conducted for this task have focused on the processing requirements for Hanford double-shell tank (DST) supernatant wastes (pumpable liquid) because this waste type is easier to retrieve than the other types (saltcake and sludge), and more tank space would become available for future processing needs. The processing requirements were based on Class A criteria set by the U.S. Nuclear Regulatory Commission and Clean Option goals provided by Pacific Northwest Laboratory

  5. Database Administrator

    Science.gov (United States)

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  6. US patent interferences vs. international first-to-file patent systems, and current GATT problems

    International Nuclear Information System (INIS)

    Parkhurst, R.W.; Serbinowski, P.A.

    1991-01-01

    Simultaneous superconductivity research activities by different entities have resulted in numerous US patent applications, some of which may claim identical inventions and thus likely will be involved in interference proceedings in the US Patent and Trademark Office to determine which inventors are entitled to priority of invention and the resulting US patent. The determination in an interference proceeding of what inventors were the first-to-invent a patentable invention is contrasted with the patent systems in the rest of the world where the first inventor to file his patent application automatically gains priority. This issue and other aspects of US patent law are the subjects of criticism of US patent law and practice in the current Uruguay round of talks on the General Agreement on Trade and Tariffs (GATT). Interesting aspects of each of these subjects will be discussed

  7. Alienation from the Objectives of the Patent System: How to Remedy the Situation of Biotechnology Patent.

    Science.gov (United States)

    Jiang, Li

    2018-03-12

    Some fundamental biotechnologies hold unprecedented potential to eradicate many incurable diseases. However, in absence of regulations, the power of patent makes the future use of some important biotechnology in few institution's hands. The excessive patents restrict researcher access to the fundamental technologies. It generates concerns and complaints of deteriorating the public health and social welfare. Furthermore, intellectual curiosities, funding, respect among colleagues etc., rather than patents, are the real motivations driving a major ground-breaking discoveries in biotechnology. These phenomena reveal that some biotechnology patents are alienated from the purpose of patent system. Therefore, it is necessary to take some approaches to stop over-patenting these fundamental biotechnology inventions. This article proposes a model regulatory framework for controlling biotechnology patent alienating from the purpose of patent system.

  8. 37 CFR 1.81 - Drawings required in patent application.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Drawings required in patent..., DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES National Processing Provisions The Drawings § 1.81 Drawings required in patent application. (a) The applicant for a patent is required to furnish...

  9. 37 CFR 1.41 - Applicant for patent.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Applicant for patent. 1.41 Section 1.41 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES National Processing Provisions Who May Apply for A...

  10. 37 CFR 1.14 - Patent applications preserved in confidence.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Patent applications preserved in confidence. 1.14 Section 1.14 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES General Provisions...

  11. 37 CFR 1.314 - Issuance of patent.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Issuance of patent. 1.314 Section 1.314 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES National Processing Provisions Allowance and Issue of...

  12. 37 CFR 11.9 - Limited recognition in patent matters.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Limited recognition in patent matters. 11.9 Section 11.9 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE REPRESENTATION OF OTHERS BEFORE THE UNITED STATES PATENT AND TRADEMARK OFFICE...

  13. 37 CFR 1.215 - Patent application publication.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Patent application publication. 1.215 Section 1.215 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES National Processing Provisions Publication...

  14. 37 CFR 1.315 - Delivery of patent.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Delivery of patent. 1.315 Section 1.315 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK OFFICE, DEPARTMENT OF COMMERCE GENERAL RULES OF PRACTICE IN PATENT CASES National Processing Provisions Allowance and Issue of...

  15. Neglected knowledge in geophysics: Patents - how to find them, how to use them and how to apply for them

    Science.gov (United States)

    Wollny, K. G.

    2013-12-01

    Geophysical departments of universities or major geophysical research institutes around the world hardly ever file for a patent, even if pioneering and marketable work is done - this is what research in patent databases shows. Patents for methods, apparatuses or scientific instruments developed during scientific projects are mostly filed by companies, i.e. more than 90% of approximately 185,000 patent documents added by May 2013 to the International Patent Classification (IPC) class G01V, which the United Nations' World Intellectual Property Organisation (WIPO) has set up mainly for inventions with key aspects in geophysics. Even inventions born of cooperations between research institutes or universities and well-known geophysical companies where both act as equal partners almost never make it to the G01V. University departments responsible for intellectual property management explain that geoscientists prefer to publish their results in journals rather than in the form of patent applications even if these departments support them and parallel publication is protected legally. This means geoscientists miss the opportunity to protect their intellectual work and to tap its economic potential. But even if scientists don't want to apply for patents, patent documents constitute a wealth of knowledge that should be used much more frequently in research e.g. to stay on top of developments in one's own scientific field. Most important databases are for free, search functionality is self-explanatory and the amount of information to be extracted is enormous. All in all, about 80 million multilingual patent documents are currently available online e.g. in DEPATIS database from the German Patent and Trade Mark Office (DPMA) or ESPACENET from the European Patent Office (EPO). From a researcher's perspective, they might also be interesting for detailed technical background information, interdisciplinary solutions for similar problems, to learn about inventions too advanced for

  16. Patents - Superconductor materials, processes and devices

    International Nuclear Information System (INIS)

    Test, A.

    1987-01-01

    A patent is a grant by a country to an inventor or his assignee of the right to exclude others for a limited period of time from making, using or selling the patented invention within its territory. It is reported that basic patents have been filed by IBM and the University of Houston to protect a broad range of warm superconducting materials or compounds. It is believed that other researchers are seeking patents to protect related or improved materials, processes and apparatus. Because of the importance of this field and to speed up the patent process, the United States Patent Office is giving, upon request, special expedited status to these patent applications. A survey of Japanese companies shows that more than 1500 patents have been applied for in Japan relating to superconducting materials, compositions, apparatus using superconductors and improvements. It appears that the goal of the Japanese companies is to obtain a patent position in Japan so that they can trade with companies wishing to do business in Japan for rights in other parts of the world

  17. Performance of Patenting Firms in Danish Manufacturing

    DEFF Research Database (Denmark)

    Madsen, Erik Strøjer; Smith, Valdemar; Nielsen, Anders Østergaard

    2000-01-01

    Most countries focus on industries with high technology and the governments grant subsidies to innovating firms. However, there has been remarkable few studies of the performance of innovative firms or industries. This study examines the performance of patent active firms compared to the non-patenting...... firms within the manufacturing sector in Denmark. Performance is measured both by growth in employment as well as in the return on equity and profit share in turnover. The results suggest that differences in performance of patenting and non-patenting firms are very small, which questions the political...

  18. Patents and Innovation: Friends or Foes?

    OpenAIRE

    Lévêque, François

    2007-01-01

    Over 2 million patents are currently in force in the EU and in the USA. Do they testify innovation is blockaded for they restrict freedom in research or do they give evidence innovation is flourishing for patent law provides incentives to invent new products and processes? In other terms do patents freeze or spur innovation? The question arises for massive anecdotal evidence shows the patent system may have turned on its head, e.g., USPTO and EPO examiners spend less than 30 hours pe...

  19. US Photovoltaic Patents, 1988--1990

    Energy Technology Data Exchange (ETDEWEB)

    1991-12-01

    This document contains US patents on terrestrial photovoltaic (PV) power applications, including systems, components, and materials, as well as manufacturing and support functions. The patent entries in this document were issued from 1988 through 1990. The entries were located by searching USPA, the data base of the US Patent Office. The final search retrieved all patents under the class ``Batteries, Thermoelectric and Photoelectric`` and the subclasses ``Photoelectric,`` ``Testing,`` and ``Applications.`` The search also located patents that contained the words ``photovoltaic(s)`` or ``solar cell(s)`` and their derivatives. A manual search of the patents in the Solar Energy Research Institute (SERI) patent file augmented the data base search. After the initial list was compiled, most of the patents on the following subjects were excluded: space photovoltaic technology, use of the photovoltaic effect for detectors and subjects only peripherally concerned with photovoltaics. Some patents on these three subjects were included when it appeared that those inventions might be of use in terrestrial PV power technologies.

  20. US Photovoltaic Patents, 1988--1990

    Energy Technology Data Exchange (ETDEWEB)

    1991-12-01

    This document contains US patents on terrestrial photovoltaic (PV) power applications, including systems, components, and materials, as well as manufacturing and support functions. The patent entries in this document were issued from 1988 through 1990. The entries were located by searching USPA, the data base of the US Patent Office. The final search retrieved all patents under the class Batteries, Thermoelectric and Photoelectric'' and the subclasses Photoelectric,'' Testing,'' and Applications.'' The search also located patents that contained the words photovoltaic(s)'' or solar cell(s)'' and their derivatives. A manual search of the patents in the Solar Energy Research Institute (SERI) patent file augmented the data base search. After the initial list was compiled, most of the patents on the following subjects were excluded: space photovoltaic technology, use of the photovoltaic effect for detectors and subjects only peripherally concerned with photovoltaics. Some patents on these three subjects were included when it appeared that those inventions might be of use in terrestrial PV power technologies.

  1. Innovación Tecnológica en Empresas Chilenas: Un Estudio Empírico Basado en Patentes

    Directory of Open Access Journals (Sweden)

    Rodrigo Fuentes Solís

    2016-12-01

    Full Text Available Technological Innovation in Chilean Firms: An Empirical Study Based on Patents Literature has focused on studying patents in particular industries, subsectors or firms, mainly in developed countries. The level or quantity of patents in Chile during the period 2007-2012 on average reached 12 triadic families, while in countries like Argentina and Mexico presented averages of 12 and 15 respectively. The overall average for the same period amounted to 48,242 OECD triadic patent families. This shows the interest of the scientific community to study the phenomenon of patent creation, and, on the other hand, the large technological gap between developed and developing countries. We propose to study the determinants of patenting in Chilean firms, as a case of a developing country. We use a probit model where the dependent variable takes value one if the firm has or is in the process of obtaining an invention patent (technological and zero if not. Our database has 4,338 Chilean firms, is cross-sectional and corresponds to an extract of the Eighth Survey of Innovation in Firms 2011-2012. The results show that the age of the firm, the base of existing knowledge, and the use of governmental instruments to support R&D have a positive effect on creation of patents.

  2. Discrimination against foreigners in the patent system : evidence from standard-essential patents

    NARCIS (Netherlands)

    de Rassenfosse, G.; Raiteri, E.; Bekkers, R.N.A.

    This paper tests for traces of discrimination against foreign firms in the patent prosecution process. It focuses on the case of China and looks specifically at patent applications declared as essential to a technological standard. The choice of standard-essential patents (SEPs) is particularly

  3. Discrimination in the patent system: evidence from standard-essential patents

    NARCIS (Netherlands)

    de Rassenfosse, G.; Raiteri, E.; Bekkers, R.N.A.

    2017-01-01

    This paper tests for traces of discrimination against foreigners in the patent prosecution process. It focuses on the case of China and looks specifically at patent applications declared as essential to a technological standard, so called standard-essential patents. The identification strategy

  4. 78 FR 51177 - Notice of Intent To Grant Partially Exclusive Patent License; ICAP Patent Brokerage, LLC

    Science.gov (United States)

    2013-08-20

    ... DEPARTMENT OF DEFENSE Department of the Navy Notice of Intent To Grant Partially Exclusive Patent License; ICAP Patent Brokerage, LLC AGENCY: Department of the Navy, DoD. ACTION: Notice. SUMMARY: The Department of the Navy hereby gives notice of its intent to grant to ICAP Patent Brokerage, LLC, a revocable...

  5. 78 FR 72872 - Notice of Intent To Grant Partially Exclusive Patent License; ICAP Patent Brokerage, LLC

    Science.gov (United States)

    2013-12-04

    ... DEPARTMENT OF DEFENSE Department of the Navy Notice of Intent To Grant Partially Exclusive Patent License; ICAP Patent Brokerage, LLC AGENCY: Department of the Navy, DoD. ACTION: Notice. SUMMARY: The Department of the Navy hereby gives notice of its intent to grant to ICAP Patent Brokerage, LLC, a revocable...

  6. Therapeutic and cosmetic applications of mangiferin: a patent review.

    Science.gov (United States)

    Telang, Manasi; Dhulap, Sivakami; Mandhare, Anita; Hirwani, Rajkumar

    2013-12-01

    Mangiferin, a natural C-glucoside xanthone [2-C-β-D-glucopyranosyl-1, 3, 6, 7-tetrahydroxyxanthone], is abundantly present in young leaves and stem bark of the mango tree. The xanthonoid structure of mangiferin with C-glycosyl linkage and polyhydroxy components contributes to its free radical-scavenging ability, leading to a potent antioxidant effect as well as multiple biological activities. An extensive search was carried out to collect patent information on mangiferin and its derivatives using various patent databases spanning all priority years to date. The patents claiming therapeutic and cosmetic applications of mangiferin and its derivatives were analyzed in detail. The technology areas covered in this article include metabolic disorders, cosmeceuticals, multiple uses of the same compound, miscellaneous uses, infectious diseases, inflammation, cancer and autoimmune disorders, and neurological disorders. Mangiferin has the potential to modulate multiple molecular targets including nuclear factor-kappa B (NF-κB) signaling and cyclooxygenase-2 (COX-2) protein expression. Mangiferin exhibits antioxidant, antidiabetic, antihyperuricemic, antiviral, anticancer and antiinflammatory activities. The molecular structure of mangiferin fulfils the four Lipinski's requisites reported to favor high bioavailability by oral administration. There is no evidence of adverse side effects of mangiferin so far. Mangiferin could thus be a promising candidate for development of a multipotent drug.

  7. [Development strategy of Paris based on combination of domestic patent and current resource application and development].

    Science.gov (United States)

    Zhao, Fei-Ya; Tao, Ai-En; Xia, Cong-Long

    2018-01-01

    Paris is a commonly used traditional Chinese medicine (TCM), and has antitumor, antibacterial, sedative, analgesic and hemostatic effects. It has been used as an ingredient of 81 Chinese patent medicines, with a wide application and large market demand. Based on the data retrieved from state Intellectual Property Office patent database, a comprehensive analysis was made on Paris patents, so as to explore the current features of Paris patents in the aspects of domestic patent output, development trend, technology field distribution, time dimension, technology growth rate and patent applicant, and reveal the development trend of China's Paris industry. In addition, based on the current Paris resource application and development, a sustainable, multi-channel and multi-level industrial development approach was built. According to the results, studies of Paris in China are at the rapid development period, with a good development trend. However, because wild Paris resources tend to be exhausted, the studies for artificial cultivation technology should be strengthened to promote the industrial development. Copyright© by the Chinese Pharmaceutical Association.

  8. A Novel Visual Interface to Foster Innovation in Mechanical Engineering and Protect from Patent Infringement

    Science.gov (United States)

    Sorce, Salvatore; Malizia, Alessio; Jiang, Pingfei; Atherton, Mark; Harrison, David

    2018-04-01

    One of the main time and money consuming tasks in the design of industrial devices and parts is the checking of possible patent infringements. Indeed, the great number of documents to be mined and the wide variety of technical language used to describe inventions are reasons why considerable amounts of time may be needed. On the other hand, the early detection of a possible patent conflict, in addition to reducing the risk of legal disputes, could stimulate a designers’ creativity to overcome similarities in overlapping patents. For this reason, there are a lot of existing patent analysis systems, each with its own features and access modes. We have designed a visual interface providing an intuitive access to such systems, freeing the designers from the specific knowledge of querying languages and providing them with visual clues. We tested the interface on a framework aimed at representing mechanical engineering patents; the framework is based on a semantic database and provides patent conflict analysis for early-stage designs. The interface supports a visual query composition to obtain a list of potentially overlapping designs.

  9. A Case Study of Pharmaceutical Pricing in China: Setting the Price for Off-Patent Originators.

    Science.gov (United States)

    Hu, Shanlian; Zhang, Yabing; He, Jiangjiang; Du, Lixia; Xu, Mingfei; Xie, Chunyan; Peng, Ying; Wang, Linan

    2015-08-01

    This article aims to define a value-based approach to pricing and reimbursement for off-patent originators using a multiple criteria decision analysis (MCDA) approach centered on a systematic analysis of current pricing and reimbursement policies in China. A drug price policy review was combined with a quantitative analysis of China's drug purchasing database. Policy preferences were identified through a MCDA performed by interviewing well-known academic experts and industry stakeholders. The study findings indicate that the current Chinese price policy includes cost-based pricing and the establishment of maximum retail prices and premiums for off-patent originators, whereas reference pricing may be adopted in the future. The literature review revealed significant differences in the dissolution profiles between originators and generics; therefore, dissolution profiles need to be improved. Market data analysis showed that the overall price ratio of generics and off-patent originators was around 0.54-0.59 in 2002-2011, with a 40% price difference, on average. Ten differentiating value attributes were identified and MCDA was applied to test the impact of three pricing policy scenarios. With the condition of implementing quality consistency regulations and controls, a reduction in the price gap between high-quality off-patent products (including originator and generics) seemed to be the preferred policy. Patents of many drugs will expire within the next 10 years; thus, pricing will be an issue of importance for off-patent originators and generic alternatives.

  10. Unveiling the geography of historical patents in the United States from 1836 to 1975

    Science.gov (United States)

    Petralia, Sergio; Balland, Pierre-Alexandre; Rigby, David L.

    2016-01-01

    It is clear that technology is a key driver of economic growth. Much less clear is where new technologies are produced and how the geography of U.S. invention has changed over the last two hundred years. Patent data report the geography, history, and technological characteristics of invention. However, those data have only recently become available in digital form and at the present time there exists no comprehensive dataset on the geography of knowledge production in the United States prior to 1975. The database presented in this paper unveils the geography of historical patents granted by the United States Patent and Trademark Office (USPTO) from 1836 to 1975. This historical dataset, HistPat, is constructed using digitalized records of original patent documents that are publicly available. We describe a methodological procedure that allows recovery of geographical information on patents from the digital records. HistPat can be used in different disciplines ranging from geography, economics, history, network science, and science and technology studies. Additionally, it is easily merged with post-1975 USPTO digital patent data to extend it until today. PMID:27576103

  11. Products with Natural Components to Heal Dermal Burns: A Patent Review.

    Science.gov (United States)

    de Melo Costa, Aida Carla Santana; Pereira Ramos, Karen Perez; Serafini, Mairim Russo; de Carvalho, Fernanda Oliveira; Teixeira, Luciana Garcez Barretto; Garcao, Diogo Costa; Shanmugam, Saravanan; de Souza Araujo, Adriano Antunes; Nunes, Paula Santos

    2015-01-01

    Burns are a global public health problem, and non-fatal burn injuries are a leading cause of morbidity. The scale of the problem has led researchers to seek to develop new prod- ucts (both synthetic and natural) for use in the treatment of burn lesions. The aim of this study was to examine all patents in databases between 2010 and 2015 related to natural prod- ucts for the treatment of burn-related wounds that targeted tissue repair and healing. The search term "burn" and the code A61K36/00 (plant and other natural derivatives used in medicinal prepara- tions) from the international classification of patents were used to identify treatments. The search was performed in the WIPO, ESPACENET and USPTO databases. The highest number of patent ap- plications was found in the WIPO data base (617), followed by ESPACENET(23) and USPTO(6). The USA and China were the countries with the most patent applications, and 2008 was the year that had the highest number of applications. Patent applications written in Spanish, English and Portuguese and that were published between 2010 and 2015 were se- lected. 559 patent applications in other languages, and 63 that did not result in the creation of new products between 2010 and 2015 were excluded and the remaining 13 patents application were selected for full reading of the text. Through this study we were able to identify and summarize the new active natural compounds that can be used in the treatment of burns, both in terms of tissue recovery and analgesia.

  12. Grant Patents on Animals? An Ethical and Legal Battle Looms.

    Science.gov (United States)

    Wheeler, David L.

    1987-01-01

    Rulings on applications for animal patents being considered by the U.S. Patent and Trademark Office could profoundly influence university patent and research income. Many animal-rights advocates have expressed philosophical objections to genetic engineering of animals. (MLW)

  13. NREL Patents Method for Continuous Monitoring of Materials During

    Science.gov (United States)

    Manufacturing | News | NREL NREL Patents Method for Continuous Monitoring of Materials During Manufacturing News Release: NREL Patents Method for Continuous Monitoring of Materials During Manufacturing NREL's Energy Systems Integration Facility (ESIF). More information, including the published patent, can

  14. Pre-empted Patents, Infringed Patents and Firms’ Participation in Markets for Technology

    DEFF Research Database (Denmark)

    Grimpe, Christoph; Hussinger, Katrin

    2014-01-01

    In recent years, firms have increasingly contributed to and been confronted with a patent landscape characterized by numerous but marginal inventions, overlapping claims and patent fences. As a result, firms risk their patent applications to be pre-empted or to be infringed upon by rivals. While...... patents on firms’ engagement in in- and cross-licensing. Based on a sample of more than 1100 German manufacturing firms our results show that firms engage in in-licensing as a reaction to pre-empted patents and in cross-licensing if their protected IP was infringed upon. However, these effects vary...

  15. The Unified Patent Court (UPC) in Action

    DEFF Research Database (Denmark)

    Petersen, Clement Salung; Schovsbo, Jens Hemmingsen; Riis, Thomas

    2015-01-01

    The new common judiciary for European patents (UPC) will play a crucial role in the future European patent system. The UPC will be a very specialised court that i.a. recruits judges from specialists’ circles and has as part of its mission to develop a coherent and autonomous body of case law...

  16. Patentability of methods of human enhancement

    DEFF Research Database (Denmark)

    Nordberg, Ana

    2015-01-01

    This article explores how to apply patentability rules to human enhancement, particularly focusing on Article 53(c) of the European Patent Convention (EPC). The global size and value of the cosmetic and wellness market and industry allow for the prediction of considerable market potential for hum...... future evolution and the corresponding public policy choices. This article seeks to provide prospective patentees with guidance and awareness concerning the patentability of methods for human enhancement.......This article explores how to apply patentability rules to human enhancement, particularly focusing on Article 53(c) of the European Patent Convention (EPC). The global size and value of the cosmetic and wellness market and industry allow for the prediction of considerable market potential for human...... enhancement. Patents will be instrumental for companies to protect investment in innovation and tap into this potentially valuable market. The European patent system contains, in Article 53(c) EPC, an exception from patentability for methods for treatment and diagnostic methods. Such rule was created...

  17. Disclosure rules and declared essential patents

    NARCIS (Netherlands)

    Bekkers, R.N.A.; Catalini, C.; Martinelli, Arianna; Righi, C.; Simcoe, T.

    Many standard setting organizations (SSOs) require participants to disclose patents that might be infringed by implementing a proposed standard, and commit to license their “essential” patents on terms that are at least fair, reasonable and non-discriminatory (FRAND). Data from these SSO

  18. Patent protection and licensing in microfluidics.

    Science.gov (United States)

    Yetisen, Ali K; Volpatti, Lisa R

    2014-07-07

    Microfluidic devices offer control over low-volume samples in order to achieve high-throughput analysis, and reduce turnaround time and costs. Their efficient commercialisation has implications for biomedical sciences, veterinary medicine, environmental monitoring and industrial applications. In particular, market diffusion of microfluidic laboratory and point-of-care diagnostic devices can contribute to the improvement of global health. In their commercialisation, consultancy and patent protection are essential elements that complement academic publishing. The awareness of knowledge transfer strategies can help academics to create value for their research. The aim of this article is to provide a guidance to (1) overview the terminology in patent law, (2) elucidate the process of filing a patent in the US, EU, Japan and internationally, (3) discuss strategies to licence a patent, and (4) explain tactics to defend a patent in a potential infringement. Awareness of the patent law and rights allows obtaining optimised, valid and valuable patents, while accelerating implementation to market route. Striking a balance between academic publishing, consultancy to industry and patent protection can increase commercial potential, enhance economic growth and create social impact.

  19. DOE patents available for licensing: a bibliography

    International Nuclear Information System (INIS)

    Thoeming, G.H.

    1982-06-01

    Abstracts and indexes are provided for 1344 DOE patents or patent applications concerning any aspect of energy production, conservation, and utilization. The entries are arranged by subject category as shown in the table of contents. The bibliography covers the period from January 1974 through December 1980

  20. When patents matter: The impact of competition and patent age on the performance contribution of intellectual property rights protection

    NARCIS (Netherlands)

    Maresch, Daniela; Fink, Matthias; Harms, Rainer

    2016-01-01

    The question whether patenting impacts patenting firms' subsequent financial performance is important for technology-oriented companies. However, relevant research has led to contradictory results. We strive to overcome this impasse by introducing innovation competition and patent age as moderators

  1. On Sharks, Trolls, and Other Patent Animals

    DEFF Research Database (Denmark)

    Reitzig, Markus; Henkel, Joachim; Heath, Christopher

    2007-01-01

    Patent trolls (or sharks) are small patent holding individuals or firms who trap R&D intense manufacturers in patent infringement situations in order to receive damage awards for the illegitimate use of their technology. While of great concern to management, their existence and impact for both...... corporate decision makers and policy makers remains to be fully analyzed from an academic standpoint. In this paper we show why patent sharks can operate profitably, why they are of growing concern, how manufacturers can forearm themselves against them, and which issues policy makers need to address. To do...... so, we map international indemnification rules with strategic rationales of small patent-holding firms within a game-theoretical model. Our central finding is that the courts’ unrealistic consideration of the trade-offs faced by inadvertent infringers is a central condition for sharks to operate...

  2. Simultaneous invention and the patent law

    DEFF Research Database (Denmark)

    Howells, John

    inventions they often find this to challenge the idea that patent law (which rewards only the first inventor with exclusive rights) is needed to encourage invention and innovation. We review the empirical evidence alleged to show that simultaneous invention is prevalent for important inventions. In general...... is typical of important pioneer inventions in both survey evidence and alleged illustrative cases of simultaneous invention. We show this in the cases of Edison, the Wright brothers, the Selden automobile patent vis a vis Ford, Watt and the steam engine. We then point out that patent law inherently ensures...... that patent protection is not extended to near simultaneous inventions. There remain a number of simultaneous inventions discovered through interference proceedings but we find the number too small to mount a serious challenge to the general operation of patent law....

  3. Are Patents used to Suppress Useful Technology?

    DEFF Research Database (Denmark)

    Howells, John

    2006-01-01

    of innovation, other than in the trivial sense of excluding third parties from the right to develop the technology covered by the patent? There are many references to this possibility in the management, economic and legal literatures, but two highly-cited papers stand out for grounding their claims of corporate......This article examines the evidence behind claims that innovation is hindered or blocked (termed technology suppression) by corporations' use of patents. In other words, are there ways in which the exploitation of the exclusive development right of the patent can be shown to retard the process...... and the difference between economic monopoly and an exclusive right. It is argued here that what is at issue in this work is the proper function of the patent institution. It is shown early in this paper that the understanding of the patent institution as a system of development prospects makes better sense...

  4. The Patent Literature As A Shortcut To Identify Knowledge Suppliers

    DEFF Research Database (Denmark)

    Søberg, Peder Veng

    patents which decreases the time span between a patent is filed and its value can be evaluated when searching the patent literature. A potential benefit thereof could be that the patent literature could become relevant in order to identify potential knowledge suppliers.......The present paper explores characteristics of valuable patents that have been subject to litigation which resulted in some of the largest fines to patent infringers reported in history. The valuable patents are compared with less valuable patents in order to identify new methods of evaluating...

  5. Section for Standard and Patents - Standardization and Patents

    International Nuclear Information System (INIS)

    Wojtowicz, S.; Trechcinski, R.; Rybka, M.; Ryszkowska, A.; Wardaszko, J.

    1997-01-01

    Standardization; cooperation with the Patent Office Republic of Poland in the areas of inventiveness and patents. (author)

  6. Fast and secure retrieval of DNA sequences

    NARCIS (Netherlands)

    2014-01-01

    Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

  7. Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing data.

    Science.gov (United States)

    Li, Cheng-Wei; Chen, Bor-Sen

    2016-10-01

    Recent studies have demonstrated that cell cycle plays a central role in development and carcinogenesis. Thus, the use of big databases and genome-wide high-throughput data to unravel the genetic and epigenetic mechanisms underlying cell cycle progression in stem cells and cancer cells is a matter of considerable interest. Real genetic-and-epigenetic cell cycle networks (GECNs) of embryonic stem cells (ESCs) and HeLa cancer cells were constructed by applying system modeling, system identification, and big database mining to genome-wide next-generation sequencing data. Real GECNs were then reduced to core GECNs of HeLa cells and ESCs by applying principal genome-wide network projection. In this study, we investigated potential carcinogenic and stemness mechanisms for systems cancer drug design by identifying common core and specific GECNs between HeLa cells and ESCs. Integrating drug database information with the specific GECNs of HeLa cells could lead to identification of multiple drugs for cervical cancer treatment with minimal side-effects on the genes in the common core. We found that dysregulation of miR-29C, miR-34A, miR-98, and miR-215; and methylation of ANKRD1, ARID5B, CDCA2, PIF1, STAMBPL1, TROAP, ZNF165, and HIST1H2AJ in HeLa cells could result in cell proliferation and anti-apoptosis through NFκB, TGF-β, and PI3K pathways. We also identified 3 drugs, methotrexate, quercetin, and mimosine, which repressed the activated cell cycle genes, ARID5B, STK17B, and CCL2, in HeLa cells with minimal side-effects.

  8. Federal databases

    International Nuclear Information System (INIS)

    Welch, M.J.; Welles, B.W.

    1988-01-01

    Accident statistics on all modes of transportation are available as risk assessment analytical tools through several federal agencies. This paper reports on the examination of the accident databases by personal contact with the federal staff responsible for administration of the database programs. This activity, sponsored by the Department of Energy through Sandia National Laboratories, is an overview of the national accident data on highway, rail, air, and marine shipping. For each mode, the definition or reporting requirements of an accident are determined and the method of entering the accident data into the database is established. Availability of the database to others, ease of access, costs, and who to contact were prime questions to each of the database program managers. Additionally, how the agency uses the accident data was of major interest

  9. Patent Keyword Extraction for Sustainable Technology Management

    Directory of Open Access Journals (Sweden)

    Jongchan Kim

    2018-04-01

    Full Text Available Recently, sustainable growth and development has become an important issue for governments and corporations. However, maintaining sustainable development is very difficult. These difficulties can be attributed to sociocultural and political backgrounds that change over time [1]. Because of these changes, the technologies for sustainability also change, so governments and companies attempt to predict and manage technology using patent analyses, but it is very difficult to predict the rapidly changing technology markets. The best way to achieve insight into technology management in this rapidly changing market is to build a technology management direction and strategy that is flexible and adaptable to the volatile market environment through continuous monitoring and analysis. Quantitative patent analysis using text mining is an effective method for sustainable technology management. There have been many studies that have used text mining and word-based patent analyses to extract keywords and remove noise words. Because the extracted keywords are considered to have a significant effect on the further analysis, researchers need to carefully check out whether they are valid or not. However, most prior studies assume that the extracted keywords are appropriate, without evaluating their validity. Therefore, the criteria used to extract keywords needs to change. Until now, these criteria have focused on how well a patent can be classified according to its technical characteristics in the collected patent data set, typically using term frequency–inverse document frequency weights that are calculated by comparing the words in patents. However, this is not suitable when analyzing a single patent. Therefore, we need keyword selection criteria and an extraction method capable of representing the technical characteristics of a single patent without comparing them with other patents. In this study, we proposed a methodology to extract valid keywords from

  10. Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species.

    Science.gov (United States)

    Arbefeville, S; Harris, A; Ferrieri, P

    2017-09-01

    Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data. 85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases. The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank. Our results indicated that the MicroSEQ® D2 LSU r

  11. AVC/H.264 patent portfolio license

    Science.gov (United States)

    Skandalis, Dean A.

    2006-08-01

    MPEG LA, LLC offers a joint patent license for the AVC (a/k/a H.264) Standard (ISO/IEC IS 14496-10:2004). Like MPEG LA's other licenses, the AVC Patent Portfolio License is offered for the convenience of the marketplace as an alternative enabling users to access essential intellectual property owned by many patent holders under a single license rather than negotiating licenses with each of them individually. The AVC Patent Portfolio License includes essential patents owned by DAEWOO Electronics Corporation; Electronics and Telecommunications Research Institute (ETRI); France Telecom, societe anonyme; Fujitsu Limited; Hitachi, Ltd.; Koninklijke Philips Electronics N.V.; LG Electronics Inc.; Matsushita Electric Industrial Co., Ltd.; Microsoft Corporation; Mitsubishi Electric Corporation; Robert Bosch GmbH; Samsung Electronics Co., Ltd.; Sedna Patent Services, LLC; Sharp Kabushiki Kaisha; Siemens AG; Sony Corporation; The Trustees of Columbia University in the City of New York; Toshiba Corporation; UB Video Inc.; and Victor Company of Japan, Limited. Another is expected also to join as of August 1, 2006. MPEG LA's objective is to provide worldwide access to as much AVC essential intellectual property as possible for the benefit of AVC users. Therefore, any party that believes it has essential patents is welcome to submit them for evaluation of their essentiality and inclusion in the License if found essential.

  12. The Transformation of Science Into Patented Inventions

    DEFF Research Database (Denmark)

    Beukel, Karin

    This paper presents the results of a grounded theory study of the transformation of scientific discoveries into patented inventions. Using an algebraic interpretive approach, the narratives collected during interviews are analyzed as Bayesian inferences and the developed theory is tested. The fin......This paper presents the results of a grounded theory study of the transformation of scientific discoveries into patented inventions. Using an algebraic interpretive approach, the narratives collected during interviews are analyzed as Bayesian inferences and the developed theory is tested....... The findings recast the relationship between science and patents as a process in which the way the transformation of the scientific invention is handled has an effect on the breadth of the patent scope. Unleashing patent scope surplus is dependent on processes related to abstraction and cognitive variety......, which can be mobilized by patent experts with both an in-depth understanding of the scientific discovery, due to their educational background in the life sciences, and capabilities within the legal framework for patenting. More specifically, the findings reveal previously unreported aspects...

  13. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  14. Identification of BKCa channel openers by molecular field alignment and patent data-driven analysis

    Directory of Open Access Journals (Sweden)

    Yaseen Gigani

    2016-01-01

    Full Text Available In this work, we present the first comprehensive molecular field analysis of patent structures on how the chemical structure of drugs impacts the biological binding. This task was formulated as searching for drug structures to reveal shared effects of substitutions across a common scaffold and the chemical features that may be responsible. We used the SureChEMBL patent database, which provides search of the patent literature using keyword-based functionality, as a query engine. The extraction of data of the BKCa channel openers and aligning them for molecular field similarity with newly designed structures did provide a probable validation method with accurate values. Therefore, in an attempt to increase the true positives, we report a procedure that functions on a multiple analyses modeled on molecular field similarity and common sub-structural search with consensus scoring and high confidence values to obtain greater accuracy during conventional virtual screening.

  15. Refactoring databases evolutionary database design

    CERN Document Server

    Ambler, Scott W

    2006-01-01

    Refactoring has proven its value in a wide range of development projects–helping software professionals improve system designs, maintainability, extensibility, and performance. Now, for the first time, leading agile methodologist Scott Ambler and renowned consultant Pramodkumar Sadalage introduce powerful refactoring techniques specifically designed for database systems. Ambler and Sadalage demonstrate how small changes to table structures, data, stored procedures, and triggers can significantly enhance virtually any database design–without changing semantics. You’ll learn how to evolve database schemas in step with source code–and become far more effective in projects relying on iterative, agile methodologies. This comprehensive guide and reference helps you overcome the practical obstacles to refactoring real-world databases by covering every fundamental concept underlying database refactoring. Using start-to-finish examples, the authors walk you through refactoring simple standalone databas...

  16. Novel methods to optimize the effects of transcranial direct current stimulation: a systematic review of transcranial direct current stimulation patents.

    Science.gov (United States)

    Malavera, Alejandra; Vasquez, Alejandra; Fregni, Felipe

    2015-01-01

    Transcranial direct current stimulation (tDCS) is a neuromodulatory technique that has been extensively studied. While there have been initial positive results in some clinical trials, there is still variability in tDCS results. The aim of this article is to review and discuss patents assessing novel methods to optimize the use of tDCS. A systematic review was performed using Google patents database with tDCS as the main technique, with patents filling date between 2010 and 2015. Twenty-two patents met our inclusion criteria. These patents attempt to address current tDCS limitations. Only a few of them have been investigated in clinical trials (i.e., high-definition tDCS), and indeed most of them have not been tested before in human trials. Further clinical testing is required to assess which patents are more likely to optimize the effects of tDCS. We discuss the potential optimization of tDCS based on these patents and the current experience with standard tDCS.

  17. Measuring science–technology interactions using patent citations and author-inventor links: an exploration analysis from Chinese nanotechnology

    International Nuclear Information System (INIS)

    Wang Gangbo; Guan Jiancheng

    2011-01-01

    This article contributes to the growing study on the interactions between science and technology with China’s evidence in the field of nanotechnology, based on the database of United States Patent and Trademark Office. The analysis is focused during the period of 1991–2008, a rapid increasing period for the development of nanotechnology. Using the non-patent references cited by patents, we first investigate the science–technology connections in the context of Chinese nanotechnology, especially in institutional sectors and its application fields. Those patents, produced by academic researchers and directed towards basic scientific knowledge, generally cite more scientific references with a higher proportion of self-citations. It is interesting to find that patents contributed by collaborations between public organizations and corporations seldom contain scientific references. Following an interesting path on matching the data of publications and patents, we establish the author-inventor links in this emerging field. Author-inventors, who are co-active in publishing and patenting, are at the very top of the most prolific and highly cited researchers. Finally, we employ social network analysis to explore the characteristics of scientific and technological networks generated by co-authorship and co-invention data, to investigate the position and the role of patenting–publishing scientists in these research networks.

  18. Exploring Contextual Models in Chemical Patent Search

    Science.gov (United States)

    Urbain, Jay; Frieder, Ophir

    We explore the development of probabilistic retrieval models for integrating term statistics with entity search using multiple levels of document context to improve the performance of chemical patent search. A distributed indexing model was developed to enable efficient named entity search and aggregation of term statistics at multiple levels of patent structure including individual words, sentences, claims, descriptions, abstracts, and titles. The system can be scaled to an arbitrary number of compute instances in a cloud computing environment to support concurrent indexing and query processing operations on large patent collections.

  19. Quinoxaline derivatives: a patent review (2006--present).

    Science.gov (United States)

    González, Mercedes; Cerecetto, Hugo

    2012-11-01

    Quinoxaline scaffold is included in a large number of therapeutic agents because of its physicochemical properties that make the difference between them and the carbono analogue, naphthalene. This review of patented products presents the quinoxaline heterocycle as part of the structural patent claims from a medicinal chemistry perspective. We centred our discussion in the various drug patent applications of the quinoxaline and its derivatives. The applications are based firstly in the specific enzyme target with very low development in the disease treatment. Only for cancer and antimicrobial agents they were specifically determined but little is mentioned in order to insight in the last development activities.

  20. An Integrated Molecular Database on Indian Insects.

    Science.gov (United States)

    Pratheepa, Maria; Venkatesan, Thiruvengadam; Gracy, Gandhi; Jalali, Sushil Kumar; Rangheswaran, Rajagopal; Antony, Jomin Cruz; Rai, Anil

    2018-01-01

    MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects. This insect resource database is available online for free at http://cib.res.in. http://cib.res.in/.

  1. RDD Databases

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database was established to oversee documents issued in support of fishery research activities including experimental fishing permits (EFP), letters of...

  2. Snowstorm Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Snowstorm Database is a collection of over 500 snowstorms dating back to 1900 and updated operationally. Only storms having large areas of heavy snowfall (10-20...

  3. Dealer Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dealer reporting databases contain the primary data reported by federally permitted seafood dealers in the northeast. Electronic reporting was implemented May 1,...

  4. National database

    DEFF Research Database (Denmark)

    Kristensen, Helen Grundtvig; Stjernø, Henrik

    1995-01-01

    Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen.......Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen....

  5. Patent border wars: defining the boundary between scientific discoveries and patentable inventions.

    Science.gov (United States)

    Holman, Christopher M

    2007-12-01

    Drawing an appropriate boundary between unpatentable natural phenomena and patentable inventions is crucial in preventing the patent laws from unduly restricting access to fundamental scientific discoveries. Some would argue that, particularly in the U.S., patents are being issued that purport to claim a novel product or process but that, in effect, encompass any practical application of a fundamental biological principle. Examples include gene patents, which Congress is considering banning, and patents relating to biological correlations and pathways, such as the patents at issue in the headline-grabbing LabCorp v. Metabolite and Ariad v. Eli Lilly litigations. In view of the mounting concern, it seems likely that Congress and/or the courts will address the issue, and perhaps substantially shift the boundary.

  6. Patent and exclusivity status of essential medicines for non-communicable disease.

    Directory of Open Access Journals (Sweden)

    Tim K Mackey

    Full Text Available OBJECTIVE: The threat of non-communicable diseases ("NCDs" is increasingly becoming a global health crisis and are pervasive in high, middle, and low-income populations resulting in an estimated 36 million deaths per year. There is a need to assess intellectual property rights ("IPRs" that may impede generic production and availability and affordability to essential NCD medicines. METHODS: Using the data sources listed below, the study design systematically eliminated NCD drugs that had no patent/exclusivity provisions on API, dosage, or administration route. The first step identified essential medicines that treat certain high disease burden NCDs. A second step examined the patent and exclusivity status of active ingredient, dosage and listed route of administration using exclusion criteria outlined in this study. MATERIALS: We examined the patent and exclusivity status of medicines listed in the World Health Organization's ("WHO" Model List of Essential Drugs (Medicines ("MLEM" and other WHO sources for drugs treating certain NCDs. i.e., cardiovascular and respiratory disease, cancers, and diabetes. We utilized the USA Food and Drug Administration Orange Book and the USA Patent and Trademark Office databases as references given the predominant number of medicines registered in the USA. RESULTS: Of the 359 MLEM medicines identified, 22% (79/359 address targeted NCDs. Of these 79, only eight required in-depth patent or exclusivity assessment. Upon further review, no NCD MLEM medicines had study patent or exclusivity protection for reviewed criteria. CONCLUSIONS: We find that ensuring availability and affordability of potential generic formulations of NCD MLEM medicines appears to be more complex than the presence of IPRs with API, dosage, or administration patent or exclusivity protection. Hence, more sophisticated analysis of NCD barriers to generic availability and affordability should be conducted in order to ensure equitable access to global

  7. Preliminary analysis of patent trends for magnetic fusion technology

    International Nuclear Information System (INIS)

    Levine, L.O.; Ashton, W.B.; Campbell, R.S.

    1984-02-01

    This study presents a preliminary analysis of development trends in magnetic fusion technology based on data from US patents. The research is limited to identification and description of general patent activity and ownership characteristics for 373 patents. The results suggest that more detailed studies of fusion patents could provide useful R and D planning information

  8. Valuing patents on cost-reducing technology: A case study

    NARCIS (Netherlands)

    van Triest, S.P.; van de Vis, Wim

    2007-01-01

    We present an approach for valuing patents on production process improvements. Specifically, we focus on valuing a patent on cost-reducing process improvements from the viewpoint of the patent holding firm. We do this by considering the relevant cash flows that result from owning the patent. The

  9. 78 FR 62367 - Changes To Implement the Patent Law Treaty

    Science.gov (United States)

    2013-10-21

    ... Office 37 CFR Parts 1, 3 and 11 Changes To Implement the Patent Law Treaty; Final Rule #0;#0;Federal... 0651-AC85 Changes To Implement the Patent Law Treaty AGENCY: United States Patent and Trademark Office, Commerce. ACTION: Final rule. SUMMARY: The Patent Law Treaties Implementation Act of 2012 (PLTIA) amends...

  10. 78 FR 21787 - Changes To Implement the Patent Law Treaty

    Science.gov (United States)

    2013-04-11

    ... Trademark Office 37 CFR Parts 1 and 3 Changes To Implement the Patent Law Treaty; Proposed Rule #0;#0...-0007] RIN 0651-AC85 Changes To Implement the Patent Law Treaty AGENCY: United States Patent and Trademark Office, Commerce. ACTION: Notice of proposed rulemaking. SUMMARY: The Patent Law Treaties...

  11. 48 CFR 1327.201 - Patent and copyright infringement liability.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Patent and copyright infringement liability. 1327.201 Section 1327.201 Federal Acquisition Regulations System DEPARTMENT OF COMMERCE GENERAL CONTRACTING REQUIREMENTS PATENTS, DATA, AND COPYRIGHTS Patents and Copyrights 1327.201 Patent and...

  12. The European Patent System: Dealing with emerging technologies.

    NARCIS (Netherlands)

    Kica, Evisa; Groenendijk, Nico

    2011-01-01

    In light of recent controversial patent decisions in biotechnology, this article argues that the current European patent examination and opposition procedures do not suffice to balance the patent system These procedures do not provide sufficient guidance for patent examiners to deal effectively with

  13. 48 CFR 970.2702-3 - Patent indemnity.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Patent indemnity. 970.2702... SUPPLEMENTARY REGULATIONS DOE MANAGEMENT AND OPERATING CONTRACTS Patents, Data, and Copyrights 970.2702-3 Patent indemnity. (a) Contracting officers must use the clause at 970.5227-6, Patent Indemnity—Subcontracts to...

  14. 14 CFR 1214.112 - Patent, data and information matters.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Patent, data and information matters. 1214... Customers § 1214.112 Patent, data and information matters. (a) Patent and data rights. NASA will not acquire rights to inventions, patents or proprietary data which may be used in, or arise from, activities for...

  15. 77 FR 269 - Matters Related to Patent Appeals

    Science.gov (United States)

    2012-01-04

    ... DEPARTMENT OF COMMERCE United States Patent and Trademark Office Matters Related to Patent Appeals ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and Trademark Office... Matters Related to Patent Appeals comment'' in the subject line of the message. Mail: Susan K. Fawcett...

  16. 48 CFR 31.205-30 - Patent costs.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Patent costs. 31.205-30....205-30 Patent costs. (a) The following patent costs are allowable to the extent that they are incurred... patent application where title or royalty-free license is to be conveyed to the Government. (b) General...

  17. 76 FR 53885 - Patent and Trademark Resource Centers Metrics

    Science.gov (United States)

    2011-08-30

    ... DEPARTMENT OF COMMERCE United States Patent and Trademark Office Patent and Trademark Resource Centers Metrics ACTION: Proposed collection; comment request. SUMMARY: The United States Patent and... ``Patent and Trademark Resource Centers Metrics comment'' in the subject line of the message. Mail: Susan K...

  18. 45 CFR 650.2 - National Science Foundation patent policy.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false National Science Foundation patent policy. 650.2... FOUNDATION PATENTS § 650.2 National Science Foundation patent policy. As authorized by the National Science... adopted the following statement of NSF patent policy. (a) In accordance with the Bayh-Dole Act and the...

  19. Prospects and trends in the development of terahertz technologies: patent landscape

    Directory of Open Access Journals (Sweden)

    D. А. Usanov

    2017-01-01

    Full Text Available The article is dedicated to the analysis of areas where terahertz radiation is applicable with the hwlp of a patent papers review, as well as to obtaining knowledge about the invention activity changes in this area over the past 35 years.Orbit patent databases’ capabilities were used to complete this analysis. Data search was conducted by keywords “terahertz” or “THz.” The searches were neither limited by submission dates, by priorities, nor by the country. A comprehensive analysis will allow to determine a more than 7389 patent-analog families’ aplications submitted in the period between 1980 and 2017 years. Statistical processing of obtained documents has been completed with the assistance of program software, indicated in the database. It was revealed that terahertz technologies have significant prospects to be applied in various areas; a fact, that is confirmed by an identified range of fields, where electromagnetic radiation of terahertz spectrum is applicable and is constantly growing. The dynamics of patenting is characterized by annual stable positive growth in the number of applications for inventions in the researched area. The highest number of inventions was identified in the field of instrumentation technologies, optics, telecommunications, semiconductor technologies, and medicine. Additionally, there was analyzed the state of patenting over the course of last five years. Examples of inventions were given. There were identified leading countries and companies in the researched area.

  20. Cyclodextrins improving the physicochemical and pharmacological properties of antidepressant drugs: a patent review.

    Science.gov (United States)

    Diniz, Tâmara Coimbra; Pinto, Tiago Coimbra Costa; Menezes, Paula Dos Passos; Silva, Juliane Cabral; Teles, Roxana Braga de Andrade; Ximenes, Rosana Christine Cavalcanti; Guimarães, Adriana Gibara; Serafini, Mairim Russo; Araújo, Adriano Antunes de Souza; Quintans Júnior, Lucindo José; Almeida, Jackson Roberto Guedes da Silva

    2018-01-01

    Depression is a serious mood disorder and is one of the most common mental illnesses. Despite the availability of several classes of antidepressants, a substantial percentage of patients are unresponsive to these drugs, which have a slow onset of action in addition to producing undesirable side effects. Some scientific evidence suggests that cyclodextrins (CDs) can improve the physicochemical and pharmacological profile of antidepressant drugs (ADDs). The purpose of this paper is to disclose current data technology prospects involving antidepressant drugs and cyclodextrins. Areas covered: We conducted a patent review to evaluate the antidepressive activity of the compounds complexed in CDs, and we analyzed whether these complexes improved their physicochemical properties and pharmacological action. The present review used 8 specialized patent databases for patent research, using the term 'cyclodextrin' combined with 'antidepressive agents' and its related terms. We found 608 patents. In the end, considering the inclusion criteria, 27 patents reporting the benefits of complexation of ADDs with CDs were included. Expert opinion: The use of CDs can be considered an important tool for the optimization of physicochemical and pharmacological properties of ADDs, such as stability, solubility and bioavailability.

  1. Database Description - AcEST | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name AcEST Alternative n...hi, Tokyo-to 192-0397 Tel: +81-42-677-1111(ext.3654) E-mail: Database classificat...eneris Taxonomy ID: 13818 Database description This is a database of EST sequences of Adiantum capillus-vene...(3): 223-227. External Links: Original website information Database maintenance site Plant Environmental Res...base Database Description Download License Update History of This Database Site Policy | Contact Us Database Description - AcEST | LSDB Archive ...

  2. Legume and Lotus japonicus Databases

    DEFF Research Database (Denmark)

    Hirakawa, Hideki; Mun, Terry; Sato, Shusei

    2014-01-01

    Since the genome sequence of Lotus japonicus, a model plant of family Fabaceae, was determined in 2008 (Sato et al. 2008), the genomes of other members of the Fabaceae family, soybean (Glycine max) (Schmutz et al. 2010) and Medicago truncatula (Young et al. 2011), have been sequenced. In this sec....... In this section, we introduce representative, publicly accessible online resources related to plant materials, integrated databases containing legume genome information, and databases for genome sequence and derived marker information of legume species including L. japonicus...

  3. Managing the patent thicket and maximizing patent lifetime in vaccine technology.

    Science.gov (United States)

    Mertes, Maria M M; Stötter, Gerd

    2010-10-01

    Patents are exclusive rights for a limited period of time that are granted to provide an incentive for innovation and in exchange for the public disclosure of an invention. Patenting in the medical field, especially in the field of human vaccine technologies, is full of pitfalls, because the products that finally access the market are often covered by a multitude of exclusive IP rights. This commentary gives an overview on obstacles in vaccine patenting and how to overcome them, and intends to provide a patenting guideline for researchers.

  4. Revising the Complex Economics of Patent Scope

    DEFF Research Database (Denmark)

    Howells, John

    Merges and Nelson claim to have provided an empirically grounded argument that pioneer patents of 'broad' scope are used to block technological development. It is widely understood in both law and economics that they have, as they claim, faulted Kitch's 'prospect theory' of patents, a theory...... that a function of patents is to enable the coordinated development of novel technical ideas. This article is a critical review of Merges and Nelson's historical empirical evidence. I find that, first, 'broad' scope is only implicated in one of the examples cited by Merges and Nelson as supportive evidence...... - the Wright brothers' warped-wing patent; second, that strict development block, defined as the prevention, or retardation of the development of technology understood to be capable of useful development, was not illustrated by any of their examples. Therefore I conclude that their general thesis...

  5. Turning Technology into Business Using University Patents

    NARCIS (Netherlands)

    Hartmann, L.

    2014-01-01

    We present an education paradigm that stimulates innovation and entrepreneurship through a master's-level university course: "Turning Technology into Business". The course was specifically designed to connect technological research with education using patented technologies developed at the research

  6. Internet: A place for patent retrieval

    African Journals Online (AJOL)

    GRACE

    2006-05-16

    May 16, 2006 ... Key words: Biotechnology, intellectual property rights, Patents, Internet application. INTRODUCTION. The principle objective of biotechnology is to produce ... Finland. France. Germany. Greek. Georgian. Hong Kong. Hungarian. Irsish. Italian. Japan. Korean. Luxemberg. Lithuania. Malaysian. Moldova.

  7. Patent documentation - comparison of two MT strategies

    DEFF Research Database (Denmark)

    Offersgaard, Lene; Povlsen, Claus

    2007-01-01

    This paper focuses on two matters: A comparison of how two different MT strategies manage translating the text type of patent documentation and a survey of what is needed to transform a MT research prototype system to a translation application for patent texts. The two MT strategies is represented....... The distinctive text type of patents pose special demands for machine translation and these aspects are discussed based on linguistic observations with focus on the users point of view. Two main demands are automatic pre processing of the documents and implementation of a module which in a flexible and user......-friendly manner offers the opportunity to extend the lexical coverage of the system. These demands and the comparison of the two MT strategies are discussed on the basis of proofread patents....

  8. The patent activity of the Czech R

    Directory of Open Access Journals (Sweden)

    Kučera Zdeněk

    2016-12-01

    Full Text Available An effective knowledge transfer between research institutions and industry is a significant bottleneck in the national innovation system. CR adopted in recent years a series of systemic measures aimed to stimulate the orientation of the R&D organizations towards the generation of knowledge directly applicable in the innovation process and more generally to improve the collaboration of the R&D establishment with the industry. In the majority of programs supporting the applied research patents and industrial designs and utility models are among the anticipated results. The Methodology of the evaluation of R&D organizations implemented in the second half of the last decade brought financial bonuses for the creation of the results in the category of industrial property. Despite of this stimulus CR lags behind the technologically advanced EU countries in the patent activities. The topic of this article is a comparison of the protection of the industrial property rights in the Czech higher education institutions and governmental R&D institutions with selected EU countries. We make use of a couple of quantitative indicators to assess the quality and the technological and the commercial potential of the produced industrial property. Despite a dynamic growth of the patent applications in the CR the number of patent applications relative to the country size is far below the EU-15 average. The Czech research organizations contribute to a higher extent to the number of patent applications then do the analogous institutions in EU-15 countries where the majority of patent applications come from the industrial sphere. The Czech research organizations mainly limit the patent rights to the Czech Republic whereas in the EU-15 countries the opposite is preponderant and only a small fraction of patent applications remains limited to the national environment. Thus the majority of the Czech patents created by research organizations cannot be commercialized on the

  9. Patent portfolio structure for single technology companies

    OpenAIRE

    Hartwell, Ian P.

    2004-01-01

    Single technology companies (STCs) are defined in this thesis as companies that (a) have the fundamental rights to a new technology, (b) have development of that technology as their core competence, (c) seek to exploit that technology primarily by licensing the patent rights, and (d) are driven primarily by 'technology push'. These factors often result in much of the value of the STC residing in its patent portfolio. This in turn may place significant - and often conflicting - ...

  10. Competition policy in patent cases and antitrust.

    Science.gov (United States)

    Sobel, Gerald

    2003-01-01

    The article that follows examines the competition policy reflected in the decisions of the Court of Appeals for the Federal Circuit in its patent cases. The court's views on this subject have been manifested most plainly in decisions that have transformed the law concerning infringement under the doctrine of equivalents and claim construction. In both categories, the court narrowed patent scope by reason of its desire to protect competitors. The article argues that the court's premise in prescribing narrower claim scope reflected an incomplete view of competition policy. The court's analysis overlooked the benefits to competition provided by patents, which stimulate inventions and their development. The article traces the development of antitrust jurisprudence and demonstrates how respect for the contribution of patents to competition and skepticism of free-riding has evolved, particularly beginning in the 1970s. The article draws a parallel between the Court's reasoning about competition policy, on the one hand, and the rejected views of Justices Hugo Black and William O. Douglas and abandoned patent-antitrust jurisprudence, on the other. The Federal Circuit's decision in Festo Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., Ltd., 234 F.3d 558 (Fed. Cir. 2000), on the subject of equivalents is considered in the paper. In that decision, the majority adopted a new rule that completely barred infringement under the doctrine of equivalents of any claim limitation where, in prosecution, there had been a narrowing amendment relating to patentability. In the past, prosecution estoppel foreclosing equivalents had been subject to a "flexible bar," which, in some circumstances, allowed for equivalence notwithstanding such an amendment. The article points out that because almost all patents are amended during prosecution, the effect would be to allow widespread copying of patented inventions by trivial modifications of any narrowed claim limitation. The incentive to innovate

  11. Patent business guide in a domestic and foreign countries

    International Nuclear Information System (INIS)

    2009-09-01

    This book explains general things on industrial property right, which includes description of industrial property right, types, qualification for application of patent, application guide, on-line application, useful procedure of application, writing methods and samples for application of patents such as design patent and trademarks patent, writing skill and examples for registration, writing ways and examples related examination and writing tips and samples on international application of patent.

  12. Patent Value: A Business Perspective for Technology Startups

    OpenAIRE

    Angela de Wilton

    2011-01-01

    In the last year, news headlines have highlighted record patent infringement settlements, multibillion dollar auctions of large corporate patent portfolios, and ongoing patent battles between key technology industry players. Despite this acknowledgment of the significant value of patents for large corporations, many small technology companies are understandably more focused on the near-term costs of obtaining a patent rather than future value. Costs may seem prohibitive to an early stage tech...

  13. Experiment Databases

    Science.gov (United States)

    Vanschoren, Joaquin; Blockeel, Hendrik

    Next to running machine learning algorithms based on inductive queries, much can be learned by immediately querying the combined results of many prior studies. Indeed, all around the globe, thousands of machine learning experiments are being executed on a daily basis, generating a constant stream of empirical information on machine learning techniques. While the information contained in these experiments might have many uses beyond their original intent, results are typically described very concisely in papers and discarded afterwards. If we properly store and organize these results in central databases, they can be immediately reused for further analysis, thus boosting future research. In this chapter, we propose the use of experiment databases: databases designed to collect all the necessary details of these experiments, and to intelligently organize them in online repositories to enable fast and thorough analysis of a myriad of collected results. They constitute an additional, queriable source of empirical meta-data based on principled descriptions of algorithm executions, without reimplementing the algorithms in an inductive database. As such, they engender a very dynamic, collaborative approach to experimentation, in which experiments can be freely shared, linked together, and immediately reused by researchers all over the world. They can be set up for personal use, to share results within a lab or to create open, community-wide repositories. Here, we provide a high-level overview of their design, and use an existing experiment database to answer various interesting research questions about machine learning algorithms and to verify a number of recent studies.

  14. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs

    DEFF Research Database (Denmark)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter

    2016-01-01

    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the......This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report...

  15. Published patent applications and patents from the promoted R + D area

    International Nuclear Information System (INIS)

    Jaeckel, G.; Zierl, I.

    1977-09-01

    The Ministry for Research and Technology of the Federal Republic of Germany has sponsored technological R + D for industrial innovations since 1969. The following compilation includes the published patent applications and patents from all projects which were sponsored up to and including 1973. (orig.) [de

  16. Can patents prohibit research? On the social epistemology of patenting and licensing in science.

    Science.gov (United States)

    Biddle, Justin B

    2014-03-01

    A topic of growing importance within philosophy of science is the epistemic implications of the organization of research. This paper identifies a promising approach to social epistemology--nonideal systems design--and uses it to examine one important aspect of the organization of research, namely the system of patenting and licensing and its role in structuring the production and dissemination of knowledge. The primary justification of patenting in science and technology is consequentialist in nature. Patenting should incentivize research and thereby promote the development of knowledge, which in turn facilitates social progress. Some have disputed this argument, maintaining that patenting actually inhibits knowledge production. In this paper, I make a stronger argument; in some areas of research in the US--in particular, research on GM seeds--patents and patent licenses can be, and are in fact being, used to prohibit some research. I discuss three potential solutions to this problem: voluntary agreements, eliminating patents, and a research exemption. I argue against eliminating patents, and I show that while voluntary agreements and a research exemption could be helpful, they do not sufficiently address the problems of access that are discussed here. More extensive changes in the organization of research are necessary.

  17. The diffusion of patented oil and gas technology with environmental uses: A forward patent citation analysis

    International Nuclear Information System (INIS)

    Duch-Brown, Néstor; Costa-Campi, María Teresa

    2015-01-01

    Relevant advances in the mitigation of environmental impact could be obtained by the appropriate diffusion of existing environmental technologies. In this paper, we look at the diffusion of knowledge related to environmental technologies developed within the oil and gas industry. To assess knowledge spillovers from oil and gas inventions as a measure of technology diffusion, we rely on forward patent citations methodology. Results show that there is a strong likelihood that the citing patent will be eventually linked to environmental technologies if the original oil and gas invention has already environmental uses. Moreover, both intra and intersectoral spillovers produce a “turnabout” effect, meaning that citing patents show the opposite quality level of the cited patent. Our results support the idea that more sector-specific environmental policies, with an emphasis on diffusion, would significantly improve the use of environmental technologies developed within the oil and gas industry. -- Highlights: •Knowledge spillovers from oil and gas inventions are of an intrasectoral nature. •Environmental uses in original patents diffuse to patents with environmental uses. •The “turnabout” effect converts low quality patents into high quality citing patents. •Diffusion of oil and gas inventions need more ad hoc instruments

  18. A Moral Economy of Patents: Case of Finnish Research Universities' Patent Policies

    Science.gov (United States)

    Kauppinen, Ilkka

    2014-01-01

    The primary objective of this paper is to demonstrate the usefulness of the concept of moral economy for higher education studies through a study of Finnish research universities' patent policies. Patent policies not only stimulate the commercialization of research, they also set norms for behavior and aim to clarify how to distribute rights and…

  19. Biological diversity in the patent system.

    Directory of Open Access Journals (Sweden)

    Paul Oldham

    Full Text Available Biological diversity in the patent system is an enduring focus of controversy but empirical analysis of the presence of biodiversity in the patent system has been limited. To address this problem we text mined 11 million patent documents for 6 million Latin species names from the Global Names Index (GNI established by the Global Biodiversity Information Facility (GBIF and Encyclopedia of Life (EOL. We identified 76,274 full Latin species names from 23,882 genera in 767,955 patent documents. 25,595 species appeared in the claims section of 136,880 patent documents. This reveals that human innovative activity involving biodiversity in the patent system focuses on approximately 4% of taxonomically described species and between 0.8-1% of predicted global species. In this article we identify the major features of the patent landscape for biological diversity by focusing on key areas including pharmaceuticals, neglected diseases, traditional medicines, genetic engineering, foods, biocides, marine genetic resources and Antarctica. We conclude that the narrow focus of human innovative activity and ownership of genetic resources is unlikely to be in the long term interest of humanity. We argue that a broader spectrum of biodiversity needs to be opened up to research and development based on the principles of equitable benefit-sharing, respect for the objectives of the Convention on Biological Diversity, human rights and ethics. Finally, we argue that alternative models of innovation, such as open source and commons models, are required to open up biodiversity for research that addresses actual and neglected areas of human need. The research aims to inform the implementation of the 2010 Nagoya Protocol on Access to Genetic Resources and the Equitable Sharing of Benefits Arising from their Utilization and international debates directed to the governance of genetic resources. Our research also aims to inform debates under the Intergovernmental Committee on

  20. Technology Trends Analysis Using Patent Landscaping

    Directory of Open Access Journals (Sweden)

    Sergey Vsevolodovich Kortov

    2017-09-01

    Full Text Available The article is devoted to the analysis and the choice of the priorities in technology development and, particularly, to the use of patent landscaping as a tool for the study of technology trends. Currently, patent activity indicators are often used for technology foresight and for competitive intelligence as well. Nevertheless, causal relationship between these indicators, on the one hand, and strategic and tactical decisions in the sphere of technological development on meso- and microeconomic level, on the other hand, are not adequately investigated to solve practical tasks. The goal of the work is to systemize the challenges of technology trends analysis, which could be effectively solved on the base of patent landscape analysis. The article analyses the patent landscaping methodology and tools, as well as their use for evaluating the current competitive environment and technology foresight. The authors formulated the generalized classification for the criteria of promising technologies for a selected region. To assess the compliance of a technology with these criteria, we propose a system of corresponding indicators of patenting activity. Using the proposed methodology, we have analysed the patent landscape to select promising technologies for the Sverdlovsk region. The research confirmed the hypothesis of the patent landscapes performance in evaluating such technology indicators as stages of the life cycle stage, universality (applicability in different industries, pace of worldwide development, innovations and science availability in the region and potential possibilities for scientific collaboration with international research institutions and universities. The results of the research may be useful to the wide audience, including representatives small and medium enterprises, large companies and regional authorities for the tasks concerned with the technology trends analysis and technology strategy design

  1. The ethics of patenting human embryonic stem cells.

    Science.gov (United States)

    Chapman, Audrey R

    2009-09-01

    Just as human embryonic stem cell research has generated controversy about the uses of human embryos for research and therapeutic applications, human embryonic stem cell patents raise fundamental ethical issues. The United States Patent and Trademark Office has granted foundational patents, including a composition of matter (or product) patent to the Wisconsin Alumni Research Foundation (WARF), the University of Wisconsin-Madison's intellectual property office. In contrast, the European Patent Office rejected the same WARF patent application for ethical reasons. This article assesses the appropriateness of these patents placing the discussion in the context of the deontological and consequentialist ethical issues related to human embryonic stem cell patenting. It advocates for a patent system that explicitly takes ethical factors into account and explores options for new types of intellectual property arrangements consistent with ethical concerns.

  2. A study of fuel cell patenting activity in Canada

    International Nuclear Information System (INIS)

    Lee, B.Y.; Sajewycz, M.

    2004-01-01

    'Full text:' A patent application is generally filed shortly after completion of research and development; therefore, patent filing statistics provide insight into the state of innovation of a technology. A study has been conducted on fuel cell patenting activity in Canada. This study examines fuel cell patenting trends between 1989-2003 and specific activity in 2001, identifies the major players in the Canadian fuel cell industry, and examines the patent landscape by fuel cell technology. Our results show that historically, Canadians have been leaders at home and abroad in fuel cell innovation. However, Canadians have recently fallen behind in protecting their patent rights at home, and now rank fourth behind German, American and Japanese fuel cell patent filers in the Canadian patent office. However, our data also shows that a significant number of new Canadian entities have emerged and have been very active filing new patent applications. These new entities as well as established Canadian companies are examined in detail. (author)

  3. The Seductive-Plausibility of Patent Hold-Up Myths — A Flawed Historiography of Patents

    DEFF Research Database (Denmark)

    Howells, John; Katznelson, Ron D

    In previous work we have shown that a flawed historiography of patents continues to be the basis for patent policy advocacy. We set out objective standards of evidence that allegations of development block due to assertion of patents must meet. We show the extent of the errors in the historical...... record in the aircraft, automobile, radio and incandescent lamp technologies. We then evaluate how they measure against the objective standards. We find many simple errors and that an absence of indicia of development block characterise scholarship alleging that assertion of patents blocked development...... of multiple case studies subjected to such standards justifies the rebuttable presumption that “pioneer patents have never blocked development”....

  4. Life after Myriad: the uncertain future of patenting biomedical innovation and personalised medicine in an international context

    DEFF Research Database (Denmark)

    M. Schwartz, Robert; Minssen, Timo

    2015-01-01

    On June 13, 2013, the U.S. Supreme Court decided the Myriad gene patent case. In a unanimous judgment the Court held that patent claims directed to isolated genomic DNA are identical to the naturally occurring sequence and thus unpatentable “products of nature”. This decision affects all isolated...... with the situation in Australia and in the EU.   Keywords: biotechnology, comparative patent law, US, Europe, Australia, DNA, Myriad, patent-eligibility,personalized medicine, genetic diagnostics, USPTO 2014 Guidelines, methods,innovation, Unified Patent Court....... of these decisions on the biomedical sector and personalized medicine,as well the methodology used by the generalist Supreme Court in reversing a specialized CAFC judgment is particularly interesting from a comparative perspective. This paper analyses and discusses these U.S. developments, and compares them...

  5. Patent foramen ovale influences the presentation of decompression illness in SCUBA divers.

    Science.gov (United States)

    Liou, Kevin; Wolfers, Darren; Turner, Robert; Bennett, Michael; Allan, Roger; Jepson, Nigel; Cranney, Greg

    2015-01-01

    Few have examined the influence of patent foramen ovale (PFO) on the phenotype of decompression illness (DCI) in affected divers. A retrospective review of our database was performed for 75 SCUBA divers over a 10-year period. Overall 4,945 bubble studies were performed at our institution during the study period. Divers with DCI were more likely to have positive bubble studies than other indications (pAustralia and New Zealand (CSANZ). Published by Elsevier B.V. All rights reserved.

  6. Science and Technology Output Indicators in the Islamic Republic of Iran: A Case Study on the Relevance between Patents and Scientific Products of Iranian Inventors

    Directory of Open Access Journals (Sweden)

    Mohamad Alaee Arani

    2012-10-01

    Full Text Available The output of scientific products represents the efforts of scientific and industrial communities. The study on this output shows scientific attitudes and approaches of a community towards world of science. Quantitative studies can give a representation of the size and extent of the scientific efforts of researchers in special occasions, or a particular society. Patents are one of these important outputs. In this study, the names of Iranian inventors were extracted by carrying a combined search and the analysis of patent data available through Europe Patent Office (EPO, the United States Patent and Trademark Office (USPTO, Japan Patent Office (JPO, and the World Intellectual Property Organization (WIPO databases. Inventors amount of scientific products were also evaluated by using citation indexes in Thompson Reuters (formerly ISI Web of Science. Content analysis research method was adopted. Results of this study reported no significant correlation was found between scientific output and patent application. Findings also indicated a 6.5 percent contribution of patent researcher in comparison with non-patent researchers of Iranian indexed articles by Web of Science.

  7. El Sistema de patentes en Colombia

    Directory of Open Access Journals (Sweden)

    Rafael Viana Barceló

    2014-01-01

    Full Text Available En este documento se realiza un análisis económico del Sistema de Patentes de Colombia. Para ello, se establece el efecto que tienen las patentes concedidas a los inventores foráneos sobre la Inversión Extranjera Directa y el Producto Interno Bruto Nacional, a través de la técnica de regresión de data panel. De igual manera, se identifican los sectores económicos que registran mayores tasas de innovación por parte de los inventores nacionales y extranjeros. Se muestra que el sistema nacional de propiedad intelectual tiene un grado de fortaleza acorde con el resto de países latinoamericanos; para ello, se construye un índice de grado de fortalecimiento de sistema de patente nacional que luego será comparado con el de otros países latinos.Palabras Clave: Sistema de Patentes; Derechos de Propiedad Intelectual; Inversión Directa extranjera; Producto Interno Bruto e innovación tecnológica. The system of patents in ColombiaAbstractIn this document an economic analysis of the System of Patents of Colombia is made. For it, the effect that has the patents granted to the foreign inventors on the Direct Foreign Investment and the Internal Product Gross National, through the technique of regression of data settles down panel. Of equal way, the economic sectors are identified that register greater rates of innovation on the part of the national and foreign inventors.Sample that the national system of intellectual property has a degree of agreed strength with the rest of Latin American countries; for it, an index of degree of fortification of system of national patent is constructed that soon will be compared with the one of other Latin countries.Keywords: System Patent; Rights of Intellectual Property; Foreign Direct Investment; Gross Domestic Product and Technology Innovation.

  8. Capacidad innovadora de la Comunidad de Madrid a partir de las patentes concedidas entre 1996 y 2007

    Directory of Open Access Journals (Sweden)

    Lascurain, M. Luisa

    2010-09-01

    Full Text Available The objective of this paper is focused on analysing the patent activity of the Madrid Community taking into account the economic and human resources assigned to cover its R&D&I activities, as well as assessing the importance of the Madrid Community’s patenting activity compared to Spain. The analysis covers patents awarded during the period 1996-2007 and included in the INVENES database of the Spanish Patent and Trade Mark Offi ce.

    El objetivo del presente trabajo es conocer algunas de las características de la actividad patentadora de la Comunidad de Madrid y analizar su relación con los recursos humanos y materiales que se dedican en dicha comunidad a las actividades de I+D+i, así como conocer el peso de esta actividad en la CM respecto al conjunto de España. Para ello, se han analizado las patentes concedidas entre 1996 y 2007 recogidas en la base de datos INVENES de la Oficina Española de Patentes y Marcas.

  9. In-depth research of domestic nuclear patent information

    International Nuclear Information System (INIS)

    Mo Dan; Gao Anna; Li Dongbin; Lu Yanjia; Ren Chao

    2014-01-01

    Based on the domestic patent information, combined with examples, this article makes an in-depth discussion on the domestic nuclear patent information. The author puts forward for the patent information research, the appropriate retrieval of patent documents is the basis,and the correct quantitative statistical analysis of patent documents is the key, and in-depth qualitative analysis of patent documents is the core. It is expected to provide information support and guarantee for the technical innovation and scientific research personnel in the nuclear field through in-depth study of domestic nuclear information. (authors)

  10. [Design and implementation of supply security monitoring and analysis system for Chinese patent medicines supply in national essential medicines].

    Science.gov (United States)

    Wang, Hui; Zhang, Xiao-Bo; Huang, Lu-Qi; Guo, Lan-Ping; Wang, Ling; Zhao, Yu-Ping; Yang, Guang

    2017-11-01

    The supply of Chinese patent medicine is influenced by the price of raw materials (Chinese herbal medicines) and the stock of resources. On the one hand, raw material prices show cyclical volatility or even irreversible soaring, making the price of Chinese patent medicine is not stable or even the highest cost of hanging upside down. On the other hand, due to lack of resources or disable some of the proprietary Chinese medicine was forced to stop production. Based on the micro-service architecture and Redis cluster deployment Based on the micro-service architecture and Redis cluster deployment, the supply security monitoring and analysis system for Chinese patent medicines in national essential medicines has realized the dynamic monitoring and intelligence warning of herbs and Chinese patent medicine by connecting and integrating the database of Chinese medicine resources, the dynamic monitoring system of traditional Chinese medicine resources and the basic medicine database of Chinese patent medicine. Copyright© by the Chinese Pharmaceutical Association.

  11. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  12. [The patents game. Generic and biosimilar drugs].

    Science.gov (United States)

    Villamañán, E; González, D; Armada, E; Ruano, M; Álvarez-Sala, R; Herrero, A

    2016-01-01

    The protection provided by patents on medicines has a limited duration. The expiry of patents expiration allows copies of the drugs to be released, competing with original. At first, they were identical to the original, known as generic drugs, but in recent years, due to the marketing of biological therapies and the expiry of many of their patents, biosimilar drugs have also emerged. These are not exact copies of the original, but, like generic drugs, biosimilar drugs have to demonstrate equivalence to the reference drugs in quality, safety and efficacy. Nevertheless, despite their importance and contribution to sustainability of health system, doctors are sometimes unaware of differences between them, and their impact in terms of clinical and economic effects. An attempt is made to review and clarify certain aspects often unknown by physicians, despite their involvement in their use. Copyright © 2015 SECA. Published by Elsevier Espana. All rights reserved.

  13. Patents, antibiotics, and autarky in Spain.

    Science.gov (United States)

    Romero De Pablos, Ana

    2014-01-01

    Patents on antibiotics were introduced in Spain in 1949. Preliminary research reveals diversification in the types of antibiotics: patents relating to penicillin were followed by those relating to streptomycin, erythromycin and tetracycline. There was also diversification in the firms that applied for patents: while Merck & Co. Incorporated and Schenley Industries Inc. were the main partners with Spanish antibiotics manufacturers in the late 1940s, this industrial space also included many others, such as Eli Lilly & Company, Abbott Laboratories, Chas. Pfizer & Co. Incorporated, and American Cyanamid Company in the mid-1970s. The introduction of these drugs in Spain adds new elements to a re-evaluation of the autarkic politics of the early years of the Franco dictatorship.

  14. Nanotechnology patents in the automotive industry (a quantitative & qualitative analysis).

    Science.gov (United States)

    Prasad, Raghavendra; Bandyopadhyay, Tapas K

    2014-01-01

    The aim of the article is to present a trend in patent filings for application of nanotechnology to the automobile sector across the world, using the keyword-based patent search. Overviews of the patents related to nano technology in the automobile industry have been provided. The current work has started from the worldwide patent search to find the patents on nanotechnology in the automobile industry and classify the patents according to the various parts of an automobile to which they are related and the solutions which they are providing. In the next step various graphs have been produced to get an insight into various trends. In next step, analysis of patents in various classifications, have been performed. The trends shown in graphs provide the quantitative analysis whereas; the qualitative analysis has been done in another section. The classifications of patents based on the solution they provide have been performed by reading the claims, titles, abstract and full texts separately. Patentability of nano technology inventions have been discussed in a view to give an idea of requirements and statutory bars to the patentability of nanotechnology inventions. Another objective of the current work is to suggest appropriate framework for the companies regarding use of nano technology in the automobile industry and a suggestive strategy for patenting of the inventions related to the same. For example, US Patent, with patent number US2008-019426A1 discusses the invention related to Lubricant composition. This patent has been studied and classified to fall under classification of automobile parts. After studying this patent, it is deduced that, the problem of friction in engine is being solved by this patent. One classification is the "automobile part" based while other is the basis of "problem being solved". Hence, two classifications, namely reduction in friction and engine were created. Similarly, after studying all the patents, a similar matrix has been created.

  15. Study the content relationship between science and technology documents: A compression of papers and patent in Autonomous Underwater Vehicle Dominos

    Directory of Open Access Journals (Sweden)

    Soraia Zolfaghari

    2016-08-01

    Full Text Available The current research aims at studying the conceptual relationship between the science and technology documents through the comparison of vocabularies that are used within the patents and the papers in the field of Autonomous Underwater Vehicles (AUV.  The research method is descriptive. To perform the research, the patents were retrieved from Google Patents and Lens websites, and the papers from IEEE Explore database. A hybrid keyword-class method was used to conduct the search. It means that the search query was consisted of "Autonomous Underwater Vehicle" keyword and “H” class. The titles and the abstracts of the patents and the papers were automatically indexed through a semi-automatic method. This resulted in 195 keywords for patents and 114 ones for papers. Co-occurrence matrices of these two sets of keywords were created through RavarMatrix software. The hierarchical maps of keywords were drawn by SPSS. Findings show that 65 percent of papers’ keywords are those that occurred within the patents but 23 percent of patents’ keywords are similar to the papers’.  The structural comparison of patents and papers clustering’s also revealed that the structural proximity between patents and papers vocabularies is equal to zero. The other finding showed that the similarity between the members of ego networks of prominent keywords is for two cases zero and for others fewer than 15 percent except for the keyword “data”. It may be concluded that the science is affected by technology in the field of AUV.

  16. Patent portfolio management: literature review and a proposed model.

    Science.gov (United States)

    Conegundes De Jesus, Camila Kiyomi; Salerno, Mario Sergio

    2018-05-09

    Patents and patent portfolios are gaining attention in the last decades, from the called 'pro-patent era' to the recent billionaire transactions involving patent portfolios. The field is growing in importance, both theoretically and practically and despite having substantial literature on new product development portfolio management, we have not found an article relating this theory to patent portfolios. Areas covered: The paper develops a systematic literature review on patent portfolio management to organize the evolution and tendencies of patent portfolio management, highlighting distinctive features of patent portfolio management. Interview with IP manager of three life sciences companies, including a leading multinational group provided relevant information about patent portfolio management. Expert opinion: Based on the systematic literature review on portfolio management, more specifically, on new product development portfolio theory, and interview the paper proposes the paper proposes a reference model to manage patent portfolios. The model comprises four stages aligned with the three goals of the NPD portfolio management: 1 - Linking strategy of the Company's NPD Portfolio to Patent Portfolio; 2 - Balancing the portfolio in buckets; 3 - Patent Valuation (maximizing valuation); 4 - Regularly reviewing the patent portfolio.

  17. Cross-Border Patent Disputes: Unified Patent Court or International Commercial Arbitration?

    Directory of Open Access Journals (Sweden)

    Ana Alba Betancourt

    2016-04-01

    Full Text Available Currently, the enforcement of a patent that is registered in several countries involves the risk of getting different and conflicting decisions from the national courts. In 2013, 25 European countries entered in an agreement that aims to homogenise the patent system by creating the European patent with unitary effect and a Unified Patent Court (UPC. This article focuses on the UPC, which aims to have a single court proceeding for cross-border patent conflicts. Does the UPC system represent an advantage compared to the current litigation system? The paper argues that it does and explores what it considers to be the two main advantages of a UPC over the current system of cross-border litigation of patents: the ability to drag several conflicts to a single procedure and the neutrality of the decision makers. These advantages are consequently compared to the characteristics of arbitration. Then, an explanation is provided with regards to how the UPC system is going to work in terms of jurisdiction, preliminary injunctions, the choice of law and enforcement of decisions, comparing those same procedural aspects to arbitration. The article finds that arbitration involves many of the same advantages (as compared to the UPC and that the procedural issues studied in both means are, so too, similar. Therefore, arbitration represents a viable alternative to the UPC when it comes to reducing the risks in solving cross-border patent conflicts.

  18. Patent Keyword Extraction Algorithm Based on Distributed Representation for Patent Classification

    Directory of Open Access Journals (Sweden)

    Jie Hu

    2018-02-01

    Full Text Available Many text mining tasks such as text retrieval, text summarization, and text comparisons depend on the extraction of representative keywords from the main text. Most existing keyword extraction algorithms are based on discrete bag-of-words type of word representation of the text. In this paper, we propose a patent keyword extraction algorithm (PKEA based on the distributed Skip-gram model for patent classification. We also develop a set of quantitative performance measures for keyword extraction evaluation based on information gain and cross-validation, based on Support Vector Machine (SVM classification, which are valuable when human-annotated keywords are not available. We used a standard benchmark dataset and a homemade patent dataset to evaluate the performance of PKEA. Our patent dataset includes 2500 patents from five distinct technological fields related to autonomous cars (GPS systems, lidar systems, object recognition systems, radar systems, and vehicle control systems. We compared our method with Frequency, Term Frequency-Inverse Document Frequency (TF-IDF, TextRank and Rapid Automatic Keyword Extraction (RAKE. The experimental results show that our proposed algorithm provides a promising way to extract keywords from patent texts for patent classification.

  19. REDIdb: the RNA editing database.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa Maria Rosaria; Brennicke, Axel; Quagliariello, Carla

    2007-01-01

    The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing information is available either by experimental inspection (in vitro) or by computational detection (in silico). Each record of REDIdb is organized in a specific flat-file containing a description of the main characteristics of the entry, a feature table with the editing events and related details and a sequence zone with both the genomic sequence and the corresponding edited transcript. REDIdb is a relational database in which the browsing and identification of editing sites has been simplified by means of two facilities to either graphically display genomic or cDNA sequences or to show the corresponding alignment. In both cases, all editing sites are highlighted in colour and their relative positions are detailed by mousing over. New editing positions can be directly submitted to REDIdb after a user-specific registration to obtain authorized secure access. This first version of REDIdb database stores 9964 editing events and can be freely queried at http://biologia.unical.it/py_script/search.html.

  20. The governance of the European patent system:

    DEFF Research Database (Denmark)

    Borras, Susana

    2006-01-01

    at the formal and informal dimensions of interactions in economic systems. This is further developed into an analytical framework which is then used in the assessment of the structural features of the current European patent system, one of the most advanced, complex, and contested economic systems in Europe....... The conclusions elaborate on the normative implications regarding the current weaknesses of the European patent system, and examine the general theoretical implications of the findings, particularly looking at the effectiveness and legitimacy of technically complex governance systems....

  1. Ghosts of inventions: Patent law's digital mediations.

    Science.gov (United States)

    Kang, Hyo Yoon

    2018-04-01

    This article examines the shifts in the material ordering of inventions in patent law organization and their effects on the meaning and scope of inventions as intellectual property. Formats and media are constitutive of the establishment and stabilization of inventions as objects of intellectual property. Modern patent law's materiality had been dominated by paper documents but ever more consists of digital images, files, and networked data. The article traces and analyzes such effects of digital media on the meaning of intellectual/intangible property and argues that inventions increasingly matter as digital data in the legal realm.

  2. Mapping patent classifications: Portfolio and statistical analysis, and the comparison of strengths and weaknesses

    NARCIS (Netherlands)

    Leydesdorff, L.; Kogler, D.F.; Yan, B.

    The Cooperative Patent Classifications (CPC) recently developed cooperatively by the European and US Patent Offices provide a new basis for mapping patents and portfolio analysis. CPC replaces International Patent Classifications (IPC) of the World Intellectual Property Organization. In this study,

  3. Transferability and Commercialization of Patent Rights: Economic and Practical Perspectives

    Directory of Open Access Journals (Sweden)

    Haim V. Levy

    2012-01-01

    Full Text Available The transformation of innovation into commercial value depends primarily on appropriate protection of the intellectual property, usually by patents, and efficient pathway(s of its transferability as well as the transfer of the protected knowledge. The key features of patents, from an economic perspective, are that they encompass new knowledge and confer monopoly rights to the owner. The exclusiveness of patent rights is generally conceived as a necessary mechanism to ensure further innovation, stimulate advanced research and facilitate efficient market transactions with patent rights. The patent holder can transfer the technology embodied by way of granting to others a license to use the patented invention in return for a share of the revenues, usually royalties. Patent rights transferability has been proven to be efficient and profitable to the industry as well as beneficial to the welfare of society. The economic and practical perspectives of the transferability and commercialization of patent rights are discussed.

  4. Constructing a unitary title regime for the European Patent System

    NARCIS (Netherlands)

    Rodriguez, V.F.

    2011-01-01

    The European Patent System without any unitary title allows Member States to retain institutional arrangements within their borders and to prevent any moves to delegate responsibility outside the national sphere. This intergovernmental patent regime suffers from fragmentation due to national

  5. Intellectual property rights in china: patents and economic ...

    African Journals Online (AJOL)

    Intellectual property rights in china: patents and economic development. ... AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search · USING ... there are still patents and other IP related rights infringement and enforcement issues.

  6. An advanced search engine for patent analytics in medicinal chemistry.

    Science.gov (United States)

    Pasche, Emilie; Gobeill, Julien; Teodoro, Douglas; Gaudinat, Arnaud; Vishnykova, Dina; Lovis, Christian; Ruch, Patrick

    2012-01-01

    Patent collections contain an important amount of medical-related knowledge, but existing tools were reported to lack of useful functionalities. We present here the development of TWINC, an advanced search engine dedicated to patent retrieval in the domain of health and life sciences. Our tool embeds two search modes: an ad hoc search to retrieve relevant patents given a short query and a related patent search to retrieve similar patents given a patent. Both search modes rely on tuning experiments performed during several patent retrieval competitions. Moreover, TWINC is enhanced with interactive modules, such as chemical query expansion, which is of prior importance to cope with various ways of naming biomedical entities. While the related patent search showed promising performances, the ad-hoc search resulted in fairly contrasted results. Nonetheless, TWINC performed well during the Chemathlon task of the PatOlympics competition and experts appreciated its usability.

  7. The availability of Misoprostol in pharmacies and patent medicine ...

    African Journals Online (AJOL)

    The availability of Misoprostol in pharmacies and patent medicine stores in two Nigerian ... AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search ... pharmacists or vendors of pharmaceutical and patent medicine outlets in two ...

  8. Patent medicine vendors are major providers antimalaria treatment

    African Journals Online (AJOL)

    management of malaria by this informal sector of healthcare delivery is however ... Methods: Fifty-five patent medicine vendors selected through a multistage sampling ... training of the patent medicine vendors, the overall appropriate treatment ...

  9. 48 CFR 27.204 - Patented technology under trade agreements.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Patented technology under trade agreements. 27.204 Section 27.204 Federal Acquisition Regulations System FEDERAL ACQUISITION... Patented technology under trade agreements. ...

  10. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  11. Chemical entity recognition in patents by combining dictionary-based and statistical approaches

    Science.gov (United States)

    Akhondi, Saber A.; Pons, Ewoud; Afzal, Zubair; van Haagen, Herman; Becker, Benedikt F.H.; Hettne, Kristina M.; van Mulligen, Erik M.; Kors, Jan A.

    2016-01-01

    We describe the development of a chemical entity recognition system and its application in the CHEMDNER-patent track of BioCreative 2015. This community challenge includes a Chemical Entity Mention in Patents (CEMP) recognition task and a Chemical Passage Detection (CPD) classification task. We addressed both tasks by an ensemble system that combines a dictionary-based approach with a statistical one. For this purpose the performance of several lexical resources was assessed using Peregrine, our open-source indexing engine. We combined our dictionary-based results on the patent corpus with the results of tmChem, a chemical recognizer using a conditional random field classifier. To improve the performance of tmChem, we utilized three additional features, viz. part-of-speech tags, lemmas and word-vector clusters. When evaluated on the training data, our final system obtained an F-score of 85.21% for the CEMP task, and an accuracy of 91.53% for the CPD task. On the test set, the best system ranked sixth among 21 teams for CEMP with an F-score of 86.82%, and second among nine teams for CPD with an accuracy of 94.23%. The differences in performance between the best ensemble system and the statistical system separately were small. Database URL: http://biosemantics.org/chemdner-patents PMID:27141091

  12. Chemical entity recognition in patents by combining dictionary-based and statistical approaches.

    Science.gov (United States)

    Akhondi, Saber A; Pons, Ewoud; Afzal, Zubair; van Haagen, Herman; Becker, Benedikt F H; Hettne, Kristina M; van Mulligen, Erik M; Kors, Jan A

    2016-01-01

    We describe the development of a chemical entity recognition system and its application in the CHEMDNER-patent track of BioCreative 2015. This community challenge includes a Chemical Entity Mention in Patents (CEMP) recognition task and a Chemical Passage Detection (CPD) classification task. We addressed both tasks by an ensemble system that combines a dictionary-based approach with a statistical one. For this purpose the performance of several lexical resources was assessed using Peregrine, our open-source indexing engine. We combined our dictionary-based results on the patent corpus with the results of tmChem, a chemical recognizer using a conditional random field classifier. To improve the performance of tmChem, we utilized three additional features, viz. part-of-speech tags, lemmas and word-vector clusters. When evaluated on the training data, our final system obtained an F-score of 85.21% for the CEMP task, and an accuracy of 91.53% for the CPD task. On the test set, the best system ranked sixth among 21 teams for CEMP with an F-score of 86.82%, and second among nine teams for CPD with an accuracy of 94.23%. The differences in performance between the best ensemble system and the statistical system separately were small.Database URL: http://biosemantics.org/chemdner-patents. © The Author(s) 2016. Published by Oxford University Press.

  13. Profile of medicinal plants utilization through patent documents: the andiroba example

    Directory of Open Access Journals (Sweden)

    Luciene F. Gaspar Amaral

    2013-06-01

    Full Text Available Today, one of the trends of the pharmaceutical, cosmetic and food market is the development of products with components of natural origin, rationally exploiting biodiversity. Brazilian population makes secular use of medicinal plants including andiroba, whose oil is used in folk medicine as febrifuge, pain-relieving, anti-parasitic, anti-allergic as well as insect repellant. The present study attempts to evaluate the profile of utilization of andiroba by analyzing the patenting trends based on information collected on the databases of the World Intellectual Property Organization, European Patent Office and Brazilian National Institute of Industrial Property in the period from 1990 to 2011. The following parameters were analyzed: chronological aspect of the applications, countries of priority, international patent classification, technologies and actors in the technological platform. The temporal analysis of the applications shows an evident increase despite a discontinuous evolution of the number of applications. Pharmaceutical, chemical and cosmetic areas were identified as the main areas for commercial application of the plant. Brazil is the country with the largest number of applications even though the majority of the patent technologies are already in public domain, indicating that the technological information contained in these documents could be used for research and investment in several areas.

  14. "Environmental Technology Strengths: International Rankings Based on US Patent Data"

    OpenAIRE

    Dora Marinova; Michael McAleer

    2003-01-01

    Patent information has been used by economists and researchers in the field of innovation to analyse current and forecast future technological directions. The recent surge in patenting activities in developed countries reaffirms the strong position of the patent system in a globalised world dominated by market mechanisms. This paper analyses the technological position of the top twelve foreign patenting countries in the USA, namely Australia, Canada, France, Germany, Italy, Japan, Korea, the ...

  15. Review and Comparison of the Search Effectiveness and User Interface of Three Major Online Chemical Databases

    Science.gov (United States)

    Bharti, Neelam; Leonard, Michelle; Singh, Shailendra

    2016-01-01

    Online chemical databases are the largest source of chemical information and, therefore, the main resource for retrieving results from published journals, books, patents, conference abstracts, and other relevant sources. Various commercial, as well as free, chemical databases are available. SciFinder, Reaxys, and Web of Science are three major…

  16. Database Description - eSOL | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name eSOL Alternative nam...eator Affiliation: The Research and Development of Biological Databases Project, National Institute of Genet...nology 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501 Japan Email: Tel.: +81-45-924-5785 Database... classification Protein sequence databases - Protein properties Organism Taxonomy Name: Escherichia coli Taxonomy ID: 562 Database...i U S A. 2009 Mar 17;106(11):4201-6. External Links: Original website information Database maintenance site

  17. Annotated chemical patent corpus: a gold standard for text mining.

    Directory of Open Access Journals (Sweden)

    Saber A Akhondi

    Full Text Available Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

  18. Why do firms give away their patents for free?

    NARCIS (Netherlands)

    Ziegler, Nicole; Gassmann, Oliver; Friesike, Sascha

    2013-01-01

    Within the trend of increasing patent commercialisation and open innovation, a recent phenomenon where firms give away their patents free of charge can be observed. This seems contradictory to the original intention of the patent system (enabling firms to create temporary monopolies to appropriate

  19. Languages, Fees and the International Scope of Patenting

    DEFF Research Database (Denmark)

    Harhoff, Dietmar; Hoisl, Karin; Van Pottelsberghe de la Potterie, Bruno

    2016-01-01

    Pottelsberghe, 2006; von Graevenitz et al., 2013) and on potential implications of their behaviour for the effectiveness of the patent system. Lately, a number of researchers have started to explore the design of the patent system itself, i.e. the role of fees and costs of patenting (Archontopoulos et al., 2007...

  20. Analysis of patents on extinguishing agent for sodium fires

    International Nuclear Information System (INIS)

    Jeong, Ji Young; Jeong, K. C.; Kim, B. H.; Kim, T. J.; Choi, J. H.

    2002-02-01

    This report relates to the extinction of sodium fires, particularly where the burning sodium is in liquid form. The total of 14 patents on extinguishing agents for sodium fires patented from 1969 to 1997 are analyzed and summarized. All of the patents analyzed were issued from USA, France and Japan

  1. Analysis of patents on extinguishing agent for sodium fires

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Ji Young; Jeong, K C; Kim, B H; Kim, T J; Choi, J H

    2002-02-01

    This report relates to the extinction of sodium fires, particularly where the burning sodium is in liquid form. The total of 14 patents on extinguishing agents for sodium fires patented from 1969 to 1997 are analyzed and summarized. All of the patents analyzed were issued from USA, France and Japan.

  2. Essential patents in industry standards : the case of UMTS

    NARCIS (Netherlands)

    Bekkers, R.N.A.; Bongard, R.; Nuvolari, A.

    2009-01-01

    We study the determinants of essential patents in industry standards. In particular, we assess the role of two main factors: the significance of the technological solution contained in the patent and the involvement of the applicant of the patent in the standardization process. To this end, we

  3. Reforming South Africa's procedures for granting patents to improve ...

    African Journals Online (AJOL)

    requires SA to grant 20 years of patent protection on products and processes ... 2010 in SA. However, secondary, evergreening patents prevented generic versions from being brought to the market at a 30% price reduction when the initial patent expired. ... and new uses (new clinical uses of medicines other than those for.

  4. 78 FR 70294 - Intent To Grant an Exclusive Patent License

    Science.gov (United States)

    2013-11-25

    ... DEPARTMENT OF DEFENSE Department of the Air Force Intent To Grant an Exclusive Patent License... interest the Air Force has in: U.S. Provisional Patent Application No. 61/354,522, filed on June 14, 2010... Anish Tuteja et al.; U.S. Non-provisional Patent Application No. 13/159,950, filed on June 14, 2011...

  5. 48 CFR 2527.7002 - NSF patent policy.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true NSF patent policy. 2527... CONTRACTING REQUIREMENTS PATENTS, DATA, AND COPYRIGHTS Disposition of Rights in Inventions 2527.7002 NSF patent policy. As authorized by the National Science Board at its 230th meeting, October 15-16, 1981, the...

  6. 25 CFR 152.5 - Issuance of patent in fee.

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Issuance of patent in fee. 152.5 Section 152.5 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER ISSUANCE OF PATENTS IN FEE, CERTIFICATES OF COMPETENCY, REMOVAL OF RESTRICTIONS, AND SALE OF CERTAIN INDIAN LANDS Issuing Patents in Fee...

  7. 77 FR 38771 - Prospective Grant of Exclusive Patent License

    Science.gov (United States)

    2012-06-29

    ... Exclusive Patent License AGENCY: National Institute of Standards and Technology, Department of Commerce. ACTION: Notice of prospective grant of exclusive patent license. SUMMARY: This is a notice in accordance... embodied in U.S. Patent Application No. 13/346,999 titled ``Chirped-Pulse Terahertz Spectroscopy for...

  8. 9 CFR 124.20 - Patent term extension calculation.

    Science.gov (United States)

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Patent term extension calculation. 124... OF AGRICULTURE VIRUSES, SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS PATENT TERM RESTORATION Regulatory Review Period § 124.20 Patent term extension calculation. (a) As provided in 37 CFR 1...

  9. 77 FR 40345 - Intent to Grant an Exclusive Patent License

    Science.gov (United States)

    2012-07-09

    ... DEPARTMENT OF DEFENSE Department of the Air Force Intent to Grant an Exclusive Patent License... William V. Stoecker, Hernan F. Gomez, Jonathan A. Green, and David L. McGlasson; U.S. Patent Number 7,927... David L. McGlasson; U.S. Patent Application Number Serial No. 12/756,875, filed on April 8, 2010...

  10. 76 FR 57720 - Intent To Grant an Exclusive Patent License

    Science.gov (United States)

    2011-09-16

    ... DEPARTMENT OF DEFENSE Department of the Air Force Intent To Grant an Exclusive Patent License... in: U.S. Patent Application No. 12/932,341, filed on February 23, 2011, entitled ``Resin-Based... INFORMATION CONTACT: An exclusive license for the invention described in this patent application will be...

  11. 77 FR 65673 - Prospective Grant of Exclusive Patent License

    Science.gov (United States)

    2012-10-30

    ... Exclusive Patent License AGENCY: National Institute of Standards and Technology, Commerce. ACTION: Notice of prospective grant of exclusive patent license. SUMMARY: This is a notice in accordance with 35 U.S.C. 209(e.... Patent Application No. 61/625,511 titled ``UV-Assisted Alcohol Sensing with Zinc Oxide Functionalized...

  12. 77 FR 48130 - Prospective Grant of Exclusive Patent License

    Science.gov (United States)

    2012-08-13

    ... Exclusive Patent License AGENCY: National Institute of Standards and Technology, Commerce. ACTION: Notice of prospective grant of exclusive patent license. SUMMARY: This is a notice in accordance with 35 U.S.C. 209(e... Provisional Application for Patent Application No. 61,638,362 titled ``Flow Cytometer Systems and Associated...

  13. Use of Patent Information : Empirical Evidence from Innovative SMEs

    NARCIS (Netherlands)

    Masurel, Enno

    2005-01-01

    This paper discusses the use of patent information by innovative SMEs. The standard literature tends to focus on obtaining patents; studies of using patent information for different purposes are underrepresented in the innovation literature. Studying the case of SMEs is especially interesting,

  14. 25 CFR 152.4 - Application for patent in fee.

    Science.gov (United States)

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Application for patent in fee. 152.4 Section 152.4 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER ISSUANCE OF PATENTS IN FEE, CERTIFICATES OF COMPETENCY, REMOVAL OF RESTRICTIONS, AND SALE OF CERTAIN INDIAN LANDS Issuing Patents in Fee...

  15. 76 FR 40339 - Patent Prosecution Highway (PPH) Program

    Science.gov (United States)

    2011-07-08

    ... any of the following methods: E-mail: [email protected] . Include ``0651- 0058 comment... Singapore (IPOS), German Patent and Trade Mark Office (DPMA), National Board of Patents and Registration of... being planned with the USPTO: CIPO, SIPO, and the Nordic Patent Institute (NPI). II. Method of...

  16. 78 FR 64925 - Request for Comments on Proposed Elimination of Patents Search Templates

    Science.gov (United States)

    2013-10-30

    ...] Request for Comments on Proposed Elimination of Patents Search Templates AGENCY: United States Patent and... Patents Search Templates from the USPTO Web site. In 2006, the United States Patent and Trademark Office (USPTO) implemented Patents Search Templates, which are United States Patent Classification (USPC...

  17. The backlog issue in patents: A look at the European case

    NARCIS (Netherlands)

    Rodriguez, V.

    2010-01-01

    Backlogs can be caused by an increase in the number of patent applications and patent size. A large number of patents granted could be explained by patent examiners' bonuses, legal and cultural contexts, claim forms, the geographical origin of patents, a firm's experience in patenting, the number of

  18. Update on Brazil's pharma patent landscape.

    Science.gov (United States)

    Gosain, Rana

    2016-09-01

    Brazil's Pharma market is a dynamic and promising one. It ranks within the top ten market. There are peculiar hurdles that patentees have to overcome, such as, a two-tier examination, a serious backlog at the Brazilian Patent and Trademark Office. Several measures to accelerate examination have been adopted given the meager number of Examiners.

  19. Savannah River Site Patented Technologies Summaries

    Energy Technology Data Exchange (ETDEWEB)

    Rabold, D.E.

    1995-07-18

    This information represents SRS`s contribution of the DOE technology information network, an internet service coordinated out of Los Alamos. The information provided is strictly DOE-SR-titled and-issued patented technologies including environmental remediation, robotics, sensors, materials science, biomedical applications, hydrogen, and consumer products.

  20. Patent, Nanotechnology, and the Role of University

    OpenAIRE

    Sardjono, Agus

    2011-01-01

    University has significant contribution tot the development of nanotechnology, The role of university can be implemented through the TTLO, particulary in an effort to build a bridge for bottom-up nanotechnology for commercial purposes. There will be an increasingly significant link betweent the patent system on the university role in the development of nanotechnology.