WorldWideScience

Sample records for annotated receipts capture

  1. 77 FR 4059 - Certain Electronic Devices for Capturing and Transmitting Images, and Components Thereof; Receipt...

    Science.gov (United States)

    2012-01-26

    ...Notice is hereby given that the U.S. International Trade Commission has received a complaint entitled In Re Certain Electronic Devices for Capturing and Transmitting Images, and Components Thereof, DN 2869; the Commission is soliciting comments on any public interest issues raised by the...

  2. Computing human image annotation.

    Science.gov (United States)

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Rubin, Daniel L

    2009-01-01

    An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human (or machine) observer. An image markup is the graphical symbols placed over the image to depict an annotation. In the majority of current, clinical and research imaging practice, markup is captured in proprietary formats and annotations are referenced only in free text radiology reports. This makes these annotations difficult to query, retrieve and compute upon, hampering their integration into other data mining and analysis efforts. This paper describes the National Cancer Institute's Cancer Biomedical Informatics Grid's (caBIG) Annotation and Image Markup (AIM) project, focusing on how to use AIM to query for annotations. The AIM project delivers an information model for image annotation and markup. The model uses controlled terminologies for important concepts. All of the classes and attributes of the model have been harmonized with the other models and common data elements in use at the National Cancer Institute. The project also delivers XML schemata necessary to instantiate AIMs in XML as well as a software application for translating AIM XML into DICOM S/R and HL7 CDA. Large collections of AIM annotations can be built and then queried as Grid or Web services. Using the tools of the AIM project, image annotations and their markup can be captured and stored in human and machine readable formats. This enables the inclusion of human image observation and inference as part of larger data mining and analysis activities. PMID:19964202

  3. Annotated English

    CERN Document Server

    Hernandez-Orallo, Jose

    2010-01-01

    This document presents Annotated English, a system of diacritical symbols which turns English pronunciation into a precise and unambiguous process. The annotations are defined and located in such a way that the original English text is not altered (not even a letter), thus allowing for a consistent reading and learning of the English language with and without annotations. The annotations are based on a set of general rules that make the frequency of annotations not dramatically high. This makes the reader easily associate annotations with exceptions, and makes it possible to shape, internalise and consolidate some rules for the English language which otherwise are weakened by the enormous amount of exceptions in English pronunciation. The advantages of this annotation system are manifold. Any existing text can be annotated without a significant increase in size. This means that we can get an annotated version of any document or book with the same number of pages and fontsize. Since no letter is affected, the ...

  4. NM Gross Receipts Baseline

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This layer represents boundaries for New Mexico's gross receipts tax districts as identified on the "Gross Receipts Tax Rate Schedule" published by the Taxation and...

  5. Annotation and Classification of Argumentative Writing Revisions

    Science.gov (United States)

    Zhang, Fan; Litman, Diane

    2015-01-01

    This paper explores the annotation and classification of students' revision behaviors in argumentative writing. A sentence-level revision schema is proposed to capture why and how students make revisions. Based on the proposed schema, a small corpus of student essays and revisions was annotated. Studies show that manual annotation is reliable with…

  6. Annotated Answer Set Programming

    OpenAIRE

    Straccia, Umberto

    2005-01-01

    We present Annotated Answer Set Programming, that extends the ex pressive power of disjunctive logic programming with annotation terms, taken from the generalized annotated logic programming framework.

  7. Annotated Videography.

    Science.gov (United States)

    United States Holocaust Memorial Museum, Washington, DC.

    This annotated list of 43 videotapes recommended for classroom use addresses various themes for teaching about the Holocaust, including: (1) overviews of the Holocaust; (2) life before the Holocaust; (3) propaganda; (4) racism, anti-Semitism; (5) "enemies of the state"; (6) ghettos; (7) camps; (8) genocide; (9) rescue; (10) resistance; (11)…

  8. US Cannery Receipts

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The data set contains receipts of tuna destined for canning, from both domestic and imported sources, at cannery locations within the 50 states, Puerto Rico, and...

  9. Gene Ontology annotations and resources.

    Science.gov (United States)

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  10. Modeling Loosely Annotated Images with Imagined Annotations

    CERN Document Server

    Tang, Hong; Chen, Yunhao

    2008-01-01

    In this paper, we present an approach to learning latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: (1) ambiguous correspondences between visual features and annotated keywords; (2) incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning topic models. In particular, some imagined keywords are poured into the incomplete annotation through measuring similarity between keywords. Then, both given and imagined annotations are used to learning probabilistic topic models for automatically annotating new images. We conduct experiments on a typical Corel dataset of images and loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods (using a set of discrete blobs to represent an image). The proposed method improves word-driven probability Latent Semantic Analysis (PLSA-words) up to ...

  11. Annotated bibliography

    International Nuclear Information System (INIS)

    Under a cooperative agreement with the U.S. Department of Energy's Office of Science and Technology, Waste Policy Institute (WPI) is conducting a five-year research project to develop a research-based approach for integrating communication products in stakeholder involvement related to innovative technology. As part of the research, WPI developed this annotated bibliography which contains almost 100 citations of articles/books/resources involving topics related to communication and public involvement aspects of deploying innovative cleanup technology. To compile the bibliography, WPI performed on-line literature searches (e.g., Dialog, International Association of Business Communicators Public Relations Society of America, Chemical Manufacturers Association, etc.), consulted past years proceedings of major environmental waste cleanup conferences (e.g., Waste Management), networked with professional colleagues and DOE sites to gather reports or case studies, and received input during the August 1996 Research Design Team meeting held to discuss the project's research methodology. Articles were selected for annotation based upon their perceived usefulness to the broad range of public involvement and communication practitioners

  12. Annotating user-defined abstractions for optimization

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, D; Schordan, M; Vuduc, R; Yi, Q

    2005-12-05

    This paper discusses the features of an annotation language that we believe to be essential for optimizing user-defined abstractions. These features should capture semantics of function, data, and object-oriented abstractions, express abstraction equivalence (e.g., a class represents an array abstraction), and permit extension of traditional compiler optimizations to user-defined abstractions. Our future work will include developing a comprehensive annotation language for describing the semantics of general object-oriented abstractions, as well as automatically verifying and inferring the annotated semantics.

  13. An Extensible, Kinematically-Based Gesture Annotation Scheme

    OpenAIRE

    Martell, Craig H.

    2002-01-01

    Chapter 1 in the book: Advances in Natural Multimodal Dialogue Systems Annotated corpora have played a critical role in speech and natural language research; and, there is an increasing interest in corpora-based research in sign language and gesture as well. We present a non-semantic, geometrically-based annotation scheme, FORM, which allows an annotator to capture the kinematic information in a gesture just from videos of speakers. In addition, FORM stores this gestural in...

  14. Interlinking Multimedia Annotations

    OpenAIRE

    Li, Yunjia; Wald, Mike; Wills, Gary

    2011-01-01

    With the fast growth of multimedia sharing and annotating applications on the Web, there is an increasing research interests in semantic annotations of multimedia. However, applying linked data principles in multimedia annotations is a relatively new topic, especially when annotations are related to media fragments. This paper, therefore, discusses this problem and further breaks it down into three fundamental sub-questions: 1) choosing media fragment URIs 2) Dereferencing media fragment URIs...

  15. 7 CFR 1421.107 - Warehouse receipts.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Warehouse receipts. 1421.107 Section 1421.107... § 1421.107 Warehouse receipts. (a) Warehouse receipts tendered to CCC under § 1421.3 for marketing... program documents. (b) Warehouse receipts must be issued in the name of the eligible producer or CCC....

  16. 7 CFR 1427.11 - Warehouse receipts.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 10 2010-01-01 2010-01-01 false Warehouse receipts. 1427.11 Section 1427.11... Deficiency Payments § 1427.11 Warehouse receipts. (a) Producers may obtain loans on eligible cotton represented by warehouse receipts only if the warehouse receipts meet the definition of a warehouse...

  17. Wearable cameras for real-time activity annotation

    OpenAIRE

    Zhou, Jiang; Duane, Aaron; Albatal, Rami; Gurrin, Cathal; Johansen, Dag

    2015-01-01

    Google Glass has potential to be a real-time data capture and annotation tool. With professional sports as a use-case, we present a platform which helps a football coach capture and annotate interesting events using Google Glass. In our implementation, an interesting event is indicated by a predefined hand gesture or motion, and our platform can automatically detect these gestures in a video without training any classifier. Three event detectors are examined and our experiment shows that the ...

  18. Annotations for Intersection Typechecking

    Directory of Open Access Journals (Sweden)

    Joshua Dunfield

    2013-07-01

    Full Text Available In functional programming languages, the classic form of annotation is a single type constraint on a term. Intersection types add complications: a single term may have to be checked several times against different types, in different contexts, requiring annotation with several types. Moreover, it is useful (in some systems, necessary to indicate the context in which each such type is to be used. This paper explores the technical design space of annotations in systems with intersection types. Earlier work (Dunfield and Pfenning 2004 introduced contextual typing annotations, which we now tease apart into more elementary mechanisms: a "right hand" annotation (the standard form, a "left hand" annotation (the context in which a right-hand annotation is to be used, a merge that allows for multiple annotations, and an existential binder for index variables. The most novel element is the left-hand annotation, which guards terms (and right-hand annotations with a judgment that must follow from the current context.

  19. Annotated Stack Trees

    OpenAIRE

    Hague, Matthew; Penelle, Vincent

    2015-01-01

    Annotated pushdown automata provide an automaton model of higher-order recursion schemes, which may in turn be used to model higher-order programs for the purposes of verification. We study Ground Annotated Stack Tree Rewrite Systems -- a tree rewrite system where each node is labelled by the configuration of an annotated pushdown automaton. This allows the modelling of fork and join constructs in higher-order programs and is a generalisation of higher-order stack trees recently introduced by...

  20. NM Gross Receipts January - June 2012

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This layer represents boundaries for New Mexico's gross receipts tax districts as identified on the "Gross Receipts Tax Rate Schedule" published by the Taxation and...

  1. NM Gross Receipts January - June 2011

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This layer represents boundaries for New Mexico's gross receipts tax districts as identified on the "Gross Receipts Tax Rate Schedule" published by the Taxation and...

  2. NM Gross Receipts July - December 2013

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This layer represents boundaries for New Mexico's gross receipts tax districts as identified on the "Gross Receipts Tax Rate Schedule" published by the Taxation and...

  3. NM Gross Receipts July - December 2012

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This layer represents boundaries for New Mexico's gross receipts tax districts as identified on the "Gross Receipts Tax Rate Schedule" published by the Taxation and...

  4. NM Gross Receipts January - June 2014

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This layer represents boundaries for New Mexico's gross receipts tax districts as identified on the "Gross Receipts Tax Rate Schedule" published by the Taxation and...

  5. NM Gross Receipts January - June 2013

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This layer represents boundaries for New Mexico's gross receipts tax districts as identified on the "Gross Receipts Tax Rate Schedule" published by the Taxation and...

  6. Graph Annotations in Modeling Complex Network Topologies

    CERN Document Server

    Dimitropoulos, Xenofontas; Vahdat, Amin; Riley, George

    2007-01-01

    The coarsest approximation of the structure of a complex network, such as the Internet, is a simple undirected unweighted graph. This approximation, however, loses too much detail. In reality, objects represented by vertices and edges in such a graph possess some non-trivial internal structure that varies across and differentiates among distinct types of links or nodes. In this work, we abstract such additional information as network annotations. We introduce a network topology modeling framework that treats annotations as an extended correlation profile of a network. Assuming we have this profile measured for a given network, we present an algorithm to rescale it in order to construct networks of varying size that still reproduce the original measured annotation profile. Using this methodology, we accurately capture the network properties essential for realistic simulations of network applications and protocols, or any other simulations involving complex network topologies, including modeling and simulation ...

  7. Personnalisation de Syst\\`emes OLAP Annot\\'es

    CERN Document Server

    Jerbi, Houssem; Ravat, Franck; Teste, Olivier

    2010-01-01

    This paper deals with personalization of annotated OLAP systems. Data constellation is extended to support annotations and user preferences. Annotations reflect the decision-maker experience whereas user preferences enable users to focus on the most interesting data. User preferences allow annotated contextual recommendations helping the decision-maker during his/her multidimensional navigations.

  8. Creating Annotation Tools with the Annotation Graph Toolkit

    OpenAIRE

    Maeda, Kazuaki; Bird, Steven; Ma, Xiaoyi; Lee, Haejoong

    2002-01-01

    The Annotation Graph Toolkit is a collection of software supporting the development of annotation tools based on the annotation graph model. The toolkit includes application programming interfaces for manipulating annotation graph data and for importing data from other formats. There are interfaces for the scripting languages Tcl and Python, a database interface, specialized graphical user interfaces for a variety of annotation tasks, and several sample applications. This paper describes all ...

  9. On Anomalies in Annotation Systems

    CERN Document Server

    Brust, Matthias R

    2007-01-01

    Today's computer-based annotation systems implement a wide range of functionalities that often go beyond those available in traditional paper-and-pencil annotations. Conceptually, annotation systems are based on thoroughly investigated psycho-sociological and pedagogical learning theories. They offer a huge diversity of annotation types that can be placed in textual as well as in multimedia format. Additionally, annotations can be published or shared with a group of interested parties via well-organized repositories. Although highly sophisticated annotation systems exist both conceptually as well as technologically, we still observe that their acceptance is somewhat limited. In this paper, we argue that nowadays annotation systems suffer from several fundamental problems that are inherent in the traditional paper-and-pencil annotation paradigm. As a solution, we propose to shift the annotation paradigm for the implementation of annotation system.

  10. Capturing Thoughts, Capturing Minds?

    DEFF Research Database (Denmark)

    Nielsen, Janni

    2004-01-01

    Think Aloud is cost effective, promises access to the user's mind and is the applied usability technique. But 'keep talking' is difficult, besides, the multimodal interface is visual not verbal. Eye-tracking seems to get around the verbalisation problem. It captures the visual focus of attention....... However, it is expensive, obtrusive and produces huge amount of data. Besides, eye-tracking do not give access to user's mind. Capturing interface/cursor tracking may be cost effective. It is easy to install, data collection is automatic and unobtrusive and replaying the captured recording to the user and...

  11. Semantic annotation of mutable data.

    Directory of Open Access Journals (Sweden)

    Robert A Morris

    Full Text Available Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology. However, electronic annotation of data differs from annotation of documents: the content of the annotations, including expectations and supporting evidence, is more often shared among members of networks. Any consequent actions taken by the holders of the annotated data could be shared as well. But even those current annotation systems that admit data as their subject often make it difficult or impossible to annotate at fine-enough granularity to use the results in this way for data quality control. We address these kinds of issues by offering simple extensions to an existing annotation ontology and describe how the results support an interest-based distribution of annotations. We are using the result to design and deploy a platform that supports annotation services overlaid on networks of distributed data, with particular application to data quality control. Our initial instance supports a set of natural science collection metadata services. An important application is the support for data quality control and provision of missing data. A previous proof of concept demonstrated such use based on data annotations modeled with XML-Schema.

  12. Algal functional annotation tool

    Energy Technology Data Exchange (ETDEWEB)

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes

  13. Algal functional annotation tool

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, D. [UCLA; Casero, D. [UCLA; Cokus, S. J. [UCLA; Merchant, S. S. [UCLA; Pellegrini, M. [UCLA

    2012-07-01

    The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

  14. Collaborative Movie Annotation

    Science.gov (United States)

    Zad, Damon Daylamani; Agius, Harry

    In this paper, we focus on metadata for self-created movies like those found on YouTube and Google Video, the duration of which are increasing in line with falling upload restrictions. While simple tags may have been sufficient for most purposes for traditionally very short video footage that contains a relatively small amount of semantic content, this is not the case for movies of longer duration which embody more intricate semantics. Creating metadata is a time-consuming process that takes a great deal of individual effort; however, this effort can be greatly reduced by harnessing the power of Web 2.0 communities to create, update and maintain it. Consequently, we consider the annotation of movies within Web 2.0 environments, such that users create and share that metadata collaboratively and propose an architecture for collaborative movie annotation. This architecture arises from the results of an empirical experiment where metadata creation tools, YouTube and an MPEG-7 modelling tool, were used by users to create movie metadata. The next section discusses related work in the areas of collaborative retrieval and tagging. Then, we describe the experiments that were undertaken on a sample of 50 users. Next, the results are presented which provide some insight into how users interact with existing tools and systems for annotating movies. Based on these results, the paper then develops an architecture for collaborative movie annotation.

  15. Annotated bibliography traceability

    NARCIS (Netherlands)

    Narain, G.

    2006-01-01

    This annotated bibliography contains summaries of articles and chapters of books, which are relevant to traceability. After each summary there is a part about the relevancy of the paper for the LEI project. The aim of the LEI-project is to gain insight in several aspects of traceability in order to

  16. Annotation: The Savant Syndrome

    Science.gov (United States)

    Heaton, Pamela; Wallace, Gregory L.

    2004-01-01

    Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

  17. The caBIG annotation and image Markup project.

    Science.gov (United States)

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Sepukar, Kastubh; Rubin, Daniel L

    2010-04-01

    Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM. PMID:19294468

  18. Functional annotation and ENU

    OpenAIRE

    Gunn, Teresa M.

    2012-01-01

    Functional annotation of every gene in the mouse genome is a herculean task that requires a multifaceted approach. Many large-scale initiatives are contributing to this undertaking. The International Knockout Mouse Consortium (IKMC) plans to mutate every protein-coding gene, using a combination of gene trapping and gene targeting in embryonic stem cells. Many other groups are performing using the chemical mutagen ethylnitrosourea (ENU) or transpon-based systems to induce mutations, screening ...

  19. 7 CFR 735.302 - Paper warehouse receipts.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Paper warehouse receipts. 735.302 Section 735.302... AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Receipts § 735.302 Paper warehouse receipts. Paper warehouse receipts must be issued as follows: (a)...

  20. 7 CFR 735.300 - Warehouse receipt requirements.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Warehouse receipt requirements. 735.300 Section 735..., DEPARTMENT OF AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Receipts § 735.300 Warehouse receipt requirements. (a) Warehouse receipts may be: (1)...

  1. Assessment of community-submitted ontology annotations from a novel database-journal partnership.

    Science.gov (United States)

    Berardini, Tanya Z; Li, Donghui; Muller, Robert; Chetty, Raymond; Ploetz, Larry; Singh, Shanker; Wensel, April; Huala, Eva

    2012-01-01

    As the scientific literature grows, leading to an increasing volume of published experimental data, so does the need to access and analyze this data using computational tools. The most commonly used method to convert published experimental data on gene function into controlled vocabulary annotations relies on a professional curator, employed by a model organism database or a more general resource such as UniProt, to read published articles and compose annotation statements based on the articles' contents. A more cost-effective and scalable approach capable of capturing gene function data across the whole range of biological research organisms in computable form is urgently needed. We have analyzed a set of ontology annotations generated through collaborations between the Arabidopsis Information Resource and several plant science journals. Analysis of the submissions entered using the online submission tool shows that most community annotations were well supported and the ontology terms chosen were at an appropriate level of specificity. Of the 503 individual annotations that were submitted, 97% were approved and community submissions captured 72% of all possible annotations. This new method for capturing experimental results in a computable form provides a cost-effective way to greatly increase the available body of annotations without sacrificing annotation quality. Database URL: www.arabidopsis.org. PMID:22859749

  2. Public Budget Database - Governmental receipts 1962-Current

    Data.gov (United States)

    Executive Office of the President — This file contains governmental receipts for 1962 through the current budget year, as well as four years of projections. It can be used to reproduce many of the...

  3. Predicting word sense annotation agreement

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier;

    2015-01-01

    High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty of...

  4. The Ensembl gene annotation system.

    Science.gov (United States)

    Aken, Bronwen L; Ayling, Sarah; Barrell, Daniel; Clarke, Laura; Curwen, Valery; Fairley, Susan; Fernandez Banet, Julio; Billis, Konstantinos; García Girón, Carlos; Hourlier, Thibaut; Howe, Kevin; Kähäri, Andreas; Kokocinski, Felix; Martin, Fergal J; Murphy, Daniel N; Nag, Rishi; Ruffier, Magali; Schuster, Michael; Tang, Y Amy; Vogel, Jan-Hinnerk; White, Simon; Zadissa, Amonida; Flicek, Paul; Searle, Stephen M J

    2016-01-01

    The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html. PMID:27337980

  5. Model and Interoperability using Meta Data Annotations

    Science.gov (United States)

    David, O.

    2011-12-01

    Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and

  6. Collective dynamics of social annotation

    CERN Document Server

    Cattuto, Ciro; Baldassarri, Andrea; Schehr, G; Loreto, Vittorio

    2009-01-01

    The enormous increase of popularity and use of the WWW has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with text keywords dubbed tags. Understanding the rich emerging structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks, and the complex networks framework, can effectively contribute to the mathematical modeling of social annotation systems. Here we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of random walks. This modeling framework reproduces several aspects, so far unexplained, of social annotation, among which the peculiar growth of the size of the...

  7. Annotation of Regular Polysemy

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector

    Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...... like “London” (Location/Organization) or “cup” (Container/Content). The goal of this dissertation is to assess whether metonymic sense underspecification justifies incorporating a third sense into our sense inventories, thereby treating the underspecified sense as independent from the literal and...... metonymic. We have conducted an analysis in English, Danish and Spanish. Later on, we have tried to replicate the human judgments by means of unsupervised and semi-supervised sense prediction. The automatic sense-prediction systems have been unable to find empiric evidence for the underspecified sense, even...

  8. Multimedia Authoring and Annotation

    NARCIS (Netherlands)

    Bulterman, D.C.A.; Cesar Garcia, P.S.; Munson, E.; Pimentel, M.G.C.

    2014-01-01

    With the massive amount of captured multimedia, authoring is more relevant than ever. Multimedia content is available in many settings including the web, mobile devices, desktop applications, as well as games and interactive TV. The authoring and production of multimedia documents demands attention

  9. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.

    Science.gov (United States)

    Beijbom, Oscar; Edmunds, Peter J; Roelfsema, Chris; Smith, Jennifer; Kline, David I; Neal, Benjamin P; Dunlap, Matthew J; Moriarty, Vincent; Fan, Tung-Yung; Tan, Chih-Jui; Chan, Stephen; Treibitz, Tali; Gamst, Anthony; Mitchell, B Greg; Kriegman, David

    2015-01-01

    Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys. PMID:26154157

  10. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.

    Directory of Open Access Journals (Sweden)

    Oscar Beijbom

    Full Text Available Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.

  11. Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

    Science.gov (United States)

    Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

    2006-12-01

    Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

  12. Enriching a biomedical event corpus with meta-knowledge annotation

    Directory of Open Access Journals (Sweden)

    Thompson Paul

    2011-10-01

    Full Text Available Abstract Background Biomedical papers contain rich information about entities, facts and events of biological relevance. To discover these automatically, we use text mining techniques, which rely on annotated corpora for training. In order to extract protein-protein interactions, genotype-phenotype/gene-disease associations, etc., we rely on event corpora that are annotated with classified, structured representations of important facts and findings contained within text. These provide an important resource for the training of domain-specific information extraction (IE systems, to facilitate semantic-based searching of documents. Correct interpretation of these events is not possible without additional information, e.g., does an event describe a fact, a hypothesis, an experimental result or an analysis of results? How confident is the author about the validity of her analyses? These and other types of information, which we collectively term meta-knowledge, can be derived from the context of the event. Results We have designed an annotation scheme for meta-knowledge enrichment of biomedical event corpora. The scheme is multi-dimensional, in that each event is annotated for 5 different aspects of meta-knowledge that can be derived from the textual context of the event. Textual clues used to determine the values are also annotated. The scheme is intended to be general enough to allow integration with different types of bio-event annotation, whilst being detailed enough to capture important subtleties in the nature of the meta-knowledge expressed in the text. We report here on both the main features of the annotation scheme, as well as its application to the GENIA event corpus (1000 abstracts with 36,858 events. High levels of inter-annotator agreement have been achieved, falling in the range of 0.84-0.93 Kappa. Conclusion By augmenting event annotations with meta-knowledge, more sophisticated IE systems can be trained, which allow interpretative

  13. 27 CFR 28.251 - Railway express receipts.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Railway express receipts... § 28.251 Railway express receipts. Where the exportation is to a contiguous foreign country and the shipment is by railway express, a receipt issued by the railway express agency may be accepted in lieu...

  14. 27 CFR 27.31 - Warehouse receipts covering distilled spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Warehouse receipts... BEER Dealer Registration and Recordkeeping § 27.31 Warehouse receipts covering distilled spirits. The sale of warehouse receipts for distilled spirits is equivalent to the sale of distilled...

  15. 27 CFR 26.211 - Warehouse receipts covering distilled spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Warehouse receipts... and Recordkeeping § 26.211 Warehouse receipts covering distilled spirits. The sale of warehouse..., warehouse receipts for distilled spirits stored in warehouses, or elsewhere, must register and keep...

  16. 27 CFR 31.47 - Warehouse receipts covering spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Warehouse receipts... Part Certain Organizations, Agencies, and Persons § 31.47 Warehouse receipts covering spirits. The sale of warehouse receipts for distilled spirits is equivalent to the sale of distilled...

  17. 27 CFR 26.45 - Warehouse receipts covering distilled spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Warehouse receipts... Recordkeeping § 26.45 Warehouse receipts covering distilled spirits. The sale of warehouse receipts for... distilled spirits into the United States from Puerto Rico who sells, or offers for sale, warehouse...

  18. 7 CFR 735.303 - Electronic warehouse receipts.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Electronic warehouse receipts. 735.303 Section 735.303... AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Receipts § 735.303 Electronic warehouse receipts. (a) Warehouse operators issuing EWR under the Act may issue...

  19. 27 CFR 28.285 - Receipt in manufacturing bonded warehouse.

    Science.gov (United States)

    2010-04-01

    ... bonded warehouse. 28.285 Section 28.285 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX... Export Receipt in Manufacturing Bonded Warehouse § 28.285 Receipt in manufacturing bonded warehouse. On..., as amended, 1380, as amended (26 U.S.C. 5214, 5362)) Receipt in Customs Bonded Warehouse...

  20. 27 CFR 28.286 - Receipt in customs bonded warehouse.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Receipt in customs bonded... in Customs Bonded Warehouse § 28.286 Receipt in customs bonded warehouse. On receipt of the distilled spirits or wine and the related TTB Form 5100.11 or 5110.30 as the case may be, the customs officer...

  1. 27 CFR 28.290 - Receipt in foreign trade zone.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Receipt in foreign trade zone. 28.290 Section 28.290 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE... in Foreign-Trade Zone § 28.290 Receipt in foreign trade zone. On receipt at the zone, the...

  2. A Study of User's Performance and Satisfaction on the Web Based Photo Annotation with Speech Interaction

    CERN Document Server

    Ramlan, Siti Azura

    2010-01-01

    This paper reports on empirical evaluation study of users' performance and satisfaction with prototype of Web Based speech photo annotation with speech interaction. Participants involved consist of Johor Bahru citizens from various background. They have completed two parts of annotation task; part A involving PhotoASys; photo annotation system with proposed speech interaction and part B involving Microsoft Microsoft Vista Speech Interaction style. They have completed eight tasks for each part including system login and selection of album and photos. Users' performance was recorded using computer screen recording software. Data were captured on the task completion time and subjective satisfaction. Participants need to complete a questionnaire on the subjective satisfaction when the task was completed. The performance data show the comparison between proposed speech interaction and Microsoft Vista Speech interaction applied in photo annotation system, PhotoASys. On average, the reduction in annotation performan...

  3. NCBI prokaryotic genome annotation pipeline.

    Science.gov (United States)

    Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat; Chetvernin, Vyacheslav; Nawrocki, Eric P; Zaslavsky, Leonid; Lomsadze, Alexandre; Pruitt, Kim D; Borodovsky, Mark; Ostell, James

    2016-08-19

    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/. PMID:27342282

  4. Do Local Elites Capture Natural Disaster Reconstruction Funds?

    OpenAIRE

    Yoshito Takasaki

    2009-01-01

    This paper examines the allocation of natural disaster reconstruction funds among cyclone victims in rural Fiji. During post-emergency periods, when good information about cyclone damage is available, do local elites, a powerful minority, capture housing construction materials? With effective targeting in both receipt and the amount received, local elites do not capture larger benefits. More severely affected victims are not early recipients, though, because the supply of reconstruction funds...

  5. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation

    OpenAIRE

    Oscar Beijbom; Edmunds, Peter J.; Chris Roelfsema; Jennifer Smith; Kline, David I.; Neal, Benjamin P.; Matthew J Dunlap; Vincent Moriarty; Tung-Yung Fan; Chih-Jui Tan; Stephen Chan; Tali Treibitz; Anthony Gamst; B. Greg Mitchell; David Kriegman

    2015-01-01

    Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images capture...

  6. Calling on a million minds for community annotation in WikiProteins

    OpenAIRE

    Mons, Barend; Ashburner, Michael; Chichester, Christine; Mulligen, Erik; Weeber, Marc; Dunnen, Johan; Ommen, Gert; Musen, Mark; Cockerill, Matthew; Hermjakob, Henning; Packer, Abel; Pacheco, Roberto; Lewis, Suzan; Berkeley, Alfred; Melton, William

    2008-01-01

    textabstractWikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a 'million minds' to annotate a 'million...

  7. Collective dynamics of social annotation.

    Science.gov (United States)

    Cattuto, Ciro; Barrat, Alain; Baldassarri, Andrea; Schehr, Gregory; Loreto, Vittorio

    2009-06-30

    The enormous increase of popularity and use of the worldwide web has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with keywords known as "tags." Understanding the rich emergent structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks (RWs), and complex networks theory, can effectively contribute to the mathematical modeling of social annotation systems. Here, we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of RWs. This modeling framework reproduces several aspects, thus far unexplained, of social annotation, among which are the peculiar growth of the size of the vocabulary used by the community and its complex network structure that represents an externalization of semantic structures grounded in cognition and that are typically hard to access. PMID:19506244

  8. SENTIMENT ANALYSIS OF DOCUMENT BASED ON ANNOTATION

    Directory of Open Access Journals (Sweden)

    Archana Shukla

    2011-11-01

    Full Text Available I present a tool which tells the quality of document or its usefulness based on annotations. Annotation mayinclude comments, notes, observation, highlights, underline, explanation, question or help etc. commentsare used for evaluative purpose while others are used for summarization or for expansion also. Furtherthese comments may be on another annotation. Such annotations are referred as meta-annotation. Allannotation may not get equal weightage. My tool considered highlights, underline as well as comments toinfer the collective sentiment of annotators. Collective sentiments of annotators are classified as positive,negative, objectivity. My tool computes collective sentiment of annotations in two manners. It counts all theannotation present on the documents as well as it also computes sentiment scores of all annotation whichincludes comments to obtain the collective sentiments about the document or to judge the quality ofdocument. I demonstrate the use of tool on research paper.

  9. Vcfanno: fast, flexible annotation of genetic variants.

    Science.gov (United States)

    Pedersen, Brent S; Layer, Ryan M; Quinlan, Aaron R

    2016-01-01

    The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. By leveraging a parallel "chromosome sweeping" algorithm, we demonstrate substantial performance gains by annotating ~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license. PMID:27250555

  10. noteEd - A web-based lecture capture system

    OpenAIRE

    Fernando, Liam Ranil; Horn, Alexander; Parson, Oliver; Porter, Matthew; Wells, Oliver

    2009-01-01

    Electronic capture and playback of lectures has long been the aim of many academic projects. Synote is an application developed under MACFoB (Multimedia Annotation and Community Folksonomy Building) project to synchronise the playback of lecture materials. However, Synote provides no functionality to capture such multimedia. This project involves the creation of a system called noteEd, which will capture a range of multimedia from lectures and make them available to Synote. This report descri...

  11. Fast Arc-Annotated Subsequence Matching in Linear Space

    CERN Document Server

    Bille, Philip

    2009-01-01

    An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$ can be obtained from $Q$ by deleting bases from $Q$. Whenever a base is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are "nested" are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive for investigating the function of RNA molecules. Gramm et al. [ACM Trans. Algorithms 2006] gave an algorithm for this problem using $O(nm)$ time and space, where $m$ and $n$ are the lengths of $P$ and $Q$, respectively. In this paper we present a new algorithm using $O(nm)$ time and $O(n + m)$ space, thereby matching the previous time bound while significantly reducing the space from a quadratic term to l...

  12. Laser capture.

    Science.gov (United States)

    Potter, S Steven; Brunskill, Eric W

    2012-01-01

    This chapter describes detailed methods used for laser capture microdissection (LCM) of discrete subpopulations of cells. Topics covered include preparing tissue blocks, cryostat sectioning, processing slides, performing the LCM, and purification of RNA from LCM samples. Notes describe the fine points of each operation, which can often mean the difference between success and failure. PMID:22639264

  13. Systems Theory and Communication. Annotated Bibliography.

    Science.gov (United States)

    Covington, William G., Jr.

    This annotated bibliography presents annotations of 31 books and journal articles dealing with systems theory and its relation to organizational communication, marketing, information theory, and cybernetics. Materials were published between 1963 and 1992 and are listed alphabetically by author. (RS)

  14. International Standard for a Linguistic Annotation Framework

    CERN Document Server

    Romary, Laurent

    2004-01-01

    This paper describes the Linguistic Annotation Framework under development within ISO TC37 SC4 WG1. The Linguistic Annotation Framework is intended to serve as a basis for harmonizing existing language resources as well as developing new ones.

  15. Annotated Bibliography, Grades K-6.

    Science.gov (United States)

    Massachusetts Dept. of Education, Boston. Bureau of Nutrition Education and School Food Services.

    This annotated bibliography on nutrition is for the use of teachers at the elementary grade level. It contains a list of books suitable for reading about nutrition and foods for pupils from kindergarten through the sixth grade. Films and audiovisual presentations for classroom use are also listed. The names and addresses from which these materials…

  16. Concept annotation in the CRAFT corpus

    OpenAIRE

    Bada Michael; Eckert Miriam; Evans Donald; Garcia Kristin; Shipley Krista; Sitnikov Dmitry; Baumgartner William A; Cohen K; Verspoor Karin; Blake Judith A; Hunter Lawrence E

    2012-01-01

    Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRA...

  17. Annotating images by mining image search results

    NARCIS (Netherlands)

    X.J. Wang; L. Zhang; X. Li; W.Y. Ma

    2008-01-01

    Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search results

  18. Eight questions about semantic web annotations

    OpenAIRE

    Euzenat, Jérôme

    2002-01-01

    Improving information retrieval is annotation¹s central goal. However, without sufficient planning, annotation - especially when running a robot and attaching automatically extracted content - risks producing incoherent information. The author recommends answering eight questions before you annotate. He provides a practical application of this approach, and discusses applying the questions to other systems.

  19. Genome re-annotation: a wiki solution?

    OpenAIRE

    Salzberg, Steven L.

    2007-01-01

    The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution.

  20. Analysis of LYSA-calculus with explicit confidentiality annotations

    DEFF Research Database (Denmark)

    Gao, Han; Nielson, Hanne Riis

    Recently there has been an increased research interest in applying process calculi in the verification of cryptographic protocols due to their ability to formally model protocols. This work presents LYSA with explicit confidentiality annotations for indicating the expected behavior of target...... malicious activities performed by attackers as specified by the confidentiality annotations. The proposed analysis approach is fully automatic without the need of human intervention and has been applied successfully to a number of protocols....... protocols. A static analysis approach is developed for analyzing protocols specified in the extended LYSA. The proposed approach will over-approximate the possible executions of protocols while keeping track of all messages communicated over the network, and furthermore it will capture the potential...

  1. Ranking of States and Commodities by Cash Receipts, 1991

    OpenAIRE

    Strickland, Roger P., Jr.; Johnson, Cheryl; Williams, Robert P.

    1992-01-01

    This publication identifies the 25 leading agricultural commodities produced in each State and the United States, ranked by the value of cash receipts. The major producing States, ranked by cash receipts, for each of the 25 leading commodities in the United States and for several major commodity groups are also identified. The information is derived from U.S. Department of Agriculture's cash receipts statistics for the marketing of agricultural commodities within States. The ranking of commod...

  2. Semantic Annotation Framework For Intelligent Information Retrieval Using KIM Architecture

    Directory of Open Access Journals (Sweden)

    Sanjay Kumar Malik

    2010-11-01

    Full Text Available Due to the explosion of information/knowledge on the web and wide use of search engines for desiredinformation,the role of knowledge management(KM is becoming more significant in an organization.Knowledge Management in an Organization is used to create ,capture, store, share, retrieve and manageinformation efficiently. The semantic web, an intelligent and meaningful web, tend to provide a promisingplatform for knowledge management systems and vice versa, since they have the potential to give eachother the real substance for machine-understandable web resources which in turn will lead to anintelligent, meaningful and efficient information retrieval on web. Today,the challenge for web communityis to integrate the distributed heterogeneous resources on web with an objective of an intelligent webenvironment focusing on data semantics and user requirements. Semantic Annotation(SA is being widelyused which is about assigning to the entities in the text and links to their semantic descriptions. Varioustools like KIM, Amaya etc may be used for semantic Annotation.In this paper, we introduce semantic annotation as one of the key technology in an intelligent webenvironment , then revisit and review, discuss and explore about Knowledge Management and SemanticAnnotation. A Knowledge Management Framework and a Framework for Semantic Annotation andSemantic Search with Knowledge Base(GATE and Ontology have been presented. Then KIM Annotationplatform architecture including KIM Ontology(KIMO, KIM Knowledge Base and KIM front ends havebeen highlighted. Finally, intelligent pattern search and concerned GATE framework with a KIMAnnotation Example have been illiustrated towards an intelligent information retrieval

  3. Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.

    Science.gov (United States)

    Foulger, R E; Denny, P; Hardy, J; Martin, M J; Sawford, T; Lovering, R C

    2016-07-01

    The Gene Ontology (GO) is widely recognised as the gold standard bioinformatics resource for summarizing functional knowledge of gene products in a consistent and computable, information-rich language. GO describes cellular and organismal processes across all species, yet until now there has been a considerable gene annotation deficit within the neurological and immunological domains, both of which are relevant to Parkinson's disease. Here we introduce the Parkinson's disease GO Annotation Project, funded by Parkinson's UK and supported by the GO Consortium, which is addressing this deficit by providing GO annotation to Parkinson's-relevant human gene products, principally through expert literature curation. We discuss the steps taken to prioritise proteins, publications and cellular processes for annotation, examples of how GO annotations capture Parkinson's-relevant information, and the advantages that a topic-focused annotation approach offers to users. Building on the existing GO resource, this project collates a vast amount of Parkinson's-relevant literature into a set of high-quality annotations to be utilized by the research community. PMID:26825309

  4. Content-based histopathology image retrieval using a kernel-based semantic annotation framework.

    Science.gov (United States)

    Caicedo, Juan C; González, Fabio A; Romero, Eduardo

    2011-08-01

    Large amounts of histology images are captured and archived in pathology departments due to the ever expanding use of digital microscopy. The ability to manage and access these collections of digital images is regarded as a key component of next generation medical imaging systems. This paper addresses the problem of retrieving histopathology images from a large collection using an example image as query. The proposed approach automatically annotates the images in the collection, as well as the query images, with high-level semantic concepts. This semantic representation delivers an improved retrieval performance providing more meaningful results. We model the problem of automatic image annotation using kernel methods, resulting in a unified framework that includes: (1) multiple features for image representation, (2) a feature integration and selection mechanism (3) and an automatic semantic image annotation strategy. An extensive experimental evaluation demonstrated the effectiveness of the proposed framework to build meaningful image representations for learning and useful semantic annotations for image retrieval. PMID:21296682

  5. Werkzeuge zur Annotation diachroner Korpora

    OpenAIRE

    Burghardt, Manuel; Wolff, Christian

    2009-01-01

    Wir diskutieren zunächst die Problematik der (syntaktischen) Annotation diachroner Korpora und stellen anschließend eine Evaluationsstudie vor, bei der mehr als 50 Annotationswerkzeuge und -frameworks vor dem Hintergrund eines funktionalen und software-ergonomischen Anforderungsprofils nach dem Qualitätsmodell von ISO/IEC 9126-1:2001 (Software engineering – Product quality – Part 1: Quality model) und ISO/IEC 25000:2005 (Software Engineering – Software product Quality Requirements and Evaluat...

  6. An Annotation Scheme for Reichenbach's Verbal Tense Structure

    CERN Document Server

    Derczynski, Leon

    2012-01-01

    In this paper we present RTMML, a markup language for the tenses of verbs and temporal relations between verbs. There is a richness to tense in language that is not fully captured by existing temporal annotation schemata. Following Reichenbach we present an analysis of tense in terms of abstract time points, with the aim of supporting automated processing of tense and temporal relations in language. This allows for precise reasoning about tense in documents, and the deduction of temporal relations between the times and verbal events in a discourse. We define the syntax of RTMML, and demonstrate the markup in a range of situations.

  7. 7 CFR 1007.30 - Reports of receipts and utilization.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Reports of receipts and utilization. 1007.30 Section... AREA Order Regulating Handling Handler Reports § 1007.30 Reports of receipts and utilization. Each... beginning and end of the month of fluid milk products and bulk fluid cream products; and (9) The...

  8. 7 CFR 1001.30 - Reports of receipts and utilization.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Reports of receipts and utilization. 1001.30 Section... AREA Order Regulating Handling Handler Reports § 1001.30 Reports of receipts and utilization. Each... products and bulk fluid cream products; (3) The utilization or disposition of all milk and milk...

  9. 7 CFR 1131.30 - Reports of receipts and utilization.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Reports of receipts and utilization. 1131.30 Section... AREA Order Regulating Handling Handler Reports § 1131.30 Reports of receipts and utilization. Each... end of the month of fluid milk products and bulk fluid cream products; and (6) The utilization...

  10. 7 CFR 1005.30 - Reports of receipts and utilization.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Reports of receipts and utilization. 1005.30 Section... MARKETING AREA Order Regulating Handling Handler Reports § 1005.30 Reports of receipts and utilization. Each... beginning and end of the month of fluid milk products and bulk fluid cream products; and (9) The...

  11. 7 CFR 1126.30 - Reports of receipts and utilization.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Reports of receipts and utilization. 1126.30 Section... AREA Order Regulating Handling Handler Reports § 1126.30 Reports of receipts and utilization. Each...) The utilization or disposition of all milk and milk products required to be reported pursuant to...

  12. 7 CFR 1006.30 - Reports of receipts and utilization.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Reports of receipts and utilization. 1006.30 Section... AREA Order Regulating Handling Handler Reports § 1006.30 Reports of receipts and utilization. Each... and bulk fluid cream products; and (6) The utilization or disposition of all milk and milk...

  13. 7 CFR 1030.30 - Reports of receipts and utilization.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Reports of receipts and utilization. 1030.30 Section... MARKETING AREA Order Regulating Handling Handler Reports § 1030.30 Reports of receipts and utilization. Each... cream products; (3) The utilization or disposition of all milk and milk products required to be...

  14. 7 CFR 1124.30 - Reports of receipts and utilization.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 9 2010-01-01 2009-01-01 true Reports of receipts and utilization. 1124.30 Section... MARKETING AREA Order Regulating Handling Handler Reports § 1124.30 Reports of receipts and utilization. Each... and end of the month of fluid milk products and bulk fluid cream products; (3) The utilization...

  15. 27 CFR 17.162 - Receipt of distilled spirits.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Receipt of distilled... BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DRAWBACK ON TAXPAID DISTILLED SPIRITS USED IN MANUFACTURING NONBEVERAGE PRODUCTS Records § 17.162 Receipt of distilled spirits. (a) Distilled spirits received in...

  16. Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

    OpenAIRE

    Schnoes, Alexandra M.; Ream, David C; Thorman, Alexander W.; Babbitt, Patricia C; Friedberg, Iddo

    2013-01-01

    The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here we investigate just how prevalent is the "few articles -- many proteins" phenomenon. We examine the experimentally val...

  17. Do Local Elites Capture Natural Disaster Reconstruction Funds?

    OpenAIRE

    Takasaki, Yoshito

    2011-01-01

    Using original survey data with rich, direct measures of local elites in rural Fiji, this article examines potential elite capture in the allocation of natural disaster reconstruction funds. Allocations of housing construction materials – both receipt and amount received – across villages, clans, and households are strongly targeted on cyclone damage, and local elites do not receive larger benefits over time. As the supply of reconstruction funds is limited during early periods, more severely...

  18. Omics data management and annotation.

    Science.gov (United States)

    Harel, Arye; Dalah, Irina; Pietrokovski, Shmuel; Safran, Marilyn; Lancet, Doron

    2011-01-01

    Technological Omics breakthroughs, including next generation sequencing, bring avalanches of data which need to undergo effective data management to ensure integrity, security, and maximal knowledge-gleaning. Data management system requirements include flexible input formats, diverse data entry mechanisms and views, user friendliness, attention to standards, hardware and software platform definition, as well as robustness. Relevant solutions elaborated by the scientific community include Laboratory Information Management Systems (LIMS) and standardization protocols facilitating data sharing and managing. In project planning, special consideration has to be made when choosing relevant Omics annotation sources, since many of them overlap and require sophisticated integration heuristics. The data modeling step defines and categorizes the data into objects (e.g., genes, articles, disorders) and creates an application flow. A data storage/warehouse mechanism must be selected, such as file-based systems and relational databases, the latter typically used for larger projects. Omics project life cycle considerations must include the definition and deployment of new versions, incorporating either full or partial updates. Finally, quality assurance (QA) procedures must validate data and feature integrity, as well as system performance expectations. We illustrate these data management principles with examples from the life cycle of the GeneCards Omics project (http://www.genecards.org), a comprehensive, widely used compendium of annotative information about human genes. For example, the GeneCards infrastructure has recently been changed from text files to a relational database, enabling better organization and views of the growing data. Omics data handling benefits from the wealth of Web-based information, the vast amount of public domain software, increasingly affordable hardware, and effective use of data management and annotation principles as outlined in this chapter

  19. Project Aloha:indexing, highlighting and annotation

    OpenAIRE

    Fallahkhair, Sanaz; Kennedy, Ian

    2010-01-01

    Lifelong learning requires many skills that are often not taught or are poorly taught. Such skills include speed reading, critical analysis, creative thinking, active reading and even a “little” skill like annotation. There are many ways that readers annotate. A short classification of some ways that reader may annotate includes underlining, using coloured highlighters, interlinear notes, marginal notes, and disassociated notes. This paper presents an investigation into the use of a tool for ...

  20. Automatic Multilevel Medical Image Annotation and Retrieval

    OpenAIRE

    Mueen, A.; Zainuddin, R.; Baba, M. Sapiyan

    2007-01-01

    Image retrieval at the semantic level mostly depends on image annotation or image classification. Image annotation performance largely depends on three issues: (1) automatic image feature extraction; (2) a semantic image concept modeling; (3) algorithm for semantic image annotation. To address first issue, multilevel features are extracted to construct the feature vector, which represents the contents of the image. To address second issue, domain-dependent concept hierarchy is constructed for...

  1. Knowledge Annotation maknig implicit knowledge explicit

    CERN Document Server

    Dingli, Alexiei

    2011-01-01

    Did you ever read something on a book, felt the need to comment, took up a pencil and scribbled something on the books' text'? If you did, you just annotated a book. But that process has now become something fundamental and revolutionary in these days of computing. Annotation is all about adding further information to text, pictures, movies and even to physical objects. In practice, anything which can be identified either virtually or physically can be annotated. In this book, we will delve into what makes annotations, and analyse their significance for the future evolutions of the web. We wil

  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. Calling on a million minds for community annotation in WikiProteins.

    Science.gov (United States)

    Mons, Barend; Ashburner, Michael; Chichester, Christine; van Mulligen, Erik; Weeber, Marc; den Dunnen, Johan; van Ommen, Gert-Jan; Musen, Mark; Cockerill, Matthew; Hermjakob, Henning; Mons, Albert; Packer, Abel; Pacheco, Roberto; Lewis, Suzanna; Berkeley, Alfred; Melton, William; Barris, Nickolas; Wales, Jimmy; Meijssen, Gerard; Moeller, Erik; Roes, Peter Jan; Borner, Katy; Bairoch, Amos

    2008-01-01

    WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org. PMID:18507872

  4. Calling on a million minds for community annotation in WikiProteins

    Science.gov (United States)

    Mons, Barend; Ashburner, Michael; Chichester, Christine; van Mulligen, Erik; Weeber, Marc; den Dunnen, Johan; van Ommen, Gert-Jan; Musen, Mark; Cockerill, Matthew; Hermjakob, Henning; Mons, Albert; Packer, Abel; Pacheco, Roberto; Lewis, Suzanna; Berkeley, Alfred; Melton, William; Barris, Nickolas; Wales, Jimmy; Meijssen, Gerard; Moeller, Erik; Roes, Peter Jan; Borner, Katy; Bairoch, Amos

    2008-01-01

    WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at . PMID:18507872

  5. The surplus value of semantic annotations

    NARCIS (Netherlands)

    M. Marx

    2010-01-01

    We compare the costs of semantic annotation of textual documents to its benefits for information processing tasks. Semantic annotation can improve the performance of retrieval tasks and facilitates an improved search experience through faceted search, focused retrieval, better document summaries, an

  6. Towards an event annotated corpus of Polish

    Directory of Open Access Journals (Sweden)

    Michał Marcińczuk

    2015-12-01

    Full Text Available Towards an event annotated corpus of PolishThe paper presents a typology of events built on the basis of TimeML specification adapted to Polish language. Some changes were introduced to the definition of the event categories and a motivation for event categorization was formulated. The event annotation task is presented on two levels – ontology level (language independent and text mentions (language dependant. The various types of event mentions in Polish text are discussed. A procedure for annotation of event mentions in Polish texts is presented and evaluated. In the evaluation a randomly selected set of documents from the Corpus of Wrocław University of Technology (called KPWr was annotated by two linguists and the annotator agreement was calculated. The evaluation was done in two iterations. After the first evaluation we revised and improved the annotation procedure. The second evaluation showed a significant improvement of the agreement between annotators. The current work was focused on annotation and categorisation of event mentions in text. The future work will be focused on description of event with a set of attributes, arguments and relations.

  7. DIMA – Annotation guidelines for German intonation

    DEFF Research Database (Denmark)

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis;

    2015-01-01

    easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were evaluated running an inter-annotator reliability study on three different speech styles (read speech, monologue and dialogue...

  8. Creating Gaze Annotations in Head Mounted Displays

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Qvarfordt, Pernilla

    To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annota- tion, ...

  9. Crowdsourcing and annotating NER for Twitter #drift

    DEFF Research Database (Denmark)

    Fromreide, Hege; Hovy, Dirk; Søgaard, Anders

    2014-01-01

    We present two new NER datasets for Twitter; a manually annotated set of 1,467 tweets (kappa=0.942) and a set of 2,975 expert-corrected, crowdsourced NER annotated tweets from the dataset described in Finin et al. (2010). In our experiments with these datasets, we observe two important points: (a...

  10. Annotation of regular polysemy and underspecification

    DEFF Research Database (Denmark)

    Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria

    2013-01-01

    We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...

  11. Harnessing Collaborative Annotations on Online Formative Assessments

    Science.gov (United States)

    Lin, Jian-Wei; Lai, Yuan-Cheng

    2013-01-01

    This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate…

  12. Manual Annotation of Translational Equivalence The Blinker Project

    CERN Document Server

    Melamed, I D

    1998-01-01

    Bilingual annotators were paid to link roughly sixteen thousand corresponding words between on-line versions of the Bible in modern French and modern English. These annotations are freely available to the research community from http://www.cis.upenn.edu/~melamed . The annotations can be used for several purposes. First, they can be used as a standard data set for developing and testing translation lexicons and statistical translation models. Second, researchers in lexical semantics will be able to mine the annotations for insights about cross-linguistic lexicalization patterns. Third, the annotations can be used in research into certain recently proposed methods for monolingual word-sense disambiguation. This paper describes the annotated texts, the specially-designed annotation tool, and the strategies employed to increase the consistency of the annotations. The annotation process was repeated five times by different annotators. Inter-annotator agreement rates indicate that the annotations are reasonably rel...

  13. Social Security Administration Percentage of Fast-Track Receipts

    Data.gov (United States)

    Social Security Administration — The dataset provides the percentage of fast-track receipts by state during the reporting fiscal year. Fast-tracked cases consist of those cases identified as Quick...

  14. Public Budget Database - Budget Authority and offsetting receipts 1976-Current

    Data.gov (United States)

    Executive Office of the President — This file contains historical budget authority and offsetting receipts for 1976 through the current budget year, as well as four years of projections. It can be...

  15. Public Budget Database - Outlays and offsetting receipts 1962-Current

    Data.gov (United States)

    Executive Office of the President — This file contains historical outlays and offsetting receipts for 1962 through the current budget year, as well as four years of projections. It can be used to...

  16. 19 CFR 24.3 - Bills and accounts; receipts.

    Science.gov (United States)

    2010-04-01

    ... account for money due the United States shall be rendered by an authorized Customs officer or employee on... constitute evidence of such payment to Customs. Should a payer desire evidence of receipt, both the...

  17. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  18. Concept annotation in the CRAFT corpus

    Directory of Open Access Journals (Sweden)

    Bada Michael

    2012-07-01

    Full Text Available Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released. Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. Conclusions As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens, our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection, the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are

  19. The GOA database: Gene Ontology annotation updates for 2015

    OpenAIRE

    Huntley, Rachael P; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria J.; O'Donovan, Claire

    2014-01-01

    The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480 000 taxonomic groups. The resource now provides annotat...

  20. A Common XML-based Framework for Syntactic Annotations

    CERN Document Server

    Ide, Nancy; Erjavec, Tomaz

    2009-01-01

    It is widely recognized that the proliferation of annotation schemes runs counter to the need to re-use language resources, and that standards for linguistic annotation are becoming increasingly mandatory. To answer this need, we have developed a framework comprised of an abstract model for a variety of different annotation types (e.g., morpho-syntactic tagging, syntactic annotation, co-reference annotation, etc.), which can be instantiated in different ways depending on the annotator's approach and goals. In this paper we provide an overview of the framework, demonstrate its applicability to syntactic annotation, and show how it can contribute to comparative evaluation of parser output and diverse syntactic annotation schemes.

  1. Annotating spatio-temporal datasets for meaningful analysis in the Web

    Science.gov (United States)

    Stasch, Christoph; Pebesma, Edzer; Scheider, Simon

    2014-05-01

    More and more environmental datasets that vary in space and time are available in the Web. This comes along with an advantage of using the data for other purposes than originally foreseen, but also with the danger that users may apply inappropriate analysis procedures due to lack of important assumptions made during the data collection process. In order to guide towards a meaningful (statistical) analysis of spatio-temporal datasets available in the Web, we have developed a Higher-Order-Logic formalism that captures some relevant assumptions in our previous work [1]. It allows to proof on meaningful spatial prediction and aggregation in a semi-automated fashion. In this poster presentation, we will present a concept for annotating spatio-temporal datasets available in the Web with concepts defined in our formalism. Therefore, we have defined a subset of the formalism as a Web Ontology Language (OWL) pattern. It allows capturing the distinction between the different spatio-temporal variable types, i.e. point patterns, fields, lattices and trajectories, that in turn determine whether a particular dataset can be interpolated or aggregated in a meaningful way using a certain procedure. The actual annotations that link spatio-temporal datasets with the concepts in the ontology pattern are provided as Linked Data. In order to allow data producers to add the annotations to their datasets, we have implemented a Web portal that uses a triple store at the backend to store the annotations and to make them available in the Linked Data cloud. Furthermore, we have implemented functions in the statistical environment R to retrieve the RDF annotations and, based on these annotations, to support a stronger typing of spatio-temporal datatypes guiding towards a meaningful analysis in R. [1] Stasch, C., Scheider, S., Pebesma, E., Kuhn, W. (2014): "Meaningful spatial prediction and aggregation", Environmental Modelling & Software, 51, 149-165.

  2. Making web annotations persistent over time

    Energy Technology Data Exchange (ETDEWEB)

    Sanderson, Robert [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory

    2010-01-01

    As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.

  3. Meteor showers an annotated catalog

    CERN Document Server

    Kronk, Gary W

    2014-01-01

    Meteor showers are among the most spectacular celestial events that may be observed by the naked eye, and have been the object of fascination throughout human history. In “Meteor Showers: An Annotated Catalog,” the interested observer can access detailed research on over 100 annual and periodic meteor streams in order to capitalize on these majestic spectacles. Each meteor shower entry includes details of their discovery, important observations and orbits, and gives a full picture of duration, location in the sky, and expected hourly rates. Armed with a fuller understanding, the amateur observer can better view and appreciate the shower of their choice. The original book, published in 1988, has been updated with over 25 years of research in this new and improved edition. Almost every meteor shower study is expanded, with some original minor showers being dropped while new ones are added. The book also includes breakthroughs in the study of meteor showers, such as accurate predictions of outbursts as well ...

  4. FolksAnnotation: A Semantic Metadata Tool for Annotating Learning Resources Using Folksonomies and Domain Ontologies

    OpenAIRE

    Hend S. Al-Khalifa; Davis, Hugh C.

    2006-01-01

    There are many resources on the Web which are suitable for educational purposes. Unfortunately the task of identifying suitable resources for a particular educational purpose is difficult as they have not typically been annotated with educational metadata. However, many resources have now been annotated in an unstructured manner within contemporary social bookmaking services. This paper describes a novel tool called ‘FolksAnnotation’ that creates annotations with educational semantics from th...

  5. SASL: A Semantic Annotation System for Literature

    Science.gov (United States)

    Yuan, Pingpeng; Wang, Guoyin; Zhang, Qin; Jin, Hai

    Due to ambiguity, search engines for scientific literatures may not return right search results. One efficient solution to the problems is to automatically annotate literatures and attach the semantic information to them. Generally, semantic annotation requires identifying entities before attaching semantic information to them. However, due to abbreviation and other reasons, it is very difficult to identify entities correctly. The paper presents a Semantic Annotation System for Literature (SASL), which utilizes Wikipedia as knowledge base to annotate literatures. SASL mainly attaches semantic to terminology, academic institutions, conferences, and journals etc. Many of them are usually abbreviations, which induces ambiguity. Here, SASL uses regular expressions to extract the mapping between full name of entities and their abbreviation. Since full names of several entities may map to a single abbreviation, SASL introduces Hidden Markov Model to implement name disambiguation. Finally, the paper presents the experimental results, which confirm SASL a good performance.

  6. Modeling Social Annotation: a Bayesian Approach

    CERN Document Server

    Plangprasopchok, Anon

    2008-01-01

    Collaborative tagging systems, such as del.icio.us, CiteULike, and others, allow users to annotate objects, e.g., Web pages or scientific papers, with descriptive labels called tags. The social annotations, contributed by thousands of users, can potentially be used to infer categorical knowledge, classify documents or recommend new relevant information. Traditional text inference methods do not make best use of socially-generated data, since they do not take into account variations in individual users' perspectives and vocabulary. In a previous work, we introduced a simple probabilistic model that takes interests of individual annotators into account in order to find hidden topics of annotated objects. Unfortunately, our proposed approach had a number of shortcomings, including overfitting, local maxima and the requirement to specify values for some parameters. In this paper we address these shortcomings in two ways. First, we extend the model to a fully Bayesian framework. Second, we describe an infinite ver...

  7. Annotation sémantique par classification

    OpenAIRE

    Toussaint, Yannick; Tenier, Sylvain

    2007-01-01

    Les systèmes actuels d'annotation sémantique exploitent peu les connaissances du domaine et fonctionnent essentiellement du texte vers l'ontologie. Pourtant, il est fréquent qu'un élément dans une page doive être annoté par un concept parce que certains autres éléments de cette même page sont annotés par d'autres concepts. Cet article propose une méthode d'annotation prenant en compte cette dépendance entre concepts, exprimée dans une ontologie sous forme de concepts définis. L'utilisation de...

  8. GRADUATE AND PROFESSIONAL EDUCATION, AN ANNOTATED BIBLIOGRAPHY.

    Science.gov (United States)

    HEISS, ANN M.; AND OTHERS

    THIS ANNOTATED BIBLIOGRAPHY CONTAINS REFERENCES TO GENERAL GRADUATE EDUCATION AND TO EDUCATION FOR THE FOLLOWING PROFESSIONAL FIELDS--ARCHITECTURE, BUSINESS, CLINICAL PSYCHOLOGY, DENTISTRY, ENGINEERING, LAW, LIBRARY SCIENCE, MEDICINE, NURSING, SOCIAL WORK, TEACHING, AND THEOLOGY. (HW)

  9. Supporting Multiple Perspectives on 3D Museum Artefacts through Interoperable Annotations

    OpenAIRE

    Hunter, Jane; Yu, Chih-Hao

    2010-01-01

    Increasing numbers of museums and cultural institutions are using 3D laser scanning techniques to preserve cultural artefacts as 3D digital models, that are then accessible to curators, scholars and the general public via Web interfaces to online galleries. Museums are finding the cost of providing metadata for such collections prohibitive and are keen to explore how they might exploit Web 2.0 social tagging and annotation services to capture community knowledge and enrich the contextual meta...

  10. Australian sea-floor survey data, with images and expert annotations

    OpenAIRE

    Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B.

    2015-01-01

    This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typic...

  11. Services for annotation of biomedical text

    OpenAIRE

    Hakenberg, Jörg

    2008-01-01

    Motivation: Text mining in the biomedical domain in recent years has focused on the development of tools for recognizing named entities and extracting relations. Such research resulted from the need for such tools as basic components for more advanced solutions. Named entity recognition, entity mention normalization, and relationship extraction now have reached a stage where they perform comparably to human annotators (considering inter--annotator agreement, measured in many studies to be aro...

  12. Multimedia Annotations on the Semantic Web

    OpenAIRE

    Stamou, G.; Ossenbruggen, J.R.; Pan, J; Schreiber, A.T.

    2006-01-01

    Multimedia in all forms (images, video, graphics, music, speech) is exploding on the Web. The content needs to be annotated and indexed to enable effective search and retrieval. However, recent standards and best practices for multimedia metadata don't provide semantically rich descriptions of multimedia content. On the other hand, the World Wide Web Consortium's (W3C's) Semantic Web effort has been making great progress in advancing techniques for annotating semantics of Web resources. To br...

  13. Fluid Annotations in a Open World

    DEFF Research Database (Denmark)

    Zellweger, Polle Trescott; Bouvin, Niels Olof; Jehøj, Henning;

    2001-01-01

    Fluid Documents use animated typographical changes to provide a novel and appealing user experience for hypertext browsing and for viewing document annotations in context. This paper describes an effort to broaden the utility of Fluid Documents by using the open hypermedia Arakne Environment to l...... layer fluid annotations and links on top of abitrary HTML pages on the World Wide Web. Changes to both Fluid Documents and Arakne are required....

  14. Learning Object Annotation for Agricultural Learning Repositories

    OpenAIRE

    Ebner, Hannes; Manouselis, Nikos; Palmér, Matthias; Enoksson, Fredrik; Palavitsinis, Nikos; Kastrantas, Kostas; Naeve, Ambjörn

    2009-01-01

    This paper introduces a Web-based tool that has been developed to facilitate learning object annotation in agricultural learning repositories with IEEE LOM-compliant metadata. More specifically, it presents how an application profile of the IEEE LOM standard has been developed for the description of learning objects on organic agriculture and agroecology. Then, it describes the design and prototype development of the Organic.Edunet repository tool: a Web-based for annotating learning objects ...

  15. Instantiation of relations for semantic annotation

    OpenAIRE

    Tenier, Sylvain; Toussaint, Yannick; Napoli, Amedeo; Polanco, Xavier

    2006-01-01

    This paper presents a methodology for the semantic annotation of web pages with individuals of a domain ontology. While most semantic annotation systems can recognize knowledge units, they usually do not establish explicit relations between them. The method presented identifies the individuals which should be related among the whole set of individuals and codes them as role instances within an OWL ontology. This is done by using a correspondence between the tree structure of a web page and th...

  16. Instructions for Temporal Annotation of Scheduling Dialogs

    OpenAIRE

    O'Hara, Tom; Wiebe, Janyce; Payne, Karen

    1997-01-01

    Human annotation of natural language facilitates standardized evaluation of natural language processing systems and supports automated feature extraction. This document consists of instructions for annotating the temporal information in scheduling dialogs, dialogs in which the participants schedule a meeting with one another. Task-oriented dialogs, such as these are, would arise in many useful applications, for instance, automated information providers and automated phone operators. Explicit ...

  17. DIMA – Annotation guidelines for German intonation

    OpenAIRE

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis; Baumann, Stefan; Braun, Bettina; Grice, Martine; Jannedy, Stefanie; Michalsky, Jan; Niebuhr, Oliver; Peters, Jörg; Ritter, Simon; Röhr, Christine T.; Schweitzer, Antje; Schweitzer, Katrin; Wagner, Petra

    2015-01-01

    This paper presents newly developed guidelines for prosodic annotation of German as a consensus system agreed upon by German intonologists. The DIMA system is rooted in the framework of autosegmental-metrical phonology. One important goal of the consensus is to make exchanging data between groups easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were e...

  18. Facilitating functional annotation of chicken microarray data

    OpenAIRE

    Buza, Teresia J; Kumar, Ranjit; Gresham, Cathy R; Burgess, Shane C.; McCarthy, Fiona M

    2009-01-01

    Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually...

  19. Annotating Honorifics Denoting Social Ranking of Referents

    OpenAIRE

    Nariyama, Shigeko; Nakaiwa, Hiromi; Siegel, Melanie

    2011-01-01

    This paper proposes an annotating scheme that encodes honorifics (respectful words). Honorifics are used extensively in Japanese, reflecting the social relationship (e.g. social ranks and age) of the referents. This referential information is vital for resolving zero pronouns and improving machine translation outputs. Annotating honorifics is a complex task that involves identifying a predicate with honorifics, assigning ranks to referents of the predicate, calibrating the ranks, and co...

  20. Related Documents Search Using User Created Annotations

    Directory of Open Access Journals (Sweden)

    Jakub Sevcech

    2013-01-01

    Full Text Available We often use various services for creating bookmarks,tags, highlights and other types of annotations while surf-ing the Internet or when reading electronic documentsas well. These services allows us to create a number oftypes of annotation that we are commonly creating intoprinted documents. Annotations attached to electronicdocuments however can be used for other purposes suchas navigation support, text summarization etc. We pro-posed a method for searching related documents to cur-rently studied document using annotations created by thedocument reader as indicators of user's interest in par-ticular parts of the document. The method is based onspreading activation in text transformed into graph. Forevaluation we created a service called Annota, which al-lows users to insert various types of annotations into webpages and PDF documents displayed in the web browser.We analyzed properties of various types of annotations in-serted by users of Annota into documents. Based on thesewe evaluated our method by simulation and we comparedit against commonly used TF-IDF based method.

  1. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  2. Determination of cost effective waste management system receipt rates

    International Nuclear Information System (INIS)

    A comprehensive logistics and cost analysis has been carried out to determine if there are potential benefits to the high-level waste management system for receipt rates other than the current 3000 MTU/yr design-basis. The analysis includes both a Repository-Only System and a Storage-Only System. Repository startup dates of 2010 and 2015 and MRS startup dates of 1988 and three years prior to the repository have been evaluated. Receipt rates ranging from 1,500 to 6, 000 MTU/yr have been considered. Higher receipt rates appear to be economically justified, for either system, minimum costs are found at a repository receipt rate of 6000 MTU/yr. However, the MRS receipt rate for minimum system costs depends on the MRS startup date. With a 1988 MRS and a 2010 repository, the added cost of providing the MRS is offset by at-reactor storage cost reductions and the total system cost of $10.0 billion is virtually the same as for the repository- only system. 9 refs., 8 figs., 3 tabs

  3. An annotation based approach to support design communication

    CERN Document Server

    Hisarciklilar, Onur

    2007-01-01

    The aim of this paper is to propose an approach based on the concept of annotation for supporting design communication. In this paper, we describe a co-operative design case study where we analyse some annotation practices, mainly focused on design minutes recorded during project reviews. We point out specific requirements concerning annotation needs. Based on these requirements, we propose an annotation model, inspired from the Speech Act Theory (SAT) to support communication in a 3D digital environment. We define two types of annotations in the engineering design context, locutionary and illocutionary annotations. The annotations we describe in this paper are materialised by a set of digital artefacts, which have a semantic dimension allowing express/record elements of technical justifications, traces of contradictory debates, etc. In this paper, we first clarify the semantic annotation concept, and we define general properties of annotations in the engineering design context, and the role of annotations in...

  4. Hybrid Generative/Discriminative Learning for Automatic Image Annotation

    CERN Document Server

    Yang, Shuang Hong; Zha, Hongyuan

    2012-01-01

    Automatic image annotation (AIA) raises tremendous challenges to machine learning as it requires modeling of data that are both ambiguous in input and output, e.g., images containing multiple objects and labeled with multiple semantic tags. Even more challenging is that the number of candidate tags is usually huge (as large as the vocabulary size) yet each image is only related to a few of them. This paper presents a hybrid generative-discriminative classifier to simultaneously address the extreme data-ambiguity and overfitting-vulnerability issues in tasks such as AIA. Particularly: (1) an Exponential-Multinomial Mixture (EMM) model is established to capture both the input and output ambiguity and in the meanwhile to encourage prediction sparsity; and (2) the prediction ability of the EMM model is explicitly maximized through discriminative learning that integrates variational inference of graphical models and the pairwise formulation of ordinal regression. Experiments show that our approach achieves both su...

  5. Algae from the arid southwestern United States: an annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, W.H.; Gaines, S.R.

    1983-06-01

    Desert algae are attractive biomass producers for capturing solar energy through photosynthesis of organic matter. They are probably capable of higher yields and efficiencies of light utilization than higher plants, and are already adapted to extremes of sunlight intensity, salinity and temperature such as are found in the desert. This report consists of an annotated bibliography of the literature on algae from the arid southwestern United States. It was prepared in anticipation of efforts to isolate desert algae and study their yields in the laboratory. These steps are necessary prior to setting up outdoor algal culture ponds. Desert areas are attractive for such applications because land, sunlight, and, to some extent, water resources are abundant there. References are sorted by state.

  6. The Annotation of RNA Motifs

    Directory of Open Access Journals (Sweden)

    Eric Westhof

    2006-04-01

    Full Text Available The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s. The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a decomposition of each motif into non-Watson–Crick base-pairs; (b geometric classification of each basepair; (c identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e acceptance or rejection of the null hypothesis that the motif is conserved.

  7. GOAnnotator: linking protein GO annotations to evidence text

    OpenAIRE

    Couto, Francisco M.; Silva, Mário J.; Lee, Vivian; Dimmer, Emily; Camon, Evelyn; Apweiler, Rolf; Kirsch, Harald; Rebholz-Schuhmann, Dietrich

    2006-01-01

    Background Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators. Results In this paper we describe an ...

  8. Web Database Query Interface Annotation Based on User Collaboration

    Institute of Scientific and Technical Information of China (English)

    LIU Wei; LIN Can; MENG Xiaofeng

    2006-01-01

    A vision based query interface annotation method is used to relate attributes and form elements in form-based web query interfaces, this method can reach accuracy of 82%.And a user participation method is used to tune the result; user can answer "yes" or "no" for existing annotations, or manually annotate form elements.Mass feedback is added to the annotation algorithm to produce more accurate result.By this approach, query interface annotation can reach a perfect accuracy.

  9. 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.

  10. Gene Ontology annotations at SGD: new data sources and annotation methods.

    Science.gov (United States)

    Hong, Eurie L; Balakrishnan, Rama; Dong, Qing; Christie, Karen R; Park, Julie; Binkley, Gail; Costanzo, Maria C; Dwight, Selina S; Engel, Stacia R; Fisk, Dianna G; Hirschman, Jodi E; Hitz, Benjamin C; Krieger, Cynthia J; Livstone, Michael S; Miyasato, Stuart R; Nash, Robert S; Oughtred, Rose; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Zhu, Kathy K; Dolinski, Kara; Botstein, David; Cherry, J Michael

    2008-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

  11. 78 FR 75905 - Credit for Increasing Research Activities: Intra-Group Gross Receipts

    Science.gov (United States)

    2013-12-13

    ...) affects the computation of gross receipts resulting from intra-group transactions between domestic... product to a customer in a transaction that does not give rise to gross receipts effectively connected... domestic member are included, but its gross receipts from the sale to the foreign corporate member are...

  12. Expanding Post-Harvest Finance Through Warehouse Receipts and Related Instruments

    OpenAIRE

    Baldwin, Marisa; Bryla, Erin; Langenbucher, Anja

    2006-01-01

    Warehouse receipt financing and similar types of collateralized lending provide an alternative to traditional lending requirements of banks and other financiers and could provide opportunities to expand this lending in emerging economies for agricultural trade. The main contents include: what is warehouse receipt financing; what is the value of warehouse receipt financing; other collater...

  13. 27 CFR 31.61 - Single sale of liquors or warehouse receipts.

    Science.gov (United States)

    2010-04-01

    ... warehouse receipts. 31.61 Section 31.61 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND... Persons Who Are Not Dealers in Liquors Or Beer § 31.61 Single sale of liquors or warehouse receipts. A single sale of distilled spirits, wines, or beer, or a single sale of one or more warehouse receipts...

  14. MPEG-7 based video annotation and browsing

    Science.gov (United States)

    Hoeynck, Michael; Auweiler, Thorsten; Wellhausen, Jens

    2003-11-01

    The huge amount of multimedia data produced worldwide requires annotation in order to enable universal content access and to provide content-based search-and-retrieval functionalities. Since manual video annotation can be time consuming, automatic annotation systems are required. We review recent approaches to content-based indexing and annotation of videos for different kind of sports and describe our approach to automatic annotation of equestrian sports videos. We especially concentrate on MPEG-7 based feature extraction and content description, where we apply different visual descriptors for cut detection. Further, we extract the temporal positions of single obstacles on the course by analyzing MPEG-7 edge information. Having determined single shot positions as well as the visual highlights, the information is jointly stored with meta-textual information in an MPEG-7 description scheme. Based on this information, we generate content summaries which can be utilized in a user-interface in order to provide content-based access to the video stream, but further for media browsing on a streaming server.

  15. Automated analysis and annotation of basketball video

    Science.gov (United States)

    Saur, Drew D.; Tan, Yap-Peng; Kulkarni, Sanjeev R.; Ramadge, Peter J.

    1997-01-01

    Automated analysis and annotation of video sequences are important for digital video libraries, content-based video browsing and data mining projects. A successful video annotation system should provide users with useful video content summary in a reasonable processing time. Given the wide variety of video genres available today, automatically extracting meaningful video content for annotation still remains hard by using current available techniques. However, a wide range video has inherent structure such that some prior knowledge about the video content can be exploited to improve our understanding of the high-level video semantic content. In this paper, we develop tools and techniques for analyzing structured video by using the low-level information available directly from MPEG compressed video. Being able to work directly in the video compressed domain can greatly reduce the processing time and enhance storage efficiency. As a testbed, we have developed a basketball annotation system which combines the low-level information extracted from MPEG stream with the prior knowledge of basketball video structure to provide high level content analysis, annotation and browsing for events such as wide- angle and close-up views, fast breaks, steals, potential shots, number of possessions and possession times. We expect our approach can also be extended to structured video in other domains.

  16. Video Screen Capture Basics

    Science.gov (United States)

    Dunbar, Laura

    2014-01-01

    This article is an introduction to video screen capture. Basic information of two software programs, QuickTime for Mac and BlueBerry Flashback Express for PC, are also discussed. Practical applications for video screen capture are given.

  17. Critical Assessment of Function Annotation Meeting, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Friedberg, Iddo

    2015-01-21

    The Critical Assessment of Function Annotation meeting was held July 14-15, 2011 at the Austria Conference Center in Vienna, Austria. There were 73 registered delegates at the meeting. We thank the DOE for this award. It helped us organize and support a scientific meeting AFP 2011 as a special interest group (SIG) meeting associated with the ISMB 2011 conference. The conference was held in Vienna, Austria, in July 2011. The AFP SIG was held on July 15-16, 2011 (immediately preceding the conference). The meeting consisted of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component provided a large-scale assessment of computational methods through participation in the Critical Assessment of Functional Annotation (CAFA).

  18. 77 FR 40375 - Receipt of Applications for Endangered Species Permits

    Science.gov (United States)

    2012-07-09

    ... (Nicrophorus americanus) for the purpose of scientific study and species recovery efforts. These activities... Fish and Wildlife Service Receipt of Applications for Endangered Species Permits AGENCY: Fish and... public to comment on the following applications to conduct certain activities with endangered...

  19. 78 FR 56924 - Receipt of Applications for Endangered Species Permits

    Science.gov (United States)

    2013-09-16

    ... the purpose of conducting presence/absence/population surveys and assisting in species recovery... Fish and Wildlife Service Receipt of Applications for Endangered Species Permits AGENCY: Fish and... public to comment on the following applications to conduct certain activities with endangered...

  20. 75 FR 31812 - Receipt of Applications for Endangered Species Permits

    Science.gov (United States)

    2010-06-04

    ... recovery efforts, Alabama beach mouse (Peromyscus polionotus ammobates), and three species of sea turtles... Fish and Wildlife Service Receipt of Applications for Endangered Species Permits AGENCY: Fish and... public to comment on the following applications to conduct certain activities with ] endangered...

  1. 78 FR 9067 - Receipt of Applications for Endangered Species Permits

    Science.gov (United States)

    2013-02-07

    ... assisting in species recovery efforts. These activities will be conducted in Escambia and Walton Counties... purpose of scientific research and species recovery. These activities will occur in North Carolina. Permit... Fish and Wildlife Service Receipt of Applications for Endangered Species Permits AGENCY: Fish...

  2. 77 FR 51819 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2012-08-27

    ... identified tasks and mandates of the recovery program for this species. This notification covers activities... Fish and Wildlife Service Endangered Species; Receipt of Applications for Permit AGENCY: Fish and... certain activities with endangered species. With some exceptions, the Endangered Species Act...

  3. 76 FR 14985 - Endangered Species; Receipt of Applications for Permit

    Science.gov (United States)

    2011-03-18

    ... Species Applicant: Tom Stehn, Whooping Crane Recovery Plan Coordinator, U.S. Fish and Wildlife Service... Fish and Wildlife Service Endangered Species; Receipt of Applications for Permit AGENCY: Fish and... certain activities with endangered species. With some exceptions, the Endangered Species Act...

  4. 77 FR 69824 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2012-11-21

    ... Register a notice of receipt of a premanufacture notice (PMN) or an application for a test marketing... under TSCA section 5(a), for ``test marketing'' purposes, which is referred to as a test marketing... linseed oil. P-12-0235 10/2/2012 9/20/2012 (G) Polyesterurethane. P-12-0392 10/5/2012 10/4/2012 (G) Mix...

  5. 77 FR 3288 - Receipt of Request for Action

    Science.gov (United States)

    2012-01-23

    ... [Federal Register Volume 77, Number 14 (Monday, January 23, 2012)] [Notices] [Page 3288] [FR Doc No: 2012-1213] NUCLEAR REGULATORY COMMISSION [NRC-2012-0004] Receipt of Request for Action Notice is..., Deputy Director for Reactor Safety Programs, Office of Nuclear Reactor Regulation. [FR Doc....

  6. 76 FR 40406 - Receipt of Request for Action

    Science.gov (United States)

    2011-07-08

    ... COMMISSION Receipt of Request for Action Notice is hereby given that by petition dated March 12, 2011, Thomas Saporito (petitioner) has requested that the Nuclear Regulatory Commission (NRC) take action to order... of Nuclear Reactor Regulation (NRR). As provided by Section 2.206, appropriate action will be...

  7. 77 FR 143 - Receipt of Request for Action

    Science.gov (United States)

    2012-01-03

    ... COMMISSION Receipt of Request for Action Notice is hereby given that by petition dated April 13, 2011, Paul... action to immediately suspend the operating licenses of General Electric boiling water reactors with Mark... ``petitioners.'' In their petition, the petitioners request: enforcement action to ensure that the public...

  8. 76 FR 72009 - Receipt of Request for Action

    Science.gov (United States)

    2011-11-21

    ... COMMISSION Receipt of Request for Action Notice is hereby given that by petition dated July 29, 2011, David...) take action to issue a Demand for Information (DFI) of all boiling-water reactor nuclear power reactors... of Nuclear Reactor Regulation (NRR). As provided by Section 2.206, appropriate action will be...

  9. 26 CFR 1.199-3 - Domestic production gross receipts.

    Science.gov (United States)

    2010-04-01

    ... order. With respect to a particular order by a customer of 100 television sets, some were manufactured... gross receipts derived from the MPGE of QPP to qualify as DPGR. (2) Packaging, repackaging, labeling, or... taxpayer engages in no other MPGE activity with respect to that QPP, the taxpayer's packaging,...

  10. Radiative electron capture

    International Nuclear Information System (INIS)

    Some data are presented for radiative electron capture by fast moving ions. The radiative electron capture spectrum is shown for O8+ in Ag, along with the energy dependence of the capture cross-section. A discrepancy between earlier data, theoretical prediction, and the present data is pointed out. (3 figs) (U.S.)

  11. An Annotated Dataset of 14 Meat Images

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille

    2002-01-01

    This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given.......This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given....

  12. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  13. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.

    Science.gov (United States)

    Mutowo-Meullenet, Prudence; Huntley, Rachael P; Dimmer, Emily C; Alam-Faruque, Yasmin; Sawford, Tony; Jesus Martin, Maria; O'Donovan, Claire; Apweiler, Rolf

    2013-01-01

    The Gene Ontology (GO) is the de facto standard for the functional description of gene products, providing a consistent, information-rich terminology applicable across species and information repositories. The UniProt Consortium uses both manual and automatic GO annotation approaches to curate UniProt Knowledgebase (UniProtKB) entries. The selection of a protein set prioritized for manual annotation has implications for the characteristics of the information provided to users working in a specific field or interested in particular pathways or processes. In this article, we describe an organelle-focused, manual curation initiative targeting proteins from the human peroxisome. We discuss the steps taken to define the peroxisome proteome and the challenges encountered in defining the boundaries of this protein set. We illustrate with the use of examples how GO annotations now capture cell and tissue type information and the advantages that such an annotation approach provides to users. Database URL: http://www.ebi.ac.uk/GOA/ and http://www.uniprot.org. PMID:23327938

  14. Capture Their Attention: Capturing Lessons Using Screen Capture Software

    Science.gov (United States)

    Drumheller, Kristina; Lawler, Gregg

    2011-01-01

    When students miss classes for university activities such as athletic and academic events, they inevitably miss important class material. Students can get notes from their peers or visit professors to find out what they missed, but when students miss new and challenging material these steps are sometimes not enough. Screen capture and recording…

  15. Annotation Method (AM): SE22_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ether with predicted molecular formulae and putative structures, were provided as metabolite annotations. Comparison with public data...bases was performed. A grading system was introduced to describe the evidence supporting the annotations. ...

  16. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  17. Multicultural Education: A Selected Annotated Bibliography.

    Science.gov (United States)

    Mathieson, Moira B.; Tatis, Rita M.

    This annotated bibliography lists 70 documents dealing with cultural differences and cross-cultural educational problems on the elementary-secondary-collegiate level and does not include material on the economically disadvantaged or inner city problems as such. The first section reports citations drawn from Research in Education and the…

  18. Semantic Annotation to Support Automatic Taxonomy Classification

    DEFF Research Database (Denmark)

    Kim, Sanghee; Ahmed, Saeema; Wallace, Ken

    2006-01-01

    This paper presents a new taxonomy classification method that generates classification criteria from a small number of important sentences identified through semantic annotations, e.g. cause-effect. Rhetorical Structure Theory (RST) is used to discover the semantics (Mann et al. 1988). Specifically...

  19. Reflective Annotations: On Becoming a Scholar

    Science.gov (United States)

    Alexander, Mark; Taylor, Caroline; Greenberger, Scott; Watts, Margie; Balch, Riann

    2012-01-01

    This article presents the authors' reflective annotations on becoming a scholar. This paper begins with a discussion on socialization for teaching, followed by a discussion on socialization for service and sense of belonging. Then, it describes how the doctoral process evolves. Finally, it talks about adult learners who pursue doctoral education.

  20. Annotated Bibliography of EDGE2D Use

    International Nuclear Information System (INIS)

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables

  1. Statistical mechanics of ontology based annotations

    CERN Document Server

    Hoyle, David C

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotate...

  2. Statistical mechanics of ontology based annotations

    Science.gov (United States)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  3. Studies of Scientific Disciplines. An Annotated Bibliography.

    Science.gov (United States)

    Weisz, Diane; Kruytbosch, Carlos

    Provided in this bibliography are annotated lists of social studies of science literature, arranged alphabetically by author in 13 disciplinary areas. These areas include astronomy; general biology; biochemistry and molecular biology; biomedicine; chemistry; earth and space sciences; economics; engineering; mathematics; physics; political science;…

  4. Food Habits: A Selected Annotated Bibliography

    Science.gov (United States)

    Wilson, Christine S.

    1973-01-01

    This is a selective annotated bibliography of material on food habits and factors affecting them, published during the period 1928-1972. References are mainly in English, although a few in European languages are included, and represent information primarily from scholarly and professional journals. Entries are organized by subject and author. (LK)

  5. An Annotated Publications List on Homelessness.

    Science.gov (United States)

    Tutunjian, Beth Ann

    This annotated publications list on homelessness contains citations for 19 publications, most of which deal with problems of alcohol or drug abuse among homeless persons. Citations are listed alphabetically by author and cover the topics of homelessness and alcoholism, drug abuse, public policy, research methodologies, mental illness, alcohol- and…

  6. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  7. Law in the Classroom. An Annotated Bibliography.

    Science.gov (United States)

    Carsello, Carmen J.

    An annotated bibliography of some 236 items relevant to discussions of school law, from novels to government-published law and court reports. The material is listed alphabetically by author within each document type (books; periodicals; documents; monographs and special reports; law reports; digests; newsletters; dictionaries, directories, and…

  8. Organizational and Intercultural Communication: An Annotated Bibliography.

    Science.gov (United States)

    Constantinides, Helen; St. Amant, Kirk; Kampf, Connie

    2001-01-01

    Presents a 27-item annotated bibliography that overviews theories of organization from the viewpoint of culture, using five themes of organizational research as a framework. Notes that each section introduces specific theories of international, intercultural, or organizational communication, building upon them through a series of related articles,…

  9. Teleconferencing, an annotated bibliography, volume 3

    Science.gov (United States)

    Shervis, K.

    1971-01-01

    In this annotated and indexed listing of works on teleconferencing, emphasis has been placed upon teleconferencing as real-time, two way audio communication with or without visual aids. However, works on the use of television in two-way or multiway nets, data transmission, regional communications networks and on telecommunications in general are also included.

  10. Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  11. Automating Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  12. Kwanzaa: A Selective Annotated Bibliography for Teachers.

    Science.gov (United States)

    Dupree, Sandra K., Comp.; Gillum, Holly A., Comp.

    This annotated bibliography about Kwanzaa, an end-of-the-year holiday that emphasizes an appreciation for the culture of African Americans, aims to provide ready access to information for classroom teachers. Noting that Kwanzaa (celebrated from December 26 to January 1) is an important cultural event, the bibliography states that the festival…

  13. Skin Cancer Education Materials: Selected Annotations.

    Science.gov (United States)

    National Cancer Inst. (NIH), Bethesda, MD.

    This annotated bibliography presents 85 entries on a variety of approaches to cancer education. The entries are grouped under three broad headings, two of which contain smaller sub-divisions. The first heading, Public Education, contains prevention and general information, and non-print materials. The second heading, Professional Education,…

  14. College Students in Transition: An Annotated Bibliography

    Science.gov (United States)

    Foote, Stephanie M., Ed.; Hinkle, Sara M., Ed.; Kranzow, Jeannine, Ed.; Pistilli, Matthew D., Ed.; Miles, LaTonya Rease, Ed.; Simmons, Jannell G., Ed.

    2013-01-01

    The transition from high school to college is an important milestone, but it is only one of many steps in the journey through higher education. This volume is an annotated bibliography of the emerging literature examining the many other transitions students make beyond the first year, including the sophomore year, the transfer experience, and the…

  15. Annotated Bibliography of EDGE2D Use

    Energy Technology Data Exchange (ETDEWEB)

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  16. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    Energy Technology Data Exchange (ETDEWEB)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  17. Classes d'annotation pour l'annotation sémantique

    OpenAIRE

    Tenier, Sylvain; Toussaint, Yannick

    2007-01-01

    Les classes d'annotation constituent une méthode d'annotation sémantique de pages web fondée sur les logiques de descriptions. Elles désignent l'annotation à la fois comme processus et comme résultat de ce processus. Cette approche est motivée par un parallèle entre la structure d'une page web et la sémantique qui lui est associée. Ces deux dimensions de structure et de sémantique sont formalisées en OWL-DL, un langage fondé sur les logiques de descriptions. L'annotation est ensuite traitée c...

  18. Ontology Learning and Semantic Annotation: a Necessary Symbiosis

    OpenAIRE

    Giovannetti, Emiliano; Marchi, Simone; Montemagni, Simonetta; Bartolini, Roberto

    2008-01-01

    Semantic annotation of text requires the dynamic merging of linguistically structured information and a ?world model?, usually represented as a domain-specific ontology. On the other hand, the process of engineering a domain-ontology through semi-automatic ontology learning system requires the availability of a considerable amount of semantically annotated documents. Facing this bootstrapping paradox requires an incremental process of annotation-acquisition-annotation, whereby domain-specific...

  19. SURFACE: a database of protein surface regions for functional annotation

    OpenAIRE

    Ferrè, Fabrizio; Ausiello, Gabriele; Zanzoni, Andreas; Helmer-Citterich, Manuela

    2004-01-01

    The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated, URL http://cbm.bio.uniroma2.it/surface/) database is a repository of annotated and compared protein surface regions. SURFACE contains the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-der...

  20. A unified representation for morphological, syntactic, semantic, and referential annotations

    OpenAIRE

    Hinrichs, Erhard W.; Kübler, Sandra; Naumann, Karin

    2008-01-01

    This paper reports on the SYN-RA (SYNtax-based Reference Annotation) project, an on-going project of annotating German newspaper texts with referential relations. The project has developed an inventory of anaphoric and coreference relations for German in the context of a unified, XML-based annotation scheme for combining morphological, syntactic, semantic, and anaphoric information. The paper discusses how this unified annotation scheme relates to other formats currently discussed in the lite...

  1. AnnaBot: A Static Verifier for Java Annotation Usage

    OpenAIRE

    Ian Darwin

    2010-01-01

    This paper describes AnnaBot, one of the first tools to verify correct use of Annotation-based metadata in the Java programming language. These Annotations are a standard Java 5 mechanism used to attach metadata to types, methods, or fields without using an external configuration file. A binary representation of the Annotation becomes part of the compiled “.class” file, for inspection by another component or library at runtime. Java Annotations were introduced into the Java language in 2004 a...

  2. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal Matoq Saeed

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  3. ePIANNO: ePIgenomics ANNOtation tool.

    Science.gov (United States)

    Liu, Chia-Hsin; Ho, Bing-Ching; Chen, Chun-Ling; Chang, Ya-Hsuan; Hsu, Yi-Chiung; Li, Yu-Cheng; Yuan, Shin-Sheng; Huang, Yi-Huan; Chang, Chi-Sheng; Li, Ker-Chau; Chen, Hsuan-Yu

    2016-01-01

    Recently, with the development of next generation sequencing (NGS), the combination of chromatin immunoprecipitation (ChIP) and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html). ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project) and gene-disease association information of GWAS (NHGRI) with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics) data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies. PMID:26859295

  4. ePIANNO: ePIgenomics ANNOtation tool.

    Directory of Open Access Journals (Sweden)

    Chia-Hsin Liu

    Full Text Available Recently, with the development of next generation sequencing (NGS, the combination of chromatin immunoprecipitation (ChIP and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html. ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project and gene-disease association information of GWAS (NHGRI with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies.

  5. Automatic annotation of head velocity and acceleration in Anvil

    DEFF Research Database (Denmark)

    Jongejan, Bart

    2012-01-01

    We describe an automatic face tracker plugin for the ANVIL annotation tool. The face tracker produces data for velocity and for acceleration in two dimensions. We compare the annotations generated by the face tracking algorithm with independently made manual annotations for head movements. The...

  6. Overriding auditory attentional capture.

    Science.gov (United States)

    Dalton, Polly; Lavie, Nilli

    2007-02-01

    Attentional capture by color singletons during shape search can be eliminated when the target is not a feature singleton (Bacon & Egeth, 1994). This suggests that a "singleton detection" search strategy must be adopted for attentional capture to occur. Here we find similar effects on auditory attentional capture. Irrelevant high-intensity singletons interfered with an auditory search task when the target itself was also a feature singleton. However, singleton interference was eliminated when the target was not a singleton (i.e., when nontargets were made heterogeneous, or when more than one target sound was presented). These results suggest that auditory attentional capture depends on the observer's attentional set, as does visual attentional capture. The suggestion that hearing might act as an early warning system that would always be tuned to unexpected unique stimuli must therefore be modified to accommodate these strategy-dependent capture effects. PMID:17557587

  7. Neutron Capture Nucleosynthesis

    OpenAIRE

    Kiss, Miklos

    2016-01-01

    Heavy elements (beyond iron) are formed in neutron capture nucleosynthesis processes. We have proposed a simple unified model to investigate the neutron capture nucleosynthesis in arbitrary neutron density environment. We have also investigated what neutron density is required to reproduce the measured abundance of nuclei assuming equilibrium processes. We found both of these that the medium neutron density has a particularly important role at neutron capture nucleosynthesis. About these resu...

  8. Overriding auditory attentional capture

    OpenAIRE

    Dalton, Polly; Lavie, Nilli

    2007-01-01

    Attentional capture by color singletons during shape search can be eliminated when the target is not a feature singleton (Bacon & Egeth, 1994). This suggests that a "singleton detection" search strategy must be adopted for attentional capture to occur. Here we find similar effects on auditory attentional capture. Irrelevant high-intensity singletons interfered with an auditory search task when the target itself was also a feature singleton. However, singleton interference was eliminated when ...

  9. Neutron Capture Nucleosynthesis

    CERN Document Server

    Kiss, Miklos

    2016-01-01

    Heavy elements (beyond iron) are formed in neutron capture nucleosynthesis processes. We have proposed a simple unified model to investigate the neutron capture nucleosynthesis in arbitrary neutron density environment. We have also investigated what neutron density is required to reproduce the measured abundance of nuclei assuming equilibrium processes. We found both of these that the medium neutron density has a particularly important role at neutron capture nucleosynthesis. About these results most of the nuclei can formed at medium neutron capture density environment e.g. in some kind of AGB stars. Besides these observations our model is capable to use educational purpose.

  10. Annotations and the Collaborative Digital Library: Effects of an Aligned Annotation Interface on Student Argumentation and Reading Strategies

    Science.gov (United States)

    Wolfe, Joanna

    2008-01-01

    Recent research on annotation interfaces provides provocative evidence that anchored, annotation-based discussion environments may lead to better conversations about a text. However, annotation interfaces raise complicated tradeoffs regarding screen real estate and positioning. It is argued that solving this screen real estate problem requires…

  11. Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.

    Science.gov (United States)

    Schnoes, Alexandra M; Ream, David C; Thorman, Alexander W; Babbitt, Patricia C; Friedberg, Iddo

    2013-01-01

    The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here, we investigate just how prevalent is the "few articles - many proteins" phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments. PMID:23737737

  12. Using Hausdorff Distance for New Medical Image Annotation

    CERN Document Server

    Bouslimi, Riadh

    2012-01-01

    Medical images annotation is most of the time a repetitive hard task. Collecting old similar annotations and assigning them to new medical images may not only enhance the annotation process, but also reduce ambiguity caused by repetitive annotations. The goal of this work is to propose an approach based on Hausdorff distance able to compute similarity between a new medical image and old stored images. User has to choose then one of the similar images and annotations related to the selected one are assigned to the new one.

  13. CONSIDERATIONS ON THE TRENDS OF INTERNATIONAL TOURISM RECEIPTS

    Directory of Open Access Journals (Sweden)

    Agatha POPESCU

    2014-12-01

    Full Text Available The paper aimed to analyze the evolution of tourism receipts at world level and by geographical area and in the main countries of tourist interest. In the period 1980-2012, the tourism income increased 10.14 times. In 2012, it accounted for USD Billion 1,075, to which Europe contributed by 42.58 %, Asia and the Pacific by 30.13 % and the Americas by 19.77 %. The USA, Spain, France, China, Macau, Italy, Germany, United Kingdom, Hong Kong and Australia are the top 10 countries according to the receipts, earning USD Billion 508.8, which represented 47.55 % of the world tourism income in 2012. The European countries with the highest contribution to tourism revenue are: Spain 12.21 %, France 11.72 %, Italy 8.99 %, Germany 8.32 %, United Kingdom 7.94 %, Turkey 5.60 %, Austria 4.12 %, Switzerland 3.62 %, Sweden 3.36 % and The Netherlands 3.03 %. Their contribution to Europe tourism receipts was 68.97 % in 2012. As a conclusion, international tourism is a very dynamic field of activity with a high contribution to the development of the world economy.

  14. TRANSPORTATION CASK RECEIPT AND RETURN FACILITY WORKER DOSE ASSESSMENT

    International Nuclear Information System (INIS)

    The purpose of this design calculation is to estimate radiation doses received by personnel working in the Transportation Cask Receipt and Return Facility (TCRRF) of the repository including the personnel at the security gate and cask staging areas. This calculation is required to support the preclosure safety analysis (PCSA) to ensure that the predicted doses are within the regulatory limits prescribed by the U.S. Nuclear Regulatory Commission (NRC). The Cask Receipt and Return Facility receives NRC licensed transportation casks loaded with spent nuclear fuel (SNF) and high-level radioactive waste (HLW). The TCRRF operation starts with the receipt, inspection, and survey of the casks at the security gate and the staging areas, and proceeds to the process facilities. The transportation casks arrive at the site via rail cars or trucks under the guidance of the national transportation system. This calculation was developed by the Environmental and Nuclear Engineering organization and is intended solely for the use of Design and Engineering in work regarding facility design. Environmental and Nuclear Engineering personnel should be consulted before using this calculation for purposes other than those stated herein or for use by individuals other than authorized personnel in the Environmental and Nuclear Engineering organization

  15. A Novel Technique to Image Annotation using Neural Network

    Directory of Open Access Journals (Sweden)

    Pankaj Savita

    2013-03-01

    Full Text Available : Automatic annotation of digital pictures is a key technology for managing and retrieving images from large image collection. Traditional image semantics extraction and representation schemes were commonly divided into two categories, namely visual features and text annotations. However, visual feature scheme are difficult to extract and are often semantically inconsistent. On the other hand, the image semantics can be well represented by text annotations. It is also easier to retrieve images according to their annotations. Traditional image annotation techniques are time-consuming and requiring lots of human effort. In this paper we propose Neural Network based a novel approach to the problem of image annotation. These approaches are applied to the Image data set. Our main work is focused on the image annotation by using multilayer perceptron, which exhibits a clear-cut idea on application of multilayer perceptron with special features. MLP Algorithm helps us to discover the concealed relations between image data and annotation data, and annotate image according to such relations. By using this algorithm we can save more memory space, and in case of web applications, transferring of images and download should be fast. This paper reviews 50 image annotation systems using supervised machine learning Techniques to annotate images for image retrieval. Results obtained show that the multi layer perceptron Neural Network classifier outperforms conventional DST Technique.

  16. Automated annotation of microbial proteomes in SWISS-PROT.

    Science.gov (United States)

    Gattiker, Alexandre; Michoud, Karine; Rivoire, Catherine; Auchincloss, Andrea H; Coudert, Elisabeth; Lima, Tania; Kersey, Paul; Pagni, Marco; Sigrist, Christian J A; Lachaize, Corinne; Veuthey, Anne Lise; Gasteiger, Elisabeth; Bairoch, Amos

    2003-02-01

    Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase. The HAMAP project, or 'High-quality Automated and Manual Annotation of microbial Proteomes', aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation process while preserving the quality of the database annotation. Automatic annotation is only applied to entries that belong to manually defined orthologous families and to entries with no identifiable similarities (ORFans). Many checks are enforced in order to prevent the propagation of wrong annotation and to spot problematic cases, which are channelled to manual curation. The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/sprot/hamap/. PMID:12798039

  17. Carbon Capture and Storage

    NARCIS (Netherlands)

    Benson, S.M.; Bennaceur, K.; Cook, P.; Davison, J.; Coninck, H. de; Farhat, K.; Ramirez, C.A.; Simbeck, D.; Surles, T.; Verma, P.; Wright, I.

    2012-01-01

    Emissions of carbon dioxide, the most important long-lived anthropogenic greenhouse gas, can be reduced by Carbon Capture and Storage (CCS). CCS involves the integration of four elements: CO 2 capture, compression of the CO2 from a gas to a liquid or a denser gas, transportation of pressurized CO 2

  18. CAPTURED India Country Evaluation

    NARCIS (Netherlands)

    O'Donoghue, R.; Brouwers, J.H.A.M.

    2012-01-01

    This report provides the findings of the India Country Evaluation and is produced as part of the overall CAPTURED End Evaluation. After five years of support by the CAPTURED project the End Evaluation has assessed that results are commendable. I-AIM was able to design an approach in which health fol

  19. A Concept Annotation System for Clinical Records

    CERN Document Server

    Kang, Ning; Afzal, Zubair; Singh, Bharat; Schuemie, Martijn J; van Mulligen, Erik M; Kors, Jan A

    2010-01-01

    Unstructured information comprises a valuable source of data in clinical records. For text mining in clinical records, concept extraction is the first step in finding assertions and relationships. This study presents a system developed for the annotation of medical concepts, including medical problems, tests, and treatments, mentioned in clinical records. The system combines six publicly available named entity recognition system into one framework, and uses a simple voting scheme that allows to tune precision and recall of the system to specific needs. The system provides both a web service interface and a UIMA interface which can be easily used by other systems. The system was tested in the fourth i2b2 challenge and achieved an F-score of 82.1% for the concept exact match task, a score which is among the top-ranking systems. To our knowledge, this is the first publicly available clinical record concept annotation system.

  20. Exploiting Social Annotation for Automatic Resource Discovery

    CERN Document Server

    Plangprasopchok, Anon

    2007-01-01

    Information integration applications, such as mediators or mashups, that require access to information resources currently rely on users manually discovering and integrating them in the application. Manual resource discovery is a slow process, requiring the user to sift through results obtained via keyword-based search. Although search methods have advanced to include evidence from document contents, its metadata and the contents and link structure of the referring pages, they still do not adequately cover information sources -- often called ``the hidden Web''-- that dynamically generate documents in response to a query. The recently popular social bookmarking sites, which allow users to annotate and share metadata about various information sources, provide rich evidence for resource discovery. In this paper, we describe a probabilistic model of the user annotation process in a social bookmarking system del.icio.us. We then use the model to automatically find resources relevant to a particular information dom...

  1. Semantic Annotation: The Mainstay of Semantic Web

    OpenAIRE

    Slimani, Thabet

    2013-01-01

    Given that semantic Web realization is based on the critical mass of metadata accessibility and the representation of data with formal knowledge, it needs to generate metadata that is specific, easy to understand and well-defined. However, semantic annotation of the web documents is the successful way to make the Semantic Web vision a reality. This paper introduces the Semantic Web and its vision (stack layers) with regard to some concept definitions that helps the understanding of semantic a...

  2. About Certain Semantic Annotation in Parallel Corpora

    OpenAIRE

    Violetta Koseska-Toszewa

    2015-01-01

    About Certain Semantic Annotation in Parallel CorporaThe semantic notation analyzed in this works is contained in the second stream of semantic theories presented here – in the direct approach semantics. We used this stream in our work on the Bulgarian-Polish Contrastive Grammar. Our semantic notation distinguishes quantificational meanings of names and predicates, and indicates aspectual and temporal meanings of verbs. It relies on logical scope-based quantification and on the contemporary t...

  3. Improving gene annotation of complete viral genomes

    OpenAIRE

    Mills, Ryan; Rozanov, Michael; Lomsadze, Alexandre; Tatusova, Tatiana; Borodovsky, Mark

    2003-01-01

    Gene annotation in viruses often relies upon similarity search methods. These methods possess high specificity but some genes may be missed, either those unique to a particular genome or those highly divergent from known homologs. To identify potentially missing viral genes we have analyzed all complete viral genomes currently available in GenBank with a specialized and augmented version of the gene finding program GeneMarkS. In particular, by implementing genome-specific self-training protoc...

  4. Html template system using java annotations

    OpenAIRE

    Speck, Peter

    2007-01-01

    The problems that motivate this project are to (1) solve the lack of separation between html templates and java code when using existing template systems (e.g. embedded language or macros), to (2) solve the lack of scoped declaration of macros and java variables inside template loops, and (3) to solve the lack of validation of template macro definitions at compile time to help finding bugs before the web applications are deployed. Annotations are used as metadata format for...

  5. EFFICIENT VIDEO ANNOTATIONS BY AN IMAGE GROUPS

    OpenAIRE

    K . Mahi balan; K . Rajakumari

    2015-01-01

    Searching desirable events in uncontrolled videos is a challenging task. So, researches mainly focus on obtaining concepts from numerous labelled videos. But it is time consuming and labour expensive to collect a large amount of required labelled videos for training event models under various condition. To avoid this problem, we propose to leverage abundant Web images for videos since Web images contain a rich source of information with many events roughly annotated and taken under various co...

  6. Deburring: an annotated bibliography. Volume V

    International Nuclear Information System (INIS)

    An annotated summary of 204 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a process, economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred

  7. Transcriptome Annotation using Tandem SAGE Tags

    OpenAIRE

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of Gene Expression (SAGE) can reveal new polyadenylated RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restric...

  8. Direct thermal neutron capture

    International Nuclear Information System (INIS)

    We discuss the direct-capture theory pertaining to primary electric dipole (E1) transitions following slow-neutron capture. For light nuclides that we have studied (including 9Be, 12C, 13C, 24Mg, 25Mg, 26Mg, 32S, 33S, 34S, 40Ca, and 44Ca), estimates of direct-capture cross sections using optical-model potentials with physically realistic parameters, are in reasonable agreement with the data. Minor disagreements that exist are consistent with extrapolations to light nuclides of generally accepted formulations of compound-nucleus capture. We also discuss the channel-capture approximation which is, in general, a good representation of these cross sections in heavier nuclei particularly if the scattering lengths are not different from the corresponding potential radii. We also draw attention to cases where the use of this formula leads to inaccurate predictions. 9 refs., 1 fig., 2 tab

  9. Muon capture in hydrogen

    International Nuclear Information System (INIS)

    In this lecture I will mainly speak about the recent results obtained by the Saclay-CERN-Bologna (SCB) collaboration on the muon capture rate at rest in liquid hydrogen.In the first talk I shall first briefly remind the theoretical description of the capture process, then describe the experimental difficulties and procedures and finally present the results obtained. In the second talk I shall compare them to other capture experiments on the proton and present the informations that are provided by muon capture in hydrogen, especially for the PCAC hypothesis, the second class currents and the μ-e universality. Finally I shall present the possible muon capture experiments on the proton that could still be undertaken in order to improve our present knowledge of the subject

  10. maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination

    OpenAIRE

    Nashar Karim; Wood A Joseph; Hulme Helen; Hayes Andrew; Morrison Norman; Velarde Giles; Wilson Michael; Hancock David; Kell Douglas B; Brass Andy

    2005-01-01

    Abstract Background maxdLoad2 is a relational database schema and Java® application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBr...

  11. Commission Versus Receipt of Violence During Pregnancy: Associations With Substance Abuse Variables

    OpenAIRE

    Tzilos, Golfo K.; Grekin, Emily R.; Beatty, Jessica R.; Chase, Sara K.; Ondersma, Steven J.

    2009-01-01

    The tendency for women to report both commission and receipt of violence is an understudied phenomenon. In particular, little is known about individual differences as a function of commission vs. receipt of partner violence among pregnant women. Using a sample of 78 cohabiting low-SES pregnant women, the current study examines three violence subtypes based on self-report (primarily commission of violence, primarily receipt of violence, and no report of violence) and investigated differences i...

  12. The GOA database: gene Ontology annotation updates for 2015.

    Science.gov (United States)

    Huntley, Rachael P; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria J; O'Donovan, Claire

    2015-01-01

    The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480,000 taxonomic groups. The resource now provides annotations to five times the number of proteins it did 4 years ago. As a member of the GO Consortium, we adhere to the most up-to-date Consortium-agreed annotation guidelines via the use of quality control checks that ensures that the GOA resource supplies high-quality functional information to proteins from a wide range of species. Annotations from GOA are freely available and are accessible through a powerful web browser as well as a variety of annotation file formats. PMID:25378336

  13. Using language to learn structured appearance models for image annotation.

    Science.gov (United States)

    Jamieson, Michael; Fazly, Afsaneh; Stevenson, Suzanne; Dickinson, Sven; Wachsmuth, Sven

    2010-01-01

    Given an unstructured collection of captioned images of cluttered scenes featuring a variety of objects, our goal is to simultaneously learn the names and appearances of the objects. Only a small fraction of local features within any given image are associated with a particular caption word, and captions may contain irrelevant words not associated with any image object. We propose a novel algorithm that uses the repetition of feature neighborhoods across training images and a measure of correspondence with caption words to learn meaningful feature configurations (representing named objects). We also introduce a graph-based appearance model that captures some of the structure of an object by encoding the spatial relationships among the local visual features. In an iterative procedure, we use language (the words) to drive a perceptual grouping process that assembles an appearance model for a named object. Results of applying our method to three data sets in a variety of conditions demonstrate that, from complex, cluttered, real-world scenes with noisy captions, we can learn both the names and appearances of objects, resulting in a set of models invariant to translation, scale, orientation, occlusion, and minor changes in viewpoint or articulation. These named models, in turn, are used to automatically annotate new, uncaptioned images, thereby facilitating keyword-based image retrieval. PMID:19926905

  14. Environment assisted electron capture

    International Nuclear Information System (INIS)

    Electrons scattering off isolated atoms or positive atomic ions may be captured in the non-resonant photorecombination or resonant dielectronic recombination processes with the excess energy carried off by a photon. We demonstrate that in a medium a new interatomic process becomes important, where in the electron capture by an atom or atomic ion the energy is transferred to a neigbouring species ionising it. We discuss different manifestations of this interatomic Coulombic electron capture and estimate its efficiency for a number of realistic systems.

  15. Neutrinoless double electron capture

    CERN Document Server

    Kotila, J; Iachello, F

    2015-01-01

    Direct determination of the neutrino mass is at the present time one of the most important aims of experimental and theoretical research in nuclear and particle physics. A possible way of detection is through neutrinoless double electron capture, $0\

  16. Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Deng Jixin

    2009-02-01

    Full Text Available Abstract Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO. In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57% being annotated with 1,957 distinct and specific GO terms. Unannotated proteins

  17. Activists versus Captured Regulators

    OpenAIRE

    Daubanes, Julien; Rochet, Jean-Charles

    2013-01-01

    We analyze the consequences of activism in a regulated industry where the regulator has been captured by the industry. Unlike ordinary economic agents, activists are insensitive to monetary incentives. Moreover, they are less well informed than regulators and their actions generate dead-weight costs. Yet we find that activism may increase social welfare because it disciplines captured regulators and reduces the social cost of imperfect regulatory systems.

  18. Muon capture by tritium

    International Nuclear Information System (INIS)

    The muon capture rate is computed with realistic wave function for the initial tritium nuclei (Faddeev equations on configuration space with realistic potentials), and plane wave approximation for the final three neutrons, with the effective Hamiltonian of Fujii and Primakoff for muon capture and via a non energy weighted sum rule. Such a forbidden transition is hoped to be a probe for exchange current contributions

  19. Factors affecting receipt of chemotherapy in women with breast cancer

    Directory of Open Access Journals (Sweden)

    Libby Morimoto

    2010-05-01

    Full Text Available Libby Morimoto1, Jenna Coalson1, Fionna Mowat1, Cynthia O’Malley21Exponent Health Sciences, Menlo Park, CA, USA; 2Amgen Global Epidemiology, Thousand Oaks, CA, USAAims: To review literature describing factors associated with receipt of chemotherapy for breast cancer, to better understand what factors are most relevant to women’s health and whether health disparities are apparent, and to assess how these factors might affect observational studies and outcomes research. Patterns of care for metastatic breast cancer, for which no standard-of-care exists, were of particular interest.Methods: Relevant studies written in English, Italian, French, or Spanish, published in 2000 or later, were identified through MEDLINE and reviewed. Review articles and clinical trials were excluded; all observational studies and surveys were considered. Articles were reviewed for any discussion of patient characteristics, hospital/physician/insurance characteristics, psychosocial characteristics, and clinical characteristics affecting receipt of chemotherapy by breast cancer patients.Results: In general, factors associated with increased likelihood of receiving chemotherapy included younger age, being Caucasian, having good general health and few co-morbidities, having more severe clinical disease, having responded well to previous treatment, and having breast cancer that is estrogen- or progesterone-receptor-negative. Many of the clinical factors found to increase the likelihood of receiving chemotherapy were consistent with current oncology guidelines. Of the relevant 19 studies identified, only six (32% reported data specific to metastatic cancer; most studies aggregated women with stage I–IV for purposes of analysis.Conclusion: Studies of patterns of care in breast cancer treatment can help identify challenges in health care provided to particular subgroups of women and can aid researchers in designing studies that account for such factors in clinical and

  20. CONSIDERATIONS ON THE TRENDS OF INTERNATIONAL TOURISM RECEIPTS

    OpenAIRE

    Agatha POPESCU

    2014-01-01

    The paper aimed to analyze the evolution of tourism receipts at world level and by geographical area and in the main countries of tourist interest. In the period 1980-2012, the tourism income increased 10.14 times. In 2012, it accounted for USD Billion 1,075, to which Europe contributed by 42.58 %, Asia and the Pacific by 30.13 % and the Americas by 19.77 %. The USA, Spain, France, China, Macau, Italy, Germany, United Kingdom, Hong Kong and Australia are the top 10 countries accor...

  1. Viewing a World of Annotations through AnnoVIP

    OpenAIRE

    Karanasos, Konstantinos; Zoupanos, Spyros

    2010-01-01

    The proliferation of electronic content has notably lead to the apparition of large corpora of interrelated structured documents (such as HTML and XML Web pages) and semantic annotations (typically expressed in RDF), which further complement these documents. Documents and annotations may be authored independently by different users or programs. We present AnnoVIP, a peer-to-peer platform, capable of efficiently exploiting a multitude of annotated documents, based on innovative materialized vi...

  2. Search-based Automatic Image Annotation Using Geotagged Community Photos

    OpenAIRE

    Mousselly Sergieh, Hatem

    2014-01-01

    In the Web 2.0 era, platforms for sharing and collaboratively annotating images with keywords, called tags, became very popular. Tags are a powerful means for organizing and retrieving photos. However, manual tagging is time consuming. Recently, the sheer amount of user-tagged photos available on the Web encouraged researchers to explore new techniques for automatic image annotation. The idea is to annotate an unlabeled image by propagating the labels of community photos that are visually sim...

  3. COFECO: composite function annotation enriched by protein complex data

    OpenAIRE

    Sun, Choong-Hyun; Kim, Min-Sung; Han, Youngwoong; Yi, Gwan-Su

    2009-01-01

    COFECO is a web-based tool for a composite annotation of protein complexes, KEGG pathways and Gene Ontology (GO) terms within a class of genes and their orthologs under study. Widely used functional enrichment tools using GO and KEGG pathways create large list of annotations that make it difficult to derive consolidated information and often include over-generalized terms. The interrelationship of annotation terms can be more clearly delineated by integrating the information of physically int...

  4. DIYA: a bacterial annotation pipeline for any genomics lab

    OpenAIRE

    Stewart, Andrew C.; Osborne, Brian; Read, Timothy D

    2009-01-01

    Summary:DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. The software is currently used to take DNA contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in Genbank file format as output. Availability: Distribution and source code are available at (https://sourceforge.net/projects/diyg/). Contact: tr...

  5. Barcode Annotations for Medical Image Retrieval: A Preliminary Investigation

    OpenAIRE

    Tizhoosh, Hamid R.

    2015-01-01

    This paper proposes to generate and to use barcodes to annotate medical images and/or their regions of interest such as organs, tumors and tissue types. A multitude of efficient feature-based image retrieval methods already exist that can assign a query image to a certain image class. Visual annotations may help to increase the retrieval accuracy if combined with existing feature-based classification paradigms. Whereas with annotations we usually mean textual descriptions, in this paper barco...

  6. Gene Ontology annotation quality analysis in model eukaryotes

    OpenAIRE

    Buza, Teresia J; McCarthy, Fiona M; Wang, Nan; Bridges, Susan M.; Burgess, Shane C.

    2008-01-01

    Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintai...

  7. Snap: An Integrated SNP Annotation Platform

    DEFF Research Database (Denmark)

    Li, S.; Ma, L.; Li, H.;

    2007-01-01

    Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...... research. Using a user-friendly web interface, genes can be searched by name, description, position, SNP ID or clone name. Several public databases are integrated, including gene information from Ensembl, protein features from Uniprot/SWISS-PROT, Pfam and DAS-CBS. Gene relationships are fetched from BIND...

  8. Evaluating Modelling Approaches for Medical Image Annotations

    CERN Document Server

    Opitz, Jasmin; Sattler, Ulrike

    2010-01-01

    Information system designers face many challenges w.r.t. selecting appropriate semantic technologies and deciding on a modelling approach for their system. However, there is no clear methodology yet to evaluate "semantically enriched" information systems. In this paper we present a case study on different modelling approaches for annotating medical images and introduce a conceptual framework that can be used to analyse the fitness of information systems and help designers to spot the strengths and weaknesses of various modelling approaches as well as managing trade-offs between modelling effort and their potential benefits.

  9. FINDING GENERIFS VIA GENE ONTOLOGY ANNOTATIONS

    OpenAIRE

    Lu, Zhiyong; Cohen, K Bretonnel; Hunter, Lawrence

    2006-01-01

    A Gene Reference Into Function (GeneRIF) is a concise phrase describing a function of a gene in the Entrez Gene database. Applying techniques from the area of natural language processing known as automatic summarization, it is possible to link the Entrez Gene database, the Gene Ontology, and the biomedical literature. A system was implemented that automatically suggests a sentence from a PubMed/MEDLINE abstract as a candidate GeneRIF by exploiting a gene’s GO annotations along with location f...

  10. A Novel Approach to Semantic and Coreference Annotation at LLNL

    Energy Technology Data Exchange (ETDEWEB)

    Firpo, M

    2005-02-04

    A case is made for the importance of high quality semantic and coreference annotation. The challenges of providing such annotation are described. Asperger's Syndrome is introduced, and the connections are drawn between the needs of text annotation and the abilities of persons with Asperger's Syndrome to meet those needs. Finally, a pilot program is recommended wherein semantic annotation is performed by people with Asperger's Syndrome. The primary points embodied in this paper are as follows: (1) Document annotation is essential to the Natural Language Processing (NLP) projects at Lawrence Livermore National Laboratory (LLNL); (2) LLNL does not currently have a system in place to meet its need for text annotation; (3) Text annotation is challenging for a variety of reasons, many related to its very rote nature; (4) Persons with Asperger's Syndrome are particularly skilled at rote verbal tasks, and behavioral experts agree that they would excel at text annotation; and (6) A pilot study is recommend in which two to three people with Asperger's Syndrome annotate documents and then the quality and throughput of their work is evaluated relative to that of their neuro-typical peers.

  11. Review of actinide-sediment reactions with an annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Ames, L.L.; Rai, D.; Serne, R.J.

    1976-02-10

    The annotated bibliography is divided into sections on chemistry and geochemistry, migration and accumulation, cultural distributions, natural distributions, and bibliographies and annual reviews. (LK)

  12. The UniProt-GO Annotation database in 2011

    Science.gov (United States)

    Dimmer, Emily C.; Huntley, Rachael P.; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J.; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek- Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  13. The UniProt-GO Annotation database in 2011.

    Science.gov (United States)

    Dimmer, Emily C; Huntley, Rachael P; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek-Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  14. Gene Ontology annotation quality analysis in model eukaryotes

    Science.gov (United States)

    Buza, Teresia J.; McCarthy, Fiona M.; Wang, Nan; Bridges, Susan M.; Burgess, Shane C.

    2008-01-01

    Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintained and optimal for the functional processes that are most relevant for their research community. We report the GO Annotation Quality (GAQ) score, a quantitative measure of GO quality that includes breadth of GO annotation, the level of detail of annotation and the type of evidence used to make the annotation. As a case study, we apply the GAQ scoring method to a set of diverse eukaryotes and demonstrate how the GAQ score can be used to track changes in GO annotations over time and to assess the quality of GO annotations available for specific biological processes. The GAQ score also allows researchers to quantitatively assess the functional data available for their experimental systems (arrays or databases). PMID:18187504

  15. Introduction to annotated logics foundations for paracomplete and paraconsistent reasoning

    CERN Document Server

    Abe, Jair Minoro; Nakamatsu, Kazumi

    2015-01-01

    This book is written as an introduction to annotated logics. It provides logical foundations for annotated logics, discusses some interesting applications of these logics and also includes the authors' contributions to annotated logics. The central idea of the book is to show how annotated logic can be applied as a tool to solve problems of technology and of applied science. The book will be of interest to pure and applied logicians, philosophers, and computer scientists as a monograph on a kind of paraconsistent logic. But, the layman will also take profit from its reading.

  16. 12 CFR 205.9 - Receipts at electronic terminals; periodic statements.

    Science.gov (United States)

    2010-01-01

    ... applicable: (1) Transaction information. For each electronic fund transfer occurring during the cycle: (i... 12 Banks and Banking 2 2010-01-01 2010-01-01 false Receipts at electronic terminals; periodic... RESERVE SYSTEM ELECTRONIC FUND TRANSFERS (REGULATION E) § 205.9 Receipts at electronic terminals;...

  17. 48 CFR 14.406 - Receipt of an unreadable electronic bid.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Receipt of an unreadable electronic bid. 14.406 Section 14.406 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION CONTRACTING METHODS AND CONTRACT TYPES SEALED BIDDING Opening of Bids and Award of Contract 14.406 Receipt of an unreadable electronic bid....

  18. Commission versus Receipt of Violence during Pregnancy: Associations with Substance Abuse Variables

    Science.gov (United States)

    Tzilos, Golfo K.; Grekin, Emily R.; Beatty, Jessica R.; Chase, Sara K.; Ondersma, Steven J.

    2010-01-01

    The tendency for women to report both commission and receipt of violence is an understudied phenomenon. In particular, little is known about individual differences as a function of commission vs. receipt of partner violence among pregnant women. Using a sample of 78 cohabiting low-SES pregnant women, the current study examines three violence…

  19. 20 CFR 702.262 - Action by district director upon receipt of notice of contest.

    Science.gov (United States)

    2010-04-01

    ... notice of contest. 702.262 Section 702.262 Employees' Benefits EMPLOYMENT STANDARDS ADMINISTRATION... AND PROCEDURE Claims Procedures Contested Claims § 702.262 Action by district director upon receipt of notice of contest. Upon receipt of the claimant's notice of contest, the district director...

  20. 77 FR 37957 - Guizhou Tyre Corporation; Receipt of Petition for Decision of Inconsequential Noncompliance

    Science.gov (United States)

    2012-06-25

    ... Statement is available for review in the Federal Register published on April 11, 2000, (65 FR 19477-78). The... National Highway Traffic Safety Administration Guizhou Tyre Corporation; Receipt of Petition for Decision...: Receipt of Petition. SUMMARY: GTC North America, Inc., on behalf of Guizhou Tyre I/E Co. LTD...

  1. 49 CFR 805.735-5 - Receipt of gifts, entertainment, and favors by Members or employees.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Receipt of gifts, entertainment, and favors by... Receipt of gifts, entertainment, and favors by Members or employees. (a) Except as provided in paragraphs..., any gift, gratuity, favor, entertainment, loan, or any other thing of monetary value, from a...

  2. 27 CFR 19.372 - Receipt of spirits, wines and alcoholic flavoring materials for processing.

    Science.gov (United States)

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Receipt of spirits, wines... Spirits, Wines and Alcoholic Flavoring Materials § 19.372 Receipt of spirits, wines and alcoholic...) Wines (i) from the storage account at the same plant, or (ii) by transfer in bond from a bonded...

  3. 7 CFR 735.401 - Electronic warehouse receipt and USWA electronic document providers.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Electronic warehouse receipt and USWA electronic... (Continued) FARM SERVICE AGENCY, DEPARTMENT OF AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Electronic Providers § 735.401 Electronic warehouse receipt and...

  4. 78 FR 69414 - Toxic Substances Control Act Chemical Testing; Receipt of Test Data

    Science.gov (United States)

    2013-11-19

    ... October 21, 2011 (76 FR 65385) (FRL-8885-5) (docket ID number EPA-HQ-OPPT-2009-0112). The table in this... AGENCY Toxic Substances Control Act Chemical Testing; Receipt of Test Data AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: This notice announces EPA's receipt of test data on...

  5. 76 FR 38170 - Toxic Substances Control Act Chemical Testing; Receipt of Test Data

    Science.gov (United States)

    2011-06-29

    ... issue of March 16, 2006 (71 FR 13708) (FRL-7335-2). Section 4(d) of TSCA (15 U.S.C. 2603(d)) requires... AGENCY Toxic Substances Control Act Chemical Testing; Receipt of Test Data AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: This notice announces EPA's receipt of test data on...

  6. 21 CFR 203.60 - Request and receipt forms, reports, and records.

    Science.gov (United States)

    2010-04-01

    ... SERVICES (CONTINUED) DRUGS: GENERAL PRESCRIPTION DRUG MARKETING Request and Receipt Forms, Reports, and Records § 203.60 Request and receipt forms, reports, and records. (a) Use of electronic records, electronic signatures, and handwritten signatures executed to electronic records. (1) Provided...

  7. 47 CFR 80.1117 - Procedure for receipt and acknowledgement of distress alerts.

    Science.gov (United States)

    2010-10-01

    ... accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of this standard can be inspected at the Federal... station acknowledging receipt, spoken three times; (5) The word RECEIVED (or RRR spoken as ROMEO ROMEO... acknowledging receipt of the distress alert; (5) The signal RRR; (6) The distress signal MAYDAY. (e)...

  8. 21 CFR 1271.265 - Receipt, predistribution shipment, and distribution of an HCT/P.

    Science.gov (United States)

    2010-04-01

    ... distribution of an HCT/P. 1271.265 Section 1271.265 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... Practice § 1271.265 Receipt, predistribution shipment, and distribution of an HCT/P. (a) Receipt. You must evaluate each incoming HCT/P for the presence and significance of microorganisms and inspect for damage...

  9. Muon capture at PSI

    CERN Document Server

    Winter, Peter

    2010-01-01

    Measuring the rate of muon capture in hydrogen provides one of the most direct ways to study the axial current of the nucleon. The MuCap experiment uses a negative muon beam stopped in a time projection chamber operated with ultra-pure hydrogen gas. Surrounded by a decay electron detector, the lifetime of muons in hydrogen can be measured to determine the singlet capture rate Lambda_s to a final precision of 1%. The capture rate determines the nucleon's pseudoscalar form factor g_p. A first result, g_p = 7.3 +- 1.1, has been published and the final analysis of the full statistics will reduce the error by a factor of up to 3. Muon capture on the deuteron probes the weak axial current in the two-nucleon system. Within the framework of effective field theories the calculation of such two-nucleon processes involving the axial current requires the knowledge of one additional low energy constant which can be extracted from the doublet capture rate Lambda_d. The same constant then allows to model-independently calcu...

  10. Analysis of high-throughput sequencing and annotation strategies for phage genomes.

    Directory of Open Access Journals (Sweden)

    Matthew R Henn

    Full Text Available BACKGROUND: Bacterial viruses (phages play a critical role in shaping microbial populations as they influence both host mortality and horizontal gene transfer. As such, they have a significant impact on local and global ecosystem function and human health. Despite their importance, little is known about the genomic diversity harbored in phages, as methods to capture complete phage genomes have been hampered by the lack of knowledge about the target genomes, and difficulties in generating sufficient quantities of genomic DNA for sequencing. Of the approximately 550 phage genomes currently available in the public domain, fewer than 5% are marine phage. METHODOLOGY/PRINCIPAL FINDINGS: To advance the study of phage biology through comparative genomic approaches we used marine cyanophage as a model system. We compared DNA preparation methodologies (DNA extraction directly from either phage lysates or CsCl purified phage particles, and sequencing strategies that utilize either Sanger sequencing of a linker amplification shotgun library (LASL or of a whole genome shotgun library (WGSL, or 454 pyrosequencing methods. We demonstrate that genomic DNA sample preparation directly from a phage lysate, combined with 454 pyrosequencing, is best suited for phage genome sequencing at scale, as this method is capable of capturing complete continuous genomes with high accuracy. In addition, we describe an automated annotation informatics pipeline that delivers high-quality annotation and yields few false positives and negatives in ORF calling. CONCLUSIONS/SIGNIFICANCE: These DNA preparation, sequencing and annotation strategies enable a high-throughput approach to the burgeoning field of phage genomics.

  11. Transcriptome annotation using tandem SAGE tags

    Science.gov (United States)

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of gene expression (SAGE) can reveal new Poly(A) RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restrictions sites of cDNAs. New transcripts are then tentatively defined by the two SAGE tags in tandem and by the spanning sequence read on the genome between these tagged sites. Having developed a new algorithm to locate these tag-delimited genomic sequences (TDGS), we first validated its capacity to recognize known genes and its ability to reveal new transcripts with two SAGE libraries built in parallel from a single RNA sample. Our algorithm proves fast enough to experiment this strategy at a large scale. We then collected and processed the complete sets of human SAGE tags to predict yet unknown transcripts. A cross-validation with tiling arrays data shows that 47% of these TDGS overlap transcriptional active regions. Our method provides a new and complementary approach for complex transcriptome annotation. PMID:17709346

  12. EFFICIENT VIDEO ANNOTATIONS BY AN IMAGE GROUPS

    Directory of Open Access Journals (Sweden)

    K . Mahi balan

    2015-10-01

    Full Text Available Searching desirable events in uncontrolled videos is a challenging task. So, researches mainly focus on obtaining concepts from numerous labelled videos. But it is time consuming and labour expensive to collect a large amount of required labelled videos for training event models under various condition. To avoid this problem, we propose to leverage abundant Web images for videos since Web images contain a rich source of information with many events roughly annotated and taken under various conditions. However, information from the Web is difficult .so,brute force knowledge transfer of images may hurt the video annotation performance. so, we propose a novel Group-based Domain Adaptation learning framework to leverage different groups of knowledge (source target queried from the Web image search engine to consumer videos (domain target. Different from old methods using multiple source domains of images, our method makes the Web images according to their intrinsic semantic relationships instead of source. Specifically, two different types of groups ( event-specific groups and concept-specific groups are exploited to respectively describe the event-level and concept-level semantic meanings of target-domain videos.

  13. Comparing functional annotation analyses with Catmap

    Directory of Open Access Journals (Sweden)

    Krogh Morten

    2004-12-01

    Full Text Available Abstract Background Ranked gene lists from microarray experiments are usually analysed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restricted to a category score based on a cutoff in the ranked list and a significance calculation based on random gene permutations as null hypothesis. Results We analysed three publicly available data sets, in each of which samples were divided in two classes and genes ranked according to their correlation to class labels. We developed a program, Catmap (available for download at http://bioinfo.thep.lu.se/Catmap, to compare different scores and null hypotheses in gene category analysis, using Gene Ontology annotations for category definition. When a cutoff-based score was used, results depended strongly on the choice of cutoff, introducing an arbitrariness in the analysis. Comparing results using random gene permutations and random sample permutations, respectively, we found that the assigned significance of a category depended strongly on the choice of null hypothesis. Compared to sample label permutations, gene permutations gave much smaller p-values for large categories with many coexpressed genes. Conclusions In gene category analyses of ranked gene lists, a cutoff independent score is preferable. The choice of null hypothesis is very important; random gene permutations does not work well as an approximation to sample label permutations.

  14. Descartes' fly: the geometry of genomic annotation.

    Science.gov (United States)

    Kim, J

    2001-03-01

    The completion of the Drosophila melanogaster genome marks another significant milestone in the growth of sequence information. But it also contributes to the ever-widening gap between sequence information and biological knowledge. One important approach to reducing this gap is theoretical inference through computational technologies. Many computer programs have been designed to annotate genomic sequence information with biologically relevant information. Here, I suggest that all of these methods have a common structure in which the sequence fragments are "coordinated" by some method of description such as Hidden Markov models. The key to the algorithms lies in constructing the most efficient set of coordinates that allow extrapolation and interpolation from existing knowledge. Efficient extrapolation and interpolation are produced if the sequence fragments acquire a natural geometrical structure in the coordinated description. Finding such a coordinate frame is an inductive problem with no algorithmic solution. The greater part of the problem of genomic annotation lies in biological modeling of the data rather than in algorithmic improvements. PMID:11793243

  15. Muon Capture in Deuterium

    CERN Document Server

    Ricci, P; Mosconi, B; Smejkal, J

    2009-01-01

    Model dependence of the capture rates of the negative muon capture in deuterium is studied starting from potential models and the weak two-body meson exchange currents constructed in the tree approximation and also from an effective field theory. The tree one-boson exchange currents are derived from the hard pion chiral Lagrangians of the $N \\Delta \\pi \\rho \\omega a_1$ system. If constructed in conjunction with the one-boson exchange potentials, the capture rates can be calculated consistently. On the other hand, the effective field theory currents, constructed within the heavy baryon chiral perturbation theory, contain a low energy constant $\\hat d ^R$ that cannot be extracted from data at the one-particle level nor determined from the first principles. Comparative analysis of the results for the doublet transition rate allows us to extract the constant $\\hat d ^R$.

  16. US Spacesuit Knowledge Capture

    Science.gov (United States)

    Chullen, Cinda; Thomas, Ken; McMann, Joe; Dolan, Kristi; Bitterly, Rose; Lewis, Cathleen

    2011-01-01

    The ability to learn from both the mistakes and successes of the past is vital to assuring success in the future. Due to the close physical interaction between spacesuit systems and human beings as users, spacesuit technology and usage lends itself rather uniquely to the benefits realized from the skillful organization of historical information; its dissemination; the collection and identification of artifacts; and the education of those in the field. The National Aeronautics and Space Administration (NASA), other organizations and individuals have been performing United States (U.S.) Spacesuit Knowledge Capture since the beginning of space exploration. Avenues used to capture the knowledge have included publication of reports; conference presentations; specialized seminars; and classes usually given by veterans in the field. More recently the effort has been more concentrated and formalized whereby a new avenue of spacesuit knowledge capture has been added to the archives in which videotaping occurs engaging both current and retired specialists in the field presenting technical scope specifically for education and preservation of knowledge. With video archiving, all these avenues of learning can now be brought to life with the real experts presenting their wealth of knowledge on screen for future learners to enjoy. Scope and topics of U.S. spacesuit knowledge capture have included lessons learned in spacesuit technology, experience from the Gemini, Apollo, Skylab and Shuttle programs, hardware certification, design, development and other program components, spacesuit evolution and experience, failure analysis and resolution, and aspects of program management. Concurrently, U.S. spacesuit knowledge capture activities have progressed to a level where NASA, the National Air and Space Museum (NASM), Hamilton Sundstrand (HS) and the spacesuit community are now working together to provide a comprehensive closed-looped spacesuit knowledge capture system which includes

  17. A Factor Graph Approach to Automated GO Annotation.

    Science.gov (United States)

    Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

  18. Product annotations - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ile name: kome_product_annotation.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...ate History of This Database Site Policy | Contact Us Product annotations - KOME | LSDB Archive ...

  19. The GATO gene annotation tool for research laboratories

    Directory of Open Access Journals (Sweden)

    A. Fujita

    2005-11-01

    Full Text Available Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

  20. The GATO gene annotation tool for research laboratories.

    Science.gov (United States)

    Fujita, A; Massirer, K B; Durham, A M; Ferreira, C E; Sogayar, M C

    2005-11-01

    Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB. PMID:16258624

  1. Behavioral Contributions to "Teaching of Psychology": An Annotated Bibliography

    Science.gov (United States)

    Karsten, A. M.; Carr, J. E.

    2008-01-01

    An annotated bibliography that summarizes behavioral contributions to the journal "Teaching of Psychology" from 1974 to 2006 is provided. A total of 116 articles of potential utility to college-level instructors of behavior analysis and related areas were identified, annotated, and organized into nine categories for ease of accessibility.…

  2. Evaluating techniques for metagenome annotation using simulated sequence data.

    Science.gov (United States)

    Randle-Boggis, Richard J; Helgason, Thorunn; Sapp, Melanie; Ashton, Peter D

    2016-07-01

    The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. PMID:27162180

  3. Annotating abstract pronominal anaphora in the DAD project

    DEFF Research Database (Denmark)

    Navarretta, Costanza; Olsen, Sussi Anni

    2008-01-01

    extended scheme, which we call the DAD annotation scheme, allows to annotate information about abstract anaphora which is important to investigate their use, see Webber (1988), Gundel et al. (2003), Navarretta (2004) and which can influence their automatic treatment. Intercoder agreement scores obtained by...

  4. Beyond annotations : a proposal for extensible java (XJ).

    OpenAIRE

    Clark, Anthony; Sammut, Paul; Willans, James

    2008-01-01

    Annotations provide a limited way of extending Java in order to tailor the language for specific tasks. This paper describes a proposal for a Java extension which generalises annotations to allow Java to be a platform for developing domain specific languages.

  5. Bioinformatics Assisted Gene Discovery and Annotation of Human Genome

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.

  6. Online Metacognitive Strategies, Hypermedia Annotations, and Motivation on Hypertext Comprehension

    Science.gov (United States)

    Shang, Hui-Fang

    2016-01-01

    This study examined the effect of online metacognitive strategies, hypermedia annotations, and motivation on reading comprehension in a Taiwanese hypertext environment. A path analysis model was proposed based on the assumption that if English as a foreign language learners frequently use online metacognitive strategies and hypermedia annotations,…

  7. CAPTURED End Evaluation Synthesis Report

    NARCIS (Netherlands)

    Brouwers, J.H.A.M.

    2012-01-01

    This report provides the findings of the Synthesis Study of the CAPTURED Evaluation and is produced as part of the overall CAPTURED End Evaluation. After five years of support by the CAPTURED project the three CAPTURED partners have achieved commendable results. Ten lessons learned are formulated th

  8. Theory of electron capture

    International Nuclear Information System (INIS)

    The historical development of a theoretical model for the electron-capture detector, sometimes called the 'classical' model, is presented and the model as it stands today is described. This is followed by a comparison of the model with experimental data obtained with other techniques since the early development of the theory and finally a section on correlations and predictions is presented. (Auth.)

  9. Semantator: annotating clinical narratives with semantic web ontologies.

    Science.gov (United States)

    Song, Dezhao; Chute, Christopher G; Tao, Cui

    2012-01-01

    To facilitate clinical research, clinical data needs to be stored in a machine processable and understandable way. Manual annotating clinical data is time consuming. Automatic approaches (e.g., Natural Language Processing systems) have been adopted to convert such data into structured formats; however, the quality of such automatically extracted data may not always be satisfying. In this paper, we propose Semantator, a semi-automatic tool for document annotation with Semantic Web ontologies. With a loaded free text document and an ontology, Semantator supports the creation/deletion of ontology instances for any document fragment, linking/disconnecting instances with the properties in the ontology, and also enables automatic annotation by connecting to the NCBO annotator and cTAKES. By representing annotations in Semantic Web standards, Semantator supports reasoning based upon the underlying semantics of the owl:disjointWith and owl:equivalentClass predicates. We present discussions based on user experiences of using Semantator. PMID:22779043

  10. On Semantic Annotation in Clarin-PL Parallel Corpora

    Directory of Open Access Journals (Sweden)

    Violetta Koseska-Toszewa

    2015-12-01

    Full Text Available On Semantic Annotation in Clarin-PL Parallel CorporaIn the article, the authors present a proposal for semantic annotation in Clarin-PL parallel corpora: Polish-Bulgarian-Russian and Polish-Lithuanian ones. Semantic annotation of quantification is a novum in developing sentence level semantics in multilingual parallel corpora. This is why our semantic annotation is manual. The authors hope it will be interesting to IT specialists working on automatic processing of the given natural languages. Semantic annotation defined the way it is defined here will make contrastive studies of natural languages more efficient, which in turn will help verify the results of those studies, and will certainly improve human and machine translations.

  11. Improving microbial genome annotations in an integrated database context.

    Directory of Open Access Journals (Sweden)

    I-Min A Chen

    Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

  12. Genotyping and annotation of Affymetrix SNP arrays

    DEFF Research Database (Denmark)

    Lamy, Philippe; Andersen, Claus Lindbjerg; Wikman, Friedrik;

    2006-01-01

    In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point...... allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose-response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree in...... 99.25% (using standard settings) of the cases, using a sample of 113 Affymetrix 10k SNP arrays. In the majority of cases where the two methods disagree, our method makes a genotype call, whereas the method by Affymetrix makes a no call, i.e. the genotype of the SNP is not determined. By visualization...

  13. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    Next generation sequencing (NGS) has revolutionized the field of genomics and its wide range of applications has resulted in the genome-wide analysis of hundreds of species and the development of thousands of computational tools. This thesis represents my work on NGS analysis of four species, Lotus...... japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... agricultural and biological importance. Its capacity to form symbiotic relationships with rhizobia and microrrhizal fungi has fascinated researchers for years. Lotus has a small genome of approximately 470 Mb and a short life cycle of 2 to 3 months, which has made Lotus a model legume plant for many molecular...

  14. Expectation-Maximization Binary Clustering for Behavioural Annotation.

    Science.gov (United States)

    Garriga, Joan; Palmer, John R B; Oltra, Aitana; Bartumeus, Frederic

    2016-01-01

    The growing capacity to process and store animal tracks has spurred the development of new methods to segment animal trajectories into elementary units of movement. Key challenges for movement trajectory segmentation are to (i) minimize the need of supervision, (ii) reduce computational costs, (iii) minimize the need of prior assumptions (e.g. simple parametrizations), and (iv) capture biologically meaningful semantics, useful across a broad range of species. We introduce the Expectation-Maximization binary Clustering (EMbC), a general purpose, unsupervised approach to multivariate data clustering. The EMbC is a variant of the Expectation-Maximization Clustering (EMC), a clustering algorithm based on the maximum likelihood estimation of a Gaussian mixture model. This is an iterative algorithm with a closed form step solution and hence a reasonable computational cost. The method looks for a good compromise between statistical soundness and ease and generality of use (by minimizing prior assumptions and favouring the semantic interpretation of the final clustering). Here we focus on the suitability of the EMbC algorithm for behavioural annotation of movement data. We show and discuss the EMbC outputs in both simulated trajectories and empirical movement trajectories including different species and different tracking methodologies. We use synthetic trajectories to assess the performance of EMbC compared to classic EMC and Hidden Markov Models. Empirical trajectories allow us to explore the robustness of the EMbC to data loss and data inaccuracies, and assess the relationship between EMbC output and expert label assignments. Additionally, we suggest a smoothing procedure to account for temporal correlations among labels, and a proper visualization of the output for movement trajectories. Our algorithm is available as an R-package with a set of complementary functions to ease the analysis. PMID:27002631

  15. The GOA database in 2009--an integrated Gene Ontology Annotation resource

    OpenAIRE

    Barrell, D.; Dimmer, E.; Huntley, R. P.; Binns, D.; O Donovan, C.; Apweiler, R.

    2009-01-01

    The Gene Ontology Annotation (GOA) project at the EBI (http://www.ebi.ac.uk/goa) provides high-quality electronic and manual associations (annotations) of Gene Ontology (GO) terms to UniProt Knowledgebase (UniProtKB) entries. Annotations created by the project are collated with annotations from external databases to provide an extensive, publicly available GO annotation resource. Currently covering over 160 000 taxa, with greater than 32 million annotations, GOA remains the largest and most c...

  16. Gene Ontology annotations at SGD: new data sources and annotation methods

    OpenAIRE

    Hong, Eurie L.; Balakrishnan, Rama; Dong, Qing; Christie, Karen R.; Park, Julie; Binkley, Gail; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Krieger, Cynthia J.; Livstone, Michael S.; Miyasato, Stuart R.

    2007-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive bo...

  17. Semi-automatic conversion of BioProp semantic annotation to PASBio annotation

    OpenAIRE

    Dai Hong-Jie; Tsai Richard; Huang Chi-Hsin; Hsu Wen-Lian

    2008-01-01

    Abstract Background Semantic role labeling (SRL) is an important text analysis technique. In SRL, sentences are represented by one or more predicate-argument structures (PAS). Each PAS is composed of a predicate (verb) and several arguments (noun phrases, adverbial phrases, etc.) with different semantic roles, including main arguments (agent or patient) as well as adjunct arguments (time, manner, or location). PropBank is the most widely used PAS corpus and annotation format in the newswire d...

  18. The Collation of Three Versions of Front Annotations of the Siku Quanshu: Based on 365 Pieces of Front Annotations

    Directory of Open Access Journals (Sweden)

    Wen-Chin Lan

    2015-06-01

    Full Text Available A bibliographic annotation (tiyao提要 is a brief description of the author and content of a book as well as a comment on, or a critique of, the book. The Siku Quanshu Zongmu (四庫全書總目 has long been viewed as a model of the traditional Chinese annotated bibliography and its bibliographic annotations have been praised by many scholars. It is suggested that these annotations can be used as examples for learning how to write bibliographic annotations. The compilation of the Siku Quanshu Zongmu went through three stages: (1 individual draft annotations (分纂稿 written by various scholars, (2 front annotations (書前提要 revised and modified by the officials of the Siku Quanshu Project, and (3 finalized annotations (總目提要 mainly edited and compiled by Ji Yun (紀昀. Initially, the Siku Quanshu had seven written copies and there were seven sets of front annotations. They were housed separately in the seven chambers that Qianlong Emperor (乾隆, r. 1736-1795 built to store the Siku Quanshu. Currently, only three of the seven sets are intact and extant, including Wenyuange (文淵閣, Wensuge (文溯閣, and Wenjinge ( 文津閣. This study attempts to conduct a collation project of the three versions of front annotations. We chose 365 pieces of front annotations from the aforementioned three sets, respectively. The results corroborate that there exist variations and differences among the three sets of front annotations. This paper presents three examples to illustrate how the collation task was done. Since these annotations were transcribed manually, it is quite common to notice that the three sets might use variant forms for the same character. The descriptions of author, title, or number of volumes might be different as well. In particular, the annotation for the same book might be different slightly or significantly among the three sets. This paper is a summary report of the preliminary findings of the collation task

  19. Gadolinium neutron capture therapy

    International Nuclear Information System (INIS)

    Gadolinium neutron capture therapy makes use of photons and electrons produced by nuclear reactions between gadolinium and lower-energy neutrons which occur within the tumor. The results of our studies have shown that its radiation effect is mostly of low LET and that the electrons are the significant component in the over-all dose. The dose from gadolinium neutron capture reactions does not seem to increase in proportion to the gadolinium concentration, and the Gd-157 concentration of about 100 μg/ml appears most optimal for therapy. Close contact between gadolinium and the cell is not necessarily required for cell inactivation, however, the effect of electrons released from intracellular gadolinium may be significant. Experimental studies on tumor-bearing mice and rabbits have shown that this is a very promising modality though further improvements in gadolinium delivery to tumors are needed. (author)

  20. Improving VAT Compliance in Romania by Implementing a New Tool – Tax Lottery Receipts

    Directory of Open Access Journals (Sweden)

    Dragos Ungureanu

    2015-12-01

    Full Text Available This paper aims to present and explain the newly implemented measure of organizing a Tax Lottery Receipts in Romania, in orderto combat tax evasion by raising awareness among consumers and make them responsible when purchasing any goods.The lottery proposes an approach to strengthen the fiscal voluntary conformation by stimulating financially those who promote respecting the law – asking for the fiscal receipt, and helpthe fiscal authorities this way in the fight against tax evasion, contrasting at the same time with punishing those who do not respect it – not issuing fiscal receipts.

  1. Supernova electron capture rates

    CERN Document Server

    Martínez-Pinedo, G

    1999-01-01

    We have calculated the Gamow-Teller strength distributions for the ground states and low lying states of several nuclei that play an important role in the precollapse evolution of supernova. The calculations reproduce the experimental GT distributions nicely. The GT distribution are used to calculate electron capture rates for typical presupernova conditions. The computed rates are noticeably smaller than the presently adopted rates. The possible implications for the supernova evolution are discussed.

  2. Inland capture fisheries

    OpenAIRE

    Welcomme, Robin L.; Cowx, Ian G.; Coates, David; Béné, Christophe; Funge-Smith, Simon; Halls, Ashley; Lorenzen, Kai

    2010-01-01

    The reported annual yield from inland capture fisheries in 2008 was over 10 million tonnes, although real catches are probably considerably higher than this. Inland fisheries are extremely complex, and in many cases poorly understood. The numerous water bodies and small rivers are inhabited by a wide range of species and several types of fisher community with diversified livelihood strategies for whom inland fisheries are extremely important. Many drivers affect the fisheries, including inter...

  3. Laser capture microscopy

    OpenAIRE

    Curran, S.; McKay, J A; McLeod, H L; Murray, G I

    2000-01-01

    Human tissues are composed of complex admixtures of different cell types and their biologically meaningful analysis necessitates the procurement of pure samples of the cells of interest. Many approaches have been used in attempts to overcome this difficulty, including a variety of microdissection methods. This review concerns a recent advance in microdissection techniques, namely laser capture microdissection (LCM). The principle underlying this technique is outlined, and practical issues per...

  4. Scoring consensus of multiple ECG annotators by optimal sequence alignment.

    Science.gov (United States)

    Haghpanahi, Masoumeh; Sameni, Reza; Borkholder, David A

    2014-01-01

    Development of ECG delineation algorithms has been an area of intense research in the field of computational cardiology for the past few decades. However, devising evaluation techniques for scoring and/or merging the results of such algorithms, both in the presence or absence of gold standards, still remains as a challenge. This is mainly due to existence of missed or erroneous determination of fiducial points in the results of different annotation algorithms. The discrepancy between different annotators increases when the reference signal includes arrhythmias or significant noise and its morphology deviates from a clean ECG signal. In this work, we propose a new approach to evaluate and compare the results of different annotators under such conditions. Specifically, we use sequence alignment techniques similar to those used in bioinformatics for the alignment of gene sequences. Our approach is based on dynamic programming where adequate mismatch penalties, depending on the type of the fiducial point and the underlying signal, are defined to optimally align the annotation sequences. We also discuss how to extend the algorithm for more than two sequences by using suitable data structures to align multiple annotation sequences with each other. Once the sequences are aligned, different heuristics are devised to evaluate the performance against a gold standard annotation, or to merge the results of multiple annotations when no gold standard exists. PMID:25570339

  5. Fuzzy Emotional Semantic Analysis and Automated Annotation of Scene Images

    Directory of Open Access Journals (Sweden)

    Jianfang Cao

    2015-01-01

    Full Text Available With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance.

  6. Fuzzy emotional semantic analysis and automated annotation of scene images.

    Science.gov (United States)

    Cao, Jianfang; Chen, Lichao

    2015-01-01

    With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP) neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance. PMID:25838818

  7. A proteogenomic update to Yersinia: enhancing genome annotation

    Directory of Open Access Journals (Sweden)

    Huang Shih-Ting

    2010-08-01

    Full Text Available Abstract Background Modern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins. Results The application of experimental proteomics data to genome annotation, called proteogenomics, can quickly and efficiently discover misannotations, yielding a more accurate and complete genome annotation. We present a comprehensive proteogenomic analysis of the plague bacterium, Yersinia pestis KIM. We discover non-annotated genes, correct protein boundaries, remove spuriously annotated ORFs, and make major advances towards accurate identification of signal peptides. Finally, we apply our data to 21 other Yersinia genomes, correcting and enhancing their annotations. Conclusions In total, 141 gene models were altered and have been updated in RefSeq and Genbank, which can be accessed seamlessly through any NCBI tool (e.g. blast or downloaded directly. Along with the improved gene models we discover new, more accurate means of identifying signal peptides in proteomics data.

  8. MimoSA: a system for minimotif annotation

    Directory of Open Access Journals (Sweden)

    Kundeti Vamsi

    2010-06-01

    Full Text Available Abstract Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to

  9. The UniProt-GO Annotation database in 2011

    OpenAIRE

    Dimmer, E. C.; Huntley, R. P.; Alam-Faruque, Y.; Sawford, T.; O'Donovan, C.; Martin, M. J.; Bely, B.; Browne, P.; Mun Chan, W.; Eberhardt, R.; Gardner, M; Laiho, K; Legge, D.; Magrane, M.; Pichler, K.

    2011-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a grea...

  10. Formalisation d'annotations produites par des apprenants

    OpenAIRE

    Mille, Dominique

    2005-01-01

    L'objet de cet article est la description d'une formalisation computable des annotations produites par des apprenants, représentée par une ontologie. Cette formalisation explicite la sémantique des annotations grâce à des attributs auxquels le lecteur devrait donner une valeur. Elle contient également les valeurs possibles de ces attributs. L'intérêt d'une telle formalisation est de couvrir toutes les annotations produites par des apprenants, et d'expliciter tout ce qui constitue leur sens, a...

  11. Annotation of the protein coding regions of the equine genome

    DEFF Research Database (Denmark)

    Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.; Zeng, Zheng; Liu, Jinze; Orlando, Ludovic Antoine Alexandre; MacLeod, James N.

    2015-01-01

    Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced m...... appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross...

  12. DDBJ in collaboration with mass-sequencing teams on annotation

    OpenAIRE

    Tateno, Y; Saitou, N; Okubo, K; Sugawara, H.; Gojobori, T

    2004-01-01

    In the past year, we at DDBJ (DNA Data Bank of Japan; http://www.ddbj.nig.ac.jp) collected and released 1 066 084 entries or 718 072 425 bases including the whole chromosome 22 of chimpanzee, the whole-genome shotgun sequences of silkworm and various others. On the other hand, we hosted workshops for human full-length cDNA annotation and participated in jamborees of mouse full-length cDNA annotation. The annotated data are made public at DDBJ. We are also in collaboration with a RIKEN team to...

  13. Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

    Energy Technology Data Exchange (ETDEWEB)

    Rutledge, Alexandra C.; Jones, Marcus B.; Chauhan, Sadhana; Purvine, Samuel O.; Sanford, James; Monroe, Matthew E.; Brewer, Heather M.; Payne, Samuel H.; Ansong, Charles; Frank, Bryan C.; Smith, Richard D.; Peterson, Scott; Motin, Vladimir L.; Adkins, Joshua N.

    2012-03-27

    Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. To date, the perceived value of manual curation for genome annotations is not offset by the real cost and time associated with the process. In order to balance the large number of sequences generated, the annotation process is now performed almost exclusively in an automated fashion for most genome sequencing projects. One possible way to reduce errors inherent to automated computational annotations is to apply data from 'omics' measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. This approach does require additional experimental and bioinformatics methods to include omics technologies; however, the approach is readily automatable and can benefit from rapid developments occurring in those research domains as well. The annotation process can be improved by experimental validation of transcription and translation and aid in the discovery of annotation errors. Here the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species, as is becoming common in sequencing efforts. Transcriptomic and proteomic data derived from three highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 previously incorrect protein-coding sequences (e.g., observed frameshifts, extended start sites, and translated pseudogenes) within the three current Yersinia genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent

  14. 76 FR 39396 - Pesticide Products; Receipt of Applications to Register New Uses

    Science.gov (United States)

    2011-07-06

    ... Nisso America Inc., 45 Broadway, Suite 2120, New York, NY 10006. Active ingredient: Acetamiprid.... Alexander Drive Research Triangle Park, NC 27709. Active ingredient: Trifloxystrobin. Proposed Use: Globe... AGENCY Pesticide Products; Receipt of Applications to Register New Uses AGENCY: Environmental...

  15. 77 FR 31875 - Certain Electronic Imaging Devices; Notice of Receipt of Complaint; Solicitation of Comments...

    Science.gov (United States)

    2012-05-30

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Certain Electronic Imaging Devices; Notice of Receipt of Complaint; Solicitation of Comments Relating to the Public Interest AGENCY: U.S. International Trade Commission. ACTION: Notice....

  16. 77 FR 32995 - Certain Electronic Imaging Devices Corrected: Notice of Receipt of Complaint; Solicitation of...

    Science.gov (United States)

    2012-06-04

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Certain Electronic Imaging Devices Corrected: Notice of Receipt of Complaint; Solicitation of Comments Relating to the Public Interest AGENCY: U.S. International Trade Commission. ACTION:...

  17. 77 FR 15390 - Certain Mobile Electronic Devices Incorporating Haptics; Receipt of Amended Complaint...

    Science.gov (United States)

    2012-03-15

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Certain Mobile Electronic Devices Incorporating Haptics; Receipt of Amended Complaint; Solicitation of Comments Relating to the Public Interest AGENCY: U.S. International Trade Commission....

  18. 78 FR 2437 - Corrected: Certain Cases For Portable Electronic Devices; Notice of Receipt of Complaint...

    Science.gov (United States)

    2013-01-11

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Corrected: Certain Cases For Portable Electronic Devices; Notice of Receipt of Complaint; Solicitation of Comments Relating to the Public Interest AGENCY: U.S. International Trade Commission....

  19. 75 FR 11875 - Spirotetramat; Receipt of Applications for Emergency Exemptions, Solicitation of Public Comment

    Science.gov (United States)

    2010-03-12

    ... development, implementation, and enforcement of environmental laws, regulations, and policies. To help address... disproportionately high and adverse human health impacts or environmental effects from exposure to the pesticide... AGENCY Spirotetramat; Receipt of Applications for Emergency Exemptions, Solicitation of Public...

  20. 48 CFR 32.609 - Delays in receipt of notices or demands.

    Science.gov (United States)

    2010-10-01

    ... REGULATION GENERAL CONTRACTING REQUIREMENTS CONTRACT FINANCING Contract Debts 32.609 Delays in receipt of... delays in the mail), the date of the debt and accrual of interest shall be extended to a time that...

  1. 76 FR 72215 - Certain Products Containing Interactive Program Guide and Parental Controls Technology; Receipt...

    Science.gov (United States)

    2011-11-22

    ... COMMISSION Certain Products Containing Interactive Program Guide and Parental Controls Technology; Receipt of... received a complaint entitled In Re Certain Products Containing Interactive Program Guide and Parental... certain products containing interactive program guide and parental controls technology. The...

  2. 77 FR 19032 - Certain Semiconductor Integrated Circuit Devices and Products Containing Same Notice of Receipt...

    Science.gov (United States)

    2012-03-29

    ... COMMISSION Certain Semiconductor Integrated Circuit Devices and Products Containing Same Notice of Receipt of... received a complaint entitled Certain Semiconductor Integrated Circuit Devices and Products Containing Same... circuit devices and products containing same. The complaint names as respondents Intersil Corporation...

  3. 7 CFR 993.172 - Reports of holdings, receipts, uses, and shipments.

    Science.gov (United States)

    2010-01-01

    ... identification tag assigned to such prunes, the numbers and dates of door receipts or weight certificates or any other identifying documents assigned to such prunes, the net weight shown on each, the total net...

  4. 26 CFR 1.927(b)-1T - Temporary regulations; Definition of gross receipts.

    Science.gov (United States)

    2010-04-01

    ... arrangement, RS could exercise its option and exclude the sale of export property A. Since F is no longer...,500 N's lease receipts for machines manufactured by M (without reduction for depreciation and...

  5. 78 FR 30934 - Certain Consumer Electronics With Display and Processing Capabilities; Notice of Receipt of...

    Science.gov (United States)

    2013-05-23

    ... COMMISSION Certain Consumer Electronics With Display and Processing Capabilities; Notice of Receipt of... received a complaint entitled Certain Consumer Electronics with Display and Processing Capabilities, DN... within the United States after importation of certain consumer electronics with display and...

  6. 77 FR 18860 - Certain Consumer Electronics, Including Mobile Phones and Tablets; Notice of Receipt of Complaint...

    Science.gov (United States)

    2012-03-28

    ... COMMISSION Certain Consumer Electronics, Including Mobile Phones and Tablets; Notice of Receipt of Complaint... complaint entitled Certain Consumer Electronics, Including Mobile Phones and Tablets, DN 2885; the... importation of certain consumer electronics, including mobile phones and tablets. The complaint names...

  7. Lunar Sulfur Capture System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Sulfur Capture System (LSCS) is an innovative method to capture greater than 90 percent of sulfur gases evolved during thermal treatment of lunar soils....

  8. Answering questions about archived, annotated meetings

    OpenAIRE

    Ailomaa, Marita

    2009-01-01

    Retrieving information from archived meetings is a new domain of information retrieval that has received increasing attention in the past few years. Search in spontaneous spoken conversations has been recognized as more difficult than text-based document retrieval because meeting discussions contain two levels of information: the content itself, i.e. what topics are discussed, but also the argumentation process, i.e. what conflicts are resolved and what decisions are made. To capture the rich...

  9. The effect of health literacy on knowledge and receipt of colorectal cancer screening: a survey study

    OpenAIRE

    Pignone Michael P; McCoy Thomas P; Brownlee Caroline D; Miller David P

    2007-01-01

    Abstract Background An estimated one-half of Americans have limited health literacy skills. Low literacy has been associated with less receipt of preventive services, but its impact on colorectal cancer (CRC) screening is unclear. We sought to determine whether low literacy affects patients' knowledge or receipt of CRC screening. Methods Pilot survey study of patients aged 50 years and older at a large, university-affiliated internal medicine practice. We assessed patients' knowledge and rece...

  10. Pathways to Service Receipt: Modeling Parent Help-Seeking for Childhood Mental Health Problems

    OpenAIRE

    Godoy, Leandra; Mian, Nicholas D.; Eisenhower, Abbey S.; Carter, Alice S.

    2014-01-01

    Understanding parent appraisals of child behavior problems and parental help-seeking can reduce unmet mental health needs. Research has examined individual contributors to help-seeking and service receipt, but use of structural equation modeling (SEM) is rare. SEM was used to examine parents’ appraisal of child behavior, thoughts about seeking help, and receipt of professional services in a diverse, urban sample (N = 189) recruited from women infant and children offices. Parents of children 1...

  11. Determinants of international tourism receipts and technical efficiency of tourism sector in Malaysia, Thailand and Singapore

    OpenAIRE

    Prad Anumat; Anuphak Saosaowapak

    2013-01-01

    The purpose of this study is to interpret factors that affect the change of international tourism receipt using the stochastic frontier model with panel data and to study the technical efficiency of tourism sector in Malaysia, Thailand, and Singapore. The secondary data from 2001 to 2010 are used for this study. Significant factors that affect the change of international tourism receipts are (1) available seat kilometer, (2) government spending on transportation and telecommunication, (3) per...

  12. Annotation et rature Annotation and Deletion: Outline of a Sociology of Forms

    Directory of Open Access Journals (Sweden)

    Axel Pohn-Weidinger

    2012-05-01

    Full Text Available Ce texte interroge les traces graphiques laissées sur un corpus de formulaires de demande de logement social telles qu’annotations, ratures, biffures et commentaires griffonnés. L’étude de ces traces, laissées en marge des catégories de l’imprimé administratif lors du remplissage, montre le recours au droit comme une opération problématique. Pour les administrés, il s’agit de décrire leur situation de vie de sorte à établir l’éligibilité à un droit, mais bien souvent il est impossible de traduire celle-ci dans les catégories préétablies du formulaire. Les annotations et commentaires laissés sur le formulaire tentent alors d’ouvrir la catégorisation juridique des situations à une prise en compte de la singularité des circonstances de vie du demandeur. Elles montrent le recours au droit comme un accomplissement réflexif, un travail à la fois sur sa propre perception de sa situation et sur celle que l’institution offre à travers le formulaire, et dont la négociation et la mise en œuvre sont au cœur de la production du dossier administratif.This text examines the graphical traces left on a collection of social housing application forms: annotations, erasures, crossed-out words and scribbled-out comments. The study of these traces, left in the margins of the categories on printed administrative forms in the process of being completed, shows the exercising of a right as a problematic operation. Citizens making applications must describe their living situation in a way that will establish their eligibility for a right, but quite often it is impossible to convey this through the form’s predetermined categories. The annotations and comments left on the form attempt to open the legal classification of situations to considering the uniqueness of the applicant’s living circumstances. They show the use of a right as an introspective accomplishment, requiring applicants to work both on their own perception of

  13. Annotated Bibliography of Recent Research Related to Academic Advising

    Science.gov (United States)

    Mottarella, Karen, Comp.

    2011-01-01

    This article presents an annotated bibliography of recent research related to academic advising. It includes research papers that focus on advising and a special section of the "Journal of Career Development" that is devoted to multicultural graduate advising relationships.

  14. Geothermal wetlands: an annotated bibliography of pertinent literature

    Energy Technology Data Exchange (ETDEWEB)

    Stanley, N.E.; Thurow, T.L.; Russell, B.F.; Sullivan, J.F.

    1980-05-01

    This annotated bibliography covers the following topics: algae, wetland ecosystems; institutional aspects; macrophytes - general, production rates, and mineral absorption; trace metal absorption; wetland soils; water quality; and other aspects of marsh ecosystems. (MHR)

  15. OntoELAN: An Ontology-based Linguistic Multimedia Annotator

    CERN Document Server

    Chebotko, Artem; Lu, Shiyong; Fotouhi, Farshad; Aristar, Anthony; Brugman, Hennie; Klassmann, Alexander; Sloetjes, Han; Russel, Albert; Wittenburg, Peter

    2009-01-01

    Despite its scientific, political, and practical value, comprehensive information about human languages, in all their variety and complexity, is not readily obtainable and searchable. One reason is that many language data are collected as audio and video recordings which imposes a challenge to document indexing and retrieval. Annotation of multimedia data provides an opportunity for making the semantics explicit and facilitates the searching of multimedia documents. We have developed OntoELAN, an ontology-based linguistic multimedia annotator that features: (1) support for loading and displaying ontologies specified in OWL; (2) creation of a language profile, which allows a user to choose a subset of terms from an ontology and conveniently rename them if needed; (3) creation of ontological tiers, which can be annotated with profile terms and, therefore, corresponding ontological terms; and (4) saving annotations in the XML format as Multimedia Ontology class instances and, linked to them, class instances of o...

  16. A Machine Learning Based Analytical Framework for Semantic Annotation Requirements

    CERN Document Server

    Hassanzadeh, Hamed; 10.5121/ijwest.2011.2203

    2011-01-01

    The Semantic Web is an extension of the current web in which information is given well-defined meaning. The perspective of Semantic Web is to promote the quality and intelligence of the current web by changing its contents into machine understandable form. Therefore, semantic level information is one of the cornerstones of the Semantic Web. The process of adding semantic metadata to web resources is called Semantic Annotation. There are many obstacles against the Semantic Annotation, such as multilinguality, scalability, and issues which are related to diversity and inconsistency in content of different web pages. Due to the wide range of domains and the dynamic environments that the Semantic Annotation systems must be performed on, the problem of automating annotation process is one of the significant challenges in this domain. To overcome this problem, different machine learning approaches such as supervised learning, unsupervised learning and more recent ones like, semi-supervised learning and active learn...

  17. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

    Science.gov (United States)

    Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  18. An Annotated Checklist of the Fishes of Samoa

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — All fishes currently known from the Samoan Islands are listed by their scientific and Samoan names. Species entries are annotated to include the initial Samoan...

  19. Annotation sémantique de pages web

    OpenAIRE

    Tenier, Sylvain; Napoli, Amedeo; Polanco, Xavier; Toussaint, Yannick

    2006-01-01

    Cet article présente un système automatique d'annotation sémantique de pages web. Les systèmes d'annotation automatique existants sont essentiellement syntaxiques, même lorsque les travaux visent à produire une annotation sémantique. La prise en compte d'informations sémantiques sur le domaine pour l'annotation d'un élément dans une page web à partir d'une ontologie suppose d'aborder conjointement deux problèmes : (1) l'identification de la structure syntaxique caractérisant cet élément dans ...

  20. Annotation Method (AM): SE28_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2013A ...

  1. Annotation Method (AM): SE4_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  2. Annotation Method (AM): SE15_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAOT201112 ...

  3. Annotation Method (AM): SE26_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  4. Annotation Method (AM): SE34_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  5. Annotation Method (AM): SE10_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  6. Annotation Method (AM): SE27_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  7. Annotation Method (AM): SE16_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  8. Annotation Method (AM): SE32_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  9. Annotation Method (AM): SE2_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2011A ...

  10. Annotation Method (AM): SE6_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAOT2012A ...

  11. Annotation Method (AM): SE11_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  12. Annotation Method (AM): SE12_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  13. Annotation Method (AM): SE14_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  14. Annotation Method (AM): SE13_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  15. Annotation Method (AM): SE20_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. Terms of chemical category

  16. Annotation Method (AM): SE17_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  17. Annotation Method (AM): SE5_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  18. Annotation Method (AM): SE30_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  19. Annotation Method (AM): SE31_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  20. Annotation Method (AM): SE33_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  1. Annotation Method (AM): SE35_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  2. Annotation Method (AM): SE25_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  3. Annotation Method (AM): SE36_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  4. Annotation Method (AM): SE8_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  5. Annotation Method (AM): SE3_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2011A ...

  6. Annotation Method (AM): SE1_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2011A ...

  7. Annotation Method (AM): SE9_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  8. Annotation Method (AM): SE7_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAOT2012A ...

  9. Annotation Method (AM): SE29_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2013A ...

  10. Creating New Medical Ontologies for Image Annotation A Case Study

    CERN Document Server

    Stanescu, Liana; Brezovan, Marius; Mihai, Cristian Gabriel

    2012-01-01

    Creating New Medical Ontologies for Image Annotation focuses on the problem of the medical images automatic annotation process, which is solved in an original manner by the authors. All the steps of this process are described in detail with algorithms, experiments and results. The original algorithms proposed by authors are compared with other efficient similar algorithms. In addition, the authors treat the problem of creating ontologies in an automatic way, starting from Medical Subject Headings (MESH). They have presented some efficient and relevant annotation models and also the basics of the annotation model used by the proposed system: Cross Media Relevance Models. Based on a text query the system will retrieve the images that contain objects described by the keywords.

  11. Collaborative Semantic Annotation of Images : Ontology-Based Model

    Directory of Open Access Journals (Sweden)

    Damien E. ZOMAHOUN

    2015-12-01

    Full Text Available In the quest for models that could help to represen t the meaning of images, some approaches have used contextual knowledge by building semantic hierarchi es. Others have resorted to the integration of imag es analysis improvement knowledge and images interpret ation using ontologies. The images are often annotated with a set of keywords (or ontologies, w hose relevance remains highly subjective and relate d to only one interpretation (one annotator. However , an image can get many associated semantics because annotators can interpret it differently. Th e purpose of this paper is to propose a collaborati ve annotation system that brings out the meaning of im ages from the different interpretations of annotato rs. The different works carried out in this paper lead to a semantic model of an image, i.e. the different means that a picture may have. This method relies o n the different tools of the Semantic Web, especial ly ontologies.

  12. 06491 Summary -- Digital Historical Corpora- Architecture, Annotation, and Retrieval

    OpenAIRE

    Burnard, Lou; Dobreva, Milena; Fuhr, Norbert; Lüdeling, Anke

    2007-01-01

    The seminar "Digital Historical Corpora" brought together scholars from (historical) linguistics, (historical) philology, computational linguistics and computer science who work with collections of historical texts. The issues that were discussed include digitization, corpus design, corpus architecture, annotation, search, and retrieval.

  13. Descriptive Cataloging: A Selected, Annotated Bibliography, 1984-1985.

    Science.gov (United States)

    Cook, C. Donald; Jones, Ellen

    1986-01-01

    This annotated bibliography of materials published during 1984-1985 on descriptive cataloging covers bibliographic control, Anglo American Cataloging Rules, 2nd edition (AACR2), specific types of materials, authority control, retrospective conversion, management issues, expert systems, and manuals. (EM)

  14. TRANSPORTATION CASK RECEIPT/RETURN FACILITY CRITICALITY SAFETY EVALUATIONS

    Energy Technology Data Exchange (ETDEWEB)

    C.E. Sanders

    2005-04-26

    The purpose of this design calculation is to demonstrate that the handling operations of transportation casks performed in the Transportation Cask Receipt and Return Facility (TCRRF) and Buffer Area meet the nuclear criticality safety design criteria specified in the ''Project Design Criteria (PDC) Document'' (BSC [Bechtel SAIC Company] 2004 [DIRS 171599], Section 4.9.2.2), and the functional nuclear criticality safety requirement described in the ''Transportation Cask Receipt/Return Facility Description Document'' (BSC 2004 [DIRS 170217], Section 3.2.3). Specific scope of work contained in this activity consists of the following items: (1) Evaluate criticality effects for both dry and fully flooded conditions pertaining to TCRRF and Buffer Area operations for defense in depth. (2) Evaluate Category 1 and 2 event sequences for the TCRRF as identified in the ''Categorization of Event Sequences for License Application'' (BSC 2004 [DIRS 167268], Section 7). This evaluation includes credible fuel reconfiguration conditions. In addition to the scope of work listed above, an evaluation was also performed of modeling assumptions for commercial spent nuclear fuel (CSNF) regarding inclusion of plenum and end regions of the active fuel. This calculation is limited to CSNF and US Department of Energy (DOE) SNF. it should be mentioned that the latter waste form is evaluated more in depth in the ''Canister Handling Facility Criticality Safety Calculations (BSC 2004 [DIRS 167614]). Further, the design and safety analyses of the naval SNF canisters are the responsibility of the US Department of the Navy (Naval Nuclear Propulsion Program) and will not be included in this document. In addition, this calculation is valid for the current design of the TCRRF and Buffer Area and may not reflect the ongoing design evolution of the facility. However, it is anticipated that design changes to the facility layout will

  15. GIFtS: annotation landscape analysis with GeneCards

    Directory of Open Access Journals (Sweden)

    Dalah Irina

    2009-10-01

    Full Text Available Abstract Background Gene annotation is a pivotal component in computational genomics, encompassing prediction of gene function, expression analysis, and sequence scrutiny. Hence, quantitative measures of the annotation landscape constitute a pertinent bioinformatics tool. GeneCards® is a gene-centric compendium of rich annotative information for over 50,000 human gene entries, building upon 68 data sources, including Gene Ontology (GO, pathways, interactions, phenotypes, publications and many more. Results We present the GeneCards Inferred Functionality Score (GIFtS which allows a quantitative assessment of a gene's annotation status, by exploiting the unique wealth and diversity of GeneCards information. The GIFtS tool, linked from the GeneCards home page, facilitates browsing the human genome by searching for the annotation level of a specified gene, retrieving a list of genes within a specified range of GIFtS value, obtaining random genes with a specific GIFtS value, and experimenting with the GIFtS weighting algorithm for a variety of annotation categories. The bimodal shape of the GIFtS distribution suggests a division of the human gene repertoire into two main groups: the high-GIFtS peak consists almost entirely of protein-coding genes; the low-GIFtS peak consists of genes from all of the categories. Cluster analysis of GIFtS annotation vectors provides the classification of gene groups by detailed positioning in the annotation arena. GIFtS also provide measures which enable the evaluation of the databases that serve as GeneCards sources. An inverse correlation is found (for GIFtS>25 between the number of genes annotated by each source, and the average GIFtS value of genes associated with that source. Three typical source prototypes are revealed by their GIFtS distribution: genome-wide sources, sources comprising mainly highly annotated genes, and sources comprising mainly poorly annotated genes. The degree of accumulated knowledge for a

  16. Combined evidence annotation of transposable elements in genome sequences.

    Directory of Open Access Journals (Sweden)

    Hadi Quesneville

    2005-07-01

    Full Text Available Transposable elements (TEs are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1, and we found a substantially higher number of TEs (n = 6,013 than previously identified (n = 1,572. Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1. We also estimated that 518 TE copies (8.6% are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other

  17. Semantic annotation of biological concepts interplaying microbial cellular responses

    Directory of Open Access Journals (Sweden)

    Carreira Rafael

    2011-11-01

    Full Text Available Abstract Background Automated extraction systems have become a time saving necessity in Systems Biology. Considerable human effort is needed to model, analyse and simulate biological networks. Thus, one of the challenges posed to Biomedical Text Mining tools is that of learning to recognise a wide variety of biological concepts with different functional roles to assist in these processes. Results Here, we present a novel corpus concerning the integrated cellular responses to nutrient starvation in the model-organism Escherichia coli. Our corpus is a unique resource in that it annotates biomedical concepts that play a functional role in expression, regulation and metabolism. Namely, it includes annotations for genetic information carriers (genes and DNA, RNA molecules, proteins (transcription factors, enzymes and transporters, small metabolites, physiological states and laboratory techniques. The corpus consists of 130 full-text papers with a total of 59043 annotations for 3649 different biomedical concepts; the two dominant classes are genes (highest number of unique concepts and compounds (most frequently annotated concepts, whereas other important cellular concepts such as proteins account for no more than 10% of the annotated concepts. Conclusions To the best of our knowledge, a corpus that details such a wide range of biological concepts has never been presented to the text mining community. The inter-annotator agreement statistics provide evidence of the importance of a consolidated background when dealing with such complex descriptions, the ambiguities naturally arising from the terminology and their impact for modelling purposes. Availability is granted for the full-text corpora of 130 freely accessible documents, the annotation scheme and the annotation guidelines. Also, we include a corpus of 340 abstracts.

  18. Integrative annotation of chromatin elements from ENCODE data

    OpenAIRE

    Hoffman, Michael M.; Ernst, Jason; Wilder, Steven P.; Kundaje, Anshul; Harris, Robert S.; Libbrecht, Max; Giardine, Belinda; Ellenbogen, Paul M.; Bilmes, Jeffrey A.; Birney, Ewan; Hardison, Ross C.; Dunham, Ian; Kellis, Manolis; Noble, William Stafford

    2012-01-01

    The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learnin...

  19. A Non-Null Annotation Inferencer for Java Bytecode

    OpenAIRE

    Hubert, Laurent

    2008-01-01

    We present a non-null annotations inferencer for the Java bytecode language. We previously proposed an analysis to infer non-null annotations and proved it soundness and completeness with respect to a state of the art type system. This paper proposes extensions to our former analysis in order to deal with the Java bytecode language. We have implemented both analyses and compared their behaviour on several benchmarks. The results show a substantial improvement in the precision and, despite bei...

  20. CATMAID: collaborative annotation toolkit for massive amounts of image data

    OpenAIRE

    Saalfeld, Stephan; Cardona, Albert; Hartenstein, Volker; Tomančák, Pavel

    2009-01-01

    Summary: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps™, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by boo...

  1. Classification and Image Annotation for Bridging the Semantic Gap

    OpenAIRE

    Muda, Zurina

    2007-01-01

    The use of digital images is rapidly increasing in digital archives, community databases, as well as on the Web. This creates new challenges for image management and retrieval and promotes the importance of automatic image classification and annotation research. In general current content-based image retrieval methods are still struggling to deal with the semantic gap between low-level visual features and the high-level abstractions perceived by humans. Manual annotation is typically a diffic...

  2. Developing a lexical resource annotated with semantic roles for Portuguese

    OpenAIRE

    Leonardo Zilio; Carlos Ramisch; Maria José Bocorny Finatto

    2014-01-01

    The objectives of this study are as follows: to present a methodology for the development of a lexical resource with semantic information; to compare semantic roles in specialized and non-specialized language; and to observe the semantic role labeling (SRL) made by a group of annotators. Two experiments revolving around SRL in Portuguese were developed: a comparison between data in specialized and non-specialized language corpora; and an annotation evaluation for verifying the agreement among...

  3. Annotation Method (AM): SE40_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available se search. Peaks with no hit to these databases are then selected to secondary sear...ch using EX-HR2 (http://webs2.kazusa.or.jp/mfsearcher/) databases. After the database search processes, each database...SE40_AM1 PowerGet annotation In annotation process, KEGG, KNApSAcK and LipidMAPS are used for primary databa

  4. Comparative omics-driven genome annotation refinement: application across Yersiniae.

    Directory of Open Access Journals (Sweden)

    Alexandra C Schrimpe-Rutledge

    Full Text Available Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic to the un-annotated genome with a proteogenomic-based approach. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+ was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation.

  5. Computational evaluation of TIS annotation for prokaryotic genomes

    OpenAIRE

    Zhu Huaiqiu; Ju Li-Ning; Zheng Xiaobin; Hu Gang-Qing; She Zhen-Su

    2008-01-01

    Abstract Background Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. Results Based on a homogeneity assumption that gene translation-related signals are uniformly distributed across a genome, we have established a computational method for a large-scale quantitative assessment o...

  6. Automatically Annotated Mapping for Indoor Mobile Robot Applications

    DEFF Research Database (Denmark)

    Özkil, Ali Gürcan; Howard, Thomas J.

    2012-01-01

    This paper presents a new and practical method for mapping and annotating indoor environments for mobile robot use. The method makes use of 2D occupancy grid maps for metric representation, and topology maps to indicate the connectivity of the ‘places-of-interests’ in the environment. Novel use of...... consistent, automatically annotated hybrid metric-topological maps that is needed by mobile service robots....

  7. Experimental Polish-Lithuanian Corpus with the Semantic Annotation Elements

    Directory of Open Access Journals (Sweden)

    Danuta Roszko

    2015-06-01

    Full Text Available Experimental Polish-Lithuanian Corpus with the Semantic Annotation ElementsIn the article the authors present the experimental Polish-Lithuanian corpus (ECorpPL-LT formed for the idea of Polish-Lithuanian theoretical contrastive studies, a Polish-Lithuanian electronic dictionary, and as help for a sworn translator. The semantic annotation being brought into ECorpPL-LT is extremely useful in Polish-Lithuanian contrastive studies, and also proves helpful in translation work.

  8. JAABA: interactive machine learning for automatic annotation of animal behavior

    OpenAIRE

    Kabra, Mayank; Robie, Alice A.; Rivera-Alba, Marta; Branson, Steven; Branson, Kristin

    2013-01-01

    We present a machine learning-based system for automatically computing interpretable, quantitative measures of animal behavior. Through our interactive system, users encode their intuition about behavior by annotating a small set of video frames. These manual labels are converted into classifiers that can automatically annotate behaviors in screen-scale data sets. Our general-purpose system can create a variety of accurate individual and social behavior classifiers for different organisms, in...

  9. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  10. Experimental Polish-Lithuanian Corpus with the Semantic Annotation Elements

    OpenAIRE

    Danuta Roszko; Roman Roszko

    2015-01-01

    Experimental Polish-Lithuanian Corpus with the Semantic Annotation ElementsIn the article the authors present the experimental Polish-Lithuanian corpus (ECorpPL-LT) formed for the idea of Polish-Lithuanian theoretical contrastive studies, a Polish-Lithuanian electronic dictionary, and as help for a sworn translator. The semantic annotation being brought into ECorpPL-LT is extremely useful in Polish-Lithuanian contrastive studies, and also proves helpful in translation work.

  11. GELATO and SAGE: An Integrated Framework for MS Annotation

    OpenAIRE

    AlJadda, Khalifeh; Ranzinger, Rene; Porterfield, Melody; Weatherly, Brent; Korayem, Mohammed; Miller, John A.; Rasheed, Khaled; Kochut, Krys J; York, William S.

    2015-01-01

    Several algorithms and tools have been developed to (semi) automate the process of glycan identification by interpreting Mass Spectrometric data. However, each has limitations when annotating MSn data with thousands of MS spectra using uncurated public databases. Moreover, the existing tools are not designed to manage MSn data where n > 2. We propose a novel software package to automate the annotation of tandem MS data. This software consists of two major components. The first, is a free, sem...

  12. Synovectomy by Neutron capture

    International Nuclear Information System (INIS)

    The Synovectomy by Neutron capture has as purpose the treatment of the rheumatoid arthritis, illness which at present does not have a definitive curing. This therapy requires a neutron source for irradiating the articulation affected. The energy spectra and the intensity of these neutrons are fundamental since these neutrons induce nuclear reactions of capture with Boron-10 inside the articulation and the freely energy of these reactions is transferred at the productive tissue of synovial liquid, annihilating it. In this work it is presented the neutron spectra results obtained with moderator packings of spherical geometry which contains in its center a Pu239 Be source. The calculations were realized through Monte Carlo method. The moderators assayed were light water, heavy water base and the both combination of them. The spectra obtained, the average energy, the neutron total number by neutron emitted by source, the thermal neutron percentage and the dose equivalent allow us to suggest that the moderator packing more adequate is what has a light water thickness 0.5 cm (radius 2 cm) and 24.5 cm heavy water (radius 26.5 cm). (Author)

  13. Stakeholder Confidence and Radioactive Waste management - An annotated glossary of key terms

    International Nuclear Information System (INIS)

    The OECD Nuclear Energy Agency (NEA) Forum on Stakeholder Confidence (FSC) Annotated Glossary is a review of concepts central to societal decision making about radioactive waste management. It records the evolution in understanding that has taken place in the group as the FSC has worked with these concepts over time. This should be a useful resource not only for new FSC participants but also for others: this annotated glossary forms a good reference handbook for future texts regarding societal aspects of radioactive waste management and its governance. Each glossary entry is structured, to the extent possible, as follows: - The term and its variants, if any, in FSC literature are identified. - The common FSC understanding of the concept and any guidance are captured, based upon a review of all FSC documents to date. - Any evolution of the concept observed over the decade of FSC work is analysed. - The FSC interpretation of the symbolic dimension is explored. - The current status of outlook in the FSC, and intended activities according to the current Programme of Work (2010 and beyond) are assessed. Overall, although different persons and groups may assign different meanings to words, and although terminology will continue to evolve, this glossary is the FSC's 'state-of-the-art' guide to key terms in use. As such, it should prove to be a handy reference for all those interested in the governance of radioactive waste management

  14. Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase.

    Science.gov (United States)

    Jungo, Florence; Bairoch, Amos

    2005-03-01

    The Tox-Prot program was initiated in order to provide the scientific community a summary of the current knowledge on animal protein toxins. The aim of this program is to systematically annotate all proteins which act as toxins and are produced by venomous and poisonous animals. Venomous animals such as snakes, scorpions, spiders, jellyfish, insects, cone snails, sea anemones, lizards, some fish, and platypus are equipped with a specialized organ to inject venom in their prey. In contrast, poisonous animals such as some fish or worms, lack such organs. Each toxin is annotated according to the quality standards of Swiss-Prot. This means providing a wealth of information that includes the description of the function, domain structure, subcellular location, tissue specificity, variants, similarities to other proteins, keywords, etc. In the framework of this program, particular care has been made to capture what is known on the function and mode of action, posttranslational modifications and 3D structural data which are all relatively abundant in the field of protein toxins. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to Swiss-Prot concerning toxins at Tox-Prot@isb-sib.ch. More information on Tox-Prot can be found at http://www.expasy.org/sprot/tox-prot. PMID:15683867

  15. GENCODE: the reference human genome annotation for The ENCODE Project.

    Science.gov (United States)

    Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J

    2012-09-01

    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. PMID:22955987

  16. A Machine Learning Based Analytical Framework for Semantic Annotation Requirements

    Directory of Open Access Journals (Sweden)

    Hamed Hassanzadeh

    2011-04-01

    Full Text Available The Semantic Web is an extension of the current web in which information is given well-defined meaning.The perspective of Semantic Web is to promote the quality and intelligence of the current web by changingits contents into machine understandable form. Therefore, semantic level information is one of thecornerstones of the Semantic Web. The process of adding semantic metadata to web resources is calledSemantic Annotation. There are many obstacles against the Semantic Annotation, such as multilinguality,scalability, and issues which are related to diversity and inconsistency in content of different web pages.Due to the wide range of domains and the dynamic environments that the Semantic Annotation systemsmust be performed on, the problem of automating annotation process is one of the significant challenges inthis domain. To overcome this problem, different machine learning approaches such as supervisedlearning, unsupervised learning and more recent ones like, semi-supervised learning and active learninghave been utilized. In this paper we present an inclusive layered classification of Semantic Annotationchallenges and discuss the most important issues in this field. Also, we review and analyze machinelearning applications for solving semantic annotation problems. For this goal, the article tries to closelystudy and categorize related researches for better understanding and to reach a framework that can mapmachine learning techniques into the Semantic Annotation challenges and requirements.

  17. AUTOMATIC ANNOTATION OF QUERY RESULTS FROM DEEP WEB DATABASE

    Directory of Open Access Journals (Sweden)

    Chaitanya Bhosale

    2015-08-01

    Full Text Available In recent years, web database extraction and annotation has received more attention from the database . When search query is submitted to the interface the search result page is generated. Search Result Records (SRRs are the result pages obtained from web database (WDB and these SRRs are used to display the result for each query. Every SRRs contains multiple data units similar to one semantic. These sea rch results can be used in many web applications such as comparison shopping, data integration, metaquerying. But to make these applications successful the search pages are annotated in a meaningful fashion. To reduce human efforts, an automatic annotation approach is used. In which, we first aligns the data units on result records into various groups such that the information in the similar group have same meaning. After this we annotate each and every group in different domains and obtain the final annota tion after aggregating them. In addition, we use New CTVS technique for extraction of QRRs from a query result page, in which we use optional labeling and dynamic tagging for the improvement. Then an annotation wrapper is generated automatically which is u sed for annotation new result records from the same web database

  18. Deep Question Answering for protein annotation.

    Science.gov (United States)

    Gobeill, Julien; Gaudinat, Arnaud; Pasche, Emilie; Vishnyakova, Dina; Gaudet, Pascale; Bairoch, Amos; Ruch, Patrick

    2015-01-01

    Biomedical professionals have access to a huge amount of literature, but when they use a search engine, they often have to deal with too many documents to efficiently find the appropriate information in a reasonable time. In this perspective, question-answering (QA) engines are designed to display answers, which were automatically extracted from the retrieved documents. Standard QA engines in literature process a user question, then retrieve relevant documents and finally extract some possible answers out of these documents using various named-entity recognition processes. In our study, we try to answer complex genomics questions, which can be adequately answered only using Gene Ontology (GO) concepts. Such complex answers cannot be found using state-of-the-art dictionary- and redundancy-based QA engines. We compare the effectiveness of two dictionary-based classifiers for extracting correct GO answers from a large set of 100 retrieved abstracts per question. In the same way, we also investigate the power of GOCat, a GO supervised classifier. GOCat exploits the GOA database to propose GO concepts that were annotated by curators for similar abstracts. This approach is called deep QA, as it adds an original classification step, and exploits curated biological data to infer answers, which are not explicitly mentioned in the retrieved documents. We show that for complex answers such as protein functional descriptions, the redundancy phenomenon has a limited effect. Similarly usual dictionary-based approaches are relatively ineffective. In contrast, we demonstrate how existing curated data, beyond information extraction, can be exploited by a supervised classifier, such as GOCat, to massively improve both the quantity and the quality of the answers with a +100% improvement for both recall and precision. Database URL: http://eagl.unige.ch/DeepQA4PA/. PMID:26384372

  19. Capturing the Daylight Dividend

    Energy Technology Data Exchange (ETDEWEB)

    Peter Boyce; Claudia Hunter; Owen Howlett

    2006-04-30

    Capturing the Daylight Dividend conducted activities to build market demand for daylight as a means of improving indoor environmental quality, overcoming technological barriers to effective daylighting, and informing and assisting state and regional market transformation and resource acquisition program implementation efforts. The program clarified the benefits of daylight by examining whole building systems energy interactions between windows, lighting, heating, and air conditioning in daylit buildings, and daylighting's effect on the human circadian system and productivity. The project undertook work to advance photosensors, dimming systems, and ballasts, and provided technical training in specifying and operating daylighting controls in buildings. Future daylighting work is recommended in metric development, technology development, testing, training, education, and outreach.

  20. Robust automated knowledge capture.

    Energy Technology Data Exchange (ETDEWEB)

    Stevens-Adams, Susan Marie; Abbott, Robert G.; Forsythe, James Chris; Trumbo, Michael Christopher Stefan; Haass, Michael Joseph; Hendrickson, Stacey M. Langfitt

    2011-10-01

    This report summarizes research conducted through the Sandia National Laboratories Robust Automated Knowledge Capture Laboratory Directed Research and Development project. The objective of this project was to advance scientific understanding of the influence of individual cognitive attributes on decision making. The project has developed a quantitative model known as RumRunner that has proven effective in predicting the propensity of an individual to shift strategies on the basis of task and experience related parameters. Three separate studies are described which have validated the basic RumRunner model. This work provides a basis for better understanding human decision making in high consequent national security applications, and in particular, the individual characteristics that underlie adaptive thinking.

  1. Particle capture device

    Energy Technology Data Exchange (ETDEWEB)

    Jayne, John T.; Worsnop, Douglas R.

    2016-02-23

    In example embodiments, particle collection efficiency in aerosol analyzers and other particle measuring instruments is improved by a particle capture device that employs multiple collisions to decrease momentum of particles until the particles are collected (e.g., vaporized or come to rest). The particle collection device includes an aperture through which a focused particle beam enters. A collection enclosure is coupled to the aperture and has one or more internal surfaces against which particles of the focused beam collide. One or more features are employed in the collection enclosure to promote particles to collide multiple times within the enclosure, and thereby be vaporized or come to rest, rather than escape through the aperture.

  2. Determination of cost-effective receipt rates for an MRS and the repository

    International Nuclear Information System (INIS)

    This paper describes results of a comprehensive logistics and cost analysis to determine if there are potential benefits to the US high-level waste management system for spent fuel receipt rates to a Monitored Retrievable Storage (MRS) facility or the repository other than the current 3000 MTU/yr design-basis receipt rate. Cases considering repository startup dates of 2010 and 2015 and MRS startup dates of 1998 and 3 years prior to the repository have been evaluated, and receipt rates ranging from 1500 to 6000 MTU/yr have been considered for both the MRS and the repository. Higher receipt rates appear to be economically justified for both the repository and an MRS. For a repository-only system, minimum costs are found at a repository receipt rate of 6000 MTU/yr. When a storage-only MRS is included in the system, minimum system costs are also achieved at a repository receipt rate of 6000 MTU/yr. However, the MRS receipt rate for minimum system costs, which ranges between 3500 and 6000 MTU/yr, depends on both the MRS startup date and whether or not the storage capacity of the MRS it constrained. With a 1998 unconstrained MRS and a 2010 repository, the added cost of providing the MRS is offset by at-reactor storage cost reductions, and the total system cost of $10.1 billion is only slightly higher than that for the repository-only system. If the MRS storage capacity is constrained to a maximum of 15,000 MTU, then this cost increases to $10.4 billion

  3. Construction of an annotated corpus to support biomedical information extraction

    Directory of Open Access Journals (Sweden)

    McNaught John

    2009-10-01

    Full Text Available Abstract Background Information Extraction (IE is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources. Results We have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs. For each event instance, all participants (arguments in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology. To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified. Using the scheme, we have created the Gene Regulation Event Corpus (GREC, consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists. A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%. Conclusion The GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions. As such, it is specifically designed to support bio-specific tool and resource development. It has already been used to acquire semantic frames for inclusion within the BioLexicon (a lexical, terminological resource to aid biomedical text mining. Initial experiments have also shown that the corpus may

  4. 75 FR 60447 - Certain New Chemicals; Receipt and Status Information

    Science.gov (United States)

    2010-09-30

    ... will be automatically captured and included as part of the comment that is placed in the docket and... / epichlorohydrin epoxy polymer reaction product with amines, neutralized with methane sulfonic acid. P-08-0187 07.... colorant for colora acid, 4-chloro-2- coloration of ([4,5-dihydro-3- plastics as per...

  5. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  6. Lunar Sulfur Capture System

    Science.gov (United States)

    Berggren, Mark; Zubrin, Robert; Bostwick-White, Emily

    2013-01-01

    The Lunar Sulfur Capture System (LSCS) protects in situ resource utilization (ISRU) hardware from corrosion, and reduces contaminant levels in water condensed for electrolysis. The LSCS uses a lunar soil sorbent to trap over 98 percent of sulfur gases and about two-thirds of halide gases evolved during hydrogen reduction of lunar soils. LSCS soil sorbent is based on lunar minerals containing iron and calcium compounds that trap sulfur and halide gas contaminants in a fixed-bed reactor held at temperatures between 250 and 400 C, allowing moisture produced during reduction to pass through in vapor phase. Small amounts of Earth-based polishing sorbents consisting of zinc oxide and sodium aluminate are used to reduce contaminant concentrations to one ppm or less. The preferred LSCS configuration employs lunar soil beneficiation to boost concentrations of reactive sorbent minerals. Lunar soils contain sulfur in concentrations of about 0.1 percent, and halogen compounds including chlorine and fluorine in concentrations of about 0.01 percent. These contaminants are released as gases such as H2S, COS, CS2,HCl, and HF during thermal ISRU processing with hydrogen or other reducing gases. Removal of contaminant gases is required during ISRU processing to prevent hardware corrosion, electrolyzer damage, and catalyst poisoning. The use of Earth-supplied, single-use consumables to entirely remove contaminants at the levels existing in lunar soils would make many ISRU processes unattractive due to the large mass of consumables relative to the mass of oxygen produced. The LSCS concept of using a primary sorbent prepared from lunar soil was identified as a method by which the majority of contaminants could be removed from process gas streams, thereby substantially reducing the required mass of Earth-supplied consumables. The LSCS takes advantage of minerals containing iron and calcium compounds that are present in lunar soil to trap sulfur and halide gases in a fixedbed reactor

  7. Neutron Capture and Neutron Halos

    OpenAIRE

    A.Mengoni; Otsuka, T; Nakamura, T.(International Center for Elementary Particle Physics and Department of Physics, The University of Tokyo, Tokyo, Japan); Ishihara, M.

    1996-01-01

    The connection between the neutron halo observed in light neutron rich nuclei and the neutron radiative capture process is outlined. We show how nuclear structure information such as spectroscopic factors and external components of the radial wave function of loosely bound states can be derived from the neutron capture cross section. The link between the direct radiative capture and the Coulomb dissociation process is elucidated.

  8. Effective and Efficient Multi-Facet Web Image Annotation

    Institute of Scientific and Technical Information of China (English)

    Jia Chen; Yi-He Zhu; Hao-Fen Wang; Wei Jin; Yong Yu

    2012-01-01

    The vast amount of images available on the Web request for an effective and efficient search service to help users find relevant images.The prevalent way is to provide a keyword interface for users to submit queries.However,the amount of images without any tags or annotations are beyond the reach of manual efforts.To overcome this,automatic image annotation techniques emerge,which are generally a process of selecting a suitable set of tags for a given image without user intervention.However,there are three main challenges with respect to Web-scale image annotation:scalability,noiseresistance and diversity.Scalability has a twofold meaning:first an automatic image annotation system should be scalable with respect to billions of images on the Web; second it should be able to automatically identify several relevant tags among a huge tag set for a given image within seconds or even faster.Noise-resistance means that the system should be robust enough against typos and ambiguous terms used in tags.Diversity represents that image content may include both scenes and objects,which are further described by multiple different image features constituting different facets in annotation.In this paper,we propose a unified framework to tackle the above three challenges for automatic Web image annotation.It mainly involves two components:tag candidate retrieval and multi-facet annotation.In the former content-based indexing and concept-based codebook are leveraged to solve scalability and noise-resistance issues.In the latter the joint feature map has been designed to describe different facets of tags in annotations and the relations between these facets.Tag graph is adopted to represent tags in the entire annotation and the structured learning technique is employed to construct a learning model on top of the tag graph based on the generated joint feature map.Millions of images from Flickr are used in our evaluation.Experimental results show that we have achieved 33% performance

  9. Applications of markerless motion capture in gait recognition.

    Science.gov (United States)

    Sandau, Martin

    2016-03-01

    This thesis is based on four manuscripts where two of them were accepted and two were submitted to peer-reviewed journals. The experimental work behind the thesis was conducted at the Institute of Neuroscience and Pharmacology, University of Copenhagen. The purpose of the studies was to explore the variability of human gait and to conduct new methods for precise estimation of the kinematic parameters applied in forensic gait analysis. The gait studies were conducted in a custom built gait laboratory designed to obtain optimal conditions for markerless motion analysis. The set-up consisted of eight synchronised cameras located in the corners of the laboratory, which were connected to a single computer. The captured images were processed with stereovision-based algorithms to provide accurate 3D reconstructions of the participants. The 3D reconstructions of the participants were obtained during normal walking and the kinematics were extracted with manual and automatic methods. The kinematic results from the automatic approach were compared to marker-based motion capture to validate the precision. The results showed that the proposed markerless motion capture method had a precision comparable to marker-based methods in the frontal plane and the sagittal plane. Similar markerless motion capture methods could therefore provide the basis for reliable gait recognition based on kinematic parameters. The manual annotations were compared to the actual anthropometric measurements obtained from MRI scans and the intra- and inter-observer variability was also quantified to observe the associated effect on recognition. The results showed not only that the kinematics in the lower extremities were important but also that the kinematics in the shoulders had a high discriminatory power. Likewise, the shank length was also highly discriminatory, which has not been previously reported. However, it is important that the same expert performs all annotations, as the inter

  10. Annotations of Mexican bullfighting videos for semantic index

    Science.gov (United States)

    Montoya Obeso, Abraham; Oropesa Morales, Lester Arturo; Fernando Vázquez, Luis; Cocolán Almeda, Sara Ivonne; Stoian, Andrei; García Vázquez, Mireya Saraí; Zamudio Fuentes, Luis Miguel; Montiel Perez, Jesús Yalja; de la O Torres, Saul; Ramírez Acosta, Alejandro Alvaro

    2015-09-01

    The video annotation is important for web indexing and browsing systems. Indeed, in order to evaluate the performance of video query and mining techniques, databases with concept annotations are required. Therefore, it is necessary generate a database with a semantic indexing that represents the digital content of the Mexican bullfighting atmosphere. This paper proposes a scheme to make complex annotations in a video in the frame of multimedia search engine project. Each video is partitioned using our segmentation algorithm that creates shots of different length and different number of frames. In order to make complex annotations about the video, we use ELAN software. The annotations are done in two steps: First, we take note about the whole content in each shot. Second, we describe the actions as parameters of the camera like direction, position and deepness. As a consequence, we obtain a more complete descriptor of every action. In both cases we use the concepts of the TRECVid 2014 dataset. We also propose new concepts. This methodology allows to generate a database with the necessary information to create descriptors and algorithms capable to detect actions to automatically index and classify new bullfighting multimedia content.

  11. APPRIS: annotation of principal and alternative splice isoforms.

    Science.gov (United States)

    Rodriguez, Jose Manuel; Maietta, Paolo; Ezkurdia, Iakes; Pietrelli, Alessandro; Wesselink, Jan-Jaap; Lopez, Gonzalo; Valencia, Alfonso; Tress, Michael L

    2013-01-01

    Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform. PMID:23161672

  12. Annotating Simplices with a Homology Basis and Its Applications

    CERN Document Server

    Busaryev, Oleksiy; Chen, Chao; Dey, Tamal K; Wang, Yusu

    2011-01-01

    Let $K$ be a simplicial complex and $g$ the rank of its $p$-th homology group $H_p(K)$ defined with $Z_2$ coefficients. We show that we can compute a basis $H$ of $H_p(K)$ and annotate each $p$-simplex of $K$ with a binary vector of length $g$ with the following property: the annotations, summed over all $p$-simplices in any $p$-cycle $z$, provide the coordinate vector of the homology class $[z]$ in the basis $H$. The basis and the annotations for all simplices can be computed in $O(n^{\\omega})$ time, where $n$ is the size of $K$ and $\\omega<2.376$ is a quantity so that two $n\\times n$ matrices can be multiplied in $O(n^{\\omega})$ time. The pre-computation of annotations permits answering queries about the independence or the triviality of $p$-cycles efficiently. Using annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1-dimensional homology. Specifically, for computing an optimal basis of $H_1(K)$, we improve the time complexity kn...

  13. Analysing Temporally Annotated Corpora with CAVaT

    CERN Document Server

    Derczynski, Leon

    2012-01-01

    We present CAVaT, a tool that performs Corpus Analysis and Validation for TimeML. CAVaT is an open source, modular checking utility for statistical analysis of features specific to temporally-annotated natural language corpora. It provides reporting, highlights salient links between a variety of general and time-specific linguistic features, and also validates a temporal annotation to ensure that it is logically consistent and sufficiently annotated. Uniquely, CAVaT provides analysis specific to TimeML-annotated temporal information. TimeML is a standard for annotating temporal information in natural language text. In this paper, we present the reporting part of CAVaT, and then its error-checking ability, including the workings of several novel TimeML document verification methods. This is followed by the execution of some example tasks using the tool to show relations between times, events, signals and links. We also demonstrate inconsistencies in a TimeML corpus (TimeBank) that have been detected with CAVaT...

  14. ESLO: from transcription to speakers' personal information annotation

    CERN Document Server

    Eshkol, Iris; Friburger, Nathalie

    2011-01-01

    This paper presents the preliminary works to put online a French oral corpus and its transcription. This corpus is the Socio-Linguistic Survey in Orleans, realized in 1968. First, we numerized the corpus, then we handwritten transcribed it with the Transcriber software adding different tags about speakers, time, noise, etc. Each document (audio file and XML file of the transcription) was described by a set of metadata stored in an XML format to allow an easy consultation. Second, we added different levels of annotations, recognition of named entities and annotation of personal information about speakers. This two annotation tasks used the CasSys system of transducer cascades. We used and modified a first cascade to recognize named entities. Then we built a second cascade to annote the designating entities, i.e. information about the speaker. These second cascade parsed the named entity annotated corpus. The objective is to locate information about the speaker and, also, what kind of information can designate ...

  15. Resource capture by single leaves

    Energy Technology Data Exchange (ETDEWEB)

    Long, S.P.

    1992-05-01

    Leaves show a variety of strategies for maximizing CO{sub 2} and light capture. These are more meaningfully explained if they are considered in the context of maximizing capture relative to the utilization of water, nutrients and carbohydrates reserves. There is considerable variation between crops in their efficiency of CO{sub 2} and light capture at the leaf level. Understanding of these mechanisms indicate some ways in which efficiency of resource capture could be level cannot be meaningfully considered without simultaneous understanding of implications at the canopy level. 36 refs., 5 figs., 1 tab.

  16. Neutron capture therapy

    International Nuclear Information System (INIS)

    The overall state of the art related with neutron capture therapy(NCT) is surveyed. Since the field related with NCT is very wide, it is not intended to survey all related subjects in depth. The primary objective of this report is to help those working for the installation of a NCT facility and a PGNAA(prompt gamma ray neutron activation analysis) system for the boron analysis understand overall NCT at Hanaro. Therefore, while the parts of reactor neutron source and PGNAA are dealt in detail, other parts are limited to the level necessary to understand related fields. For example, the subject of chemical compound which requires intensive knowledge on chemistry, is not dealt as a separated item. However, the requirement of a compound for NCT, currently available compounds, their characteristics, etc. could be understood through this report. Although the subject of cancer treated by NCT is out of the capability of the author, it is dealt focussing its characteristics related with the success of NCT. Each detailed subject is expected to be dealt more detail by specialists in future. This report would be helpful for the researchers working for the NCT to understand related fields. (author). 128 refs., 3 tabs., 12 figs

  17. An Investigation into Automatically Captured Autobiographical Metadata, and the Support for Autobiographical Narrative Generation. Mini-Thesis: PhD upgrade report

    OpenAIRE

    Tuffield, Mischa M; Millard, David E.; Shadbolt, Nigel R.

    2006-01-01

    Personal information and the act of publishing multimedia artifacts to the World Wide Web is becoming more and more observable. This report presents an infrastructure for the capturing and exploitation of personal metadata to drive research into context aware systems. I aim to expose ongoing research in the areas of capture of personal experiences, context aware systems, multimedia annotation systems, narrative generation, and that of Semantic Web enabling technologies. This report details th...

  18. Optical character recognition of camera-captured images based on phase features

    Science.gov (United States)

    Diaz-Escobar, Julia; Kober, Vitaly

    2015-09-01

    Nowadays most of digital information is obtained using mobile devices specially smartphones. In particular, it brings the opportunity for optical character recognition in camera-captured images. For this reason many recognition applications have been recently developed such as recognition of license plates, business cards, receipts and street signal; document classification, augmented reality, language translator and so on. Camera-captured images are usually affected by geometric distortions, nonuniform illumination, shadow, noise, which make difficult the recognition task with existing systems. It is well known that the Fourier phase contains a lot of important information regardless of the Fourier magnitude. So, in this work we propose a phase-based recognition system exploiting phase-congruency features for illumination/scale invariance. The performance of the proposed system is tested in terms of miss classifications and false alarms with the help of computer simulation.

  19. Functional identification in correlation networks using gene ontology edge annotation.

    Science.gov (United States)

    Dempsey, Kathryn; Thapa, Ishwor; Bastola, Dhundy; Ali, Hesham

    2012-01-01

    Correlation networks identify mechanisms behind observed change in temporal data sets; however, it is often difficult to discriminate between causative versus coincidental structures in such networks. We propose a method to enhance causative relationships based on annotations derived from the Gene Ontology (GO). Enriching correlation networks with biological relationships is likely to conserve relevant signals while reducing the network size. The obtained results are structures enriched in GO functions, despite reduction in network size. Our proposed method annotates edges according to the shortest path between elements and the position of the deepest common parent in the GO tree. Our results show that such enrichment brings functional relationships to the forefront which allows for the identification of clusters with significant biological relevance. Further, this method impacts the identification of essential genes within a network model. This approach for uncovering true function of relationships provides annotation beyond traditional statistical analysis. PMID:23013651

  20. SNP annotation-based whole genomic prediction and selection

    DEFF Research Database (Denmark)

    Do, Duy Ngoc; Janss, Luc; Jensen, Just;

    2015-01-01

    into a training (968 pigs) and a validation dataset (304 pigs) by assigning records as before and after January 1, 2012, respectively. SNP were annotated by 14 different classes using Ensembl variant effect prediction. Predictive accuracy and prediction bias were calculated using Bayesian Power LASSO...... SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from randomized SNP groups. Genomic prediction has accuracy comparable to observed phenotype, and use of genomic prediction can be cost...... effective by replacing feed intake measurement. Genomic annotation had less impact on predictive accuracy traits considered here but may be different for other traits. It is the first study to provide useful insights into biological classes of SNP driving the whole genomic prediction for complex traits in...

  1. Image Annotation by Latent Community Detection and Multikernel Learning.

    Science.gov (United States)

    Gu, Yun; Qian, Xueming; Li, Qing; Wang, Meng; Hong, Richang; Tian, Qi

    2015-11-01

    Automatic image annotation is an attractive service for users and administrators of online photo sharing websites. In this paper, we propose an image annotation approach that exploits latent semantic community of labels and multikernel learning (LCMKL). First, a concept graph is constructed for labels indicating the relationship between the concepts. Based on the concept graph, semantic communities are explored using an automatic community detection method. For an image to be annotated, a multikernel support vector machine is used to determine the image's latent community from its visual features. Then, a candidate label ranking based approach is determined by intracommunity and intercommunity ranking. Experiments on the NUS-WIDE database and IAPR TC-12 data set demonstrate that LCMKL outperforms some state-of-the-art approaches. PMID:26068319

  2. ProSAT+: visualizing sequence annotations on 3D structure.

    Science.gov (United States)

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org. PMID:27284084

  3. Arc-preserving subsequences of arc-annotated sequences

    CERN Document Server

    Popov, Vladimir Yu

    2011-01-01

    Arc-annotated sequences are useful in representing the structural information of RNA and protein sequences. The longest arc-preserving common subsequence problem has been introduced as a framework for studying the similarity of arc-annotated sequences. In this paper, we consider arc-annotated sequences with various arc structures. We consider the longest arc preserving common subsequence problem. In particular, we show that the decision version of the 1-{\\sc fragment LAPCS(crossing,chain)} and the decision version of the 0-{\\sc diagonal LAPCS(crossing,chain)} are {\\bf NP}-complete for some fixed alphabet $\\Sigma$ such that $|\\Sigma| = 2$. Also we show that if $|\\Sigma| = 1$, then the decision version of the 1-{\\sc fragment LAPCS(unlimited, plain)} and the decision version of the 0-{\\sc diagonal LAPCS(unlimited, plain)} are {\\bf NP}-complete.

  4. 3D annotation and manipulation of medical anatomical structures

    Science.gov (United States)

    Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

    2009-02-01

    Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

  5. Aldo-keto reductase (AKR) superfamily: genomics and annotation.

    Science.gov (United States)

    Mindnich, Rebekka D; Penning, Trevor M

    2009-07-01

    Aldo-keto reductases (AKRs) are phase I metabolising enzymes that catalyse the reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H)-dependent reduction of carbonyl groups to yield primary and secondary alcohols on a wide range of substrates, including aliphatic and aromatic aldehydes and ketones, ketoprostaglandins, ketosteroids and xenobiotics. In so doing they functionalise the carbonyl group for conjugation (phase II enzyme reactions). Although functionally diverse, AKRs form a protein superfamily based on their high sequence identity and common protein fold, the (alpha/beta) 8 -barrel structure. Well over 150 AKR enzymes, from diverse organisms, have been annotated so far and given systematic names according to a nomenclature that is based on multiple protein sequence alignment and degree of identity. Annotation of non-vertebrate AKRs at the National Center for Biotechnology Information or Vertebrate Genome Annotation (vega) database does not often include the systematic nomenclature name, so the most comprehensive overview of all annotated AKRs is found on the AKR website (http://www.med.upenn.edu/akr/). This site also hosts links to more detailed and specialised information (eg on crystal structures, gene expression and single nucleotide polymorphisms [SNPs]). The protein-based AKR nomenclature allows unambiguous identification of a given enzyme but does not reflect the wealth of genomic and transcriptomic variation that exists in the various databases. In this context, identification of putative new AKRs and their distinction from pseudogenes are challenging. This review provides a short summary of the characteristic features of AKR biochemistry and structure that have been reviewed in great detail elsewhere, and focuses mainly on nomenclature and database entries of human AKRs that so far have not been subject to systematic annotation. Recent developments in the annotation of SNP and transcript variance in AKRs are also summarised. PMID:19706366

  6. Aldo-keto reductase (AKR superfamily: Genomics and annotation

    Directory of Open Access Journals (Sweden)

    Mindnich Rebekka D

    2009-07-01

    Full Text Available Abstract Aldo-keto reductases (AKRs are phase I metabolising enzymes that catalyse the reduced nicotinamide adenine dinucleotide (phosphate (NAD(PH-dependent reduction of carbonyl groups to yield primary and secondary alcohols on a wide range of substrates, including aliphatic and aromatic aldehydes and ketones, ketoprostaglan-dins, ketosteroids and xenobiotics. In so doing they functionalise the carbonyl group for conjugation (phase II enzyme reactions. Although functionally diverse, AKRs form a protein superfamily based on their high sequence identity and common protein fold, the (α/(β8-barrel structure. Well over 150 AKR enzymes, from diverse organisms, have been annotated so far and given systematic names according to a nomenclature that is based on multiple protein sequence alignment and degree of identity. Annotation of non-vertebrate AKRs at the National Center for Biotechnology Information or Vertebrate Genome Annotation (vega database does not often include the systematic nomenclature name, so the most comprehensive overview of all annotated AKRs is found on the AKR website (http://www.med.upenn.edu/akr/. This site also hosts links to more detailed and specialised information (eg on crystal structures, gene expression and single nucleotide polymorphisms [SNPs]. The protein-based AKR nomenclature allows unambiguous identification of a given enzyme but does not reflect the wealth of genomic and transcriptomic variation that exists in the various databases. In this context, identification of putative new AKRs and their distinction from pseudogenes are challenging. This review provides a short summary of the characteristic features of AKR biochemistry and structure that have been reviewed in great detail elsewhere, and focuses mainly on nomenclature and database entries of human AKRs that so far have not been subject to systematic annotation. Recent developments in the annotation of SNP and transcript variance in AKRs are also summarised.

  7. Thomas-forbidden particle capture

    OpenAIRE

    Carter, John H.; Lieber, Michael

    2010-01-01

    At high energies, in particle-capture processes between ions and atoms, classical kinematic requirements show that generally double collision Thomas processes dominate. However, for certain mass-ratios these processes are kinematically forbidden. This paper explores the possibility of capture for such processes by triple or higher order collision processes.

  8. Web Image Retrieval Search Engine based on Semantically Shared Annotation

    Directory of Open Access Journals (Sweden)

    Alaa Riad

    2012-03-01

    Full Text Available This paper presents a new majority voting technique that combines the two basic modalities of Web images textual and visual features of image in a re-annotation and search based framework. The proposed framework considers each web page as a voter to vote the relatedness of keyword to the web image, the proposed approach is not only pure combination between image low level feature and textual feature but it take into consideration the semantic meaning of each keyword that expected to enhance the retrieval accuracy. The proposed approach is not used only to enhance the retrieval accuracy of web images; but also able to annotated the unlabeled images.

  9. Context, Dependency and Annotation Analysis in Java EE

    OpenAIRE

    Božidar, Darko

    2012-01-01

    The goal of this bachelor’s thesis is to analyze two of Java EE’s features, CDI and annotations, and to use the acquired knowledge to build a simple web application based on CDI and developed annotations. For this purpose it was necessary to clarify what CDI does and what it offers. Previously mentioned features were therefore firstly thoroughly examined to find out what improvements to the Java EE platform, if any, they provide. The main purpose of this thesis is to explore and analyse how t...

  10. Annotation-Based Whole Genomic Prediction and Selection

    DEFF Research Database (Denmark)

    Kadarmideen, Haja; Do, Duy Ngoc; Janss, Luc;

    using the BayesCπ method and applied to 1,272 Duroc pigs with both genotypic and phenotypic records including residual (RFI) and daily feed intake (DFI), average daily gain (ADG) and back fat (BF)). Records were split into a training (968 pigs) and a validation dataset (304 pigs). SNPs were annotated by...... 14 different classes. Predictive accuracy was 0.531, 0.532, 0.302, and 0.344 for DFI, RFI, ADG and BF, respectively. The contribution per SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from...

  11. ONEMercury: Towards Automatic Annotation of Earth Science Metadata

    Science.gov (United States)

    Tuarob, S.; Pouchard, L. C.; Noy, N.; Horsburgh, J. S.; Palanisamy, G.

    2012-12-01

    Earth sciences have become more data-intensive, requiring access to heterogeneous data collected from multiple places, times, and thematic scales. For example, research on climate change may involve exploring and analyzing observational data such as the migration of animals and temperature shifts across the earth, as well as various model-observation inter-comparison studies. Recently, DataONE, a federated data network built to facilitate access to and preservation of environmental and ecological data, has come to exist. ONEMercury has recently been implemented as part of the DataONE project to serve as a portal for discovering and accessing environmental and observational data across the globe. ONEMercury harvests metadata from the data hosted by multiple data repositories and makes it searchable via a common search interface built upon cutting edge search engine technology, allowing users to interact with the system, intelligently filter the search results on the fly, and fetch the data from distributed data sources. Linking data from heterogeneous sources always has a cost. A problem that ONEMercury faces is the different levels of annotation in the harvested metadata records. Poorly annotated records tend to be missed during the search process as they lack meaningful keywords. Furthermore, such records would not be compatible with the advanced search functionality offered by ONEMercury as the interface requires a metadata record be semantically annotated. The explosion of the number of metadata records harvested from an increasing number of data repositories makes it impossible to annotate the harvested records manually, urging the need for a tool capable of automatically annotating poorly curated metadata records. In this paper, we propose a topic-model (TM) based approach for automatic metadata annotation. Our approach mines topics in the set of well annotated records and suggests keywords for poorly annotated records based on topic similarity. We utilize the

  12. Knowledge Representation and Management. From Ontology to Annotation

    Science.gov (United States)

    Darmoni, S.J.

    2015-01-01

    Summary Objective To summarize the best papers in the field of Knowledge Representation and Management (KRM). Methods A comprehensive review of medical informatics literature was performed to select some of the most interesting papers of KRM published in 2014. Results Four articles were selected, two focused on annotation and information retrieval using an ontology. The two others focused mainly on ontologies, one dealing with the usage of a temporal ontology in order to analyze the content of narrative document, one describing a methodology for building multilingual ontologies. Conclusion Semantic models began to show their efficiency, coupled with annotation tools. PMID:26293860

  13. Biocuration of functional annotation at the European nucleotide archive.

    Science.gov (United States)

    Gibson, Richard; Alako, Blaise; Amid, Clara; Cerdeño-Tárraga, Ana; Cleland, Iain; Goodgame, Neil; Ten Hoopen, Petra; Jayathilaka, Suran; Kay, Simon; Leinonen, Rasko; Liu, Xin; Pallreddy, Swapna; Pakseresht, Nima; Rajan, Jeena; Rosselló, Marc; Silvester, Nicole; Smirnov, Dmitriy; Toribio, Ana Luisa; Vaughan, Daniel; Zalunin, Vadim; Cochrane, Guy

    2016-01-01

    The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achievements. This is followed by a focus on sustainable biocuration of functional annotation, an area which has particularly felt the pressure of sequencing growth. The importance of functional annotation, how it can be submitted and the shifting role of the biocurator in the context of increasing volumes of data are all discussed. PMID:26615190

  14. Application of Annotated Logic Program to Pipeline Process Safety Verification

    Science.gov (United States)

    Nakamatsu, Kazumi

    We have developed a paraconsistent annotated logic program called Extended Vector Annotated Logic Program with Strong Negation (abbr. EVALPSN), which can deal with defeasible deontic reasoning and contradiction, and we have already applied it to safety verification and control such as railway interlocking safety verification and traffic signal control. In this paper, we introduce process safety verification as an application of EVALPSN with a small example for brewery pipeline valve control. The safety verification control is based on EVALPSN defeasible deontic reasoning to avoid unexpected mix of different sorts of liquid in pipeline networks.

  15. Neutron capture reactions at DANCE

    International Nuclear Information System (INIS)

    The Detector for Advanced Neutron Capture Experiments (DANCE) is a 4π BaF2 array consisting of 160 active detector elements. The primary purpose of the array is to perform neutron capture cross section measurements on small (> or approx.100 μg) and/or radioactive (241,243Am, neutron capture and neutron-induced fission cross sections and capture-to-fission ratio (α = σγ/σf) for 235U using a new fission-tagging detector as well as neutron capture cross sections for several astrophysics branch-point nuclei. Results from several of these measurements will be presented along with a discussion of additional physics information that can be extracted from the DANCE data

  16. Annotated Bibliography for the MATADOR Project

    Energy Technology Data Exchange (ETDEWEB)

    Janik, Tadeusz; White, Amanda M.; Pawley, Norma H.; Myers, Kary L.; Oehmen, Christopher S.

    2012-06-07

    The MATADOR project is focused on developing methods to infer the operational mode of facilities that have the potential to be used in weapons development programs. Our central hypothesis is that by persistent, non-intrusive monitoring of such facilities, differences between various use scenarios can be reliably discovered. The impact of success in this area is that new tools and techniques for monitoring and treaty verification would make it easier to reliably discover and document weapons development activities. This document captures the literature that will serve as a basis to approach this task. The relevant literature is divided into topical areas that relate to the various aspects of expected MATADOR project development. We have found that very little work that is directly applicable for our purposes has been published, which has motivated the development of novel methods under the project. Therefore, the manuscripts referenced in this document were selected based on their potential use as foundational blocks for the methods we anticipate developing, or so that we can understand the limitations of existing methods.

  17. Disparities in receipt of modern concurrent chemoradiotherapy in glioblastoma.

    Science.gov (United States)

    Rhome, Ryan; Fisher, Rebecca; Hormigo, Adília; Parikh, Rahul R

    2016-06-01

    Temozolomide given concurrently with radiation after resection/biopsy improves survival in glioblastoma (GBM). The disparities in receipt of adjuvant single-agent chemotherapy and their association with outcome have not been well established. Observational study of a prospectively collected database, the National Cancer Database (NCDB), from 1998 to 2012 with median follow-up 12.4 months. Among the 114,979 patients in the NCDB with GBM, 44,531 patients were analyzed for disparities, and 28,279 patients were analyzed for overall survival (OS). Associations were assessed in a multivariable Cox proportional hazards regression model. Survival was estimated using the Kaplan-Meier method. Median age was 58 years. Chemotherapy use was associated with male gender, white race, younger age (≤50), higher performance status (≥70), more extensive surgery, insurance status, higher income/education, and treatment at academic centers (all p < 0.05). We found improved OS associated with type of insurance (private insurance HR 0.91, 95 % CI 0.85-0.96 and Medicare HR 1.24, 95 % CI 1.16-1.33, both p < 0.01 compared to uninsured) and treatment at academic programs (HR 0.86; p < 0.01). MGMT methylation status predicted improved OS (HR 0.54; 95 % CI 0.41-0.70, p < 0.01). 1-year OS for patients receiving chemotherapy was 55.9 % versus 35.3 % for those without (p < 0.0001). After adjustment for confounders, chemotherapy use remained associated with improved OS (HR 0.64, 95 % CI 0.63-0.66, p < 0.01). Chemotherapy utilization increased from 26.9 to 93.3 % during the study period. We have identified specific disparities in the use of chemotherapy that may be targeted to improve patient access to care. Widespread adoption of adjuvant chemoradiotherapy after resection or biopsy for GBM appears to improve OS. PMID:26970981

  18. 48 CFR 52.232-35 - Designation of Office for Government Receipt of Electronic Funds Transfer Information.

    Science.gov (United States)

    2010-10-01

    ... Government Receipt of Electronic Funds Transfer Information. 52.232-35 Section 52.232-35 Federal Acquisition... CONTRACT CLAUSES Text of Provisions and Clauses 52.232-35 Designation of Office for Government Receipt of Electronic Funds Transfer Information. As prescribed in 32.1110(c), insert the following clause:...

  19. 32 CFR 37.905 - Must I make receipt of the final performance report a condition for final payment?

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Must I make receipt of the final performance report a condition for final payment? 37.905 Section 37.905 National Defense Department of Defense OFFICE... make receipt of the final performance report a condition for final payment? If a final report...

  20. 20 CFR 10.500 - What are the basic rules governing continuing receipt of compensation benefits and return to work?

    Science.gov (United States)

    2010-04-01

    ... receipt of compensation benefits and return to work? 10.500 Section 10.500 Employees' Benefits OFFICE OF... to return each disabled employee to suitable work as soon as he or she is medically able. In... § 10.500 What are the basic rules governing continuing receipt of compensation benefits and return...

  1. 77 FR 37956 - BMW of North America, LLC, a Subsidiary of BMW AG; Receipt of Petition for Decision of...

    Science.gov (United States)

    2012-06-25

    ... Register published on April 11, 2000, (65 FR 19477-78). The petition, supporting materials, and all... National Highway Traffic Safety Administration BMW of North America, LLC, a Subsidiary of BMW AG; Receipt... Administration, DOT. ACTION: Receipt of Petition. SUMMARY: BMW of North America, LLC,\\1\\ a subsidiary of BMW...

  2. 77 FR 63415 - BMW of North America, LLC, a Subsidiary of BMW AG, Receipt of Petition for Decision of...

    Science.gov (United States)

    2012-10-16

    ... Statement is available for review in the Federal Register published on April 11, 2000, (65 FR 19477-78). The... National Highway Traffic Safety Administration BMW of North America, LLC, a Subsidiary of BMW AG, Receipt... Administration, DOT. ACTION: Receipt of petition. SUMMARY: BMW North America, LLC,\\1\\ a subsidiary of BMW...

  3. 76 FR 51468 - BMW of North America, LLC, a subsidiary of BMW AG, Receipt of Petition for Decision of...

    Science.gov (United States)

    2011-08-18

    ..., (65 FR 19477-78). The petition, supporting materials, and all comments received before the close of... National Highway Traffic Safety Administration BMW of North America, LLC, a subsidiary of BMW AG, Receipt... Administration, DOT. ACTION: Receipt of Petition for Inconsequential Noncompliance. SUMMARY: BMW of North...

  4. 77 FR 56700 - BMW of North America, LLC, a Subsidiary of BMW AG, Receipt of Petition for Decision of...

    Science.gov (United States)

    2012-09-13

    ... Statement is available for review in the Federal Register published on April 11, 2000, (65 FR 19477-78). The... National Highway Traffic Safety Administration BMW of North America, LLC, a Subsidiary of BMW AG, Receipt... Administration, DOT. ACTION: Receipt of petition. SUMMARY: BMW of North America, LLC (BMW),\\1\\ a subsidiary...

  5. 77 FR 56698 - Mercedes-Benz USA, LLC, on Behalf of Daimler AG, Receipt of Petition for Decision of...

    Science.gov (United States)

    2012-09-13

    ... National Highway Traffic Safety Administration Mercedes-Benz USA, LLC, on Behalf of Daimler AG, Receipt of... Administration, DOT. ACTION: Receipt of petition. SUMMARY: Mercedes-Benz USA, LLC (MBUSA),\\1\\ on behalf of itself and its parent company Daimler AG (DAG) \\2\\, has determined that certain model year 2012...

  6. 78 FR 48769 - Mercedes-Benz USA, LLC and Daimler AG, Receipt of Petition for Decision of Inconsequential...

    Science.gov (United States)

    2013-08-09

    ... TRANSPORTATION National Highway Traffic Safety Administration Mercedes-Benz USA, LLC and Daimler AG, Receipt of... Administration, DOT. ACTION: Receipt of petition. SUMMARY: Mercedes-Benz USA, LLC (MBUSA) \\1\\ on behalf of itself...'', have determined that certain model year (MY) 2013 Mercedes-Benz GLK-Class (X204 platform)...

  7. 77 FR 38391 - Mercedes-Benz USA, LLC, and Daimler AG (DAG), Receipt of Petition for Decision of Inconsequential...

    Science.gov (United States)

    2012-06-27

    ... National Highway Traffic Safety Administration Mercedes-Benz USA, LLC, and Daimler AG (DAG), Receipt of... Administration, DOT. ACTION: Receipt of petition. SUMMARY: Mercedes-Benz USA, LLC \\1\\ (MBUSA) and its parent... and 2012 Mercedes-Benz S-Class (221 platform) passenger cars do not fully comply with paragraph...

  8. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

    Directory of Open Access Journals (Sweden)

    Hamilton John P

    2007-10-01

    Full Text Available Abstract Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation. This requires tools that facilitate 1 the submission of gene annotation to an annotation project, 2 the review of the submitted models by project annotators, and 3 the incorporation of the submitted models in the ongoing annotation effort. Results We have developed the Eukaryotic Community Annotation Package (EuCAP, an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website http://rice.tigr.org, as well as in the Community Annotation track of the Genome Browser. Conclusion We have applied EuCAP to rice. As of July 2007, the

  9. Software tool for researching annotations of proteins: open-source protein annotation software with data visualization.

    Science.gov (United States)

    Bhatia, Vivek N; Perlman, David H; Costello, Catherine E; McComb, Mark E

    2009-12-01

    In order that biological meaning may be derived and testable hypotheses may be built from proteomics experiments, assignments of proteins identified by mass spectrometry or other techniques must be supplemented with additional notation, such as information on known protein functions, protein-protein interactions, or biological pathway associations. Collecting, organizing, and interpreting this data often requires the input of experts in the biological field of study, in addition to the time-consuming search for and compilation of information from online protein databases. Furthermore, visualizing this bulk of information can be challenging due to the limited availability of easy-to-use and freely available tools for this process. In response to these constraints, we have undertaken the design of software to automate annotation and visualization of proteomics data in order to accelerate the pace of research. Here we present the Software Tool for Researching Annotations of Proteins (STRAP), a user-friendly, open-source C# application. STRAP automatically obtains gene ontology (GO) terms associated with proteins in a proteomics results ID list using the freely accessible UniProtKB and EBI GOA databases. Summarized in an easy-to-navigate tabular format, STRAP results include meta-information on the protein in addition to complementary GO terminology. Additionally, this information can be edited by the user so that in-house expertise on particular proteins may be integrated into the larger data set. STRAP provides a sortable tabular view for all terms, as well as graphical representations of GO-term association data in pie charts (biological process, cellular component, and molecular function) and bar charts (cross comparison of sample sets) to aid in the interpretation of large data sets and differential analyses experiments. Furthermore, proteins of interest may be exported as a unique FASTA-formatted file to allow for customizable re-searching of mass spectrometry

  10. Materials For Gas Capture, Methods Of Making Materials For Gas Capture, And Methods Of Capturing Gas

    KAUST Repository

    Polshettiwar, Vivek

    2013-06-20

    In accordance with the purpose(s) of the present disclosure, as embodied and broadly described herein, embodiments of the present disclosure, in one aspect, relate to materials that can be used for gas (e.g., CO.sub.2) capture, methods of making materials, methods of capturing gas (e.g., CO.sub.2), and the like, and the like.

  11. Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes

    Directory of Open Access Journals (Sweden)

    Danchin Antoine

    2002-02-01

    Full Text Available Abstract Background Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with close relatives among other organisms during the annotation process, accurate gene prediction remains quite difficult. A major reason for this situation is that genes are tightly packed in prokaryotes, resulting in frequent overlap. Thus, detection of translation initiation sites and/or selection of the correct coding regions remain difficult unless appropriate biological knowledge (about the structure of a gene is imbedded in the approach. Results We have developed a new program that automatically identifies biologically significant candidate genes in a bacterial genome. Twenty-six complete prokaryotic genomes were analyzed using this tool, and the accuracy of gene finding was assessed by comparison with existing annotations. This analysis revealed that, despite the enormous effort of genome program annotators, a small but not negligible number of genes annotated within the framework of sequencing projects are likely to be partially inaccurate or plainly wrong. Moreover, the analysis of several putative new genes shows that, as expected, many short genes have escaped annotation. In most cases, these new genes revealed frameshifts that could be either artifacts or genuine frameshifts. Some entirely unexpected new genes have also been identified. This allowed us to get a more complete picture of prokaryotic genomes. The results of this procedure are progressively integrated into the SWISS-PROT reference databank. Conclusions The results described in the present study show that our procedure is very satisfactory in terms of gene finding accuracy. Except in few cases, discrepancies between our results and annotations provided by individual authors can be accounted for by the nature of each annotation process or by specific

  12. 34 CFR 370.15 - What must the Governor of a State do upon receipt of a copy of a designated agency's written...

    Science.gov (United States)

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false What must the Governor of a State do upon receipt of a... Redesignation? § 370.15 What must the Governor of a State do upon receipt of a copy of a designated agency's... with § 370.14, the Governor shall, within 15 days of receipt of the designated agency's appeal,...

  13. Evaluation of Three Automated Genome Annotations for Halorhabdus utahensis

    DEFF Research Database (Denmark)

    Bakke, Peter; Carney, Nick; DeLoache, Will;

    2009-01-01

    Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in...... databases such as NCBI and used to validate subsequent annotation errors. We submitted the genome sequence of halophilic archaeon Halorhabdus utahensis to be analyzed by three genome annotation services. We have examined the output from each service in a variety of ways in order to compare the methodology...... and effectiveness of the annotations, as well as to explore the genes, pathways, and physiology of the previously unannotated genome. The annotation services differ considerably in gene calls, features, and ease of use. We had to manually identify the origin of replication and the species...

  14. Annotated Bibliography on Offender Job Training and Placement. Second Edition.

    Science.gov (United States)

    Clem, Constance, Ed.

    This second edition of an annotated bibliography on offender job training and placement lists nearly 400 items from the collection of the National Institute of Corrections (NIC) Information Center in Longmont, Colorado, including 85 items added since the first edition in 1997. Items new to this edition are marked with an asterisk. Citations have…

  15. Effects of E-Textbook Instructor Annotations on Learner Performance

    Science.gov (United States)

    Dennis, Alan R.; Abaci, Serdar; Morrone, Anastasia S.; Plaskoff, Joshua; McNamara, Kelly O.

    2016-01-01

    With additional features and increasing cost advantages, e-textbooks are becoming a viable alternative to paper textbooks. One important feature offered by enhanced e-textbooks (e-textbooks with interactive functionality) is the ability for instructors to annotate passages with additional insights. This paper describes a pilot study that examines…

  16. Social Change and Teacher Education: An Annotated Bibliography.

    Science.gov (United States)

    Mathieson, Moira B.; Tatis, Rita M.

    This annotated bibliography lists 137 published and unpublished documents, the majority of them dated between 1967 and 1969. Included are research reports, program descriptions, addresses, articles, and conference papers. The citations are organized into six sections: 1) Teacher Education and Changing Social Order--25 items; 2) Insights into…

  17. Understanding Disadvantaged Youth: Their Problems and Potentials. An Annotated Bibliography.

    Science.gov (United States)

    Mathieson, Moira B., Comp.; Tatis, Rita M., Comp.

    Designed as a resource guide for teachers and teacher educators, this annotated bibliography contains 102 citations (e.g., journal articles, program descriptions, research reports) most of them dated between 1968 and 1970. There are five sections: 1) Characteristics and Problems of the Disadvantaged--22 items; 2) Attitudes Toward the…

  18. Certifying and reasoning on cost annotations of functional programs

    CERN Document Server

    Amadio, Roberto M

    2011-01-01

    We present a so-called labelling method to insert cost annotations in a higher-order functional program, to certify their correctness with respect to a standard compilation chain to assembly code, and to reason on them in a higher-order Hoare logic.

  19. The Dartmouth/Rassias Method: An Annotated Bibliography.

    Science.gov (United States)

    Horner, Jeanne; Stansfield, Charles

    The Dartmouth/Rassias method of foreign language instruction, which is used in many American colleges and universities, has inspired much comment in the media. This annotated bibliography describes 17 books, articles, and monographs, as well as a film, which focus on the method. (JB)

  20. Asian American Literature of Hawaii: An Annotated Bibliography.

    Science.gov (United States)

    Hiura, Arnold T.; Sumida, Stephen H.

    This annotated bibllography focuses on the drama, prose fiction, and poetry of people of Chinese, Japanese, Korean, and Filipino descent in Hawaii. All works cited were written in English, between the 1920s and 1970, with the exception of poems translated into English by their authors. The bibliography begins with an overview of the cultural and…

  1. An Annotated Bibliography of Gay and Lesbian Communication Studies.

    Science.gov (United States)

    Park, Jan Carl

    1979-01-01

    The 22 entries in this annotated bibliography represent articles that have lesbian women or gay men as subjects and that deal with a specific verbal or nonverbal communication factor. Topics covered in the entries include patterns of self-disclosure in homosexual and heterosexual college students, interpersonal conflict in homosexual relations,…

  2. Pertinent Discussions Toward Modeling the Social Edition: Annotated Bibliographies

    NARCIS (Netherlands)

    R. Siemens; M. Timney; C. Leitch; C. Koolen; A. Garnett

    2012-01-01

    The two annotated bibliographies present in this publication document and feature pertinent discussions toward the activity of modeling the social edition, first exploring reading devices, tools and social media issues and, second, social networking tools for professional readers in the Humanities.

  3. Coping with Workplace Change: An Annotated Bibliography of Resources.

    Science.gov (United States)

    Kilcullen, Maureen

    1997-01-01

    Presents an annotated bibliography of print sources published between 1990 and 1996 that provide strategies and solutions to coping with workplace change. Includes four sections: an overview of books about downsizing, books for those still employed after a downsizing, books for those who lose their jobs, and governmental and private resources…

  4. Educational Leadership: A Selective Annotated Bibliography, 1981-1985.

    Science.gov (United States)

    1985

    This bibliography consists of annotations of selected journal articles, magazine articles, books, and unpublished doctoral dissertations pertinent to the topic of educational leadership. The selections encompass a time frame ranging from 1981 to 1985. "Education Index" and "Psychological Abstracts" were the primary sources for journal and magazine…

  5. The Holocaust in Books and Films. A Selected, Annotated List.

    Science.gov (United States)

    Muffs, Judith Herschlag, Ed.

    This is an annotated list of over 400 resource books and films on Jewish history before the Holocaust, the history and development of Nazism, experiences during the Holocaust and its aftermath, and the phenomenon of prejudice and anti-Semitism. Designed primarily for teachers and librarians in secondary schools and to some extent in elementary…

  6. Resources for Teaching about Human Rights: An Annotated List.

    Science.gov (United States)

    Totten, Samuel

    1985-01-01

    The following resources are cited in this annotated bibliography dealing with human rights: general references (background readings for teachers and students); classroom materials; fiction; audiovisuals; periodicals; and organizations and associations dedicated to the investigation of human rights infractions or education and communication on…

  7. Folklore around the World: An Annotated Bibliography of Folk Literature.

    Science.gov (United States)

    Eastman, Kristen Paletti, Ed.; Omura, Grace Inokuchi, Ed.

    Fourth in a series, the annotated bibliographies in this collection were compiled by students in the Traditional Literature and Oral Narration class at the School of Library and Information Studies, University of Hawaii at Manoa. These bibliographies are designed to make information about specific topics in traditional literature easily accessible…

  8. Social Sciences in the People's Republic of China: Annotated Bibliography.

    Science.gov (United States)

    Parker, Franklin

    This annotated bibliography includes 18 journal articles, books, newspaper stories, and confernce papers focusing on official Chinese policy toward the role of the social sciences. The impact of the Chinese Cultural Revolution and the establishment of the Chinese Academy of Social Sciences in 1977 are the subjects of most of the listed sources.…

  9. Recall Oriented Search on the Web using Semantic Annotations

    NARCIS (Netherlands)

    Kaptein, A.M.; Broek, E.L. van den; Koot, G.; Huis in't Veld, M.A.A.

    2013-01-01

    Web search engines are optimized for early precision, which makes it difficult to perform recall oriented tasks with them. In this article, we propose several ways to leverage semantic annotations and, thereby, increase the efficiency of recall oriented search tasks, with a focus on forensic investi

  10. Know Your Neighbor's Faith: An Annotated Interfaith Bibliography.

    Science.gov (United States)

    Deitrick, Bernard A., Comp.

    General interest books on North American religions are cited in this annotated bibliography for church and synagogue librarians. Over 130 publications, including references, children's books, and adult literature, are listed under the following categories: general books, Judaism, Christianity, and interfaith dialogue. The section on Christianity…

  11. Child Drama: A Selected and Annotated Bibliography, 1974-1979.

    Science.gov (United States)

    Kennedy, Carol Jean

    The more than 200 entries in this annotated bibliography deal with drama, creative dramatics, and children's theatre. The entries for articles, papers, and books are arranged according to the following categories: (1) bibliographies and references in child drama; (2) theory, research, and methods in preschool dramatic play; (3) theory and research…

  12. Annotating Evidence Based Clinical Guidelines: A Lightweight Ontology

    NARCIS (Netherlands)

    R. Hoekstra; A. de Waard; R. Vdovjak

    2012-01-01

    This paper describes a lightweight ontology for representing annotations of declarative evidence based clinical guidelines. We present the motivation and requirements for this representation, based on an analysis of several guidelines. The ontology provides the means to connect clinical questions an

  13. Annotation des structures discursives : l'expérience ANNODIS

    Directory of Open Access Journals (Sweden)

    Ho-Dac Lydia-Mai

    2014-07-01

    Full Text Available La ressource ANNODIS est un corpus diversifié de français écrit enrichi d'annotations concernant le niveau discursif. Son originalité réside dans sa mutualisation de deux approches complémentaires qui permettent, par leur oppositions et rapprochements, de poser un certain nombre de questions concernant l'annotation de structures discursives. cet article propose de revenir sur les enjeux principaux qui ont motivés les membres du projet ANNODIS : 1 stabiliser un certain nombre de définition linguistique de phénomènes discursives ciblées et 2 confronter aux données réelles une certaine modélisation de la construction de la cohérence discursive. Ce double objectif est révélateur des deux approches mises à l'épreuve dans l'expérience ANNODIS. Cet article revient sur les enjeux de cette ressource en terme à la fois de structures discursives et de campagne d'annotation. Un regard particulier sera porté sur la question du devenir des annotations, notamment dans un domaine encore peu stabilisé.

  14. Sequence-based feature prediction and annotation of proteins

    DEFF Research Database (Denmark)

    Juncker, Agnieszka; Jensen, Lars J.; Pierleoni, Andrea; Bernsel, Andreas; Tress, Michael L.; Bork, Peer; Von Heijne, Gunnar; Valencia, Alfonso; A Ouzounis, Christos; Casadio, Rita; Brunak, Søren

    2009-01-01

    A recent trend in computational methods for annotation of protein function is that many prediction tools are combined in complex workflows and pipelines to facilitate the analysis of feature combinations, for example, the entire repertoire of kinase-binding motifs in the human proteome....

  15. Annotation: Neurofeedback--Train Your Brain to Train Behaviour

    Science.gov (United States)

    Heinrich, Hartmut; Gevensleben, Holger; Strehl, Ute

    2007-01-01

    Background: Neurofeedback (NF) is a form of behavioural training aimed at developing skills for self-regulation of brain activity. Within the past decade, several NF studies have been published that tend to overcome the methodological shortcomings of earlier studies. This annotation describes the methodical basis of NF and reviews the evidence…

  16. Rapid reconstruction and annotation of vaccinium macrocarpon organellar genomes

    Science.gov (United States)

    The mitochondria genome of the American cranberry (Vaccinium macrocarpon Ait.) cultivar “HyRed” is being reconstructed using sequence 454 shotgun data and in silico procedures. We previously reconstructed and annotated a putative plastid cranberry genome with an approximate length of 176kb. The reli...

  17. Functional annotation of the human retinal pigment epithelium transcriptome

    NARCIS (Netherlands)

    J.C. Booij (Judith); S. van Soest (Simone); S.M.A. Swagemakers (Sigrid); A.H.W. Essing (Anke); J.H.M. Verkerk (Annemieke); P.J. van der Spek (Peter); T.G.M.F. Gorgels (Theo); A.A.B. Bergen (Arthur)

    2009-01-01

    textabstractBackground: To determine level, variability and functional annotation of gene expression of the human retinal pigment epithelium (RPE), the key tissue involved in retinal diseases like age-related macular degeneration and retinitis pigmentosa. Macular RPE cells from six selected healthy

  18. Annotated Bibliography on Ethology in Education. Ecological Theory of Teaching.

    Science.gov (United States)

    Miller, Kevin; Frey, Susan

    This annotated bibliography focuses on the ethological study of child development and the educational process. Topics covered include: (1) evolution; (2) dominance hierarchies and social organization; (3) agonistic, affiliative, and epistemic behaviors; (4) nonverbal communication; (5) play; (6) biological constraints on learning; and (7) relevant…

  19. An Annotated Bibliography of Games and Simulations in Consumer Education.

    Science.gov (United States)

    Blucker, Gwen

    Thirty-two games and simulations relating to consumer education comprise this annotated bibliography designed to aid the teacher of adult basic education students and others in their search for teaching devices. Topics covered in the various simulations include money management, insurance, credit, credit unions, consumer law, consumer frauds,…

  20. The Challenges of Blended Learning Using a Media Annotation Tool

    Science.gov (United States)

    Douglas, Kathy A.; Lang, Josephine; Colasante, Meg

    2014-01-01

    Blended learning has been evolving as an important approach to learning and teaching in tertiary education. This approach incorporates learning in both online and face-to-face modes and promotes deep learning by incorporating the best of both approaches. An innovation in blended learning is the use of an online media annotation tool (MAT) in…

  1. An Annotated Dataset of 14 Cardiac MR Images

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille

    2002-01-01

    This note describes a dataset consisting of 14 annotated cardiac MR images. Points of correspondence are placed on each image at the left ventricle (LV). As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given....

  2. Bibliographies and Annotations from Speakers and Class Participants.

    Science.gov (United States)

    California Univ., Berkeley. Office of Resources for International and Area Studies.

    This annotated bibliography focuses on recent children's literature that deals with other cultures. The books in the bibliography are set in or about Africa (29 selections), Ancient Egypt (3 selections), East Asia (20 selections), India (7 selections), Latin America (3 selections), Middle East (5 selections), and Russia (9 selections). The…

  3. PROSITE, a protein domain database for functional characterization and annotation.

    Science.gov (United States)

    Sigrist, Christian J A; Cerutti, Lorenzo; de Castro, Edouard; Langendijk-Genevaux, Petra S; Bulliard, Virginie; Bairoch, Amos; Hulo, Nicolas

    2010-01-01

    PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 ( approximately 70%) are annotated with PROSITE descriptors using information from ProRule. In order to allow better functional characterization of domains, PROSITE developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/. PMID:19858104

  4. Systematic Functional Annotation and Visualization of Biological Networks.

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-06-22

    Large-scale biological networks represent relationships between genes, but our understanding of how networks are functionally organized is limited. Here, I describe spatial analysis of functional enrichment (SAFE), a systematic method for annotating biological networks and examining their functional organization. SAFE visualizes the network in 2D space and measures the continuous distribution of functional enrichment across local neighborhoods, producing a list of the associated functions and a map of their relative positioning. I applied SAFE to annotate the Saccharomyces cerevisiae genetic interaction similarity network and protein-protein interaction network with gene ontology terms. SAFE annotations of the genetic network matched manually derived annotations, while taking less than 1% of the time, and proved robust to noise and sensitive to biological signal. Integration of genetic interaction and chemical genomics data using SAFE revealed a link between vesicle-mediate transport and resistance to the anti-cancer drug bortezomib. These results demonstrate the utility of SAFE for examining biological networks and understanding their functional organization. PMID:27237738

  5. Biochemical Space: A Framework for Systemic Annotation of Biological Models

    Czech Academy of Sciences Publication Activity Database

    Klement, M.; Děd, T.; Šafránek, D.; Červený, Jan; Müller, Stefan; Steuer, Ralf

    2014-01-01

    Roč. 306, JUL (2014), s. 31-44. ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * cyanobacteria Subject RIV: EH - Ecology, Behaviour

  6. Protein function annotation by homology-based inference

    OpenAIRE

    Loewenstein, Yaniv; Raimondo, Domenico; Redfern, Oliver C.; Watson, James; Frishman, Dmitrij; Linial, Michal; Orengo, Christine; Thornton, Janet; Tramontano, Anna

    2009-01-01

    With many genomes now sequenced, computational annotation methods to characterize genes and proteins from their sequence are increasingly important. The BioSapiens Network has developed tools to address all stages of this process, and here we review progress in the automated prediction of protein function based on protein sequence and structure.

  7. The Olympic Games and World Politics: A Select Annotated Bibliography.

    Science.gov (United States)

    Meyer, Evelyn S.

    1984-01-01

    This 62-item annotated bibliography lists books and journal articles published over last decade (historical guides and surveys, memoirs, speeches, essays, biographies, government documents, critical analyses) on the history of politics in modern Olympic games and use of games in politics. A brief history of the games is included with 24…

  8. ACOUSTICS IN ARCHITECTURAL DESIGN, AN ANNOTATED BIBLIOGRAPHY ON ARCHITECTURAL ACOUSTICS.

    Science.gov (United States)

    DOELLE, LESLIE L.

    THE PURPOSE OF THIS ANNOTATED BIBLIOGRAPHY ON ARCHITECTURAL ACOUSTICS WAS--(1) TO COMPILE A CLASSIFIED BIBLIOGRAPHY, INCLUDING MOST OF THOSE PUBLICATIONS ON ARCHITECTURAL ACOUSTICS, PUBLISHED IN ENGLISH, FRENCH, AND GERMAN WHICH CAN SUPPLY A USEFUL AND UP-TO-DATE SOURCE OF INFORMATION FOR THOSE ENCOUNTERING ANY ARCHITECTURAL-ACOUSTIC DESIGN…

  9. JAFA: a protein function annotation meta-server

    DEFF Research Database (Denmark)

    Friedberg, Iddo; Harder, Tim; Godzik, Adam

    Function Annotations, or JAFA server. JAFA queries several function prediction servers with a protein sequence and assembles the returned predictions in a legible, non-redundant format. In this manner, JAFA combines the predictions of several servers to provide a comprehensive view of what are the...

  10. An annotated corpus for the analysis of VP ellipsis

    NARCIS (Netherlands)

    Bos, Johan; Spenader, J.

    2011-01-01

    Verb Phrase Ellipsis (VPE) has been studied in great depth in theoretical linguistics, but empirical studies of VPE are rare. We extend the few previous corpus studies with an annotated corpus of VPE in all 25 sections of the Wall Street Journal corpus (WSJ) distributed with the Penn Treebank. We an

  11. Intra-species sequence comparisons for annotating genomes

    Energy Technology Data Exchange (ETDEWEB)

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  12. Automatic image annotation and retrieval using group sparsity.

    Science.gov (United States)

    Zhang, Shaoting; Huang, Junzhou; Li, Hongsheng; Metaxas, Dimitris N

    2012-06-01

    Automatically assigning relevant text keywords to images is an important problem. Many algorithms have been proposed in the past decade and achieved good performance. Efforts have focused upon model representations of keywords, whereas properties of features have not been well investigated. In most cases, a group of features is preselected, yet important feature properties are not well used to select features. In this paper, we introduce a regularization-based feature selection algorithm to leverage both the sparsity and clustering properties of features, and incorporate it into the image annotation task. Using this group-sparsity-based method, the whole group of features [e.g., red green blue (RGB) or hue, saturation, and value (HSV)] is either selected or removed. Thus, we do not need to extract this group of features when new data comes. A novel approach is also proposed to iteratively obtain similar and dissimilar pairs from both the keyword similarity and the relevance feedback. Thus, keyword similarity is modeled in the annotation framework. We also show that our framework can be employed in image retrieval tasks by selecting different image pairs. Extensive experiments are designed to compare the performance between features, feature combinations, and regularization-based feature selection methods applied on the image annotation task, which gives insight into the properties of features in the image annotation task. The experimental results demonstrate that the group-sparsity-based method is more accurate and stable than others. PMID:22249744

  13. Reliability and effectiveness of clickthrough data for automatic image annotation

    NARCIS (Netherlands)

    Tsikrika, T.; Diou, C.; De Vries, A.P.; Delopoulos, A.

    2010-01-01

    Automatic image annotation using supervised learning is performed by concept classifiers trained on labelled example images. This work proposes the use of clickthrough data collected from search logs as a source for the automatic generation of concept training data, thus avoiding the expensive manua

  14. Geothermal power economics: an annotated bibliography. Volume I

    Energy Technology Data Exchange (ETDEWEB)

    El-Ramly, N.; Peterson, R.; Seo, K.K.

    1974-02-01

    Volume 1 contains annotations and abstracts of thirty-two papers on geothermal exploration, worldwide geothermal development, geothermal by-products, economic aspects, and environmental and legal aspects. A bibliography of 192 citations is also included. Individual items were previously indexed for the energy data base. (LBS)

  15. Genome Annotation in a Community College Cell Biology Lab

    Science.gov (United States)

    Beagley, C. Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning…

  16. Electron capture and stellar collapse

    International Nuclear Information System (INIS)

    In order, to investigate the function of electron capture in the phenomenon of pre-supernovae gravitacional collapse, an hydrodynamic caculation was carried out, coupling capture, decay and nuclear reaction equation system. A star simplified model (homogeneous model) was adopted using fermi ideal gas approximation for tthe sea of free electrons and neutrons. The non simplified treatment from quasi-static evolution to collapse is presented. The capture and beta decay rates, as wellas neutron delayed emission, were calculated by beta decay crude theory, while the other reaction rates were determined by usual theories. The preliminary results are presented. (M.C.K.)

  17. An Improved microRNA Annotation of the Canine Genome

    Science.gov (United States)

    Swofford, Ross; Johnson, Jeremy; Alföldi, Jessica; Lindblad-Toh, Kerstin; Swarbreck, David; Moxon, Simon; Di Palma, Federica

    2016-01-01

    The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions. PMID:27119849

  18. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

    OpenAIRE

    Hamilton John P; Campbell Matthew; Thibaud-Nissen Françoise; Zhu Wei; Buell C

    2007-01-01

    Abstract Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation) is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging k...

  19. Creating reference gene annotation for the mouse C57BL6/J genome assembly

    OpenAIRE

    Mudge, Jonathan M; Harrow, Jennifer

    2015-01-01

    Annotation on the reference genome of the C57BL6/J mouse has been an ongoing project ever since the draft genome was first published. Initially, the principle focus was on the identification of all protein-coding genes, although today the importance of describing long non-coding RNAs, small RNAs, and pseudogenes is recognized. Here, we describe the progress of the GENCODE mouse annotation project, which combines manual annotation from the HAVANA group with Ensembl computational annotation, al...

  20. Annotation Graphs and Servers and Multi-Modal Resources: Infrastructure for Interdisciplinary Education, Research and Development

    OpenAIRE

    Cieri, Christopher; Bird, Steven

    2002-01-01

    Annotation graphs and annotation servers offer infrastructure to support the analysis of human language resources in the form of time-series data such as text, audio and video. This paper outlines areas of common need among empirical linguists and computational linguists. After reviewing examples of data and tools used or under development for each of several areas, it proposes a common framework for future tool development, data annotation and resource sharing based upon annotation graphs an...