LEGO mindstorm masterpieces building and programming advanced robots

CERN Document Server

2003-01-01

In LEGO Mindstorm Masterpieces, some of the world's leading LEGO Mindstorms inventors share their knowledge and development secrets. The unique style of this book will allow it to cover an incredibly broad range of topics in unparalleled detail. Chapters within the book will include detailed discussions of the mechanics that drive the robot - and also provide step-by-step construction diagrams for each of the robots. This is perfect book for LEGO hobbyists looking to take their skills to the next level whether they build world-class competitive robots or just like to mess around for the fun of it.For experienced users of LEGO Mindstorms, LEGO Mindstorms Masterpiece is composed of three fundamental sections:·Part One: A review of the advanced robot building concepts and theories.·Part Two: Step-by-step building instructions for a series of complex models. The companion programming code is included, along with in-depth explanations of concepts needed for the specific models. Robots include Line Followers, Bip...

LEGO products have become more complex.

Science.gov (United States)

Bartneck, Christoph; Moltchanova, Elena

2018-01-01

The LEGO Group has become the largest toy company in the world and they can look back to a proud history of more than 50 years of producing bricks and other toys. Starting with a simple set of basic bricks their range of toys appeared to have increased in complexity over the years. We processed the inventories of most sets from 1955-2015 and our analysis showed that LEGO sets have become bigger, more colorful and more specialized. The vocabulary of bricks has increased significantly resulting in sets sharing fewer bricks. The increased complexity of LEGO sets and bricks enables skilled builders to design ever more amazing models but it may also overwhelm less skilled or younger builders.

Introduction for Freshmen to Embedded Systems Using LEGO Mindstorms

Science.gov (United States)

Kim, Seung Han; Jeon, Jae Wook

2009-01-01

The purpose of the course presented here is to introduce freshmen to embedded systems using LEGO Mindstorms, under an ANSI-C programming environment. The students build their own LEGO robots, make programs for them using ANSI-C, and operate them. By creating these LEGO robots, the students become more motivated, learning the basic concepts of…

LEGO products have become more complex.

Directory of Open Access Journals (Sweden)

Christoph Bartneck

Full Text Available The LEGO Group has become the largest toy company in the world and they can look back to a proud history of more than 50 years of producing bricks and other toys. Starting with a simple set of basic bricks their range of toys appeared to have increased in complexity over the years. We processed the inventories of most sets from 1955-2015 and our analysis showed that LEGO sets have become bigger, more colorful and more specialized. The vocabulary of bricks has increased significantly resulting in sets sharing fewer bricks. The increased complexity of LEGO sets and bricks enables skilled builders to design ever more amazing models but it may also overwhelm less skilled or younger builders.

LEGO Robotics: An Authentic Problem Solving Tool?

Science.gov (United States)

Castledine, Alanah-Rei; Chalmers, Chris

2011-01-01

With the current curriculum focus on correlating classroom problem solving lessons to real-world contexts, are LEGO robotics an effective problem solving tool? This present study was designed to investigate this question and to ascertain what problem solving strategies primary students engaged with when working with LEGO robotics and whether the…

On the asymptotic enumeration of LEGO structures

DEFF Research Database (Denmark)

Abrahamsen, Mikkel; Eilers, Søren

2011-01-01

We investigate experimentally the growth regimes of the number of LEGO structures that can be constructed contiguously from n blocks of equal shape and color.......We investigate experimentally the growth regimes of the number of LEGO structures that can be constructed contiguously from n blocks of equal shape and color....

Modular Lego-Electronics

KAUST Repository

Shaikh, Sohail F.; Ghoneim, Mohamed T.; Bahabry, Rabab R.; Khan, Sherjeel M.; Hussain, Muhammad Mustafa

2017-01-01

. Here, a generic manufacturable method of converting state-of-the-art complementary metal oxide semiconductor-based ICs into modular Lego-electronics is shown with unique geometry that is physically identifiable to ease manufacturing and enhance

LEGO Diorama Images

Data.gov (United States)

Allegheny County / City of Pittsburgh / Western PA Regional Data Center — We often create dioramas from LEGO bricks for use with our presentations, blogs, and social media posts. We find it's much more fun and effective to reenact...

Lego Robotics: STEM Sport of the Mind

Science.gov (United States)

Gura, Mark

2012-01-01

Lego robotics is engaging, hands-on, and encompasses every one of the NETS for Students. It also inspires a love of science, technology, engineering, and mathematics (STEM) and provides the experience students need to use digital age skills in the real world. In this article, the author discusses how schools get involved with Lego Robotics and…

A Lego version of ATLAS

CERN Multimedia

Laëtitia Pedroso

2010-01-01

There's nothing very unusual about a small child making simple objects out of Lego. But wouldn't you be surprised to learn that one six-year old has just made a life-like model of the ATLAS detector?   Bastian with his Lego ATLAS detector. © Photo provided by Kai Nicklas, Bastian's father. It all began a month ago when the boy's father was watching a video about the construction of the ATLAS detector on the Internet. He hadn't noticed that his son was watching it over his shoulder. The small boy was fascinated by what he was seeing on the computer screen and his first reaction was to exclaim: "Wow! That's a terrific machine! I think the people who built it must be really clever." The detector must have really fired his imagination because, after asking his father a few questions, he decided to make a Lego model of it. Look at the photo and you will see how closely the model he produced resembles the actual ATLAS detector. Is the little boy in question, Bastia...

LEGO Koncern 2000 - 2003 - en årsagsanalyse

OpenAIRE

Rosenberg, Morten; Özbudak, Devrim; Møller, Mads; Herneth, Daniel

2006-01-01

Denne rapport omhandler LEGO Koncernens økonomiske krise i årene 2000-2003. Vores videnskabsteoretiske er Kritisk realisme og vi bruger i projektet; en regnskabsanalyse, komparativ rapport og en PEST-analyse Denne rapport omhandler LEGO Koncernens økonomiske krise i årene 2000-2003. Vores videnskabsteoretiske er Kritisk realisme og vi bruger i projektet; en regnskabsanalyse, komparativ rapport og en PEST-analyse

LEGO-Method--New Strategy for Chemistry Calculation

Science.gov (United States)

Molnar, Jozsef; Molnar-Hamvas, Livia

2011-01-01

The presented strategy of chemistry calculation is based on mole-concept, but it uses only one fundamental relationship of the amounts of substance as a basic panel. The name of LEGO-method comes from the famous toy of LEGO[R] because solving equations by grouping formulas is similar to that. The relations of mole and the molar amounts, as small…

Lego Group: An Outsourcing Journey

DEFF Research Database (Denmark)

Larsen, Marcus Møller; Pedersen, Torben; Slepniov, Dmitrij

2010-01-01

The last years’ rather adventurous journey from 2004 to 2009 had taught the fifth-largest toy-maker in the world - the LEGO Group - the importance of managing the global supply chain effectively. In order to survive the largest internal financial crisis in its roughly 70 years of existence......, the management had, among many initiatives, decided to offshore and outsource a major chunk of its production to Flextronics. In this pursuit of rapid cost-cutting sourcing advantages, the LEGO Group planned to license out as much as 80 per cent of its production besides closing down major parts...

Using LEGO for learning fractions, supporting or distracting?

Science.gov (United States)

Rejeki, Sri; Setyaningsih, Nining; Toyib, Muhamad

2017-05-01

The role of games used for learning mathematics is still in debate. However, many research revealed that it gave positive effects on both students' motivation and performance in mathematics. Therefore, this study aims at investigating the effects of using LEGO-as one of games which students are familiar with, for learning mathematics, on both students' conceptual knowledge of fractions and students' attitude in learning mathematics. A set of learning activities consisting three meetings of fractions learning was designed for this study. The activities were mainly about solving word-context problems using LEGO as the model. Thirty students of seven grade with high-ability in mathematics and thirty two students with low-ability in mathematics were involved in this study. The data were collected through students' written works, video registration and field notes during the teaching and learning activities. The results indicate that in general the use of LEGO in learning activities support the conceptual understanding on fractions for both students with high-ability and low-ability in mathematics. Moreover, for students with low-ability in mathematics, it promotes the computational skill of fractions operation. The evidences also suggest that bringing LEGO into classroom activities improve students' motivation and engagement. However, in some cases, students were more focus on playing than learning. Therefore, teachers play important roles on providing clear pedagogical instructions about the way to use LEGO properly.

Orthognathic model surgery with LEGO key-spacer.

Science.gov (United States)

Tsang, Alfred Chee-Ching; Lee, Alfred Siu Hong; Li, Wai Keung

2013-12-01

A new technique of model surgery using LEGO plates as key-spacers is described. This technique requires less time to set up compared with the conventional plaster model method. It also retains the preoperative setup with the same set of models. Movement of the segments can be measured and examined in detail with LEGO key-spacers. Copyright © 2013 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

IMPLEMENTASI ALGORITMA BREADTH FIRST SEARCH DAN OBSTACLE DETECTION DALAM PENELUSURAN LABIRIN DINAMIS MENGGUNAKAN ROBOT LEGO

Directory of Open Access Journals (Sweden)

Adi Wibowo

2012-05-01

Full Text Available Dewasa ini perkembangan teknologi di dunia robot edukasi berkembang pesat. Robot-robot edukasi ini sering digunakan dalam riset penelitian karena kemudahan-kemudahan yang diberikannya dari segi perangkat keras. Salah satu contoh robot edukasi adalah robot LEGO Mindstorms NXT. Pada penelitian ini robot LEGO dibangun dalam bentuk robot line follower. Robot ini mampu menelusuri dan mencari jalan keluar dari labirin dinamis. Dalam menelusuri dan mencari jalan keluar, robot LEGO menggunakan algoritma Breadth First Search dan Manhattan Distance dalam memutuskan jalan mana yang harus diambil. Ketika menemui objek halangan, robot LEGO akan mengenali dan menghindari objek halangan tersebut dengan algoritma Obstacle Detection yang dimilikinya. Hasil implementasi membuktikan bahwa algoritma penelusuran labirin dinamis ini dapat diimplementasikan pada robot LEGO meskipun terdapat banyak keterbatasan dalam robot LEGO. Nowadays, the development of technology in educational robots is rapidly evolving. Educational robots are often used in research studies because they provide convenience in terms of hardware. One example is the educational robot LEGO Mindstorms NXT robot. In this research, LEGO robots built in the form of line follower robot. Robot is able to browse and find a way out of the dynamic labyrinth. In track and find a way out, LEGO robot uses an algorithm Breadth First Search and Manhattan Distance in deciding which path to take. When encountering an obstacle object, LEGO robot will recognize and avoid that obstacle objects with Obstacle Detection algorithm. The results prove that the implementation of a dynamic maze search algorithm can be implemented on a LEGO robot even though there are many limitations in LEGO robot.

Lego Car Race

Science.gov (United States)

Preston, Christine

2017-01-01

Familiar toys can be used to scaffold young children's learning about basic physics as well as guide scientific inquiry. Teachers looking for resources to engage young children and develop science inquiry skills need look no further than the toy box. In this two-part activity, children first construct a Lego® car and use it to explore the effects…

Konstruksi Genre Dalam Film “the Lego Movie”

OpenAIRE

Natalia, Vivi

2014-01-01

“The Lego Movie” adalah film animasi dari produsen film Warner Bros yang menceritakan kehidupan dan petualangan Emmet, seorang konstruksi bangunan yang salah terdeteksi sebagai orang spesial yang mampu menyelesaikan masalah dunia. Film ini adalah sebuah film yang membawa konvensi-konvensi genre yang berbeda dibanding film-film animasi lainnya. Peneliti melakukan analisis genre terhadap film “The Lego Movie” menggunakan 6 elemen menurut Jane Stoke, yaitu setting, lokasi, peristiwa naratif, plo...

LEGO: A Modular Approach to Accelerator Alignment Data Analysis

Energy Technology Data Exchange (ETDEWEB)

LeCocq, Catherine M

2003-05-14

The underlying unity of the numerous surveying computational methods is hidden by many practical differences in data acquisition. Traditional programming languages have added to the confusion by requiring programmers to describe the numeric data in very concrete and low-level structures (mostly arrays). In fact the algorithms behind all coordinate determination from surveying observations come down to basic methods of linear algebra. Lego uses the paradigm of object oriented programming (OOP) to more closely model the fundamental mathematical structures of all geodetic methods. Once the methods are in OOP form, the commonality across them becomes more obvious and a general architecture for a wide range of geodetic treatments becomes possible. This paper describes the fundamental concepts of this architecture and its advantages in terms of clarity (maintainability, testability and multi-author), portability and extensibility (observation types, resolution techniques and storage methods). The very first version of Lego was built in 1994 as a set of C routines to be used for the adjustment of theodolite data and tracker data. The routines were organized into six modules. Each module answered a specific task. The tasks had been identified as followed: general implementation, input, generic surveying formulas, statistical functions, matrix manipulation and specific resolution technique. This organization was the reason for the name Lego, but more seriously the purpose of this separation was to make Lego easily adaptable to any environment and easily expandable to new resolution techniques. At a second look, it was also a cry for being converted into a more modern language. Because C++ is primarily a superset of C, most C++ compilers have no problems compiling regular C code and may also handle a mixture of C and C++. This made the transformation of Lego very fast and painless. Up to now Lego is still using C functions for file access and dynamic memory allocation but is

LEGO: A Modular Approach to Accelerator Alignment Data Analysis

International Nuclear Information System (INIS)

LeCocq, Catherine M

2003-01-01

The underlying unity of the numerous surveying computational methods is hidden by many practical differences in data acquisition. Traditional programming languages have added to the confusion by requiring programmers to describe the numeric data in very concrete and low-level structures (mostly arrays). In fact the algorithms behind all coordinate determination from surveying observations come down to basic methods of linear algebra. Lego uses the paradigm of object oriented programming (OOP) to more closely model the fundamental mathematical structures of all geodetic methods. Once the methods are in OOP form, the commonality across them becomes more obvious and a general architecture for a wide range of geodetic treatments becomes possible. This paper describes the fundamental concepts of this architecture and its advantages in terms of clarity (maintainability, testability and multi-author), portability and extensibility (observation types, resolution techniques and storage methods). The very first version of Lego was built in 1994 as a set of C routines to be used for the adjustment of theodolite data and tracker data. The routines were organized into six modules. Each module answered a specific task. The tasks had been identified as followed: general implementation, input, generic surveying formulas, statistical functions, matrix manipulation and specific resolution technique. This organization was the reason for the name Lego, but more seriously the purpose of this separation was to make Lego easily adaptable to any environment and easily expandable to new resolution techniques. At a second look, it was also a cry for being converted into a more modern language. Because C++ is primarily a superset of C, most C++ compilers have no problems compiling regular C code and may also handle a mixture of C and C++. This made the transformation of Lego very fast and painless. Up to now Lego is still using C functions for file access and dynamic memory allocation but is

Long-term outcome of social skills intervention based on interactive LEGO play.

Science.gov (United States)

Legoff, Daniel B; Sherman, Michael

2006-07-01

LEGO building materials have been adapted as a therapeutic modality for increasing motivation to participate in social skills intervention, and providing a medium through which children with social and communication handicaps can effectively interact. A 3 year retrospective study of long-term outcome for autistic spectrum children participating in LEGO therapy (N = 60) compared Vineland Adaptive Behavior Scale socialization domain (VABS-SD) and Gilliam Autism Rating Scale social interaction subscale (GARS-SI) scores preand post-treatment with a matched comparison sample (N = 57) who received comparable non-LEGO therapy. Although both groups made significant gains on the two outcome measures, LEGO participants improved significantly more than the comparison subjects. Diagnosis and pre-treatment full-scale IQ scores did not predict outcome scores; however, Vineland adaptive behavior composite, Vineland communication domain, and verbal IQ all predicted outcome on the VABS-SD, especially for the LEGO therapy group. Results are discussed in terms of implications for methods of social skills intervention for autistic spectrum disorders.

Learning with LEGO

Science.gov (United States)

Durrani, Matin

2017-12-01

I have lost count of the number of wheezes to get people hooked on particle physics. There have been straightforward scientific accounts, personal tales of discovery, books filled with cartoons, essays and even historical vignettes. In Particle Physics Brick by Brick, science communicator Ben Still has decided to use LEGO bricks to coax readers into learning more about the subatomic world.

LEGO-inspired drug design

DEFF Research Database (Denmark)

Thanh Tung, Truong; Dao, Trong Tuan; Grifell Junyent, Marta

2018-01-01

The fungal plasma membrane H+-ATPase (Pma1p) is a potential target for the discovery of new antifungal agents. Surprisingly, no structure-activity relationship studies for small molecules targeting Pma1p have been reported. Herein, we disclose a LEGO-inspired fragment assembly strategy for design...

Anmeldelse af Eigil Lego Andersen: Dirigent og generalforsamling

DEFF Research Database (Denmark)

Werlauff, Erik

2011-01-01

Artiklen er en anmeldelse af advokat, adj. professor, dr. jur. Eigil Lego Andersens juridiske monografi om dirigenten og generalforsamlingen, herunder med lancering af en række nye afstemningsmetoder til brug for generalforsamlingen i (større) aktieselskaber.......Artiklen er en anmeldelse af advokat, adj. professor, dr. jur. Eigil Lego Andersens juridiske monografi om dirigenten og generalforsamlingen, herunder med lancering af en række nye afstemningsmetoder til brug for generalforsamlingen i (større) aktieselskaber....

Control Systems Lab Using a LEGO Mindstorms NXT Motor System

Science.gov (United States)

Kim, Y.

2011-01-01

This paper introduces a low-cost LEGO Mindstorms NXT motor system for teaching classical and modern control theories in standard third-year undergraduate courses. The LEGO motor system can be used in conjunction with MATLAB, Simulink, and several necessary toolboxes to demonstrate: 1) a modeling technique; 2) proportional-integral-differential…

Supramolecular Lego assembly towards three-dimensional multi-responsive hydrogels.

Science.gov (United States)

Ma, Chunxin; Li, Tiefeng; Zhao, Qian; Yang, Xuxu; Wu, Jingjun; Luo, Yingwu; Xie, Tao

2014-08-27

Inspired by the assembly of Lego toys, hydrogel building blocks with heterogeneous responsiveness are assembled utilizing macroscopic supramolecular recognition as the adhesion force. The Lego hydrogel provides 3D transformation upon pH variation. After disassembly of the building blocks by changing the oxidation state, they can be re-assembled into a completely new shape. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

LEGO Dimensions meets Doctor Who: Transbranding and New Dimensions of Transmedia Storytelling?

Directory of Open Access Journals (Sweden)

Matt Hills

2016-01-01

Full Text Available This article explores how the ‘toys-to-life’ videogame LEGO Dimensions (WarnerBros. Interactive Entertainment/Traveller’s Tales/The LEGO Group, 2015 mashes upmany different franchise storyworlds and brands. Specifically, I focus on how DoctorWho (BBC, 1963—, the British TV science fiction series, is licensed and transmediallyengaged with in Dimensions. I consider how the transbranding of LEGO Dimensionsappears to co-opt children’s “transgressive play” (Nørgård and Toft-Nielsen, 2014by combining intellectual properties, but actually continues to operate according tologics of shared corporate ownership where many of the combined storyworlds areultimately owned by Time Warner (placing Dimensions in competition with Disney’sown ‘toys-to-life’ game. Considering what value might accrue to the brand of DoctorWho by participating in LEGO Dimensions, I identify this as a particular example of“What If?” transmedia (Mittell, 2015, arguing that LEGO Dimensions’ Doctor Whonevertheless fluctuates in terms of its brand (inauthenticity. The Starter Pack remainscloser to LEGO Games’/Traveller’s Tales’ established format, subordinating Who, whilstthe separate Level Pack engages more precisely with Doctor Who’s history, albeit stilldisplaying some notable divergences from the TV series (Booth, 2015. Although LEGODimensions challenges influential theories of transmedia storytelling (Jenkins, 2006;Aldred, 2014, its transbranding and child/adult targeting accord with established approachesto transmedia licensing (Santo 2015 and fan-consumer socialization (Kinder1991.

Listening and Legos[TM

Science.gov (United States)

Morris, Pamela

2012-01-01

This simple exercise, performed in teams, gives students practice in listening to instructions, particularly when there are restrictions for the communication. The teams compete in a limited amount of time to build a Lego[TM] structure based on the instructions of one team member. Which team listens the best and is most successful?

FIRST LEGO League Kickoff

Science.gov (United States)

2007-01-01

Randall Hicks (right), Jacobs Technology's Education Services manager at NASA John C. Stennis Space Center, answers questions about the playing field for FIRST (For Inspiration and Recognition of Science and Technology) LEGO League's 2007 Challenge, `Power Puzzle.' More than 140 teachers, mentors, parents and students from 15 schools attended the Sept. 15 FLL season kickoff at StenniSphere, the visitor center at SSC. The teams from southern and central Mississippi and Mobile, Ala., who came to SSC heard rules for and asked questions about `Power Puzzle,' and saw robot demonstrations by Gulfport and Picayune high schools' past FIRST Robotics competitions. Using LEGO Mindstorms NXT kits, FLL teams of children ages 9-14 will spend the next three months building and programming robots to perform 'Power Puzzle's' challenge tasks, then pit them in competitions. They also will submit a research project about how energy choices impact the environment and the economy. The season will culminate at the Mississippi Championship Tournament on Dec. 8 at the Mississippi Gulf Coast Community College. FLL, considered the `little league' of the FIRST Robotics Competition, partners FIRST and the LEGO Group. Competitions aim to inspire and celebrate science and technology using real-world context and hands-on experimentation. NASA recognizes FIRST activities as an excellent hands-on method to increase student knowledge of science, engineering, technology and mathematics. Schools represented in this year's kickoff were: Madison Avenue Upper Elementary, the Mississippi Band of Choctaw Indians' Conehatta Elementary, Hattiesburg's Lillie Burney Elementary, Pearl Upper Elementary, Long Beach Middle, Oktibehha Elementary, d'Iberville Middle, Saucier's West Wortham Middle, Picayune's Nicholson Elementary and Roseland Park Baptist Church Academy, Bay St. Louis' St. Stanislaus College and Mobile's Davidson High, as well as two home-school groups from the Jackson area.

Innovation management based on proactive engagement of customers: A case study on LEGO Group. Part I: Innovation Management at Lego Group

Science.gov (United States)

Rusu, G.; Avasilcăi, S.

2015-11-01

Customers' proactive engagement in the innovation process represents a business priority for companies which adopt the open innovation business model. In such a context, it is of outmost importance for companies to use the online environment and social media, in order to create an interactive and open dialogue with customers and other important external stakeholders, achieving to gather creative solutions and innovative ideas by involving them in the process of co-creating value. Thus, the current paper is based on a case study approach, which aims to highlight the open innovation business model of the LEGO Group, one of the most successful and active company in engaging customers in submitting ideas and creative solutions for developing new products and new technologies, through online platforms. The study then proceeds to analyze the innovation management at LEGO Group, emphasizing the most important elements regarding the management team, the success and failures, the evolution of the LEGO products focusing on the innovation efforts of the company, its mission, vision, and values, emphasizing the innovation terms which guide the actions and objectives of the LEGO Group. Also, the research based on the case study approach, outlines the most important policies and strategies of the company, the organizational structure consisting of flat structures which facilitate the orientation of the team management on the innovation process and the proactive involvement of consumers and other external stakeholders in product development, highlighting also the most important activities developed by the management team in exploring the new opportunities which may occur on the market, involving customers in sharing their ideas at festivals, participating to discussions of adult fans on web-based platforms and establishing partnerships with the external stakeholders in order to create value. Moreover, the paper is focused on identifying the company's concerns regarding the

Alle ønsker sig en Lego-aktie til jul

DEFF Research Database (Denmark)

Iversen, Martin Jes

2014-01-01

Både små og store investorer får julelys i øjnene ved tanken om at eje et stykke af Lego. På sigt kunne en børsnotering gøre Danmark til et rigere land.......Både små og store investorer får julelys i øjnene ved tanken om at eje et stykke af Lego. På sigt kunne en børsnotering gøre Danmark til et rigere land....

Using LEGO Blocks for Technology-Mediated Task-Based English Language Learning

Science.gov (United States)

Gadomska, Agnieszka

2015-01-01

LEGO blocks have been played with by generations of children worldwide since the 1950s. It is undeniable that they boost creativity, eye-hand coordination, focus, planning, problem solving and many other skills. LEGO bricks have been also used by educators across the curricula as they are extremely motivating and engaging and, in effect, make…

Using a Lego-based communications simulation to introduce medical students to patient-centered interviewing.

Science.gov (United States)

Harding, S R; D'Eon, M F

2001-01-01

Teaching patient-centered interviewing skills to medical students can be challenging. We have observed that 1st-year medical students, in particular, do not feel free to concentrate on the interviewing skills because they are preoccupied with complicated technical medical knowledge. The Lego simulation we use with our 1st-year students as part of a professional-skills course overcomes that difficulty. The Lego activity is a role play analogous to a doctor-patient interview that uses identical sets of Legos for the "doctor" and for the "patients" and a small construction that represents a patient history. With a simple questionnaire, data were collected from students at different points during instruction. Results indicate that the Lego activity was very effective in helping students learn the importance of open-ended questioning. It also was rated as highly as the very dynamic interactive part of the instructional session. The effectiveness of the Lego activity may be due to the properties of analogies.

PLAYING LEGO INCREASE COGNITIVE DEVELOPMENT ON PRESCHOOL CHILD (4-5 YEARS OLD

Directory of Open Access Journals (Sweden)

Sri Utami

2017-07-01

Full Text Available Introduction: The preschool cognitive development can be stimulated with playing activity. The preschool child who stimulateless, their creativity will be checked and it can effect their cognitive development. Playing lego is one of the stimulation which give chance to the preschool child to express creativity and explorate their skill in playing construction. This research was aimed to analyze the effect of playing lego to the preschool cognitive development. Method: Quasy experimental pre post test design was used in this research. Total sample were 18 preschool child (4-5 years old. The independent variable was playing lego and the dependent variable was the cognitive development. Data were analyzed by Wilcoxon Signed Rank Test and Mann Whitney U Test with the significance α<0.05. Result: Result showed that the control group has significance level p=0.059 and the treatment group has significance level p=0.008. The result of Mann Whitney U Test showed p=0.001. Discussion: It can be concluded that playing lego can effect the preschool cognitive development in spatial factor, reasoning, memory, and perceptual speed. It can be suggested to the further research to examine the effect of playing lego to the motoric development or social development.

Lego Group: An Outsourcing Journey

DEFF Research Database (Denmark)

Larsen, Marcus Møller; Pedersen, Torben; Slepniov, Dmitrij

2010-01-01

, the management had, among many initiatives, decided to offshore and outsource a major chunk of its production to Flextronics. In this pursuit of rapid cost-cutting sourcing advantages, the LEGO Group planned to license out as much as 80 per cent of its production besides closing down major parts...

On the entropy of LEGO

DEFF Research Database (Denmark)

Durhuus, Bergfinnur; Eilers, Søren

We propose the further study of the rate of growth of the number of contiguous buildings which may be made from n LEGO blocks of the same size and color. Specializing to blocks of dimension 2x4 we give upper and lower bounds, and speculate on the true value....

Method of dynamic fuzzy symptom vector in intelligent diagnosis

International Nuclear Information System (INIS)

Sun Hongyan; Jiang Xuefeng

2010-01-01

Aiming at the requirement of diagnostic symptom real-time updating brought from diagnostic knowledge accumulation and great gap in unit and value of diagnostic symptom in multi parameters intelligent diagnosis, the method of dynamic fuzzy symptom vector is proposed. The concept of dynamic fuzzy symptom vector is defined. Ontology is used to specify the vector elements, and the vector transmission method based on ontology is built. The changing law of symptom value is analyzed and fuzzy normalization method based on fuzzy membership functions is built. An instance proved method of dynamic fussy symptom vector is efficient to solve the problems of symptom updating and unify of symptom value and unit. (authors)

Live LEGO House: a Mixed Reality Game for the Edutainment

OpenAIRE

Portalés Ricart, Cristina

2007-01-01

Gaming is a natural way of learning and multimedia technologies bring new possibilities in the field of edutainment. Live LEGO House in an interactive space to explore coexistence and multicultural factors through gaming based on the Mixed Reality(MXR)technology. The system consists basically on a physical/real house built with the LEGO blocks, which is enriched with different non-physical/virtual multimedia files, including sounds, videos and 3D animations with multicultural content. Childre...

A 'LEGO' Hybrid Photon Detector - assembled from standard mass-produced vacuum components

International Nuclear Information System (INIS)

Ferenc, Daniel; Lorenz, Eckart; Mirzoyan, Razmik

2000-01-01

Motivated primarily by the MAGIC atmospheric Cherenkov telescope project, we have developed a 'LEGO' Hybrid Photon Detector (HPD) comprising excellent focusing properties and protection against positive ion feedback. LEGO-HPD is supposed to be assembled from standard high vacuum components, which insures simplicity in the assembly procedure and reliability of operation

Use artificial neural network to align biological ontologies.

Science.gov (United States)

Huang, Jingshan; Dang, Jiangbo; Huhns, Michael N; Zheng, W Jim

2008-09-16

Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics. In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others. The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.

Project Luna Succendo: The Lunar Evolutionary Growth-Optimized (LEGO) Reactor

Science.gov (United States)

Bess, John Darrell

A final design has been established for a basic Lunar Evolutionary Growth-Optimized (LEGO) Reactor using current and near-term technologies. The LEGO Reactor is a modular, fast-fission, heatpipe-cooled, clustered-reactor system for lunar-surface power generation. The reactor is divided into subcritical units that can be safely launched within lunar shipments from the Earth, and then emplaced directly into holes drilled into the lunar regolith to form a critical reactor assembly. The regolith would not just provide radiation shielding, but serve as neutron-reflector material as well. The reactor subunits are to be manufactured using proven and tested materials for use in radiation environments, such as uranium-dioxide fuel, stainless-steel cladding and structural support, and liquid-sodium heatpipes. The LEGO Reactor system promotes reliability, safety, and ease of manufacture and testing at the cost of an increase in launch mass per overall rated power level and a reduction in neutron economy when compared to a single-reactor system. A single unshielded LEGO Reactor subunit has an estimated mass of approximately 448 kg and provides 5 kWe using a free-piston Stirling space converter. The overall envelope for a single unit with fully extended radiator panels has a height of 8.77 m and a diameter of 0.50 m. The subunits can be placed with centerline distances of approximately 0.6 m in a hexagonal-lattice pattern to provide sufficient neutronic coupling while allowing room for heat rejection and interstitial control. A lattice of six subunits could provide sufficient power generation throughout the initial stages of establishing a lunar outpost. Portions of the reactor may be neutronically decoupled to allow for reduced power production during unmanned periods of base operations. During later stages of lunar-base development, additional subunits may be emplaced and coupled into the existing LEGO Reactor network Future improvements include advances in reactor control

Calling all LEGO lovers! Add a mini control room to your collection

CERN Multimedia

Katarina Anthony

2015-01-01

The mini LHC Lego project launched in March (see here) now has almost 6,000 supporters - well on its way to the 10,000 votes needed for it to (hopefully!) hit store shelves. This week, the project added a new feature to its line: a mini control centre! The new LEGO Control centre, featuring operators "Kerstin" and "Marco".   The mini LHC project is the brainchild of ATLAS PhD student Nathan Readioff, who designed Lego replicas of the LHC and the ALICE, ATLAS, CMS and LHCb experiments on a micro scale. Each detector model is small enough to fit in the palm of your hand but crammed with detailed internal systems revealed by cutaway walls. Every major detector component is represented by a Lego piece. Now, Nathan has created a control centre to complement the mini LHC project. This would be an add-on feature for Lego’s consideration, should they decide to develop the accelerator into a box set. “The control centre is ...

Bright bricks, dark play: On the impossibility of studying LEGO

OpenAIRE

Giddings, S.

2014-01-01

It is generally recognized that the pleasures of LEGO do not end once the instructions in a particular set have been followed and the model depicted on the box is accurately realized. Generations of children have —just as the manufacturers intended— pulled apart the pristine model and begun again, making new vehicles, environments and creatures. The new set joins the larger box of LEGO full of older bricks, and is mixed and hybridized. This hybridization has become particularly evident in rec...

Implementation of Reconfigurable Manufacturing Systems, the Case of The LEGO Group

DEFF Research Database (Denmark)

Wang, Ying; Bilberg, Arne; Hadar, Ronen

of reconfigurable manufacturing systems (RMS). A literature review is made to describe the advantages and core characteristics of RMS. Based on the theory, a conceptual model is developed to analyze where RMS would be most suitable and have most benefits in The LEGO Group. Finally, the conclusion is drawn based...... on the analysis through the model. Keywords: Reconfigurable Manufacturing Systems, Conceptual Model of RMS, Production of The LEGO Group...

FIRST LEGO League announces State Championship winners

Science.gov (United States)

2007-01-01

PEAK Home School Network Team 1832 'Techno Warriors' of Brandon sport the Champions Award they won during the Dec. 8 FIRST (For Inspiration and Recognition of Science and Technology) LEGO League 2007 Mississippi Championship Tournament.

LEGO for Two-Party Secure Computation

DEFF Research Database (Denmark)

Nielsen, Jesper Buus; Orlandi, Claudio

2009-01-01

This paper continues the recent line of work of making Yao’s garbled circuit approach to two-party computation secure against an active adversary. We propose a new cut-and-choose based approach called LEGO (Large Efficient Garbled-circuit Optimization): It is specifically aimed at large circuits...

Race to improve student understanding of uncertainty: Using LEGO race cars in the physics lab

Science.gov (United States)

Parappilly, Maria; Hassam, Christopher; Woodman, Richard J.

2018-01-01

Laboratories using LEGO race cars were developed for students in an introductory physics topic with a high early drop-out rate. In a 2014 pilot study, the labs were offered to improve students' confidence with experiments and laboratory skills, especially uncertainty propagation. This intervention was extended into the intro level physics topic the next year, for comparison and evaluation. Considering the pilot study, we subsequently adapted the delivery of the LEGO labs for a large Engineering Mechanics cohort. A qualitative survey of the students was taken to gain insight into their perception of the incorporation of LEGO race cars into physics labs. For Engineering, the findings show that LEGO physics was instrumental in teaching students the measurement and uncertainty, improving their lab reporting skills, and was a key factor in reducing the early attrition rate. This paper briefly recalls the results of the pilot study, and how variations in the delivery yielded better learning outcomes. A novel method is proposed for how LEGO race cars in a physics lab can help students increase their understanding of uncertainty and motivate them towards physics practicals.

Liquid-handling Lego robots and experiments for STEM education and research

OpenAIRE

Gerber, Lukas C.; Calasanz-Kaiser, Agnes; Hyman, Luke; Voitiuk, Kateryna; Patil, Uday; Riedel-Kruse, Ingmar H.

2017-01-01

Liquid-handling robots have many applications for biotechnology and the life sciences, with increasing impact on everyday life. While playful robotics such as Lego Mindstorms significantly support education initiatives in mechatronics and programming, equivalent connections to the life sciences do not currently exist. To close this gap, we developed Lego-based pipetting robots that reliably handle liquid volumes from 1 ml down to the sub-μl range and that operate on standard laboratory plasti...

Transforming LEGO for the Digital Economy

DEFF Research Database (Denmark)

Andersen, Peter; Ross, Jeanne

2016-01-01

processes. The goal of the new transformation is “to become a digital company.” Although the company already looked digital in 2016, management felt it had not become digital—in its products and processes. This case describes the LEGO Group’s journey to become a successful digital company....

Programación de LEGO MindStorms bajo GNU/Linux

OpenAIRE

Matellán Olivera, Vicente; Heras Quirós, Pedro de las; Centeno González, José; González Barahona, Jesús

2002-01-01

GNU/Linux sobre un ordenador personal es la opción libre preferida por muchos desarrolladores de aplicaciones, pero también es una plataforma de desarrollo muy popular para otros sistemas, incluida la programación de robots, en particular es muy adecuada para jugar con los LEGO Mindstorms. En este artículo presentaremos las dos opciones más extendidas a la hora de programar estos juguetes: NQC y LegOS. NQC es una versión reducida de C que permite el desarrollo rápido de programas ...

A Basic LEGO Reactor Design for the Provision of Lunar Surface Power

International Nuclear Information System (INIS)

John Darrell Bess

2008-01-01

A final design has been established for a basic Lunar Evolutionary Growth-Optimized (LEGO) Reactor using current and near-term technologies. The LEGO Reactor is a modular, fast-fission, heatpipe-cooled, clustered-reactor system for lunar-surface power generation. The reactor is divided into subcritical units that can be safely launched with lunar shipments from Earth, and then emplaced directly into holes drilled into the lunar regolith to form a critical reactor assembly. The regolith would not just provide radiation shielding, but serve as neutron-reflector material as well. The reactor subunits are to be manufactured using proven and tested materials for use in radiation environments, such as uranium-dioxide fuel, stainless-steel cladding and structural support, and liquid-sodium heatpipes. The LEGO Reactor system promotes reliability, safety, and ease of manufacture and testing at the cost of an increase in launch mass per overall rated power level and a reduction in neutron economy when compared to a single-reactor system. A single unshielded LEGO Reactor subunit has an estimated mass of approximately 448 kg and provides approximately 5 kWe. The overall envelope for a single subunit with fully extended radiator panels has a height of 8.77 m and a diameter of 0.50 m. Six subunits could provide sufficient power generation throughout the initial stages of establishing a lunar outpost. Portions of the reactor may be neutronically decoupled to allow for reduced power production during unmanned periods of base operations. During later stages of lunar-base development, additional subunits may be emplaced and coupled into the existing LEGO Reactor network, subject to lunar base power demand. Improvements in reactor control methods, fuel form and matrix, shielding, as well as power conversion and heat rejection techniques can help generate an even more competitive LEGO Reactor design. Further modifications in the design could provide power generative opportunities for

Color dithering methods for LEGO-like 3D printing

Science.gov (United States)

Sun, Pei-Li; Sie, Yuping

2015-01-01

Color dithering methods for LEGO-like 3D printing are proposed in this study. The first method is work for opaque color brick building. It is a modification of classic error diffusion. Many color primaries can be chosen. However, RGBYKW is recommended as its image quality is good and the number of color primary is limited. For translucent color bricks, multi-layer color building can enhance the image quality significantly. A LUT-based method is proposed to speed the dithering proceeding and make the color distribution even smoother. Simulation results show the proposed multi-layer dithering method can really improve the image quality of LEGO-like 3D printing.

A Day at FIRST Lego League

Science.gov (United States)

McIntyre, Nancy

2012-01-01

This article features an after-school FIRST Lego League (FLL) program at Chaminade Middle School in Chatsworth, California, USA. The after-school FLL program feeds into the high school FIRST Robotics Competition (FRC) program wherein aspiring young engineers come to the high school team with several years of FLL experience. Through the FLL…

Wave propagation in complex structures with LEGO

NARCIS (Netherlands)

Lancellotti, V.; Hon, de B.P.; Tijhuis, A.G.

2012-01-01

We present the extension of the linear embedding via Green's operators (LEGO) scheme to problems that involve elementary sources localized inside complex structures made of different dielectric media with inclusions. We show how this new feature allows solving problems of wave propagation within,

Exploring New Firm Creation Out of Brand Communities: The Case of LEGO

DEFF Research Database (Denmark)

Hienerth, Christoph; Lettl, Christopher; Biskjaer, Michael Mose

2011-01-01

In the field of new product development, brand communities have attracted a great deal of attention from both academics and practitioners as a means of facilitating consumer-producer co-creation processes. In this paper, we extend the line of research on brand communities to the field...... brand community enjoys a broader range of LEGO products and services. Our findings reveal the emergence of a hybrid organizational form in which new business ideas are neither exploited solely within the boundaries of the focal producer firm, nor pursued by fully independent new firms alone. We observe...... of entrepreneurship studies by examining the conditions under which new firms emerge out of these social networks. Our empirical setting is the global LEGO brand community. As a well-known pioneering firm that is constantly experimenting with new ways of collaborating with its fan and customer base, LEGO recently...

Building ontologies with basic formal ontology

CERN Document Server

Arp, Robert; Spear, Andrew D.

2015-01-01

In the era of "big data," science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now u...

Spiral CT scanning technique in the detection of aspiration of LEGO foreign bodies.

Science.gov (United States)

Applegate, K E; Dardinger, J T; Lieber, M L; Herts, B R; Davros, W J; Obuchowski, N A; Maneker, A

2001-12-01

Radiolucent foreign bodies (FBs) such as plastic objects and toys remain difficult to identify on conventional radiographs of the neck and chest. Children may present with a variety of respiratory complaints, which may or may not be due to a FB. To determine whether radiolucent FBs such as plastic LEGOs and peanuts can be seen in the tracheobronchial tree or esophagus using low-dose spiral CT, and, if visible, to determine the optimal CT imaging technique. Multiple spiral sequences were performed while varying the CT parameters and the presence and location of FBs in either the trachea or the esophagus first on a neck phantom and then a cadaver. Sequences were rated by three radiologists blinded to the presence of a FB using a single scoring system. The LEGO was well visualized in the trachea by all three readers (both lung and soft-tissue windowing: combined sensitivity 89 %, combined specificity 89 %) and to a lesser extent in the esophagus (combined sensitivity 31 %, combined specificity 100 %). The peanut was not well visualized (combined sensitivity LEGO was 120 kV, 90 mA, 3-mm collimation, 0.75 s/revolution, and 2.0 pitch. This allowed for coverage of the cadaver tracheobronchial tree (approximately 11 cm) in about 18 s. Although statistical power was low for detecting significant differences, all three readers noted higher average confidence ratings with lung windowing among 18 LEGO-in-trachea scans. Rapid, low-dose spiral CT may be used to visualize LEGO FBs in the airway or esophagus. Peanuts were not well visualized.

Elite weapons for lego fanatics build working handcuffs, body armor, batons, sunglasses, and the world's hardest hitting brick guns

CERN Document Server

Hüdepohl, Martin

2015-01-01

The last LEGO brick weapon construction book and design guide you'll ever need, Elite Weapons for LEGO Fanatics features building instructions for thirteen fully functional LEGO masterpieces, including the monstrous, 27-inch-long Dinosaur Superior, a fully automatic combat rifle that can puncture aluminum cans, and a highly detailed HK G3 brick replica. Also featuring a helmet, a baton, handcuffs, sunglasses, and a grappling hook gun, which allows you to retrieve distant objects without ever leaving your seat, Elite Weapons for LEGO Fanatics includes a chapter on how to find the LEGO pieces you need and a comic book story featuring a hero using the weapons in action. LEGO fans of all ages and skill levels will find a treasure trove of models, including: • Hammerhead Jr., a single-shot crossbow and it's big brother, the heavy-duty Hammerhead Sr. • Panzer Pod combat helmet • KlopSTOCK baton • Melody, a rubber-firing machine pistol • Nice-1, a pocket-sized pistol that packs a punch • Chinahook harpoon gun ...

Post-processing of Deep Web Information Extraction Based on Domain Ontology

Directory of Open Access Journals (Sweden)

PENG, T.

2013-11-01

Full Text Available Many methods are utilized to extract and process query results in deep Web, which rely on the different structures of Web pages and various designing modes of databases. However, some semantic meanings and relations are ignored. So, in this paper, we present an approach for post-processing deep Web query results based on domain ontology which can utilize the semantic meanings and relations. A block identification model (BIM based on node similarity is defined to extract data blocks that are relevant to specific domain after reducing noisy nodes. Feature vector of domain books is obtained by result set extraction model (RSEM based on vector space model (VSM. RSEM, in combination with BIM, builds the domain ontology on books which can not only remove the limit of Web page structures when extracting data information, but also make use of semantic meanings of domain ontology. After extracting basic information of Web pages, a ranking algorithm is adopted to offer an ordered list of data records to users. Experimental results show that BIM and RSEM extract data blocks and build domain ontology accurately. In addition, relevant data records and basic information are extracted and ranked. The performances precision and recall show that our proposed method is feasible and efficient.

Particle physics brick by brick atomic and subatomic physics explained... in LEGO

CERN Document Server

Still, Ben

2017-01-01

Using LEGO (R) blocks to create a uniquely visual and clear depiction of the way our universe is put together. This is the perfect introduction to the enigmatic and fascinating world of Quantum Physics.Our story starts with the Big Bang, and along the way, the constructs and interactions within and among atoms and sub-atomic particles, and the forces that play upon them, are clearly explained, with each LEGO (R) block representing a different atomic or sub-atomic particle. The different colours and size denote what that particle is and its relationship with the other 'building blocks'.Each chapter is presented in digestible chunks, using toy building blocks to illustrate the ideas and experiments that have led to some of the biggest discoveries of the past 150 years.Soon you'll be able to construct every element in the Universe using a box of LEGO (R) and this book!

LEGO, Legoland og Billund Lalandia nr. 2

DEFF Research Database (Denmark)

Leth Pasgaard, Jens Chr.

2007-01-01

kant af Ribe Amt. Ud over LEGO koncernens produktionsudflytning påvirkes Ny Billund Kommune endvidere af lukningen af Danish Crowns slagteri i Grindsted, hvor 700 arbejdspladser for nyligt blev nedlagt. Det er således forståeligt at kommunen byder nye investorer velkommen. Kommunen har potentialet til...

Innovation management based on proactive engagement of customers: A case study on LEGO Group. Part II: Challenge of engaging the digital customer

Science.gov (United States)

Avasilcăi, S.; Rusu, G.

2015-11-01

To foster the development of innovative products and new technologies, nowadays companies use an open innovation system, encouraging stakeholders to contribute, using the companies’ online platforms for open innovation or social media, bringing and sharing creative solutions and ideas in order to respond to challenging needs the company directly expresses. Accordingly, the current research continues the analysis of the LEGO Group innovation efforts, aiming to provide a case study approach based on describing the most important projects and online instruments company uses to interact with customers and other external stakeholders. Thus, by analysing the experience of the company in developing projects of involving stakeholders in the innovation processes, the article emphasizes the objective of these past projects developed by LEGO Group, outlining their objectives regarding the focus on the product or process innovation, the team management and stakeholders involved in the innovation actions and the results they obtained. Moreover, the case study highlights the features of the most important online instruments LEGO Group uses at the moment for engaging LEGO fans, children, parents, and other external stakeholders in developing new LEGO sets. Thus, LEGO online instruments provide the opportunity for customers to be creative and to respond to LEGO management team challenges. Accordingly, LEGO involve customers in bringing innovative ideas for LEGO sets through LEGO Ideas instrument, which aims to engage customers in submitting projects, voting and supporting ideas and also sharing them on social media. Also, the research emphasizes the role of supporting the open dialogue and interaction with customers and other external stakeholders through LEGO.com Create & Share Galleries instrument, using their creativity to upload innovative models in the public galleries. The continuous challenges LEGO launches for their fans create a long-term connection between company and

Block Party: Legos in the Library

Science.gov (United States)

Klebanoff, Abbe

2009-01-01

Toys don't belong in the library. That's probably what some people still think. But the author's library outside Philadelphia was having such a hard time attracting boys who had outgrown storytime that he and his colleagues decided to try something new. So his school started a Lego club. Since their June 2008 kickoff, they've been amazed by how…

The parametric resonance—from LEGO Mindstorms to cold atoms

Science.gov (United States)

Kawalec, Tomasz; Sierant, Aleksandra

2017-07-01

We show an experimental setup based on a popular LEGO Mindstorms set, allowing us to both observe and investigate the parametric resonance phenomenon. The presented method is simple but covers a variety of student activities like embedded software development, conducting measurements, data collection and analysis. It may be used during science shows, as part of student projects and to illustrate the parametric resonance in mechanics or even quantum physics, during lectures or classes. The parametrically driven LEGO pendulum gains energy in a spectacular way, increasing its amplitude from 10° to about 100° within a few tens of seconds. We provide also a short description of a wireless absolute orientation sensor that may be used in quantitative analysis of driven or free pendulum movement.

The parametric resonance—from LEGO Mindstorms to cold atoms

International Nuclear Information System (INIS)

Kawalec, Tomasz; Sierant, Aleksandra

2017-01-01

We show an experimental setup based on a popular LEGO Mindstorms set, allowing us to both observe and investigate the parametric resonance phenomenon. The presented method is simple but covers a variety of student activities like embedded software development, conducting measurements, data collection and analysis. It may be used during science shows, as part of student projects and to illustrate the parametric resonance in mechanics or even quantum physics, during lectures or classes. The parametrically driven LEGO pendulum gains energy in a spectacular way, increasing its amplitude from 10° to about 100° within a few tens of seconds. We provide also a short description of a wireless absolute orientation sensor that may be used in quantitative analysis of driven or free pendulum movement. (paper)

Design of a Two-level Adaptive Multi-Agent System for Malaria Vectors driven by an ontology

Directory of Open Access Journals (Sweden)

Etang Josiane

2007-07-01

Full Text Available Abstract Background The understanding of heterogeneities in disease transmission dynamics as far as malaria vectors are concerned is a big challenge. Many studies while tackling this problem don't find exact models to explain the malaria vectors propagation. Methods To solve the problem we define an Adaptive Multi-Agent System (AMAS which has the property to be elastic and is a two-level system as well. This AMAS is a dynamic system where the two levels are linked by an Ontology which allows it to function as a reduced system and as an extended system. In a primary level, the AMAS comprises organization agents and in a secondary level, it is constituted of analysis agents. Its entry point, a User Interface Agent, can reproduce itself because it is given a minimum of background knowledge and it learns appropriate "behavior" from the user in the presence of ambiguous queries and from other agents of the AMAS in other situations. Results Some of the outputs of our system present a series of tables, diagrams showing some factors like Entomological parameters of malaria transmission, Percentages of malaria transmission per malaria vectors, Entomological inoculation rate. Many others parameters can be produced by the system depending on the inputted data. Conclusion Our approach is an intelligent one which differs from statistical approaches that are sometimes used in the field. This intelligent approach aligns itself with the distributed artificial intelligence. In terms of fight against malaria disease our system offers opportunities of reducing efforts of human resources who are not obliged to cover the entire territory while conducting surveys. Secondly the AMAS can determine the presence or the absence of malaria vectors even when specific data have not been collected in the geographical area. In the difference of a statistical technique, in our case the projection of the results in the field can sometimes appeared to be more general.

Liquid-handling Lego robots and experiments for STEM education and research.

Directory of Open Access Journals (Sweden)

Lukas C Gerber

2017-03-01

Full Text Available Liquid-handling robots have many applications for biotechnology and the life sciences, with increasing impact on everyday life. While playful robotics such as Lego Mindstorms significantly support education initiatives in mechatronics and programming, equivalent connections to the life sciences do not currently exist. To close this gap, we developed Lego-based pipetting robots that reliably handle liquid volumes from 1 ml down to the sub-μl range and that operate on standard laboratory plasticware, such as cuvettes and multiwell plates. These robots can support a range of science and chemistry experiments for education and even research. Using standard, low-cost household consumables, programming pipetting routines, and modifying robot designs, we enabled a rich activity space. We successfully tested these activities in afterschool settings with elementary, middle, and high school students. The simplest robot can be directly built from the widely used Lego Education EV3 core set alone, and this publication includes building and experiment instructions to set the stage for dissemination and further development in education and research.

Liquid-handling Lego robots and experiments for STEM education and research.

Science.gov (United States)

Gerber, Lukas C; Calasanz-Kaiser, Agnes; Hyman, Luke; Voitiuk, Kateryna; Patil, Uday; Riedel-Kruse, Ingmar H

2017-03-01

Liquid-handling robots have many applications for biotechnology and the life sciences, with increasing impact on everyday life. While playful robotics such as Lego Mindstorms significantly support education initiatives in mechatronics and programming, equivalent connections to the life sciences do not currently exist. To close this gap, we developed Lego-based pipetting robots that reliably handle liquid volumes from 1 ml down to the sub-μl range and that operate on standard laboratory plasticware, such as cuvettes and multiwell plates. These robots can support a range of science and chemistry experiments for education and even research. Using standard, low-cost household consumables, programming pipetting routines, and modifying robot designs, we enabled a rich activity space. We successfully tested these activities in afterschool settings with elementary, middle, and high school students. The simplest robot can be directly built from the widely used Lego Education EV3 core set alone, and this publication includes building and experiment instructions to set the stage for dissemination and further development in education and research.

Spiral CT scanning technique in the detection of aspiration of LEGO foreign bodies

International Nuclear Information System (INIS)

Applegate, K.E.; Dardinger, J.T.; Herts, B.R.; Davros, W.J.; Obuchowski, N.A.; Lieber, M.L.; Maneker, A.

2001-01-01

Background:. Radiolucent foreign bodies (FBs) such as plastic objects and toys remain difficult to identify on conventional radiographs of the neck and chest. Children may present with a variety of respiratory complaints, which may or may not be due to a FB. Objective: To determine whether radiolucent FBs such as plastic LEGOs and peanuts can be seen in the tracheobronchial tree or esophagus using low-dose spiral CT, and, if visible, to determine the optimal CT imaging technique. Materials and methods: Multiple spiral sequences were performed while varying the CT parameters and the presence and location of FBs in either the trachea or the esophagus first on a neck phantom and then a cadaver. Sequences were rated by three radiologists blinded to the presence of a FB using a single scoring system. Results: The LEGO was well visualized in the trachea by all three readers (both lung and soft-tissue windowing: combined sensitivity 89 %, combined specificity 89 %) and to a lesser extent in the esophagus (combined sensitivity 31 %, combined specificity 100 %). The peanut was not well visualized (combined sensitivity < 35 %). The optimal technique for visualizing the LEGO was 120 kV, 90 mA, 3-mm collimation, 0.75 s/revolution, and 2.0 pitch. This allowed for coverage of the cadaver tracheobronchial tree (approximately 11 cm) in about 18 s. Although statistical power was low for detecting significant differences, all three readers noted higher average confidence ratings with lung windowing among 18 LEGO-in-trachea scans. Conclusion: Rapid, low-dose spiral CT may be used to visualize LEGO FBs in the airway or esophagus. Peanuts were not well visualized. (orig.)

Lego Serious Play in Law

Directory of Open Access Journals (Sweden)

Frederico de Andrade Gabrich

2016-12-01

Full Text Available The legal education is not fully following the significant changes in society in the XXI century, and this determines significant lack of student motivation. The teaching methodologies used in legal courses continued to follow the teacher's knowledge and books, grounded in instructionism. It takes the development and application of new teaching methodologies that favor the change of the dominant mental model, systems thinking, innovation and real problems solution that motivate students for learning. The Lego Serious

How LEGO Built the Foundations and Enterprise Capabilities for Digital Leadership

DEFF Research Database (Denmark)

El Sawy, Omar; Henrik, Amsinck; Kræmmergaard, Pernille

2016-01-01

We define digital leadership as doing the right things for the strategic success of digitalization for the enterprise and its business ecosystem. Digital leadership means thinking differently about business strategy, business models, the IT function, enterprise platforms, mindsets and skill sets......, and the workplace. Based on the decade-long digitalization journey and experiences of the LEGO Group, this article provides insights on building the foundations for enhancing enterprise capabilities for digital leadership. Leveraging digitalization is one of the LEGO Group’s four strategic priorities...... and is fundamental to it being a world leader in its industry...

Generation NXT: Building Young Engineers with LEGOs

Science.gov (United States)

Karp, T.; Gale, R.; Lowe, L. A.; Medina, V.; Beutlich, E.

2010-01-01

This paper describes key success factors for the implementation and development of a LEGO robotics engineering outreach program for elementary school students in West Texas. The outreach program not only aims at getting young students excited about engineering but at the same time aims at improving retention rates among electrical and computer…

Correlating Information Contents of Gene Ontology Terms to Infer Semantic Similarity of Gene Products

Directory of Open Access Journals (Sweden)

Mingxin Gan

2014-01-01

Full Text Available Successful applications of the gene ontology to the inference of functional relationships between gene products in recent years have raised the need for computational methods to automatically calculate semantic similarity between gene products based on semantic similarity of gene ontology terms. Nevertheless, existing methods, though having been widely used in a variety of applications, may significantly overestimate semantic similarity between genes that are actually not functionally related, thereby yielding misleading results in applications. To overcome this limitation, we propose to represent a gene product as a vector that is composed of information contents of gene ontology terms annotated for the gene product, and we suggest calculating similarity between two gene products as the relatedness of their corresponding vectors using three measures: Pearson’s correlation coefficient, cosine similarity, and the Jaccard index. We focus on the biological process domain of the gene ontology and annotations of yeast proteins to study the effectiveness of the proposed measures. Results show that semantic similarity scores calculated using the proposed measures are more consistent with known biological knowledge than those derived using a list of existing methods, suggesting the effectiveness of our method in characterizing functional relationships between gene products.

Designing and implementing nervous system simulations on LEGO robots.

Science.gov (United States)

Blustein, Daniel; Rosenthal, Nikolai; Ayers, Joseph

2013-05-25

We present a method to use the commercially available LEGO Mindstorms NXT robotics platform to test systems level neuroscience hypotheses. The first step of the method is to develop a nervous system simulation of specific reflexive behaviors of an appropriate model organism; here we use the American Lobster. Exteroceptive reflexes mediated by decussating (crossing) neural connections can explain an animal's taxis towards or away from a stimulus as described by Braitenberg and are particularly well suited for investigation using the NXT platform.(1) The nervous system simulation is programmed using LabVIEW software on the LEGO Mindstorms platform. Once the nervous system is tuned properly, behavioral experiments are run on the robot and on the animal under identical environmental conditions. By controlling the sensory milieu experienced by the specimens, differences in behavioral outputs can be observed. These differences may point to specific deficiencies in the nervous system model and serve to inform the iteration of the model for the particular behavior under study. This method allows for the experimental manipulation of electronic nervous systems and serves as a way to explore neuroscience hypotheses specifically regarding the neurophysiological basis of simple innate reflexive behaviors. The LEGO Mindstorms NXT kit provides an affordable and efficient platform on which to test preliminary biomimetic robot control schemes. The approach is also well suited for the high school classroom to serve as the foundation for a hands-on inquiry-based biorobotics curriculum.

History and Educational Potential of LEGO Mindstorms NXT

Directory of Open Access Journals (Sweden)

Memet ÜÇGÜL

2013-01-01

Full Text Available Abstract: Educational usage of the robotics has accelerated recently because of educational potential of robotics has been recognized by educators and popularity of international robotics tournaments. Many university and schools prepare technology and robotics related summer schools for children. LEGO Mindstorms NXT is the most popular and commonly used robotics set for educational purposes. This robot sets rooted to Seymour Papert’s LOGO studies which have much influence Instructional Technology in 1960’s. This study aims to present a literature review on educational potential of LEGO Mindstorms NXT robotics sets. Robotics mainly used in education for supporting the STEM (Science, Technology, Engineering and Mathematics education. Most of the related studies resulted with positive effects of the robotics activities in STEM education. Robotics also used in education to increase some skills of the children such as discovery learning, critical thinking and social skills.Özet - LEGO Mindstorms NXT’lerin Tarihi ve Eğitsel Potansiyeli: Robotların eğitsel amaçlarla kullanımı giderek artmaktadır. Eğitimcilerin robotların eğitsel potansiyelinin farkına varmaları ve uluslararası robot turnuvalarının popülerlik kazanmasının robotların eğitsel kullanımına katkısı büyüktür. Birçok üniversite ve okul, teknoloji ve robotlar konulu yaz kampları düzenlemektedirler. LEGO Mindstorms NXT en popüler ve en çok kullanılan eğitsel robot setleridir. Bu robot setlerinin geçmişi, Seymour Papert’in LOGO çalışmalarına dayanmaktadır. Bu çalışmaların 1960’larda eğitim teknolojisine büyük etkileri olmuştur. Bu tarama çalışmasının amacı son zamanlarda eğitimcilerin ilgisini çeken, robotların eğitsel amaçlarla kullanımına yönelik çalışmaları inceleyerek, LEGO Mindstorms NXT robot setlerinin  eğitim amaçlı kullanım potansiyellerinin belirlenmesidir. Robotlar eğitimde en çok FTMM (Fen, Teknoloji

A LEGO Mindstorms Brewster angle microscope

Science.gov (United States)

Fernsler, Jonathan; Nguyen, Vincent; Wallum, Alison; Benz, Nicholas; Hamlin, Matthew; Pilgram, Jessica; Vanderpoel, Hunter; Lau, Ryan

2017-09-01

A Brewster Angle Microscope (BAM) built from a LEGO Mindstorms kit, additional LEGO bricks, and several standard optics components, is described. The BAM was built as part of an undergraduate senior project and was designed, calibrated, and used to image phospholipid, cholesterol, soap, and oil films on the surface of water. A BAM uses p-polarized laser light reflected off a surface at the Brewster angle, which ideally yields zero reflectivity. When a film of different refractive index is added to the surface a small amount of light is reflected, which can be imaged in a microscope camera. Films of only one molecule (approximately 1 nm) thick, a monolayer, can be observed easily in the BAM. The BAM was used in a junior-level Physical Chemistry class to observe phase transitions of a monolayer and the collapse of a monolayer deposited on the water surface in a Langmuir trough. Using a photometric calculation, students observed a change in thickness of a monolayer during a phase transition of 7 Å, which was accurate to within 1 Å of the value determined by more advanced methods. As supplementary material, we provide a detailed manual on how to build the BAM, software to control the BAM and camera, and image processing software.

Scaling limits for the Lego discrepancy

International Nuclear Information System (INIS)

Hameren, Andre van; Kleiss, Ronald

1999-01-01

For the Lego discrepancy with M bins, which is equivalent with a χ 2 -statistic with M bins, we present a procedure to calculate the moment generating function of the probability distribution perturbatively if M and N, the number of uniformly and randomly distributed data points, become large. Furthermore, we present a phase diagram for various limits of the probability distribution in terms of the standardized variable if M and N become infinite

Ontology Update in the Cognitive Model of Ontology Learning

Directory of Open Access Journals (Sweden)

Zhang De-Hai

2016-01-01

Full Text Available Ontology has been used in many hot-spot fields, but most ontology construction methods are semiautomatic, and the construction process of ontology is still a tedious and painstaking task. In this paper, a kind of cognitive models is presented for ontology learning which can simulate human being’s learning from world. In this model, the cognitive strategies are applied with the constrained axioms. Ontology update is a key step when the new knowledge adds into the existing ontology and conflict with old knowledge in the process of ontology learning. This proposal designs and validates the method of ontology update based on the axiomatic cognitive model, which include the ontology update postulates, axioms and operations of the learning model. It is proved that these operators subject to the established axiom system.

MiniLEGO

DEFF Research Database (Denmark)

Frederiksen, Tore Kasper; Jakobsen, Thomas Pelle; Nielsen, Jesper Buus

2013-01-01

One of the main tools to construct secure two-party computation protocols are Yao garbled circuits. Using the cut-and-choose technique, one can get reasonably efficient Yao-based protocols with security against malicious adversaries. At TCC 2009, Nielsen and Orlandi [28] suggested to apply cut......-and-choose at the gate level, while previously cut-and-choose was applied on the circuit as a whole. This idea allows for a speed up with practical significance (in the order of the logarithm of the size of the circuit) and has become known as the “LEGO” construction. Unfortunately the construction in [28] is based...... on a specific number-theoretic assumption and requires public-key operations per gate of the circuit. The main technical contribution of this work is a new XOR-homomorphic commitment scheme based on oblivious transfer, that we use to cope with the problem of connecting the gates in the LEGO construction. Our...

LEGO A Modular Approach to Accelerator Alignment Data Analysis

CERN Document Server

Lecocq, C M

2003-01-01

The underlying unity of the numerous surveying computational methods is hidden by many practical differences in data acquisition. Traditional programming languages have added to the confusion by requiring programmers to describe the numeric data in very concrete and low-level structures (mostly arrays). In fact the algorithms behind all coordinate determination from surveying observations come down to basic methods of linear algebra. Lego uses the paradigm of object oriented programming (OOP) to more closely model the fundamental mathematical structures of all geodetic methods. Once the methods are in OOP form, the commonality across them becomes more obvious and a general architecture for a wide range of geodetic treatments becomes possible. This paper describes the fundamental concepts of this architecture and its advantages in terms of clarity (maintainability, testability and portability and extensibility (observation types, resolution techniques and storage methods). The very first version of Lego was bu...

An Exploration of the Nanoworld with LEGO Bricks

Science.gov (United States)

Campbell, Dean J.; Miller, Josiah D.; Bannon, Stephen J.; Obermaier, Lauren M.

2011-01-01

LEGO bricks can be used for a number of demonstrations of chemical structures and properties, especially at the nanoscale level. These bricks can also be used to model instrumentation that probes these structures and properties. Detailed resources about many of these demonstrations are located on the extensive Web site "Exploring the Nanoworld…

Lego Bricks and the Octet Rule: Molecular Models for Biochemical Pathways with Plastic, Interlocking Toy Bricks

Science.gov (United States)

Lin, Henry J.; Lehoang, Jennifer; Kwan, Isabel; Baghaee, Anita; Prasad, Priya; Ha-Chen, Stephanie J.; Moss, Tanesha; Woods, Jeremy D.

2018-01-01

The 8 studs on a 2 × 4 Lego brick conveniently represent the outer shell of electrons for carbon, nitrogen, and oxygen atoms. We used Lego bricks to model these atoms, which are then joined together to form molecules by following the Lewis octet rule. A variety of small biological molecules can be modeled in this way, such as most amino acids,…

METODE BERMAIN LEGO DALAM UPAYA MENUMBUHKEMBANGKAN KECERDASAN KINESTETIK PADA ANAK USIA DINI (Sudi Kasus di Lembaga Pendidikan Manusia Unggul

Directory of Open Access Journals (Sweden)

Fitria Yulianti Ningtyas

2018-01-01

Full Text Available Penelitian ini membahas tentang upaya menumbuhkembangkan kecerdasan kinestetik pada anak usia dini melalui metode bermain Lego di Lembaga Pendidikan Manusia Unggul. Melalui permainan Lego, anak yang memiliki gaya belajar kinestetik akan terstimulasi kecerdasan dan kemampuannya, terutama kecerdasan kinestetiknya. Sebab pada dasarnya, anak dengan gaya belajar kinestetik, memiliki kelebihan dalam ruang gerak serta berlebih energinya. Sehingga saat belajar, anak membutuhkan ruang yang cukup luas, serta permainan yang menantang. Penelitian ini bertujuan: 1 Untuk mengetahui dan menganalisis bagaimana langkah-langkah dalam menerapkan metode bermain Lego dalam upaya menumbuhkembangkan kecerdasan kinestetik pada anak usia dini di Lembaga Pendidikan Manusia Unggul. 2 Untuk mengetahui dan menganalisis bagaimana pelaksanaan dalam menerapkan metode bermain Lego dalam upaya menumbuhkembangkan kecerdasan kinestetik pada anak usia dini di Lembaga Manusia Unggul. 3 Untuk mengetahui dan menganalisis dampak dan hasil dari penerapan metode bermain Lego dalam upaya menumbuhkembangkan kecerdasan kinestetik pada anak usia dini di Lembaga Pendidikan Manusia Unggul. 4 Untuk mengetahui dan menganalisis apa saja faktor pendukung dan penghambat dalam menerapkan metode bermain Lego dalam upaya menumbuhkembangkan kecerdasan kinestetik pada anak usia dini di Lembaga Manusia Unggul. Penelitian ini menggunakan pendekatan kualitatif naturalistik. Ciri yang menonjol dari penelitian ini adalah cara pengamatan dan pengumpulan datanya dilakukan dalam latar/setting alamiah. Artinya tanpa memanipulasi subyek yang diteliti. Penelitian ini mencakup juga keyakinan terhadap sifat dasar dari realitas (yang diamati, hubungan antara orang yang mencoba mengetahui sesuatu (peneliti dan hal yang mereka coba ketahui (yang diteliti, peranan/pengaruh dari nilai-nilai (yang dianut peneliti dan variable-variabel lainnya yang serupa itu.Kajian data pada penelitian ini didapat dari hasil pengamatan

PENGARUH PENGGUNAAN BUKU AJAR BERBASIS STEM BERBANTUAN LEGO MINDSTORM EV3 TERHADAP PEMAHAMAN KONSEP MOMENTUM SISWA

Directory of Open Access Journals (Sweden)

Ratih Mega Ayu Afifah

2017-10-01

Full Text Available The purpose of this research is to figure out the effect of using STEM (Science, Technology, Engineering, and Mathematic based textbook that assisted by using LEGO mindstorm EV3 toward the students’s understanding of momentum subject. The design of this research that is pretest-postest group design. The Samples are composed of 12 students from experimental class and 12 students from control class. The results of this research show that the conceptual understanding of experimental class that using STEM-based textbook that assisted by using LEGO mindstorm EV3 is beter than the understanding of control class which using the conventional textbook in the ordinary class. The implication of this research is applying this textbook to measure the other cognitive dimention such as reasoning. Abstrak Tujuan penelitian ini adalah untuk mengetahui pengaruh penggunaan buku ajar berbasis STEM (Science, Technology, Engineering, dan Mathematics berbantuan LEGO mindstorm EV3 dalam pembelajaran fisika terhadap pemahaman konsep siswa pada materi momentum. Penelitian ini menggunakan desain eksperimen pretest postest group design. Sampel penelitian terdiri dari 12  siswa kelompok eksperimen dan 12 siswa kelompok kontrol. Berdasarkan hasil analisis menunjukkan bahwa pemahaman konsep kelompok siswa yang menggunakan buku ajar berbasis STEM berbantuan LEGO mindstorm EV3 secara signifikan lebih meningkat dibandingkan dengan kelompok yang menggunakan buku yang biasa digunakan di sekolah. Hasil penelitian menunjukkan bahwa penggunaan buku ajar berbasis STEM berbantuan robot LEGO mindstorm EV3 dapat meningkatkan pemahaman konsep siswa pada materi momentum. Implikasi pada penelitian ini adalah menerapkan buku ajar tersebut untuk mengukur dimensi kognitif lainnya seperti penalaran.

The Lego Story: Remolding Education Policy and Practice

Science.gov (United States)

Pirrie, Anne

2017-01-01

The aim of this article is to develop a more nuanced understanding of the complex nature of learning as it relates to both the educational and social aims of education as manifested in contemporary European education policy. The article explores tensions in education policy and practice by exploring the evolution of the global brand Lego. The…

Lightweight Expression of Granular Objects (LEGO) Content Modeling Using the SNOMED CT Observables Model to Represent Nursing Assessment Data.

Science.gov (United States)

Johnson, Christie

2016-01-01

This poster presentation presents a content modeling strategy using the SNOMED CT Observable Model to represent large amounts of detailed clinical data in a consistent and computable manner that can support multiple use cases. Lightweight Expression of Granular Objects (LEGOs) represent question/answer pairs on clinical data collection forms, where a question is modeled by a (usually) post-coordinated SNOMED CT expression. LEGOs transform electronic patient data into a normalized consumable, which means that the expressions can be treated as extensions of the SNOMED CT hierarchies for the purpose of performing subsumption queries and other analytics. Utilizing the LEGO approach for modeling clinical data obtained from a nursing admission assessment provides a foundation for data exchange across disparate information systems and software applications. Clinical data exchange of computable LEGO patient information enables the development of more refined data analytics, data storage and clinical decision support.

Ontological foundations for evolutionary economics: A Darwinian social ontology

NARCIS (Netherlands)

Stoelhorst, J.W.

2008-01-01

The purpose of this paper is to further the project of generalized Darwinism by developing a social ontology on the basis of a combined commitment to ontological continuity and ontological commonality. Three issues that are central to the development of a social ontology are addressed: (1) the

Use of LEGO as a therapeutic medium for improving social competence.

Science.gov (United States)

LeGoff, Daniel B

2004-10-01

A repeated-measures, waiting list control design was used to assess efficacy of a social skills intervention for autistic spectrum children focused on individual and group LEGO play. The intervention combined aspects of behavior therapy, peer modeling and naturalistic communication strategies. Close interaction and joint attention to task play an important role in both group and individual therapy activities. The goal of treatment was to improve social competence (SC) which was construed as reflecting three components: (1) motivation to initiate social contact with peers; (2) ability to sustain interaction with peers for a period of time: and (3) overcoming autistic symptoms of aloofness and rigidity. Measures for the first two variables were based on observation of subjects in unstructured situations with peers; and the third variable was assessed using a structured rating scale, the SI subscale of the GARS. Results revealed significant improvement on all three measures at both 12 and 24 weeks with no evidence of gains during the waiting list period. No gender differences were found on outcome, and age of clients was not correlated with outcome. LEGO play appears to be a particularly effective medium for social skills intervention, and other researchers and clinicians are encouraged to attempt replication of this work, as well as to explore use of LEGO in other methodologies, or with different clinical populations.

LEGO therapy and the social use of language programme: an evaluation of two social skills interventions for children with high functioning autism and Asperger Syndrome.

Science.gov (United States)

Owens, Gina; Granader, Yael; Humphrey, Ayla; Baron-Cohen, Simon

2008-11-01

LEGO therapy and the Social Use of Language Programme (SULP) were evaluated as social skills interventions for 6-11 year olds with high functioning autism and Asperger Syndrome. Children were matched on CA, IQ, and autistic symptoms before being randomly assigned to LEGO or SULP. Therapy occurred for 1 h/week over 18 weeks. A no-intervention control group was also assessed. Results showed that the LEGO therapy group improved more than the other groups on autism-specific social interaction scores (Gilliam Autism Rating Scale). Maladaptive behaviour decreased significantly more in the LEGO and SULP groups compared to the control group. There was a non-significant trend for SULP and LEGO groups to improve more than the no-intervention group in communication and socialisation skills.

Enriching K-12 Science and Mathematics Education Using LEGOs

Science.gov (United States)

Williams, Keeshan; Igel, Irina; Poveda, Ronald; Kapila, Vikram; Iskander, Magued

2012-01-01

This paper presents a series of illustrative LEGO Mindstorms-based science and math activities, developed under an NSF GK-12 Fellows project, for elementary, middle, and high school grades. The activities, developed by engineering and science graduate Fellows in partnership with K-12 teachers, are grade appropriate, address pertinent learning…

MIRO and IRbase: IT Tools for the Epidemiological Monitoring of Insecticide Resistance in Mosquito Disease Vectors

Science.gov (United States)

Dialynas, Emmanuel; Topalis, Pantelis; Vontas, John; Louis, Christos

2009-01-01

Background Monitoring of insect vector populations with respect to their susceptibility to one or more insecticides is a crucial element of the strategies used for the control of arthropod-borne diseases. This management task can nowadays be achieved more efficiently when assisted by IT (Information Technology) tools, ranging from modern integrated databases to GIS (Geographic Information System). Here we describe an application ontology that we developed de novo, and a specially designed database that, based on this ontology, can be used for the purpose of controlling mosquitoes and, thus, the diseases that they transmit. Methodology/Principal Findings The ontology, named MIRO for Mosquito Insecticide Resistance Ontology, developed using the OBO-Edit software, describes all pertinent aspects of insecticide resistance, including specific methodology and mode of action. MIRO, then, forms the basis for the design and development of a dedicated database, IRbase, constructed using open source software, which can be used to retrieve data on mosquito populations in a temporally and spatially separate way, as well as to map the output using a Google Earth interface. The dependency of the database on the MIRO allows for a rational and efficient hierarchical search possibility. Conclusions/Significance The fact that the MIRO complies with the rules set forward by the OBO (Open Biomedical Ontologies) Foundry introduces cross-referencing with other biomedical ontologies and, thus, both MIRO and IRbase are suitable as parts of future comprehensive surveillance tools and decision support systems that will be used for the control of vector-borne diseases. MIRO is downloadable from and IRbase is accessible at VectorBase, the NIAID-sponsored open access database for arthropod vectors of disease. PMID:19547750

Build Your Own Particle Detector. Education and outreach through ATLAS LEGO models and events

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00220289; The ATLAS collaboration

2016-01-01

To support the outreach activities of ATLAS institutes and to grasp people’s attention in science exhibitions and during public events, a very detailed model of the experiment built entirely out of LEGO bricks as well as an outreach programme using LEGO bricks to get people to think about particle detectors and involve them into a conversation about particle physics in general have been created. A large LEGO model, consisting of about 9500 pieces, has been exported to more than 55 ATLAS institutes and has been used in numerous exhibitions to explain the proportion and composition of the experiment to the public. As part of the Build Your Own Particle Detector programme (byopd.org) more than 15 events have been conducted, either involving a competition to design and build the best particle detector from a random pile of pieces or to take part in the construction of one of the large models, as part of a full day outreach event. Recently, miniature models of all four main LHC experiments, that will be used at ...

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms

Directory of Open Access Journals (Sweden)

Skene JH Pate

2007-09-01

Full Text Available Abstract Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD, which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO website 1. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1 install Apache Tomcat 2 on one's web server, (2 download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3 create an html (HyperText Markup Language file that refers to the OntologyWidget using a simple, well-defined format. Conclusion We have developed Ontology

LEGO bricks used as chemotactic chambers: evaluation by a computer-assisted image analysis technique.

Science.gov (United States)

Azzarà, A; Chimenti, M

2004-01-01

One of the main techniques used to explore neutrophil motility, employs micropore filters in chemotactic chambers. Many new models have been proposed, in order to perform multiple microassays in a rapid, inexpensive and reproducible way. In this work, LEGO bricks have been used as chemotactic chambers in the evaluation of neutrophil random motility and chemotaxis and compared with conventional Boyden chambers in a "time-response" experiment. Neutrophil motility throughout the filters was evaluated by means of an image-processing workstation, in which a dedicated algorithm recognizes and counts the cells in several fields and focal planes throughout the whole filter; correlates counts and depth values; performs a statistical analysis of data; calculates the true value of neutrophil migration; determines the distribution of cells; and displays the migration pattern. By this method, we found that the distances travelled by the cells in conventional chambers and in LEGO bricks were perfectly identical, both in random migration and under chemotactic conditions. Moreover, no interference with the physiological behaviour of neutrophils was detectable. In fact, the kinetics of migration was identical both in random migration (characterized by a gaussian pattern) and in chemotaxis (characterized by a typical stimulation peak, previously identified by our workstation). In conclusion, LEGO bricks are extremely precise devices. They are simple to use and allow the use of small amounts of chemoattractant solution and cell suspension, supplying by itself a triplicate test. LEGO bricks are inexpensive, fast and suitable for current diagnostic activity or for research investigations in every laboratory.

Where to Publish and Find Ontologies? A Survey of Ontology Libraries

Science.gov (United States)

d'Aquin, Mathieu; Noy, Natalya F.

2011-01-01

One of the key promises of the Semantic Web is its potential to enable and facilitate data interoperability. The ability of data providers and application developers to share and reuse ontologies is a critical component of this data interoperability: if different applications and data sources use the same set of well defined terms for describing their domain and data, it will be much easier for them to “talk” to one another. Ontology libraries are the systems that collect ontologies from different sources and facilitate the tasks of finding, exploring, and using these ontologies. Thus ontology libraries can serve as a link in enabling diverse users and applications to discover, evaluate, use, and publish ontologies. In this paper, we provide a survey of the growing—and surprisingly diverse—landscape of ontology libraries. We highlight how the varying scope and intended use of the libraries a ects their features, content, and potential exploitation in applications. From reviewing eleven ontology libraries, we identify a core set of questions that ontology practitioners and users should consider in choosing an ontology library for finding ontologies or publishing their own. We also discuss the research challenges that emerge from this survey, for the developers of ontology libraries to address. PMID:22408576

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

Science.gov (United States)

Martínez-Romero, Marcos; Jonquet, Clement; O'Connor, Martin J; Graybeal, John; Pazos, Alejandro; Musen, Mark A

2017-06-07

Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios. Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability

Quantum ontologies

International Nuclear Information System (INIS)

Stapp, H.P.

1988-12-01

Quantum ontologies are conceptions of the constitution of the universe that are compatible with quantum theory. The ontological orientation is contrasted to the pragmatic orientation of science, and reasons are given for considering quantum ontologies both within science, and in broader contexts. The principal quantum ontologies are described and evaluated. Invited paper at conference: Bell's Theorem, Quantum Theory, and Conceptions of the Universe, George Mason University, October 20-21, 1988. 16 refs

There is no quantum ontology without classical ontology

Energy Technology Data Exchange (ETDEWEB)

Fink, Helmut [Institut fuer Theoretische Physik, Univ. Erlangen-Nuernberg (Germany)

2011-07-01

The relation between quantum physics and classical physics is still under debate. In his recent book ''Rational Reconstructions of Modern Physics'', Peter Mittelstaedt explores a route from classical to quantum mechanics by reduction and elimination of (some of) the ontological hypotheses underlying classical mechanics. While, according to Mittelstaedt, classical mechanics describes a fictitious world that does not exist in reality, he claims to achieve a universal quantum ontology that can be improved by incorporating unsharp properties and equipped with Planck's constant without any need to refer to classical concepts. In this talk, we argue that quantum ontology in Mittelstaedt's sense is not enough. Quantum ontology can never be universal as long as the difference between potential and real properties is not represented adequately. Quantum properties are potential, not (yet) real, be they sharp or unsharp. Hence, preparation and measurement presuppose classical concepts, even in quantum theory. We end up with a classical-quantum sandwich ontology, which is still less extravagant than Bohmian or many-worlds ontologies are.

Automated concept and relationship extraction for the semi-automated ontology management (SEAM) system.

Science.gov (United States)

Doing-Harris, Kristina; Livnat, Yarden; Meystre, Stephane

2015-01-01

We develop medical-specialty specific ontologies that contain the settled science and common term usage. We leverage current practices in information and relationship extraction to streamline the ontology development process. Our system combines different text types with information and relationship extraction techniques in a low overhead modifiable system. Our SEmi-Automated ontology Maintenance (SEAM) system features a natural language processing pipeline for information extraction. Synonym and hierarchical groups are identified using corpus-based semantics and lexico-syntactic patterns. The semantic vectors we use are term frequency by inverse document frequency and context vectors. Clinical documents contain the terms we want in an ontology. They also contain idiosyncratic usage and are unlikely to contain the linguistic constructs associated with synonym and hierarchy identification. By including both clinical and biomedical texts, SEAM can recommend terms from those appearing in both document types. The set of recommended terms is then used to filter the synonyms and hierarchical relationships extracted from the biomedical corpus. We demonstrate the generality of the system across three use cases: ontologies for acute changes in mental status, Medically Unexplained Syndromes, and echocardiogram summary statements. Across the three uses cases, we held the number of recommended terms relatively constant by changing SEAM's parameters. Experts seem to find more than 300 recommended terms to be overwhelming. The approval rate of recommended terms increased as the number and specificity of clinical documents in the corpus increased. It was 60% when there were 199 clinical documents that were not specific to the ontology domain and 90% when there were 2879 documents very specific to the target domain. We found that fewer than 100 recommended synonym groups were also preferred. Approval rates for synonym recommendations remained low varying from 43% to 25% as the

The KINA neutronic module of the LEGO code for steady-state and transient PWR plant simulations

International Nuclear Information System (INIS)

Nicolopoulos, D.; Pollacchini, L.; Vimercati, G.; Spelta, S.

1989-01-01

The Automation Research Center (CRA) of ENEl has implemented some models for analyzing both incidental and operational transients in PWR power plants. For such models an axial neutron kinetics module characterized by high computational efficency with adequate results accuracy was called for. CISE has been entrusted with the task of implementing such a module named KINA and based on IQS (Improved Quasi Static) method, to be included in the library of LEGO modular code used by CRA to set up PWR power models. Moreover, The KINA module has been adapted to the neutron constants computing model developed by the EdF-SEPTEN, which has been using and improving the LEGO code for a long time in cooperation with ENEL-CRA. In this paper, after some remarks on the LEGO code, a general description of KINA neutronic module is given. The resylts of a preliminary validation activity of KINA for an EdF 1300 MWe PWR plant are also presented

The Proteasix Ontology.

Science.gov (United States)

Arguello Casteleiro, Mercedes; Klein, Julie; Stevens, Robert

2016-06-04

The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides) The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis. The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results. The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO . This ontology is free and open for use by everyone.

Another brick in the whole: estrategias de adaptación, remediación y transmediación en LEGO Batman: La Película

Directory of Open Access Journals (Sweden)

Sergio ALBALADEJO-ORTEGA

2018-01-01

Full Text Available El estreno en 2014 de La Lego Película (The Lego Movie, Phil Lord y Chris Miller supuso un importante hito en la historia de la empresa danesa LEGO, erigiendo el filme como pieza clave de la estrategia transmediática que empezaba a tomar forma en el ámbito cinematográfico. Aquel filme, en el que el personaje de Batman gozaba de un especial protagonismo, ha dado paso a un particular spin-off que, bajo el título LEGO Batman: La Película (The LEGO Batman Movie, Chris McKay, 2017, repite algunas de las fórmulas puestas en práctica en La Lego Película e introduce otras nuevas de igual o mayor interés desde un punto de vista intertextual. Este artículo se aproxima al largometraje del superhéroe de DC Comics atendiendo a las particulares estrategias de adaptación, remediación y transmediación que lleva a cabo. A través del análisis de los componentes narrativos que constituyen la propuesta del filme, así como de su puesta en relación con los presentes en los textos impresos, audiovisuales y videolúdicos pertenecientes a la franquicia LEGO Batman, se estudian las distintas estrategias que posibilitan la interconexión entre ellos y moldean el ‘macrorrelato’ (Scolari, 2009 que, de manera paradigmática, toma forma en la narrativa transmediática resultante.

Maternal Experience of Lego Therapy in Families with Children with Autism Spectrum Conditions: What Is the Impact on Family Relationships?

Science.gov (United States)

Peckett, Helen; MacCallum, Fiona; Knibbs, Jacky

2016-01-01

This study aimed to explore mothers' experience of implementing Lego Therapy at home within the family. Following a Lego Therapy training session, mothers carried out hourly sessions with their child with an autism spectrum condition and the child's sibling, once a week, for 6 weeks. Mothers were interviewed following the intervention, and the…

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

Science.gov (United States)

2013-01-01

Background The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community. PMID:24093723

Toxicology ontology perspectives.

Science.gov (United States)

Hardy, Barry; Apic, Gordana; Carthew, Philip; Clark, Dominic; Cook, David; Dix, Ian; Escher, Sylvia; Hastings, Janna; Heard, David J; Jeliazkova, Nina; Judson, Philip; Matis-Mitchell, Sherri; Mitic, Dragana; Myatt, Glenn; Shah, Imran; Spjuth, Ola; Tcheremenskaia, Olga; Toldo, Luca; Watson, David; White, Andrew; Yang, Chihae

2012-01-01

The field of predictive toxicology requires the development of open, public, computable, standardized toxicology vocabularies and ontologies to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. In this article we review ontology developments based on a set of perspectives showing how ontologies are being used in predictive toxicology initiatives and applications. Perspectives on resources and initiatives reviewed include OpenTox, eTOX, Pistoia Alliance, ToxWiz, Virtual Liver, EU-ADR, BEL, ToxML, and Bioclipse. We also review existing ontology developments in neighboring fields that can contribute to establishing an ontological framework for predictive toxicology. A significant set of resources is already available to provide a foundation for an ontological framework for 21st century mechanistic-based toxicology research. Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated in an extended future framework. OpenTox has provided a semantic web framework for the implementation of such ontologies into software applications and linked data resources. Bioclipse developers have shown the benefit of interoperability obtained through ontology by being able to link their workbench application with remote OpenTox web services. Although these developments are promising, an increased international coordination of efforts is greatly needed to develop a more unified, standardized, and open toxicology ontology framework.

Epistemology and ontology in core ontologies: FOLaw and LRI-Core, two core ontologies for law

NARCIS (Netherlands)

Breukers, J.A.P.J.; Hoekstra, R.J.

2004-01-01

For more than a decade constructing ontologies for legal domains, we, at the Leibniz Center for Law, felt really the need to develop a core ontology for law that would enable us to re-use the common denominator of the various legal domains. In this paper we present two core ontologies for law. The

Modelamiento y programación de un juego de legos en un entorno de brealidad virtual

OpenAIRE

Arboleda, Freddy; Laica, Ricardo; Loor, Magdalena; García, Sixto

2010-01-01

This project seeks by the use of the techniques of Virtual Reality to create a virtual world of a traditional game of Lego blocks, in order to check the applicability of the concepts learned throughout the topic. The present abstract specifies the general ideas on the modeling, design and implementation of an application of Virtual Reality of Lego blocks. First, we focus in the creation of the 3D objects and scenes, which are going to constitute the virtual environment. Later, we are going t...

LEGO-based Robotics in Higher Education: 15 Years of Student Creativity

Directory of Open Access Journals (Sweden)

Ethan Danahy

2014-02-01

Full Text Available Our goal in this article is to reflect on the role LEGO robotics has played in college engineering education over the last 15 years, starting with the introduction of the RCX in 1998 and ending with the introduction of the EV3 in 2013. By combining a modular computer programming language with a modular building platform, LEGO Education has allowed students (of all ages to become active leaders in their own education as they build everything from animals for a robotic zoo to robots that play children's games. Most importantly, it allows all students to develop different solutions to the same problem to provide a learning community. We look first at how the recent developments in the learning sciences can help in promoting student learning in robotics. We then share four case studies of successful college-level implementations that build on these developments.

SPONGY (SPam ONtoloGY): email classification using two-level dynamic ontology.

Science.gov (United States)

Youn, Seongwook

2014-01-01

Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user's background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance.

SPONGY (SPam ONtoloGY: Email Classification Using Two-Level Dynamic Ontology

Directory of Open Access Journals (Sweden)

Seongwook Youn

2014-01-01

Full Text Available Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user’s background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1 to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2 to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance.

SPONGY (SPam ONtoloGY): Email Classification Using Two-Level Dynamic Ontology

Science.gov (United States)

2014-01-01

Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user's background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance. PMID:25254240

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Science.gov (United States)

Diehl, Alexander D; Meehan, Terrence F; Bradford, Yvonne M; Brush, Matthew H; Dahdul, Wasila M; Dougall, David S; He, Yongqun; Osumi-Sutherland, David; Ruttenberg, Alan; Sarntivijai, Sirarat; Van Slyke, Ceri E; Vasilevsky, Nicole A; Haendel, Melissa A; Blake, Judith A; Mungall, Christopher J

2016-07-04

The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class 'cell in vitro' have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning. The CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs. The ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the wider scientific community, and we continue to experience increased interest in the

Long-term LEGO therapy with humanoid robot for children with ASD

NARCIS (Netherlands)

Barakova, E.I.; Bajracharya, P.; Willemsen, M.H.J.; Lourens, T.; Huskens, B.

2015-01-01

To utilise the knowledge gained from highly specialised domains as autism therapy to robot-based interactive training platforms, an innovative design approach is needed. We present the process of content creation and co-design of LEGO therapy for children with autism spectrum disorders performed by

"Creative Blocs": Action Research Study on the Implementation of Lego as a Tool for Reflective Practice with Social Care Practitioners

Science.gov (United States)

Cavaliero, Tamsin

2017-01-01

The aim of this study is to investigate whether Lego could be used as a tool for reflective practice with social care practitioners (SCPs) and student practitioners. This article outlines an action research study conducted in an institute of higher education in Ireland. Findings from this study suggest that Lego can be used to support student…

Alignment of ICNP® 2.0 ontology and a proposed INCP® Brazilian ontology.

Science.gov (United States)

Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; Nóbrega, Maria Miriam Lima da

2014-01-01

to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology. document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence, their names, and their sibling, parent, and child classes. there were 2,682 concepts present in the ICNP® 2.0 Ontology that were missing in the Brazilian Ontology; 717 concepts present in the Brazilian Ontology were missing in the ICNP® 2.0 Ontology; and there were 215 pairs of matching concepts. it is believed that the correspondences identified in this study might contribute to the interoperability between the representations of nursing practice elements in ICNP®, thus allowing the standardization of nursing records based on this classification system.

Does Lego Training Stimulate Pupils' Ability to Solve Logical Problems?

Science.gov (United States)

Lindh, Jorgen; Holgersson, Thomas

2007-01-01

The purpose of this study is to investigate the effect of a one-year regular robotic toys (lego) training on school pupils' performance. The underlying pedagogical perspective is the "constructionist theory," where the main idea is that knowledge is constructed in the mind of the pupil by active learning. The investigation has been made…

The Serious Use of Play and Metaphor: Legos and Labyrinths

Science.gov (United States)

James, Alison; Brookfield, Stephen

2013-01-01

In this paper the authors wish to examine kinesthetic forms of learning involving the body and the physical realm. The authors look at two particular techniques; using Legos to build metaphorical models and living the physical experience of metaphors in the shape of labyrinth-walking and its attendant activities. The authors begin by discussing…

Using a Foundational Ontology for Reengineering a Software Enterprise Ontology

Science.gov (United States)

Perini Barcellos, Monalessa; de Almeida Falbo, Ricardo

The knowledge about software organizations is considerably relevant to software engineers. The use of a common vocabulary for representing the useful knowledge about software organizations involved in software projects is important for several reasons, such as to support knowledge reuse and to allow communication and interoperability between tools. Domain ontologies can be used to define a common vocabulary for sharing and reuse of knowledge about some domain. Foundational ontologies can be used for evaluating and re-designing domain ontologies, giving to these real-world semantics. This paper presents an evaluating of a Software Enterprise Ontology that was reengineered using the Unified Foundation Ontology (UFO) as basis.

Towards Lego Snapping; Integration of Carbon Nanotubes and Few-Layer Graphene

Science.gov (United States)

Nasseri, Mohsen; Boland, Mathias; Farrokhi, M. Javad; Strachan, Douglas

Integration of semiconducting, conducting, and insulating nanomaterials into precisely aligned complicated systems is one of the main challenges to the ultimate size scaling of electronic devices, which is a key goal in nanoscience and nanotechnology. This integration could be made more effective through controlled alignment of the crystallographic lattices of the nanoscale components. Of the vast number of materials of atomically-thin materials, two of the sp2 bonded carbon structures, graphene and carbon nanotubes, are ideal candidates for this type of application since they are built from the same backbone carbon lattice. Here we report carbon nanotube and graphene hybrid nanostructures fabricated through their catalytic synthesis and etching. The growth formations we have investigated through various high-resolution microscopy techniques provide evidence of lego-snapped interfaces between nanotubes and graphene into device-relevant orientations. We will finish with a discussion of the various size and energy regimes relevant to these lego-snapped interfaces and their implications on developing these integrated formations.

Building a Chemical Ontology using Methontology and the Ontology Design Environment

OpenAIRE

Fernández López, Mariano; Gómez-Pérez, A.; Pazos Sierra, Alejandro; Pazos Sierra, Juan

1999-01-01

METHONTOLOGY PROVIDES GUIDELINES FOR SPECIFYING ONTOLOGIES AT THE KNOWLEDGE LEVEL, AS A SPECIFICATION OF A CONCEPTUALIZATION. ODE ENABLES ONTOLOGY CONSTRUCTION, COVERING THE ENTIRE LIFE CYCLE AND AUTOMATICALLY IMPLEMENTING ONTOLOGIES

Integration of low level and ontology derived features for automatic weapon recognition and identification

Science.gov (United States)

Sirakov, Nikolay M.; Suh, Sang; Attardo, Salvatore

2011-06-01

This paper presents a further step of a research toward the development of a quick and accurate weapons identification methodology and system. A basic stage of this methodology is the automatic acquisition and updating of weapons ontology as a source of deriving high level weapons information. The present paper outlines the main ideas used to approach the goal. In the next stage, a clustering approach is suggested on the base of hierarchy of concepts. An inherent slot of every node of the proposed ontology is a low level features vector (LLFV), which facilitates the search through the ontology. Part of the LLFV is the information about the object's parts. To partition an object a new approach is presented capable of defining the objects concavities used to mark the end points of weapon parts, considered as convexities. Further an existing matching approach is optimized to determine whether an ontological object matches the objects from an input image. Objects from derived ontological clusters will be considered for the matching process. Image resizing is studied and applied to decrease the runtime of the matching approach and investigate its rotational and scaling invariance. Set of experiments are preformed to validate the theoretical concepts.

Towards Process-Ontology: A Critical Study of Substance-Ontological Premises

DEFF Research Database (Denmark)

Seibt, Johanna

The thesis proposes therapeutic revision of fundamental assumptions in contemporary ontological thought. I show that non of the prevalent theories of objects, by virtue of certain implicit substance-ontological assumptions provides a viable account of the numerical, qualitative, and trans-tempora......-ontological presuppositions, I finally explore the result of rejecting all of them and sketch a scheme basic on dynamic masses which promises to yield coherent explanation of the ontological features of those complex processes that we commonly call objects....

COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance.

Science.gov (United States)

Cui, Licong

Biomedical ontologies play a vital role in healthcare information management, data integration, and decision support. Ontology quality assurance (OQA) is an indispensable part of the ontology engineering cycle. Most existing OQA methods are based on the knowledge provided within the targeted ontology. This paper proposes a novel cross-ontology analysis method, Cross-Ontology Hierarchical Relation Examination (COHeRE), to detect inconsistencies and possible errors in hierarchical relations across multiple ontologies. COHeRE leverages the Unified Medical Language System (UMLS) knowledge source and the MapReduce cloud computing technique for systematic, large-scale ontology quality assurance work. COHeRE consists of three main steps with the UMLS concepts and relations as the input. First, the relations claimed in source vocabularies are filtered and aggregated for each pair of concepts. Second, inconsistent relations are detected if a concept pair is related by different types of relations in different source vocabularies. Finally, the uncovered inconsistent relations are voted according to their number of occurrences across different source vocabularies. The voting result together with the inconsistent relations serve as the output of COHeRE for possible ontological change. The highest votes provide initial suggestion on how such inconsistencies might be fixed. In UMLS, 138,987 concept pairs were found to have inconsistent relationships across multiple source vocabularies. 40 inconsistent concept pairs involving hierarchical relationships were randomly selected and manually reviewed by a human expert. 95.8% of the inconsistent relations involved in these concept pairs indeed exist in their source vocabularies rather than being introduced by mistake in the UMLS integration process. 73.7% of the concept pairs with suggested relationship were agreed by the human expert. The effectiveness of COHeRE indicates that UMLS provides a promising environment to enhance

SUGOI: automated ontology interchangeability

CSIR Research Space (South Africa)

Khan, ZC

2015-04-01

Full Text Available A foundational ontology can solve interoperability issues among the domain ontologies aligned to it. However, several foundational ontologies have been developed, hence such interoperability issues exist among domain ontologies. The novel SUGOI tool...

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

Science.gov (United States)

He, Yongqun; Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; Overton, James A; Ong, Edison

2018-01-12

Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).

Practical ontologies for information professionals

CERN Document Server

AUTHOR|(CDS)2071712

2016-01-01

Practical Ontologies for Information Professionals provides an introduction to ontologies and their development, an essential tool for fighting back against information overload. The development of robust and widely used ontologies is an increasingly important tool in the fight against information overload. The publishing and sharing of explicit explanations for a wide variety of conceptualizations, in a machine readable format, has the power to both improve information retrieval and identify new knowledge. This new book provides an accessible introduction to the following: * What is an ontology? Defining the concept and why it is increasingly important to the information professional * Ontologies and the semantic web * Existing ontologies, such as SKOS, OWL, FOAF, schema.org, and the DBpedia Ontology * Adopting and building ontologies, showing how to avoid repetition of work and how to build a simple ontology with Protege * Interrogating semantic web ontologies * The future of ontologies and the role of the ...

PENERAPAN LEGO BRICKS DALAM PEMBELAJARAN SEBAGAI STRATEGI UNTUK MENINGKATKAN KECERDASAN MATEMATIS SISWA DALAM MENGHITUNG BILANGAN BERPANGKAT

Directory of Open Access Journals (Sweden)

Mutia Rahma Setyani

2017-12-01

Full Text Available Penelitian ini bertujuan untuk mengetahui hasil pembelajaran dan mendeskripsikan kecerdasan matematis siswa dalam menghitung bilangan berpangkat setelah menggunakan lego bricks pada siswa kelas III Tahassus MIS Ta’allamul Huda. Penelitian ini menggunakan Penelitian Tindakan Kelas ini dengan model pembelajaran Cooperative Learning. Subjek penelitian adalah siswa kelas III ahassus MIS a’allamul Huda yang berjumlah 24 siswa. Data dikumpulkan melalui observasi dan wawancara, selanjutnya dianalisis secara kualitatif. Hasil penelitian menunjukkan bahwa keberhasilan penerapan lego bricks pada perhitungan bilangan berpangkat meningkat pada setiap siklusnya. Pada tahap Pra Siklus, hanya 40% siswa yang lulus dalam mengerjakan soal-soal dari bilangan berpangkat, kemudian pada Siklus I berdasarkan hasil observasi didapatkan kenaikan yang signifikan yaitu 80% siswa yang lulus dalam mengerjakan soal mengenai bilangan berpangkat. Masih ada 20% siswa yang masih kesulitan dalam mengerjakan soal tersebut. Selanjutnya setelah dilakukan perbaikan, pada Siklus II didapat kenaikan yang luar biasa yaitu seluruh kelompok siswa lulus dalam mengerjakan soal mengenai bilangan berpangkat. Hal tersebut dibuktikan kembali melalui hasil post test pada tahap Pasca Siklus dimana nilai seluruh siswa berada diatas kriteria ketuntasan minimum, yaitu 85-100 sehingga penerapan lego bricks untuk meningkatkan kecerdasan matematis siswa dalam menghitung bilangan berpangkat dikatakan berhasil.

Alignment of ICNP? 2.0 Ontology and a proposed INCP? Brazilian Ontology1

OpenAIRE

Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; da N?brega, Maria Miriam Lima

2014-01-01

OBJECTIVE: to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology.METHOD: document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence...

Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

Science.gov (United States)

Ochs, Christopher; He, Zhe; Zheng, Ling; Geller, James; Perl, Yehoshua; Hripcsak, George; Musen, Mark A

2016-06-01

An Abstraction Network is a compact summary of an ontology's structure and content. In previous research, we showed that Abstraction Networks support quality assurance (QA) of biomedical ontologies. The development of an Abstraction Network and its associated QA methodologies, however, is a labor-intensive process that previously was applicable only to one ontology at a time. To improve the efficiency of the Abstraction-Network-based QA methodology, we introduced a QA framework that uses uniform Abstraction Network derivation techniques and QA methodologies that are applicable to whole families of structurally similar ontologies. For the family-based framework to be successful, it is necessary to develop a method for classifying ontologies into structurally similar families. We now describe a structural meta-ontology that classifies ontologies according to certain structural features that are commonly used in the modeling of ontologies (e.g., object properties) and that are important for Abstraction Network derivation. Each class of the structural meta-ontology represents a family of ontologies with identical structural features, indicating which types of Abstraction Networks and QA methodologies are potentially applicable to all of the ontologies in the family. We derive a collection of 81 families, corresponding to classes of the structural meta-ontology, that enable a flexible, streamlined family-based QA methodology, offering multiple choices for classifying an ontology. The structure of 373 ontologies from the NCBO BioPortal is analyzed and each ontology is classified into multiple families modeled by the structural meta-ontology. Copyright © 2016 Elsevier Inc. All rights reserved.

Ontology-based Information Retrieval

DEFF Research Database (Denmark)

Styltsvig, Henrik Bulskov

In this thesis, we will present methods for introducing ontologies in information retrieval. The main hypothesis is that the inclusion of conceptual knowledge such as ontologies in the information retrieval process can contribute to the solution of major problems currently found in information...... retrieval. This utilization of ontologies has a number of challenges. Our focus is on the use of similarity measures derived from the knowledge about relations between concepts in ontologies, the recognition of semantic information in texts and the mapping of this knowledge into the ontologies in use......, as well as how to fuse together the ideas of ontological similarity and ontological indexing into a realistic information retrieval scenario. To achieve the recognition of semantic knowledge in a text, shallow natural language processing is used during indexing that reveals knowledge to the level of noun...

Extracting Cross-Ontology Weighted Association Rules from Gene Ontology Annotations.

Science.gov (United States)

Agapito, Giuseppe; Milano, Marianna; Guzzi, Pietro Hiram; Cannataro, Mario

2016-01-01

Gene Ontology (GO) is a structured repository of concepts (GO Terms) that are associated to one or more gene products through a process referred to as annotation. The analysis of annotated data is an important opportunity for bioinformatics. There are different approaches of analysis, among those, the use of association rules (AR) which provides useful knowledge, discovering biologically relevant associations between terms of GO, not previously known. In a previous work, we introduced GO-WAR (Gene Ontology-based Weighted Association Rules), a methodology for extracting weighted association rules from ontology-based annotated datasets. We here adapt the GO-WAR algorithm to mine cross-ontology association rules, i.e., rules that involve GO terms present in the three sub-ontologies of GO. We conduct a deep performance evaluation of GO-WAR by mining publicly available GO annotated datasets, showing how GO-WAR outperforms current state of the art approaches.

Organizational System for the LEGO WeDo 2.0 Robotics System

Science.gov (United States)

Dolecheck, Suzann Hagan; Ewers, Timothy

2017-01-01

In this article, we explain an organizational system for the new LEGO Education WeDo 2.0 Core Set used in 4-H robotics; in school enrichment, afterschool, and other youth robotics programs; and by hobbyists. The system presented is for organizing WeDo parts into a translucent parts tray that includes part names and numbers. The article provides…

How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects.

Science.gov (United States)

Strohmaier, Markus; Walk, Simon; Pöschko, Jan; Lamprecht, Daniel; Tudorache, Tania; Nyulas, Csongor; Musen, Mark A; Noy, Natalya F

2013-05-01

Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product . In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to its construction is critical not only in understanding but consequently also in evaluating the ontology. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches.

How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects

Science.gov (United States)

Strohmaier, Markus; Walk, Simon; Pöschko, Jan; Lamprecht, Daniel; Tudorache, Tania; Nyulas, Csongor; Musen, Mark A.; Noy, Natalya F.

2013-01-01

Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product. In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to its construction is critical not only in understanding but consequently also in evaluating the ontology. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches. PMID:24311994

Biomedical ontologies: toward scientific debate.

Science.gov (United States)

Maojo, V; Crespo, J; García-Remesal, M; de la Iglesia, D; Perez-Rey, D; Kulikowski, C

2011-01-01

Biomedical ontologies have been very successful in structuring knowledge for many different applications, receiving widespread praise for their utility and potential. Yet, the role of computational ontologies in scientific research, as opposed to knowledge management applications, has not been extensively discussed. We aim to stimulate further discussion on the advantages and challenges presented by biomedical ontologies from a scientific perspective. We review various aspects of biomedical ontologies going beyond their practical successes, and focus on some key scientific questions in two ways. First, we analyze and discuss current approaches to improve biomedical ontologies that are based largely on classical, Aristotelian ontological models of reality. Second, we raise various open questions about biomedical ontologies that require further research, analyzing in more detail those related to visual reasoning and spatial ontologies. We outline significant scientific issues that biomedical ontologies should consider, beyond current efforts of building practical consensus between them. For spatial ontologies, we suggest an approach for building "morphospatial" taxonomies, as an example that could stimulate research on fundamental open issues for biomedical ontologies. Analysis of a large number of problems with biomedical ontologies suggests that the field is very much open to alternative interpretations of current work, and in need of scientific debate and discussion that can lead to new ideas and research directions.

Data mining for ontology development.

Energy Technology Data Exchange (ETDEWEB)

Davidson, George S.; Strasburg, Jana (Pacific Northwest National Laboratory, Richland, WA); Stampf, David (Brookhaven National Laboratory, Upton, NY); Neymotin,Lev (Brookhaven National Laboratory, Upton, NY); Czajkowski, Carl (Brookhaven National Laboratory, Upton, NY); Shine, Eugene (Savannah River National Laboratory, Aiken, SC); Bollinger, James (Savannah River National Laboratory, Aiken, SC); Ghosh, Vinita (Brookhaven National Laboratory, Upton, NY); Sorokine, Alexandre (Oak Ridge National Laboratory, Oak Ridge, TN); Ferrell, Regina (Oak Ridge National Laboratory, Oak Ridge, TN); Ward, Richard (Oak Ridge National Laboratory, Oak Ridge, TN); Schoenwald, David Alan

2010-06-01

A multi-laboratory ontology construction effort during the summer and fall of 2009 prototyped an ontology for counterfeit semiconductor manufacturing. This effort included an ontology development team and an ontology validation methods team. Here the third team of the Ontology Project, the Data Analysis (DA) team reports on their approaches, the tools they used, and results for mining literature for terminology pertinent to counterfeit semiconductor manufacturing. A discussion of the value of ontology-based analysis is presented, with insights drawn from other ontology-based methods regularly used in the analysis of genomic experiments. Finally, suggestions for future work are offered.

Expressivity in Open-ended Constructive Play: Building and Playing Musical Lego Instruments

DEFF Research Database (Denmark)

Jakobsen, Kasper; Stougaard, Jeppe; Petersen, Marianne Graves

2016-01-01

This paper presents the findings from a case study in designing for open-ended constructive play for children. The study is based on a workshop where more that 150 children in ages 3-13 built and played their own musical instruments from Lego. The children used different sensors for playing...

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

Science.gov (United States)

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-01

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

Feasibility of automated foundational ontology interchangeability

CSIR Research Space (South Africa)

Khan, ZC

2014-11-01

Full Text Available the Source Domain Ontology (sOd), with the domain knowledge com- ponent of the source ontology, the Source Foundational Ontology (sOf ) that is the foundational ontology component of the source ontology that is to be interchanged, and any equivalence... or subsumption mappings between enti- ties in sOd and sOf . – The Target Ontology (tO) which has been interchanged, which comprises the Target Domain Ontology (tOd), with the domain knowledge component of the target ontology, and the Target Foundational Ontology...

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms

OpenAIRE

Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, JH Pate; Ball, Catherine A; Sherlock, Gavin

2007-01-01

Abstract Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to r...

The educational affordances of Lego-based play in primary school

Directory of Open Access Journals (Sweden)

Luisa Salmaso

2013-12-01

Full Text Available Questo articolo presenta un’esperienza didattica attuata in una classe prima e in una classe seconda della Scuola Primaria mediante l’utilizzo di mattoncini Lego. Al termine di questo percorso è stato possibile delineare alcuni elementi utili per sostenere l’efficacia del gioco a favore dello sviluppo delle abilità visuo-spaziali e di pianificazione, anche in una prospettiva inclusiva e di pari opportunità di genere.

Ontology authoring with Forza

CSIR Research Space (South Africa)

Keet, CM

2014-11-01

Full Text Available Generic, reusable ontology elements, such as a foundational ontology's categories and part-whole relations, are essential for good and interoperable knowledge representation. Ontology developers, which include domain experts and novices, face...

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.

Science.gov (United States)

Thacker, Robert W; Díaz, Maria Cristina; Kerner, Adeline; Vignes-Lebbe, Régine; Segerdell, Erik; Haendel, Melissa A; Mungall, Christopher J

2014-01-01

Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/. By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative.

Science.gov (United States)

Harrow, Ian; Jiménez-Ruiz, Ernesto; Splendiani, Andrea; Romacker, Martin; Woollard, Peter; Markel, Scott; Alam-Faruque, Yasmin; Koch, Martin; Malone, James; Waaler, Arild

2017-12-02

The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease. Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results. Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

Science.gov (United States)

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-04

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A model of Alto Lazio boiling water reactor using the LEGO code balance of plant simulation

International Nuclear Information System (INIS)

Spelta, S.; Garbossa, G.B.

1989-01-01

An extensive effort has been made at the Italian National Electricity Board (ENEL) to construct and validate a LEGO model capable of simulating the operational transients of the Alto Lazio Nuclear Station, a two twin-units site with BWR/6 class reactors, rated at 2894 MWt and with Mark III containment. LEGO is a modular package developed at the Research and development Department of the Italian National Electricity Board (CRA-ENEL) for computer aided modeling of fossil-fired and nuclear steam power plants. In this paper a system analysis model capable of describing steady-state and transient performance of the Balance of Plant (BOP) of the Alto Lazio Power Station is presented. This is one of two companion papers devoted to the description of the overall plant model including both the Nuclear Steam Supply System (NSSS) and the BOP. In the paper, after a brief summary of the main LEGO characteristics, a description of the BOP lay-out is presented. The overall model, which has been set-up, including control systems and automation, is very detailed and consists of almost 2000 differential or algebraic equations. After a brief description of the mathematical model, two significant transients obtained using the overall model are presented and discussed

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

Science.gov (United States)

Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; He, Yongqun

2015-01-01

It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. Because ontology terms often follow specific ODPs, the Ontology for Biomedical Investigations (OBI) developers proposed a Quick Term Templates (QTTs) process targeted at generating new ontology classes following the same pattern, using term templates in a spreadsheet format. Inspired by the ODPs and QTTs, the Ontorat web application is developed to automatically generate new ontology terms, annotations of terms, and logical axioms based on a specific ODP(s). The inputs of an Ontorat execution include axiom expression settings, an input data file, ID generation settings, and a target ontology (optional). The axiom expression settings can be saved as a predesigned Ontorat setting format text file for reuse. The input data file is generated based on a template file created by a specific ODP (text or Excel format). Ontorat is an efficient tool for ontology expansion. Different use cases are described. For example, Ontorat was applied to automatically generate over 1,000 Japan RIKEN cell line cell terms with both logical axioms and rich annotation axioms in the Cell Line Ontology (CLO). Approximately 800 licensed animal vaccines were represented and annotated in the Vaccine Ontology (VO) by Ontorat. The OBI team used Ontorat to add assay and device terms required by ENCODE project. Ontorat was also used to add missing annotations to all existing Biobank specific terms in the Biobank Ontology. A collection of ODPs and templates with examples are provided on the Ontorat website and can be reused to facilitate ontology development. With ever increasing ontology development and applications, Ontorat provides a timely platform for generating and annotating a large number of ontology terms by following

Ontologies vs. Classification Systems

DEFF Research Database (Denmark)

Madsen, Bodil Nistrup; Erdman Thomsen, Hanne

2009-01-01

What is an ontology compared to a classification system? Is a taxonomy a kind of classification system or a kind of ontology? These are questions that we meet when working with people from industry and public authorities, who need methods and tools for concept clarification, for developing meta...... data sets or for obtaining advanced search facilities. In this paper we will present an attempt at answering these questions. We will give a presentation of various types of ontologies and briefly introduce terminological ontologies. Furthermore we will argue that classification systems, e.g. product...... classification systems and meta data taxonomies, should be based on ontologies....

Fast generation of macro basis functions for LEGO through the adaptive cross approximation

NARCIS (Netherlands)

Lancellotti, V.

2015-01-01

We present a method for the fast generation of macro basis functions in the context of the linear embedding via Green's operators approach (LEGO) which is a domain decomposition technique based on the combination of electromagnetic bricks in turn described by means of scattering operators. We show

‘Everything is awesome’ : The LEGO movie and the affective politics of security

NARCIS (Netherlands)

Goggin, J.

2017-01-01

Scholarship on the finance-security nexus has typically been concerned with ‘first order’ phenomena, such as the interpenetration of the finance and security sectors. This article contributes to the debate by turning to an apparent epiphenomenon, namely The LEGO Movie, and using it to address some

Culture's building blocks: investigating cultural evolution in a LEGO construction task.

Science.gov (United States)

McGraw, John J; Wallot, Sebastian; Mitkidis, Panagiotis; Roepstorff, Andreas

2014-01-01

ONE OF THE MOST ESSENTIAL BUT THEORETICALLY VEXING ISSUES REGARDING THE NOTION OF CULTURE IS THAT OF CULTURAL EVOLUTION AND TRANSMISSION: how a group's accumulated solutions to invariant challenges develop and persevere over time. But at the moment, the notion of applying evolutionary theory to culture remains little more than a suggestive trope. Whereas the modern synthesis of evolutionary theory has provided an encompassing scientific framework for the selection and transmission of biological adaptations, a convincing theory of cultural evolution has yet to emerge. One of the greatest challenges for theorists is identifying the appropriate time scales and units of analysis in order to reduce the intractably large and complex phenomenon of "culture" into its component "building blocks." In this paper, we present a model for scientifically investigating cultural processes by analyzing the ways people develop conventions in a series of LEGO construction tasks. The data revealed a surprising pattern in the selection of building bricks as well as features of car design across consecutive building sessions. Our findings support a novel methodology for studying the development and transmission of culture through the microcosm of interactive LEGO design and assembly.

A line follower robot implementation using Lego's Mindstorms Kit and Q-Learning

Directory of Open Access Journals (Sweden)

Hector-Gabriel Acosta-Mesa

2012-03-01

Full Text Available Un problema común al trabajar con robots móviles es que la fase de programación puede ser un proceso largo, costoso y difícil para los programadores. Los Algoritmos de Aprendizaje por Refuerzo ofrecen uno de los marcos de trabajo más generales en el ámbito de aprendizaje de máquina. Este trabajo presenta un enfoque usando el algoritmo de Q-Learning en un robot Lego para que aprenda "por sí mismo" a seguir una línea negra dibujada en una superficie blanca. El entorno de programación utilizado en este trabajo es Matlab.A common problem working with mobile robots is that programming phase could be a long, expensive and heavy process for programmers. The reinforcement learning algorithms offer one of the most general frameworks in learning subjects. This work presents an approach using the Q-Learning algorithm on a Lego robot in order for it to learn by itself how to follow a blackline drawn down on a white surface, using Matlab [5] as programming environment.

Merged ontology for engineering design: Contrasting empirical and theoretical approaches to develop engineering ontologies

DEFF Research Database (Denmark)

Ahmed, Saeema; Storga, M

2009-01-01

to developing the ontology engineering design integrated taxonomies (EDIT) with a theoretical approach in which concepts and relations are elicited from engineering design theories ontology (DO) The limitations and advantages of each approach are discussed. The research methodology adopted is to map......This paper presents a comparison of two previous and separate efforts to develop an ontology in the engineering design domain, together with an ontology proposal from which ontologies for a specific application may be derived. The research contrasts an empirical, user-centered approach...

Ontological Planning

Directory of Open Access Journals (Sweden)

Ahmet Alkan

2017-12-01

• Is it possible to redefine ontology within the hierarchical structure of planning? We are going to seek answers to some of these questions within the limited scope of this paper and we are going to offer the rest for discussion by just asking them. In light of these assessments, drawing attention, based on ontological knowledge relying on the wholeness of universe, to the question, on macro level planning, of whether or not the ontological realities of man, energy and movements of thinking can provide macro data for planning on a universal level as important factors affecting mankind will be one of the limited objectives of the paper.

Teaching of Computer Science Topics Using Meta-Programming-Based GLOs and LEGO Robots

Science.gov (United States)

Štuikys, Vytautas; Burbaite, Renata; Damaševicius, Robertas

2013-01-01

The paper's contribution is a methodology that integrates two educational technologies (GLO and LEGO robot) to teach Computer Science (CS) topics at the school level. We present the methodology as a framework of 5 components (pedagogical activities, technology driven processes, tools, knowledge transfer actors, and pedagogical outcomes) and…

Long-Term Outcome of Social Skills Intervention Based on Interactive LEGO[C] Play

Science.gov (United States)

Legoff, Daniel B.; Sherman, Michael

2006-01-01

LEGO[C] building materials have been adapted as a therapeutic modality for increasing motivation to participate in social skills intervention, and providing a medium through which children with social and communication handicaps can effectively interact. A 3 year retrospective study of long-term outcome for autistic spectrum children participating…

Comparison of the LEGO Mindstorms NXT and EV3 Robotics Education Platforms

Science.gov (United States)

Sherrard, Ann; Rhodes, Amy

2014-01-01

The release of the latest LEGO Mindstorms EV3 robotics platform in September 2013 has provided a dilemma for many youth robotics leaders. There is a need to understand the differences in the Mindstorms NXT and EV3 in order to make future robotics purchases. In this article the differences are identified regarding software, hardware, sensors, the…

Modular Lego-Electronics

KAUST Repository

Shaikh, Sohail F.

2017-10-24

Electronic system components have thousands of individual field effect transistors (FETs) interconnected executing dedicated functions. Assembly yield of >80% will guarantee system failure since a single interconnect failure will result in undesired performance. Hence, a paradigm shift is needed in the self-assembly or integration of state-of-the-art integrated circuits (ICs) for a physically compliant system. Traditionally, most ICs share same geometry with only variations in dimensions and packaging. Here, a generic manufacturable method of converting state-of-the-art complementary metal oxide semiconductor-based ICs into modular Lego-electronics is shown with unique geometry that is physically identifiable to ease manufacturing and enhance throughput. Various geometries at the backside of the silicon die and on the destination site having the same geometry with relaxed dimension (up to 50 µm extra) allow targeted site binding like DNA assembly. Different geometries, angles, and heights for different modules provide a unique identity to each of the ICs. A two-level geometric combination presented here helps in maintaining the uniqueness of individual module to assemble at exact matching site like a perfect lock-and-key model. The assembled ICs offer uncompromised electrical performance, higher yield, and fabrication ease. In future, this method can further be expanded for fluidic assisted self-assembly.

Business Process Innovation: The LEGO Case

DEFF Research Database (Denmark)

Møller, Charles; Hansen, P.K.

2006-01-01

Most organizations today are required not only to establish effective business processes but they are required to accommodate for changing business conditions at an increasing rate. Many business processes extend beyond the boundary of the enterprise into the supply chain and the information...... process innovation (BPI) in future organizations. This paper explores the applicability of one particular methodology for Business Process Innovation to deal with the challenge that the LEGO organization is facing with the alignment of their product development process and their supply chain. The paper...... infrastructure therefore is critical. Today nearly every business relies on their Enterprise System (ES) for process integration and the future generations of Enterprise Systems will increasingly be driven by business process models. Consequently process modelling and improvement will become vital for business...

A method of constructing geo-object ontology in disaster system for prevention and decrease

Science.gov (United States)

Li, Bin; Liu, Jiping; Shi, Lihong; Wang, Zhenfeng

2009-10-01

A kind of formal system, which can express clearly a certain entity or information, is needed to express geographical concept. Besides, some rules explaining the interrelationship and action between different components are also required. Therefore, the conception of geo-object ontology is introduced. It is a shared formalization and display specification of conceptual knowledge system in the field of concrete application of spatial information science. It can constitute hierarchy structure, which derives from the concept classification system in the geographical area. Its concepts can be described by the property. Property sets can form a vector space with multi-dimensional characteristics. Geographic space is composed of different types of geographic entities. And its concept is formed by a series of geographic entities with the same properties and actions. Moreover, each of the geographic entities can be mapped to an object, and each object has its spatial property, time information and topology, semantic relationships associated with other objects. The biggest difference between ecumenical information ontology and geo-ontology is that the latter has the spatial characteristics. During the construction process of geo-object ontology, some important components, such as geographic type, spatial relation, spatial entity type and coordinates, time, should be included to make further research. Here, taking disaster as an example, by using Protégé and OWL, combined methods used by constructing the geo-object ontology in the form of being manual made by domanial experts and semi-automatic are investigated oriented to disaster to serve ultimately geographic information retrieval service driven by ontology.

Towards Agile Ontology Maintenance

Science.gov (United States)

Luczak-Rösch, Markus

Ontologies are an appropriate means to represent knowledge on the Web. Research on ontology engineering reached practices for an integrative lifecycle support. However, a broader success of ontologies in Web-based information systems remains unreached while the more lightweight semantic approaches are rather successful. We assume, paired with the emerging trend of services and microservices on the Web, new dynamic scenarios gain momentum in which a shared knowledge base is made available to several dynamically changing services with disparate requirements. Our work envisions a step towards such a dynamic scenario in which an ontology adapts to the requirements of the accessing services and applications as well as the user's needs in an agile way and reduces the experts' involvement in ontology maintenance processes.

Benchmarking ontologies: bigger or better?

Directory of Open Access Journals (Sweden)

Lixia Yao

2011-01-01

Full Text Available A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1 four of the most common medical ontologies with respect to a corpus of medical documents and (2 seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them.

DIME Students Show Off their Lego(TM) Challenge Creation

Science.gov (United States)

2002-01-01

Two students show the Lego (TM) Challenge device they designed and built to operate in the portable drop tower demonstrator as part of the second Dropping in a Microgravity Environment (DIME) competition held April 23-25, 2002, at NASA's Glenn Research Center. Competitors included two teams from Sycamore High School, Cincinnati, OH, and one each from Bay High School, Bay Village, OH, and COSI Academy, Columbus, OH. DIME is part of NASA's education and outreach activities. Details are on line at http://microgravity.grc.nasa.gov/DIME_2002.html.

Introduction to autonomous mobile robotics using Lego Mindstorms NXT

Science.gov (United States)

Akın, H. Levent; Meriçli, Çetin; Meriçli, Tekin

2013-12-01

Teaching the fundamentals of robotics to computer science undergraduates requires designing a well-balanced curriculum that is complemented with hands-on applications on a platform that allows rapid construction of complex robots, and implementation of sophisticated algorithms. This paper describes such an elective introductory course where the Lego Mindstorms NXT kits are used as the robot platform. The aims, scope and contents of the course are presented, and the design of the laboratory sessions as well as the term projects, which address several core problems of robotics and artificial intelligence simultaneously, are explained in detail.

Assessment Applications of Ontologies.

Science.gov (United States)

Chung, Gregory K. W. K.; Niemi, David; Bewley, William L.

This paper discusses the use of ontologies and their applications to assessment. An ontology provides a shared and common understanding of a domain that can be communicated among people and computational systems. The ontology captures one or more experts' conceptual representation of a domain expressed in terms of concepts and the relationships…

The Impact of Lean Thinking on Workforce Motivation: A Success Factor at LEGO Manufacturing Ltd.

Directory of Open Access Journals (Sweden)

Oláh Judit

2017-06-01

Full Text Available Several enterprises have tried to introduce the lean approach in order to enhance competitiveness. However, the only successful ones were the companies which understood that lean is not only about methods and tools, but the people using them: employees. The only way an enterprise can become a lean organisation is if all of its members deeply identify with the organisation’s principles, which is then manifested in all decisions and actions of the organisation. The aim of this study is to present the practical use of the lean approach in the Nyíregyháza plant of LEGO. Based on the questionnaire results and our observations, we present the current situation of LEGO in accordance with the same points and compare it to an ideal situation. We then make improvement recommendations in all cases when negative changes were observed.

Highly Manufacturable Deep (Sub-Millimeter) Etching Enabled High Aspect Ratio Complex Geometry Lego-Like Silicon Electronics

KAUST Repository

Ghoneim, Mohamed T.; Hussain, Muhammad Mustafa

2017-01-01

A highly manufacturable deep reactive ion etching based process involving a hybrid soft/hard mask process technology shows high aspect ratio complex geometry Lego-like silicon electronics formation enabling free-form (physically flexible

Survey on Ontology Mapping

Science.gov (United States)

Zhu, Junwu

To create a sharable semantic space in which the terms from different domain ontology or knowledge system, Ontology mapping become a hot research point in Semantic Web Community. In this paper, motivated factors of ontology mapping research are given firstly, and then 5 dominating theories and methods, such as information accessing technology, machine learning, linguistics, structure graph and similarity, are illustrated according their technology class. Before we analyses the new requirements and takes a long view, the contributions of these theories and methods are summarized in details. At last, this paper suggest to design a group of semantic connector with the ability of migration learning for OWL-2 extended with constrains and the ontology mapping theory of axiom, so as to provide a new methodology for ontology mapping.

A Method for Evaluating and Standardizing Ontologies

Science.gov (United States)

Seyed, Ali Patrice

2012-01-01

The Open Biomedical Ontology (OBO) Foundry initiative is a collaborative effort for developing interoperable, science-based ontologies. The Basic Formal Ontology (BFO) serves as the upper ontology for the domain-level ontologies of OBO. BFO is an upper ontology of types as conceived by defenders of realism. Among the ontologies developed for OBO…

A Method for Building Personalized Ontology Summaries

OpenAIRE

Queiroz-Sousa, Paulo Orlando; Salgado, Ana Carolina; Pires, Carlos Eduardo

2013-01-01

In the context of ontology engineering, the ontology understanding is the basis for its further developmentand reuse. One intuitive eective approach to support ontology understanding is the process of ontology summarizationwhich highlights the most important concepts of an ontology. Ontology summarization identies an excerpt from anontology that contains the most relevant concepts and produces an abridged ontology. In this article, we present amethod for summarizing ontologies that represent ...

The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications.

Science.gov (United States)

Dönitz, Jürgen; Wingender, Edgar

2012-01-01

The semantic web depends on the use of ontologies to let electronic systems interpret contextual information. Optimally, the handling and access of ontologies should be completely transparent to the user. As a means to this end, we have developed a service that attempts to bridge the gap between experts in a certain knowledge domain, ontologists, and application developers. The ontology-based answers (OBA) service introduced here can be embedded into custom applications to grant access to the classes of ontologies and their relations as most important structural features as well as to information encoded in the relations between ontology classes. Thus computational biologists can benefit from ontologies without detailed knowledge about the respective ontology. The content of ontologies is mapped to a graph of connected objects which is compatible to the object-oriented programming style in Java. Semantic functions implement knowledge about the complex semantics of an ontology beyond the class hierarchy and "partOf" relations. By using these OBA functions an application can, for example, provide a semantic search function, or (in the examples outlined) map an anatomical structure to the organs it belongs to. The semantic functions relieve the application developer from the necessity of acquiring in-depth knowledge about the semantics and curation guidelines of the used ontologies by implementing the required knowledge. The architecture of the OBA service encapsulates the logic to process ontologies in order to achieve a separation from the application logic. A public server with the current plugins is available and can be used with the provided connector in a custom application in scenarios analogous to the presented use cases. The server and the client are freely available if a project requires the use of custom plugins or non-public ontologies. The OBA service and further documentation is available at http://www.bioinf.med.uni-goettingen.de/projects/oba.

Surreptitious, Evolving and Participative Ontology Development: An End-User Oriented Ontology Development Methodology

Science.gov (United States)

Bachore, Zelalem

2012-01-01

Ontology not only is considered to be the backbone of the semantic web but also plays a significant role in distributed and heterogeneous information systems. However, ontology still faces limited application and adoption to date. One of the major problems is that prevailing engineering-oriented methodologies for building ontologies do not…

Using LEGO NXT Mobile Robots with LabVIEW for Undergraduate Courses on Mechatronics

Science.gov (United States)

Gomez-de-Gabriel, J. M.; Mandow, A.; Fernandez-Lozano, J.; Garcia-Cerezo, A.

2011-01-01

The paper proposes lab work and student competitions based on the LEGO NXT Mindstorms kits and standard LabVIEW. The goal of this combination is to stimulate design and experimentation with real hardware and representative software in courses where mobile robotics is adopted as a motivating platform to introduce mechatronics competencies. Basic…

An Ontology for Software Engineering Education

Science.gov (United States)

Ling, Thong Chee; Jusoh, Yusmadi Yah; Adbullah, Rusli; Alwi, Nor Hayati

2013-01-01

Software agents communicate using ontology. It is important to build an ontology for specific domain such as Software Engineering Education. Building an ontology from scratch is not only hard, but also incur much time and cost. This study aims to propose an ontology through adaptation of the existing ontology which is originally built based on a…

Electromagnetic modelling of large complex 3-D structures with LEGO and the eigencurrent expansion method

NARCIS (Netherlands)

Lancellotti, V.; Hon, de B.P.; Tijhuis, A.G.

2009-01-01

Linear embedding via Green's operators (LEGO) is a computational method in which the multiple scattering between adjacent objects - forming a large composite structure - is determined through the interaction of simple-shaped building domains, whose electromagnetic (EM) behavior is accounted for by

OntoMaven: Maven-based Ontology Development and Management of Distributed Ontology Repositories

OpenAIRE

Paschke, Adrian

2013-01-01

In collaborative agile ontology development projects support for modular reuse of ontologies from large existing remote repositories, ontology project life cycle management, and transitive dependency management are important needs. The Apache Maven approach has proven its success in distributed collaborative Software Engineering by its widespread adoption. The contribution of this paper is a new design artifact called OntoMaven. OntoMaven adopts the Maven-based development methodology and ada...

Conceptual querying through ontologies

DEFF Research Database (Denmark)

Andreasen, Troels; Bulskov, Henrik

2009-01-01

is motivated by an obvious need for users to survey huge volumes of objects in query answers. An ontology formalism and a special notion of-instantiated ontology" are introduced. The latter is a structure reflecting the content in the document collection in that; it is a restriction of a general world......We present here ail approach to conceptual querying where the aim is, given a collection of textual database objects or documents, to target an abstraction of the entire database content in terms of the concepts appearing in documents, rather than the documents in the collection. The approach...... knowledge ontology to the concepts instantiated in the collection. The notion of ontology-based similarity is briefly described, language constructs for direct navigation and retrieval of concepts in the ontology are discussed and approaches to conceptual summarization are presented....

Improving the Teaching of Discrete-Event Control Systems Using a LEGO Manufacturing Prototype

Science.gov (United States)

Sanchez, A.; Bucio, J.

2012-01-01

This paper discusses the usefulness of employing LEGO as a teaching-learning aid in a post-graduate-level first course on the control of discrete-event systems (DESs). The final assignment of the course is presented, which asks students to design and implement a modular hierarchical discrete-event supervisor for the coordination layer of a…

Form, Content, and Gender Differences in Lego[R] Block Creations by Japanese Adolescents

Science.gov (United States)

Kato, Daiki; Morita, Miyako

2009-01-01

This study examined general features of Lego block creations produced by Japanese adolescents with no known mental health disorders. The block creations of 33 participants were assessed for form, content, and gender differences. Time spent on the task, amount of area covered, and quantity and types of blocks used were measured and correlated with…

Culture’s building blocks: investigating cultural evolution in a LEGO construction task

Science.gov (United States)

McGraw, John J.; Wallot, Sebastian; Mitkidis, Panagiotis; Roepstorff, Andreas

2014-01-01

One of the most essential but theoretically vexing issues regarding the notion of culture is that of cultural evolution and transmission: how a group’s accumulated solutions to invariant challenges develop and persevere over time. But at the moment, the notion of applying evolutionary theory to culture remains little more than a suggestive trope. Whereas the modern synthesis of evolutionary theory has provided an encompassing scientific framework for the selection and transmission of biological adaptations, a convincing theory of cultural evolution has yet to emerge. One of the greatest challenges for theorists is identifying the appropriate time scales and units of analysis in order to reduce the intractably large and complex phenomenon of “culture” into its component “building blocks.” In this paper, we present a model for scientifically investigating cultural processes by analyzing the ways people develop conventions in a series of LEGO construction tasks. The data revealed a surprising pattern in the selection of building bricks as well as features of car design across consecutive building sessions. Our findings support a novel methodology for studying the development and transmission of culture through the microcosm of interactive LEGO design and assembly. PMID:25309482

Culture’s building blocks: investigating cultural evolution in a LEGO construction task

Directory of Open Access Journals (Sweden)

John Joseph Mcgraw

2014-09-01

Full Text Available One of the most essential but theoretically vexing issues regarding the notion of culture is that of cultural evolution and transmission: how a group’s accumulated solutions to invariant challenges develop and persevere over time. But at the moment, the notion of applying evolutionary theory to culture remains little more than a suggestive trope. Whereas the modern synthesis of evolutionary theory has provided an encompassing scientific framework for the selection and transmission of biological adaptations, a convincing theory of cultural evolution has yet to emerge. One of the greatest challenges for theorists is identifying the appropriate time scales and units of analysis in order to reduce the intractably large and complex phenomenon of culture into its component building blocks. In this paper, we present a model for scientifically investigating cultural processes by analyzing the ways people develop conventions in a series of LEGO construction tasks. The data revealed a surprising pattern in the selection of building bricks as well as features of car design across consecutive building sessions. Our findings support a novel methodology for studying the development and transmission of culture through the microcosm of interactive LEGO design and assembly.

LEGO[R] Therapy and the Social Use of Language Programme: An Evaluation of Two Social Skills Interventions for Children with High Functioning Autism and Asperger Syndrome

Science.gov (United States)

Owens, Gina; Granader, Yael; Humphrey, Ayla; Baron-Cohen, Simon

2008-01-01

LEGO[R] therapy and the Social Use of Language Programme (SULP) were evaluated as social skills interventions for 6-11 year olds with high functioning autism and Asperger Syndrome. Children were matched on CA, IQ, and autistic symptoms before being randomly assigned to LEGO or SULP. Therapy occurred for 1 h/week over 18 weeks. A no-intervention…

Protein-protein interaction inference based on semantic similarity of Gene Ontology terms.

Science.gov (United States)

Zhang, Shu-Bo; Tang, Qiang-Rong

2016-07-21

Identifying protein-protein interactions is important in molecular biology. Experimental methods to this issue have their limitations, and computational approaches have attracted more and more attentions from the biological community. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most powerful indicators for protein interaction. However, conventional methods based on GO similarity fail to take advantage of the specificity of GO terms in the ontology graph. We proposed a GO-based method to predict protein-protein interaction by integrating different kinds of similarity measures derived from the intrinsic structure of GO graph. We extended five existing methods to derive the semantic similarity measures from the descending part of two GO terms in the GO graph, then adopted a feature integration strategy to combines both the ascending and the descending similarity scores derived from the three sub-ontologies to construct various kinds of features to characterize each protein pair. Support vector machines (SVM) were employed as discriminate classifiers, and five-fold cross validation experiments were conducted on both human and yeast protein-protein interaction datasets to evaluate the performance of different kinds of integrated features, the experimental results suggest the best performance of the feature that combines information from both the ascending and the descending parts of the three ontologies. Our method is appealing for effective prediction of protein-protein interaction. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Use of Lego Technologies in Elementary Teacher Preparation

Science.gov (United States)

Hadjiachilleos, Stella; Avraamidou, Lucy; Papastavrou, Stavros

2013-10-01

The need to reform science teacher preparation programs has been pointed out in research (Bryan and Abell in J Res Sci Teach 36:121-140, 1999; Bryan and Atwater in Sci Educ 8(6):821-839, 2002; Harrington and Hathaway in J Teach Educ 46(4):275-284, 1995). Science teachers are charged with the responsibility of incorporating both cognitive and non-cognitive parameters in their everyday teaching practices. This often results in their reluctance to teach science because they often lack disciplinary and/or pedagogical expertise required to promote science learning. The purpose of this study is to propose an alternative instructional approach in which Lego vehicles were used as a tool to promote pre-service elementary teachers' development and to examine whether there are non-cognitive parameters that promote or obstruct them from using Lego Technologies as a teaching tool. The context of the study was defined by a teacher preparation program of a private university in a small Mediterranean country. A sample of 28 pre-service elementary teachers, working in five 5-6-member groups were involved in scientific inquiries, during which they had to use vehicles in order to solve scientific problems related to concepts such as gear functioning, force, and motion. The nature of their cognitive engagement in the scientific inquiry process, non-cognitive parameters contributing to their cognitive engagement, and the impact of their involvement in the process on their development were examined through qualitative analysis of pre- and post-inquiry interviews, presentations of their solutions to the scientific problems and of their personal reflective journals.

Inferring ontology graph structures using OWL reasoning

KAUST Repository

Rodriguez-Garcia, Miguel Angel

2018-01-05

Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies\\' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies\\' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph .Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

Inferring ontology graph structures using OWL reasoning.

Science.gov (United States)

Rodríguez-García, Miguel Ángel; Hoehndorf, Robert

2018-01-05

Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies' semantic content remains a challenge. We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph . Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

Integrated learning of mathematics, science and technology concepts through LEGO/Logo projects

Science.gov (United States)

Wu, Lina

This dissertation examined integrated learning in the domains of mathematics, science and technology based on Piaget's constructivism, Papert's constructionism, and project-based approach to education. Ten fifth grade students were involved in a two-month long after school program where they designed and built their own computer-controlled LEGO/Logo projects that required the use of gears, ratios and motion concepts. The design of this study centered on three notions of integrated learning: (1) integration in terms of what educational materials/settings provide, (2) integration in terms of students' use of those materials, and (3) integration in the psychological sense. In terms of the first notion, the results generally showed that the LEGO/Logo environment supported the integrated learning of math, science and technology concepts. Regarding the second notion, the students all completed impressive projects of their own design. They successfully combined gears, motors, and LEGO parts together to create motion and writing control commands to manipulate the motion. But contrary to my initial expectations, their successful designs did not require numerical reasoning about ratios in designing effective gear systems. When they did reason about gear relationships, they worked with "qualitative" ratios, e.g., "a larger driver gear with a smaller driven gear increases the speed." In terms of the third notion of integrated learning, there was evidence in all four case study students of the psychological processes involved in linking mathematical, scientific, and/or technological concepts together to achieve new conceptual units. The students not only made connections between ideas and experiences, but also recognized decisive patterns and relationships in their project work. The students with stronger overall project performances showed more evidence of synthesis than the students with relatively weaker performances did. The findings support the conclusion that all three

Highly Manufacturable Deep (Sub-Millimeter) Etching Enabled High Aspect Ratio Complex Geometry Lego-Like Silicon Electronics

KAUST Repository

Ghoneim, Mohamed T.

2017-02-01

A highly manufacturable deep reactive ion etching based process involving a hybrid soft/hard mask process technology shows high aspect ratio complex geometry Lego-like silicon electronics formation enabling free-form (physically flexible, stretchable, and reconfigurable) electronic systems.

Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies.

Science.gov (United States)

Lamy, Jean-Baptiste

2017-07-01

Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated "role-filler" constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Owlready has been successfully

The Ontology for Biomedical Investigations.

Science.gov (United States)

Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

2016-01-01

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

Ontology-aided Data Fusion (Invited)

Science.gov (United States)

Raskin, R.

2009-12-01

An ontology provides semantic descriptions that are analogous to those in a dictionary, but are readable by both computers and humans. A data or service is semantically annotated when it is formally associated with elements of an ontology. The ESIP Federation Semantic Web Cluster has developed a set of ontologies to describe datatypes and data services that can be used to support automated data fusion. The service ontology includes descriptors of the service function, its inputs/outputs, and its invocation method. The datatype descriptors resemble typical metadata fields (data format, data model, data structure, originator, etc.) augmented with descriptions of the meaning of the data. These ontologies, in combination with the SWEET science ontology, enable a registered data fusion service to be chained together and implemented that is scientifically meaningful based on machine understanding of the associated data and services. This presentation describes initial results and experiences in automated data fusion.

Geo-Ontologies Are Scale Dependent

Science.gov (United States)

Frank, A. U.

2009-04-01

Philosophers aim at a single ontology that describes "how the world is"; for information systems we aim only at ontologies that describe a conceptualization of reality (Guarino 1995; Gruber 2005). A conceptualization of the world implies a spatial and temporal scale: what are the phenomena, the objects and the speed of their change? Few articles (Reitsma et al. 2003) seem to address that an ontology is scale specific (but many articles indicate that ontologies are scale-free in another sense namely that they are scale free in the link densities between concepts). The scale in the conceptualization can be linked to the observation process. The extent of the support of the physical observation instrument and the sampling theorem indicate what level of detail we find in a dataset. These rules apply for remote sensing or sensor networks alike. An ontology of observations must include scale or level of detail, and concepts derived from observations should carry this relation forward. A simple example: in high resolution remote sensing image agricultural plots and roads between them are shown, at lower resolution, only the plots and not the roads are visible. This gives two ontologies, one with plots and roads, the other with plots only. Note that a neighborhood relation in the two different ontologies also yield different results. References Gruber, T. (2005). "TagOntology - a way to agree on the semantics of tagging data." Retrieved October 29, 2005., from http://tomgruber.org/writing/tagontology-tagcapm-talk.pdf. Guarino, N. (1995). "Formal Ontology, Conceptual Analysis and Knowledge Representation." International Journal of Human and Computer Studies. Special Issue on Formal Ontology, Conceptual Analysis and Knowledge Representation, edited by N. Guarino and R. Poli 43(5/6). Reitsma, F. and T. Bittner (2003). Process, Hierarchy, and Scale. Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information ScienceInternational Conference

Ontology of fractures

Science.gov (United States)

Zhong, Jian; Aydina, Atilla; McGuinness, Deborah L.

2009-03-01

Fractures are fundamental structures in the Earth's crust and they can impact many societal and industrial activities including oil and gas exploration and production, aquifer management, CO 2 sequestration, waste isolation, the stabilization of engineering structures, and assessing natural hazards (earthquakes, volcanoes, and landslides). Therefore, an ontology which organizes the concepts of fractures could help facilitate a sound education within, and communication among, the highly diverse professional and academic community interested in the problems cited above. We developed a process-based ontology that makes explicit specifications about fractures, their properties, and the deformation mechanisms which lead to their formation and evolution. Our ontology emphasizes the relationships among concepts such as the factors that influence the mechanism(s) responsible for the formation and evolution of specific fracture types. Our ontology is a valuable resource with a potential to applications in a number of fields utilizing recent advances in Information Technology, specifically for digital data and information in computers, grids, and Web services.

Constructive Ontology Engineering

Science.gov (United States)

Sousan, William L.

2010-01-01

The proliferation of the Semantic Web depends on ontologies for knowledge sharing, semantic annotation, data fusion, and descriptions of data for machine interpretation. However, ontologies are difficult to create and maintain. In addition, their structure and content may vary depending on the application and domain. Several methods described in…

Summarization by domain ontology navigation

DEFF Research Database (Denmark)

Andreasen, Troels; Bulskov, Henrik

2013-01-01

of the subject. In between these two extremes, conceptual summaries encompass selected concepts derived using background knowledge. We address in this paper an approach where conceptual summaries are provided through a conceptualization as given by an ontology. The ontology guiding the summarization can...... be a simple taxonomy or a generative domain ontology. A domain ontology can be provided by a preanalysis of a domain corpus and can be used to condense improved summaries that better reflects the conceptualization of a given domain....

Ion Channel ElectroPhysiology Ontology (ICEPO) - a case study of text mining assisted ontology development.

Science.gov (United States)

Elayavilli, Ravikumar Komandur; Liu, Hongfang

2016-01-01

Computational modeling of biological cascades is of great interest to quantitative biologists. Biomedical text has been a rich source for quantitative information. Gathering quantitative parameters and values from biomedical text is one significant challenge in the early steps of computational modeling as it involves huge manual effort. While automatically extracting such quantitative information from bio-medical text may offer some relief, lack of ontological representation for a subdomain serves as impedance in normalizing textual extractions to a standard representation. This may render textual extractions less meaningful to the domain experts. In this work, we propose a rule-based approach to automatically extract relations involving quantitative data from biomedical text describing ion channel electrophysiology. We further translated the quantitative assertions extracted through text mining to a formal representation that may help in constructing ontology for ion channel events using a rule based approach. We have developed Ion Channel ElectroPhysiology Ontology (ICEPO) by integrating the information represented in closely related ontologies such as, Cell Physiology Ontology (CPO), and Cardiac Electro Physiology Ontology (CPEO) and the knowledge provided by domain experts. The rule-based system achieved an overall F-measure of 68.93% in extracting the quantitative data assertions system on an independently annotated blind data set. We further made an initial attempt in formalizing the quantitative data assertions extracted from the biomedical text into a formal representation that offers potential to facilitate the integration of text mining into ontological workflow, a novel aspect of this study. This work is a case study where we created a platform that provides formal interaction between ontology development and text mining. We have achieved partial success in extracting quantitative assertions from the biomedical text and formalizing them in ontological

HybridGO-Loc: mining hybrid features on gene ontology for predicting subcellular localization of multi-location proteins.

Science.gov (United States)

Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

2014-01-01

Protein subcellular localization prediction, as an essential step to elucidate the functions in vivo of proteins and identify drugs targets, has been extensively studied in previous decades. Instead of only determining subcellular localization of single-label proteins, recent studies have focused on predicting both single- and multi-location proteins. Computational methods based on Gene Ontology (GO) have been demonstrated to be superior to methods based on other features. However, existing GO-based methods focus on the occurrences of GO terms and disregard their relationships. This paper proposes a multi-label subcellular-localization predictor, namely HybridGO-Loc, that leverages not only the GO term occurrences but also the inter-term relationships. This is achieved by hybridizing the GO frequencies of occurrences and the semantic similarity between GO terms. Given a protein, a set of GO terms are retrieved by searching against the gene ontology database, using the accession numbers of homologous proteins obtained via BLAST search as the keys. The frequency of GO occurrences and semantic similarity (SS) between GO terms are used to formulate frequency vectors and semantic similarity vectors, respectively, which are subsequently hybridized to construct fusion vectors. An adaptive-decision based multi-label support vector machine (SVM) classifier is proposed to classify the fusion vectors. Experimental results based on recent benchmark datasets and a new dataset containing novel proteins show that the proposed hybrid-feature predictor significantly outperforms predictors based on individual GO features as well as other state-of-the-art predictors. For readers' convenience, the HybridGO-Loc server, which is for predicting virus or plant proteins, is available online at http://bioinfo.eie.polyu.edu.hk/HybridGoServer/.

A Simple, Small-Scale Lego Colorimeter with a Light-Emitting Diode (LED) Used as Detector

Science.gov (United States)

Asheim, Jonas; Kvittingen, Eivind V.; Kvittingen, Lise; Verley, Richard

2014-01-01

This article describes how to construct a simple, inexpensive, and robust colorimeter from a few Lego bricks, in which one light-emitting diode (LED) is used as a light source and a second LED as a light detector. The colorimeter is suited to various grades and curricula.

A LEGO Watt balance: An apparatus to determine a mass based on the new SI

Science.gov (United States)

Chao, L. S.; Schlamminger, S.; Newell, D. B.; Pratt, J. R.; Seifert, F.; Zhang, X.; Sineriz, G.; Liu, M.; Haddad, D.

2015-11-01

A global effort to redefine our International System of Units (SI) is underway, and the change to the new system is expected to occur in 2018. Within the newly redefined SI, the present base units will still exist but be derived from fixed numerical values of seven reference constants. In particular, the unit of mass (the kilogram) will be realized through a fixed value of the Planck constant h. A so-called watt balance, for example, can then be used to realize the kilogram unit of mass within a few parts in 108. Such a balance has been designed and constructed at the National Institute of Standards and Technology. For educational outreach and to demonstrate the principle, we have constructed a LEGO tabletop watt balance capable of measuring a gram-level masses to 1% relative uncertainty. This article presents the design, construction, and performance of the LEGO watt balance and its ability to determine h.

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.

Gene Ontology Consortium: going forward.

Science.gov (United States)

2015-01-01

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Building a developmental toxicity ontology.

Science.gov (United States)

Baker, Nancy; Boobis, Alan; Burgoon, Lyle; Carney, Edward; Currie, Richard; Fritsche, Ellen; Knudsen, Thomas; Laffont, Madeleine; Piersma, Aldert H; Poole, Alan; Schneider, Steffen; Daston, George

2018-04-03

As more information is generated about modes of action for developmental toxicity and more data are generated using high-throughput and high-content technologies, it is becoming necessary to organize that information. This report discussed the need for a systematic representation of knowledge about developmental toxicity (i.e., an ontology) and proposes a method to build one based on knowledge of developmental biology and mode of action/ adverse outcome pathways in developmental toxicity. This report is the result of a consensus working group developing a plan to create an ontology for developmental toxicity that spans multiple levels of biological organization. This report provide a description of some of the challenges in building a developmental toxicity ontology and outlines a proposed methodology to meet those challenges. As the ontology is built on currently available web-based resources, a review of these resources is provided. Case studies on one of the most well-understood morphogens and developmental toxicants, retinoic acid, are presented as examples of how such an ontology might be developed. This report outlines an approach to construct a developmental toxicity ontology. Such an ontology will facilitate computer-based prediction of substances likely to induce human developmental toxicity. © 2018 Wiley Periodicals, Inc.

Building a biomedical ontology recommender web service

Directory of Open Access Journals (Sweden)

Jonquet Clement

2010-06-01

Full Text Available Abstract Background Researchers in biomedical informatics use ontologies and terminologies to annotate their data in order to facilitate data integration and translational discoveries. As the use of ontologies for annotation of biomedical datasets has risen, a common challenge is to identify ontologies that are best suited to annotating specific datasets. The number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use. Methods We present the Biomedical Ontology Recommender web service. The system uses textual metadata or a set of keywords describing a domain of interest and suggests appropriate ontologies for annotating or representing the data. The service makes a decision based on three criteria. The first one is coverage, or the ontologies that provide most terms covering the input text. The second is connectivity, or the ontologies that are most often mapped to by other ontologies. The final criterion is size, or the number of concepts in the ontologies. The service scores the ontologies as a function of scores of the annotations created using the National Center for Biomedical Ontology (NCBO Annotator web service. We used all the ontologies from the UMLS Metathesaurus and the NCBO BioPortal. Results We compare and contrast our Recommender by an exhaustive functional comparison to previously published efforts. We evaluate and discuss the results of several recommendation heuristics in the context of three real world use cases. The best recommendations heuristics, rated ‘very relevant’ by expert evaluators, are the ones based on coverage and connectivity criteria. The Recommender service (alpha version is available to the community and is embedded into BioPortal.

The malleability of spatial ability under treatment of a FIRST LEGO League-based robotics unit

Science.gov (United States)

Coxon, Steven Vincent

Spatial ability is important to science, technology, engineering, and math (STEM) success, but spatial talents are rarely developed in schools. Likewise, the gifted may become STEM innovators, but they are rarely provided with pedagogy appropriate to develop their abilities in schools. A stratified random sample of volunteer participants (n=75) ages 9-14 was drawn from 16 public school districts' gifted programs, including as many females (n=28) and children from groups traditionally underrepresented in gifted programs (n=18) as available. Participants were randomly divided into an experimental (n=38) and a control group (n=37) for an intervention study. All participants took the CogAT (form 6) Verbal Battery and the Project TALENT Spatial Ability Assessments. The experimental group participated in a simulation of the FIRST LEGO League (FLL) competition for 20 hours total over five consecutive days. All participants took the spatial measure another time. Experimental males evidenced significant and meaningful gains in measured spatial ability (Cohen's d = 0.87). Females did not evidence significant gains in measured spatial ability. This may be due to sampling error, gender differences in prior experience with LEGO, or differences in facets of spatial ability in the treatment or measurements. Further research studies with larger samples of females, other treatments and measurement tools, and longer treatment periods are recommended. The literature review revealed that FLL is beneficial for STEM engagement in both genders and its use in schools is recommended. The present study provides additional evidence for FLL's usefulness in increasing the number of individuals in the STEM pipeline. Keywords: spatial, gilled, talent, robotics, FIRST LEGO League, science

A Hydrological Sensor Web Ontology Based on the SSN Ontology: A Case Study for a Flood

Directory of Open Access Journals (Sweden)

Chao Wang

2017-12-01

Full Text Available Accompanying the continuous development of sensor network technology, sensors worldwide are constantly producing observation data. However, the sensors and their data from different observation platforms are sometimes difficult to use collaboratively in response to natural disasters such as floods for the lack of semantics. In this paper, a hydrological sensor web ontology based on SSN ontology is proposed to describe the heterogeneous hydrological sensor web resources by importing the time and space ontology, instantiating the hydrological classes, and establishing reasoning rules. This work has been validated by semantic querying and knowledge acquiring experiments. The results demonstrate the feasibility and effectiveness of the proposed ontology and its potential to grow into a more comprehensive ontology for hydrological monitoring collaboratively. In addition, this method of ontology modeling is generally applicable to other applications and domains.

Gradient Learning Algorithms for Ontology Computing

Science.gov (United States)

Gao, Wei; Zhu, Linli

2014-01-01

The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting. PMID:25530752

Gradient Learning Algorithms for Ontology Computing

Directory of Open Access Journals (Sweden)

Wei Gao

2014-01-01

Full Text Available The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting.

Perspectives on ontology learning

CERN Document Server

Lehmann, J

2014-01-01

Perspectives on Ontology Learning brings together researchers and practitioners from different communities − natural language processing, machine learning, and the semantic web − in order to give an interdisciplinary overview of recent advances in ontology learning.Starting with a comprehensive introduction to the theoretical foundations of ontology learning methods, the edited volume presents the state-of-the-start in automated knowledge acquisition and maintenance. It outlines future challenges in this area with a special focus on technologies suitable for pushing the boundaries beyond the c

Towards Ontology-Driven Information Systems: Guidelines to the Creation of New Methodologies to Build Ontologies

Science.gov (United States)

Soares, Andrey

2009-01-01

This research targeted the area of Ontology-Driven Information Systems, where ontology plays a central role both at development time and at run time of Information Systems (IS). In particular, the research focused on the process of building domain ontologies for IS modeling. The motivation behind the research was the fact that researchers have…

Database Concepts in a Domain Ontology

Directory of Open Access Journals (Sweden)

Gorskis Henrihs

2017-12-01

Full Text Available There are multiple approaches for mapping from a domain ontology to a database in the task of ontology-based data access. For that purpose, external mapping documents are most commonly used. These documents describe how the data necessary for the description of ontology individuals and other values, are to be obtained from the database. The present paper investigates the use of special database concepts. These concepts are not separated from the domain ontology; they are mixed with domain concepts to form a combined application ontology. By creating natural relationships between database concepts and domain concepts, mapping can be implemented more easily and with a specific purpose. The paper also investigates how the use of such database concepts in addition to domain concepts impacts ontology building and data retrieval.

On Algebraic Spectrum of Ontology Evaluation

OpenAIRE

Adekoya Adebayo Felix; kinwale Adio Taofiki; Sofoluwe Adetokunbo

2011-01-01

Ontology evaluation remains an important open problem in the area of its application. The ontology structure evaluation framework for benchmarking the internal graph structures was proposed. The framework was used in transport and biochemical ontology. The corresponding adjacency, incidence matrices and other structural properties due to the class hierarchical structure of the transport and biochemical ontology were computed using MATLAB. The results showed that the choice of suitable choice ...

ONTOGRABBING: Extracting Information from Texts Using Generative Ontologies

DEFF Research Database (Denmark)

Nilsson, Jørgen Fischer; Szymczak, Bartlomiej Antoni; Jensen, P.A.

2009-01-01

We describe principles for extracting information from texts using a so-called generative ontology in combination with syntactic analysis. Generative ontologies are introduced as semantic domains for natural language phrases. Generative ontologies extend ordinary finite ontologies with rules...... for producing recursively shaped terms representing the ontological content (ontological semantics) of NL noun phrases and other phrases. We focus here on achieving a robust, often only partial, ontology-driven parsing of and ascription of semantics to a sentence in the text corpus. The aim of the ontological...... analysis is primarily to identify paraphrases, thereby achieving a search functionality beyond mere keyword search with synsets. We further envisage use of the generative ontology as a phrase-based rather than word-based browser into text corpora....

Formal Ontologies and Uncertainty. In Geographical Knowledge

Directory of Open Access Journals (Sweden)

Matteo Caglioni

2014-05-01

Full Text Available Formal ontologies have proved to be a very useful tool to manage interoperability among data, systems and knowledge. In this paper we will show how formal ontologies can evolve from a crisp, deterministic framework (ontologies of hard knowledge to new probabilistic, fuzzy or possibilistic frameworks (ontologies of soft knowledge. This can considerably enlarge the application potential of formal ontologies in geographic analysis and planning, where soft knowledge is intrinsically linked to the complexity of the phenomena under study.  The paper briefly presents these new uncertainty-based formal ontologies. It then highlights how ontologies are formal tools to define both concepts and relations among concepts. An example from the domain of urban geography finally shows how the cause-to-effect relation between household preferences and urban sprawl can be encoded within a crisp, a probabilistic and a possibilistic ontology, respectively. The ontology formalism will also determine the kind of reasoning that can be developed from available knowledge. Uncertain ontologies can be seen as the preliminary phase of more complex uncertainty-based models. The advantages of moving to uncertainty-based models is evident: whether it is in the analysis of geographic space or in decision support for planning, reasoning on geographic space is almost always reasoning with uncertain knowledge of geographic phenomena.

A meta-ontological framework for multi-agent systems design

OpenAIRE

Sokolova, Marina; Fernández Caballero, Antonio

2007-01-01

The paper introduces an approach to using a meta-ontology framework for complex multi-agent systems design, and illustrates it in an application related to ecological-medical issues. The described shared ontology is pooled from private sub-ontologies, which represent a problem area ontology, an agent ontology, a task ontology, an ontology of interactions, and the multi-agent system architecture ontology.

Basic concepts of automation and mechatronics with LEGO mindstorms NXT

Directory of Open Access Journals (Sweden)

Matijević Milan S.

2014-01-01

Full Text Available Mindstorsms LEGO NXT is using in engineering education at well recognized engineering schools like RWTH Aachen University where is created the RWTH - Mindstorms NXT Toolbox for Matlab. MATLAB / Simulink is widely available and popular for students around the world, but software toolboxes which are required for work with the real time systems are too expensive for the universities, especially those in developing countries. This paper describes an approach that is currently used in introductory subjects in the field of automation and mechatronics at the University of Kragujevac, and that does not require expensive software support.

Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

Science.gov (United States)

Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Ó Tuama, Éamonn; Schildhauer, Mark; Smith, Barry; Stucky, Brian J; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

2014-01-01

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

Science.gov (United States)

Baskauf, Steve; Blum, Stanley; Bowers, Shawn; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Tuama, Éamonn Ó.; Schildhauer, Mark; Smith, Barry; Stucky, Brian J.; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

2014-01-01

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers

Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us FANTOM....biosciencedbc.jp/archive/fantom5/datafiles/LATEST/extra/Ontology/ File size: 1.8 MB Simple search URL - Dat...t Us Sample ontology, GOstat and ontology term enrichment - FANTOM5 | LSDB Archive ...

An ontological approach to domain engineering

NARCIS (Netherlands)

Falbo, R.A.; Guizzardi, G.; Duarte, K.

2002-01-01

Domain engineering aims to support systematic reuse, focusing on modeling common knowledge in a problem domain. Ontologies have also been pointed as holding great promise for software reuse. In this paper, we present ODE (Ontology-based Domain Engineering), an ontological approach for domain

OIntEd: online ontology instance editor enabling a new approach to ontology development

NARCIS (Netherlands)

Wibisono, A.; Koning, R.; Grosso, P.; Belloum, A.; Bubak, M.; de Laat, C.

2013-01-01

Ontology development involves people with different background knowledge and expertise. It is an elaborate process, where sophisticated tools for experienced knowledge engineers are available. However, domain experts need simple tools that they can use to focus on ontology instantiation. In this

Ontology and medical diagnosis.

Science.gov (United States)

Bertaud-Gounot, Valérie; Duvauferrier, Régis; Burgun, Anita

2012-03-01

Ontology and associated generic tools are appropriate for knowledge modeling and reasoning, but most of the time, disease definitions in existing description logic (DL) ontology are not sufficient to classify patient's characteristics under a particular disease because they do not formalize operational definitions of diseases (association of signs and symptoms=diagnostic criteria). The main objective of this study is to propose an ontological representation which takes into account the diagnostic criteria on which specific patient conditions may be classified under a specific disease. This method needs as a prerequisite a clear list of necessary and sufficient diagnostic criteria as defined for lots of diseases by learned societies. It does not include probability/uncertainty which Web Ontology Language (OWL 2.0) cannot handle. We illustrate it with spondyloarthritis (SpA). Ontology has been designed in Protégé 4.1 OWL-DL2.0. Several kinds of criteria were formalized: (1) mandatory criteria, (2) picking two criteria among several diagnostic criteria, (3) numeric criteria. Thirty real patient cases were successfully classified with the reasoner. This study shows that it is possible to represent operational definitions of diseases with OWL and successfully classify real patient cases. Representing diagnostic criteria as descriptive knowledge (instead of rules in Semantic Web Rule Language or Prolog) allows us to take advantage of tools already available for OWL. While we focused on Assessment of SpondyloArthritis international Society SpA criteria, we believe that many of the representation issues addressed here are relevant to using OWL-DL for operational definition of other diseases in ontology.

Resident Space Object Characterization and Behavior Understanding via Machine Learning and Ontology-based Bayesian Networks

Science.gov (United States)

Furfaro, R.; Linares, R.; Gaylor, D.; Jah, M.; Walls, R.

2016-09-01

In this paper, we present an end-to-end approach that employs machine learning techniques and Ontology-based Bayesian Networks (BN) to characterize the behavior of resident space objects. State-of-the-Art machine learning architectures (e.g. Extreme Learning Machines, Convolutional Deep Networks) are trained on physical models to learn the Resident Space Object (RSO) features in the vectorized energy and momentum states and parameters. The mapping from measurements to vectorized energy and momentum states and parameters enables behavior characterization via clustering in the features space and subsequent RSO classification. Additionally, Space Object Behavioral Ontologies (SOBO) are employed to define and capture the domain knowledge-base (KB) and BNs are constructed from the SOBO in a semi-automatic fashion to execute probabilistic reasoning over conclusions drawn from trained classifiers and/or directly from processed data. Such an approach enables integrating machine learning classifiers and probabilistic reasoning to support higher-level decision making for space domain awareness applications. The innovation here is to use these methods (which have enjoyed great success in other domains) in synergy so that it enables a "from data to discovery" paradigm by facilitating the linkage and fusion of large and disparate sources of information via a Big Data Science and Analytics framework.

A UML profile for the OBO relation ontology

Science.gov (United States)

2012-01-01

Background Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions The use of an established and well-known graphical language in the development of biomedical ontologies provides a more

Highly Manufacturable Deep (Sub-Millimeter) Etching Enabled High Aspect Ratio Complex Geometry Lego-Like Silicon Electronics.

Science.gov (United States)

Ghoneim, Mohamed Tarek; Hussain, Muhammad Mustafa

2017-04-01

A highly manufacturable deep reactive ion etching based process involving a hybrid soft/hard mask process technology shows high aspect ratio complex geometry Lego-like silicon electronics formation enabling free-form (physically flexible, stretchable, and reconfigurable) electronic systems. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aspects of ontology visualization and integration

NARCIS (Netherlands)

Dmitrieva, Joelia Borisovna

2011-01-01

In this thesis we will describe and discuss methodologies for ontology visualization and integration. Two visualization methods will be elaborated. In one method the ontology is visualized with the node-link technique, and with the other method the ontology is visualized with the containment

Proposed actions are no actions: re-modeling an ontology design pattern with a realist top-level ontology.

Science.gov (United States)

Seddig-Raufie, Djamila; Jansen, Ludger; Schober, Daniel; Boeker, Martin; Grewe, Niels; Schulz, Stefan

2012-09-21

Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies. As a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans. The proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as

LEGO Mindstorms NXT for elderly and visually impaired people in need: A platform.

Science.gov (United States)

Al-Halhouli, Ala'aldeen; Qitouqa, Hala; Malkosh, Nancy; Shubbak, Alaa; Al-Gharabli, Samer; Hamad, Eyad

2016-07-27

This paper presents the employment of LEGO Mindstorms NXT robotics as core component of low cost multidisciplinary platform for assisting elderly and visually impaired people. LEGO Mindstorms system offers a plug-and-play programmable robotics toolkit, incorporating construction guides, microcontrollers and sensors, all connected via a comprehensive programming language. It facilitates, without special training and at low cost, the use of such device for interpersonal communication and for handling multiple tasks required for elderly and visually impaired people in-need. The research project provides a model for larger-scale implementation, tackling the issues of creating additional functions in order to assist people in-need. The new functions were built and programmed using MATLAB through a user friendly Graphical User Interface (GUI). Power consumption problem, besides the integration of WiFi connection has been resolved, incorporating GPS application on smart phones enhanced the guiding and tracking functions. We believe that developing and expanding the system to encompass a range of applications beyond the initial design schematics to ease conducting a limited number of pre-described protocols. However, the beneficiaries for the proposed research would be limited to elderly people who require assistance within their household as assistive-robot to facilitate a low-cost solution for a highly demanding health circumstance.

Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor.

Science.gov (United States)

Levy, Yaakov

2017-09-26

Proteins, like other biomolecules, have a modular and hierarchical structure. Various building blocks are used to construct proteins of high structural complexity and diverse functionality. In multidomain proteins, for example, domains are fused to each other in different combinations to achieve different functions. Although the LEGO brick metaphor is justified as a means of simplifying the complexity of three-dimensional protein structures, several fundamental properties (such as allostery or the induced-fit mechanism) make deviation from it necessary to respect the plasticity, softness, and cross-talk that are essential to protein function. In this work, we illustrate recently reported protein behavior in multidomain proteins that deviates from the LEGO brick analogy. While earlier studies showed that a protein domain is often unaffected by being fused to another domain or becomes more stable following the formation of a new interface between the tethered domains, destabilization due to tethering has been reported for several systems. We illustrate that tethering may sometimes result in a multidomain protein behaving as "less than the sum of its parts". We survey these cases for which structure additivity does not guarantee thermodynamic additivity. Protein destabilization due to fusion to other domains may be linked in some cases to biological function and should be taken into account when designing large assemblies.

Mapping between the OBO and OWL ontology languages.

Science.gov (United States)

Tirmizi, Syed Hamid; Aitken, Stuart; Moreira, Dilvan A; Mungall, Chris; Sequeda, Juan; Shah, Nigam H; Miranker, Daniel P

2011-03-07

Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical ontologies. These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language (OWL). OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. In comparison, OWL is a Semantic Web language, and is supported by the World Wide Web consortium together with integral query languages, rule languages and distributed infrastructure for information interchange. These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL. We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web itself to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to decompose the problem into two parts. Most OBO constructs have easy and obvious equivalence to a construct in OWL. A small subset of OBO constructs requires deeper consideration. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source. Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge. In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.

Vaccine and Drug Ontology Studies (VDOS 2014).

Science.gov (United States)

Tao, Cui; He, Yongqun; Arabandi, Sivaram

2016-01-01

The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat human and animal diseases. Work in both (drugs and vaccines) areas is closely related - from preclinical research and development to manufacturing, clinical trials, government approval and regulation, and post-licensure usage surveillance and monitoring. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs - extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, developing new models such as the Vaccine Ontology (VO) and Ontology of Adverse Events (OAE), vernacular medical terminologies such as the Consumer Health Vocabulary (CHV). The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The five full-length papers included in this 2014 thematic issue focus on two main themes: (i) General vaccine/drug-related ontology development and exploration, and (ii) Interaction and network-related ontology studies.

Ontological Engineering for the Cadastral Domain

DEFF Research Database (Denmark)

Stubkjær, Erik; Stuckenschmidt, Heiner

2000-01-01

conceptualization of the world is that much information remains implicit. Ontologies have set out to overcome the problem of implicit and hidden knowledge by making the conceptualization of a domain (e.g. mathematics) explicit. Ontological engineering is thus an approach to achieve a conceptual rigor...... that characterizes established academic disciplines, like geodesy. Many university courses address more application oriented fields, like cadastral law, and spatial planning, and they may benefit from the ontological engineering approach. The paper provides an introduction to the field of ontological engineering...

Learning Resources Organization Using Ontological Framework

Science.gov (United States)

Gavrilova, Tatiana; Gorovoy, Vladimir; Petrashen, Elena

The paper describes the ontological approach to the knowledge structuring for the e-learning portal design as it turns out to be efficient and relevant to current domain conditions. It is primarily based on the visual ontology-based description of the content of the learning materials and this helps to provide productive and personalized access to these materials. The experience of ontology developing for Knowledge Engineering coursetersburg State University is discussed and “OntolingeWiki” tool for creating ontology-based e-learning portals is described.

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.

Leave-two-out stability of ontology learning algorithm

International Nuclear Information System (INIS)

Wu, Jianzhang; Yu, Xiao; Zhu, Linli; Gao, Wei

2016-01-01

Ontology is a semantic analysis and calculation model, which has been applied to many subjects. Ontology similarity calculation and ontology mapping are employed as machine learning approaches. The purpose of this paper is to study the leave-two-out stability of ontology learning algorithm. Several leave-two-out stabilities are defined in ontology learning setting and the relationship among these stabilities are presented. Furthermore, the results manifested reveal that leave-two-out stability is a sufficient and necessary condition for ontology learning algorithm.

Semantic similarity between ontologies at different scales

Energy Technology Data Exchange (ETDEWEB)

Zhang, Qingpeng; Haglin, David J.

2016-04-01

In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

Use of the CIM Ontology

Energy Technology Data Exchange (ETDEWEB)

Neumann, Scott; Britton, Jay; Devos, Arnold N.; Widergren, Steven E.

2006-02-08

There are many uses for the Common Information Model (CIM), an ontology that is being standardized through Technical Committee 57 of the International Electrotechnical Commission (IEC TC57). The most common uses to date have included application modeling, information exchanges, information management and systems integration. As one should expect, there are many issues that become apparent when the CIM ontology is applied to any one use. Some of these issues are shortcomings within the current draft of the CIM, and others are a consequence of the different ways in which the CIM can be applied using different technologies. As the CIM ontology will and should evolve, there are several dangers that need to be recognized. One is overall consistency and impact upon applications when extending the CIM for a specific need. Another is that a tight coupling of the CIM to specific technologies could limit the value of the CIM in the longer term as an ontology, which becomes a larger issue over time as new technologies emerge. The integration of systems is one specific area of interest for application of the CIM ontology. This is an area dominated by the use of XML for the definition of messages. While this is certainly true when using Enterprise Application Integration (EAI) products, it is even more true with the movement towards the use of Web Services (WS), Service-Oriented Architectures (SOA) and Enterprise Service Buses (ESB) for integration. This general IT industry trend is consistent with trends seen within the IEC TC57 scope of power system management and associated information exchange. The challenge for TC57 is how to best leverage the CIM ontology using the various XML technologies and standards for integration. This paper will provide examples of how the CIM ontology is used and describe some specific issues that should be addressed within the CIM in order to increase its usefulness as an ontology. It will also describe some of the issues and challenges that will

DEPONTO: A Reusable Dependability Domain Ontology

Directory of Open Access Journals (Sweden)

Teodora Sanislav

2015-08-01

Full Text Available This paper proposes a dependability reusable ontology for knowledge representation. The fundamental knowledge related to dependability follows its taxonomy. Thus, this paper gives an analysis of what is the dependability domain ontology andof its components.The dependability domain ontology plays an important role in ensuring the dependability of information systems by providing support for their diagnosis in case of faults, errors and failures.The proposed ontology is used as a dependability framework in two case study Cyber-Physical Systemswhich demonstrate its reusability within this category of systems.

Anatomy Ontology Matching Using Markov Logic Networks

Directory of Open Access Journals (Sweden)

Chunhua Li

2016-01-01

Full Text Available The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relationships between ontologies describing different species. Ontology matching is a kind of solutions to find semantic correspondences between entities of different ontologies. Markov logic networks which unify probabilistic graphical model and first-order logic provide an excellent framework for ontology matching. We combine several different matching strategies through first-order logic formulas according to the structure of anatomy ontologies. Experiments on the adult mouse anatomy and the human anatomy have demonstrated the effectiveness of proposed approach in terms of the quality of result alignment.

Core Semantics for Public Ontologies

National Research Council Canada - National Science Library

Suni, Niranjan

2005-01-01

... (schemas or ontologies) with respect to objects. The DARPA Agent Markup Language (DAML) through the use of ontologies provides a very powerful way to describe objects and their relationships to other objects...

Model Driven Engineering with Ontology Technologies

Science.gov (United States)

Staab, Steffen; Walter, Tobias; Gröner, Gerd; Parreiras, Fernando Silva

Ontologies constitute formal models of some aspect of the world that may be used for drawing interesting logical conclusions even for large models. Software models capture relevant characteristics of a software artifact to be developed, yet, most often these software models have limited formal semantics, or the underlying (often graphical) software language varies from case to case in a way that makes it hard if not impossible to fix its semantics. In this contribution, we survey the use of ontology technologies for software modeling in order to carry over advantages from ontology technologies to the software modeling domain. It will turn out that ontology-based metamodels constitute a core means for exploiting expressive ontology reasoning in the software modeling domain while remaining flexible enough to accommodate varying needs of software modelers.

A model of Altio Lazio boiling water reactor using the LEGO code nuclear steam supply system simulation

International Nuclear Information System (INIS)

Garbossa, G.B.; Spelta, S.; Cori, R.; Mosca, R.; Cento, P.

1989-01-01

An extensive effort has been made at the Italian National Electricity Board (ENEL) to construct and validate a LEGO model capable of simulating the operational transients of the Alto Lazio Nuclear Station, a two-twin units site with BWR/6 class reactors, rated at 2894 MWt and with Mark III containment. The desired end-product of this effort is an overall plant model consisting of the Nuclear Steam Supply System model, described in this paper, and the Balance of Plant model, capable of simulating the transient response of Alto Lazio Station. The models utilize the in-house developed LEGO code, which is a modular package oriented to power plant modeling and suitable to perform transient analyses to assist during power plant design, control system design and operating procedure verification. The ability of the NSSS model to predict correctly the plant response is demonstrated through comparison with results calculated by the vendor, using REDY code, and by an in-house RETRAN-02 model

Methodology for Automatic Ontology Generation Using Database Schema Information

Directory of Open Access Journals (Sweden)

JungHyen An

2018-01-01

Full Text Available An ontology is a model language that supports the functions to integrate conceptually distributed domain knowledge and infer relationships among the concepts. Ontologies are developed based on the target domain knowledge. As a result, methodologies to automatically generate an ontology from metadata that characterize the domain knowledge are becoming important. However, existing methodologies to automatically generate an ontology using metadata are required to generate the domain metadata in a predetermined template, and it is difficult to manage data that are increased on the ontology itself when the domain OWL (Ontology Web Language individuals are continuously increased. The database schema has a feature of domain knowledge and provides structural functions to efficiently process the knowledge-based data. In this paper, we propose a methodology to automatically generate ontologies and manage the OWL individual through an interaction of the database and the ontology. We describe the automatic ontology generation process with example schema and demonstrate the effectiveness of the automatically generated ontology by comparing it with existing ontologies using the ontology quality score.

An ontology for major histocompatibility restriction.

Science.gov (United States)

Vita, Randi; Overton, James A; Seymour, Emily; Sidney, John; Kaufman, Jim; Tallmadge, Rebecca L; Ellis, Shirley; Hammond, John; Butcher, Geoff W; Sette, Alessandro; Peters, Bjoern

2016-01-01

MHC molecules are a highly diverse family of proteins that play a key role in cellular immune recognition. Over time, different techniques and terminologies have been developed to identify the specific type(s) of MHC molecule involved in a specific immune recognition context. No consistent nomenclature exists across different vertebrate species. To correctly represent MHC related data in The Immune Epitope Database (IEDB), we built upon a previously established MHC ontology and created an ontology to represent MHC molecules as they relate to immunological experiments. This ontology models MHC protein chains from 16 species, deals with different approaches used to identify MHC, such as direct sequencing verses serotyping, relates engineered MHC molecules to naturally occurring ones, connects genetic loci, alleles, protein chains and multi-chain proteins, and establishes evidence codes for MHC restriction. Where available, this work is based on existing ontologies from the OBO foundry. Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building efforts into web resources.

Process attributes in bio-ontologies

Directory of Open Access Journals (Sweden)

Andrade André Q

2012-08-01

Full Text Available Abstract Background Biomedical processes can provide essential information about the (mal- functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attributes, such as rates or regularities. The adequate representation of such process attributes has been a contentious issue in bio-ontologies recently; and domain ontologies have correspondingly developed ad hoc workarounds that compromise interoperability and logical consistency. Results We present a design pattern for the representation of process attributes that is compatible with upper ontology frameworks such as BFO and BioTop. Our solution rests on two key tenets: firstly, that many of the sorts of process attributes which are biomedically interesting can be characterised by the ways that repeated parts of such processes constitute, in combination, an overall process; secondly, that entities for which a full logical definition can be assigned do not need to be treated as primitive within a formal ontology framework. We apply this approach to the challenge of modelling and automatically classifying examples of normal and abnormal rates and patterns of heart beating processes, and discuss the expressivity required in the underlying ontology representation language. We provide full definitions for process attributes at increasing levels of domain complexity. Conclusions We show that a logical definition of process attributes is feasible, though limited by the expressivity of DL languages so that the creation of primitives is still necessary. This finding may endorse current formal upper-ontology frameworks as a way of ensuring consistency, interoperability and clarity.

Ontology Mapping Neural Network: An Approach to Learning and Inferring Correspondences among Ontologies

Science.gov (United States)

Peng, Yefei

2010-01-01

An ontology mapping neural network (OMNN) is proposed in order to learn and infer correspondences among ontologies. It extends the Identical Elements Neural Network (IENN)'s ability to represent and map complex relationships. The learning dynamics of simultaneous (interlaced) training of similar tasks interact at the shared connections of the…

Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO relationships.

Science.gov (United States)

Manda, Prashanti; McCarthy, Fiona; Bridges, Susan M

2013-10-01

The Gene Ontology (GO), a set of three sub-ontologies, is one of the most popular bio-ontologies used for describing gene product characteristics. GO annotation data containing terms from multiple sub-ontologies and at different levels in the ontologies is an important source of implicit relationships between terms from the three sub-ontologies. Data mining techniques such as association rule mining that are tailored to mine from multiple ontologies at multiple levels of abstraction are required for effective knowledge discovery from GO annotation data. We present a data mining approach, Multi-ontology data mining at All Levels (MOAL) that uses the structure and relationships of the GO to mine multi-ontology multi-level association rules. We introduce two interestingness measures: Multi-ontology Support (MOSupport) and Multi-ontology Confidence (MOConfidence) customized to evaluate multi-ontology multi-level association rules. We also describe a variety of post-processing strategies for pruning uninteresting rules. We use publicly available GO annotation data to demonstrate our methods with respect to two applications (1) the discovery of co-annotation suggestions and (2) the discovery of new cross-ontology relationships. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Ontology-based multi-agent systems

Energy Technology Data Exchange (ETDEWEB)

Hadzic, Maja; Wongthongtham, Pornpit; Dillon, Tharam; Chang, Elizabeth [Digital Ecosystems and Business Intelligence Institute, Perth, WA (Australia)

2009-07-01

The Semantic web has given a great deal of impetus to the development of ontologies and multi-agent systems. Several books have appeared which discuss the development of ontologies or of multi-agent systems separately on their own. The growing interaction between agents and ontologies has highlighted the need for integrated development of these. This book is unique in being the first to provide an integrated treatment of the modeling, design and implementation of such combined ontology/multi-agent systems. It provides clear exposition of this integrated modeling and design methodology. It further illustrates this with two detailed case studies in (a) the biomedical area and (b) the software engineering area. The book is, therefore, of interest to researchers, graduate students and practitioners in the semantic web and web science area. (orig.)

Scientific Digital Libraries, Interoperability, and Ontologies

Science.gov (United States)

Hughes, J. Steven; Crichton, Daniel J.; Mattmann, Chris A.

2009-01-01

Scientific digital libraries serve complex and evolving research communities. Justifications for the development of scientific digital libraries include the desire to preserve science data and the promises of information interconnectedness, correlative science, and system interoperability. Shared ontologies are fundamental to fulfilling these promises. We present a tool framework, some informal principles, and several case studies where shared ontologies are used to guide the implementation of scientific digital libraries. The tool framework, based on an ontology modeling tool, was configured to develop, manage, and keep shared ontologies relevant within changing domains and to promote the interoperability, interconnectedness, and correlation desired by scientists.

Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease

Directory of Open Access Journals (Sweden)

Nicola Mulder

2016-06-01

The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology.

Audit Validation Using Ontologies

Directory of Open Access Journals (Sweden)

Ion IVAN

2015-01-01

Full Text Available Requirements to increase quality audit processes in enterprises are defined. It substantiates the need for assessment and management audit processes using ontologies. Sets of rules, ways to assess the consistency of rules and behavior within the organization are defined. Using ontologies are obtained qualifications that assess the organization's audit. Elaboration of the audit reports is a perfect algorithm-based activity characterized by generality, determinism, reproducibility, accuracy and a well-established. The auditors obtain effective levels. Through ontologies obtain the audit calculated level. Because the audit report is qualitative structure of information and knowledge it is very hard to analyze and interpret by different groups of users (shareholders, managers or stakeholders. Developing ontology for audit reports validation will be a useful instrument for both auditors and report users. In this paper we propose an instrument for validation of audit reports contain a lot of keywords that calculates indicators, a lot of indicators for each key word there is an indicator, qualitative levels; interpreter who builds a table of indicators, levels of actual and calculated levels.

An Ontology for Knowledge Representation and Applications

OpenAIRE

Nhon Do

2008-01-01

Ontology is a terminology which is used in artificial intelligence with different meanings. Ontology researching has an important role in computer science and practical applications, especially distributed knowledge systems. In this paper we present an ontology which is called Computational Object Knowledge Base Ontology. It has been used in designing some knowledge base systems for solving problems such as the system that supports studying knowledge and solving analytic ...

A priorean approach to time ontologies

DEFF Research Database (Denmark)

Øhrstrøm, Peter; Schärfe, Henrik

2004-01-01

Any non-trivial top-level ontology should take temporal notions into account. The details of how this should be done, however, are frequently debated. In this paper it is argued that "the four grades of tense-logical involvement" suggested by A.N. Prior form a useful framework for discussing how...... various temporal notions are related in a top-level ontology. Furthermore, a number of modern ontologies are analysed with respect to their incorporation of temporal notions. It is argued that all of them correspond to Prior's first and second grade, and that none of them reflect the views which Prior......'s third and fourth grade represent. Finally, the paper deals with Prior's ideas on a tensed ontology and it is argued that a logic based on the third grade and will be useful in the further development of tensed ontology....

A methodology for creating ontologies for engineering design

DEFF Research Database (Denmark)

Ahmed, Saeema; Kim, S.; Wallace, K.M.

2007-01-01

This paper describes a six-stage methodology for developing ontologies for engineering design, together with the research methods and evaluation of each stage. The methodology focuses upon understanding a user's domain models through empirical research. A case study of an ontology for searching......, indexing, and retrieving engineering knowledge is described. The root concepts of the ontology were elicited from engineering designers. Relationships between concepts are extracted as the ontology is populated. The contribution of this research is a methodology to allow researchers. and industry to create...... ontologies for their particular purpose and a thesaurus for the terms within the ontology....

BiOSS: A system for biomedical ontology selection.

Science.gov (United States)

Martínez-Romero, Marcos; Vázquez-Naya, José M; Pereira, Javier; Pazos, Alejandro

2014-04-01

In biomedical informatics, ontologies are considered a key technology for annotating, retrieving and sharing the huge volume of publicly available data. Due to the increasing amount, complexity and variety of existing biomedical ontologies, choosing the ones to be used in a semantic annotation problem or to design a specific application is a difficult task. As a consequence, the design of approaches and tools addressed to facilitate the selection of biomedical ontologies is becoming a priority. In this paper we present BiOSS, a novel system for the selection of biomedical ontologies. BiOSS evaluates the adequacy of an ontology to a given domain according to three different criteria: (1) the extent to which the ontology covers the domain; (2) the semantic richness of the ontology in the domain; (3) the popularity of the ontology in the biomedical community. BiOSS has been applied to 5 representative problems of ontology selection. It also has been compared to existing methods and tools. Results are promising and show the usefulness of BiOSS to solve real-world ontology selection problems. BiOSS is openly available both as a web tool and a web service. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

An ontological case base engineering methodology for diabetes management.

Science.gov (United States)

El-Sappagh, Shaker H; El-Masri, Samir; Elmogy, Mohammed; Riad, A M; Saddik, Basema

2014-08-01

Ontology engineering covers issues related to ontology development and use. In Case Based Reasoning (CBR) system, ontology plays two main roles; the first as case base and the second as domain ontology. However, the ontology engineering literature does not provide adequate guidance on how to build, evaluate, and maintain ontologies. This paper proposes an ontology engineering methodology to generate case bases in the medical domain. It mainly focuses on the research of case representation in the form of ontology to support the case semantic retrieval and enhance all knowledge intensive CBR processes. A case study on diabetes diagnosis case base will be provided to evaluate the proposed methodology.

ONSET: Automated foundational ontology selection and explanation

CSIR Research Space (South Africa)

Khan, Z

2012-10-01

Full Text Available It has been shown that using a foundational ontology for domain ontology development is beneficial in theory and practice. However, developers have difficulty with choosing the appropriate foundational ontology, and why. In order to solve...

The mouse-human anatomy ontology mapping project.

Science.gov (United States)

Hayamizu, Terry F; de Coronado, Sherri; Fragoso, Gilberto; Sioutos, Nicholas; Kadin, James A; Ringwald, Martin

2012-01-01

The overall objective of the Mouse-Human Anatomy Project (MHAP) was to facilitate the mapping and harmonization of anatomical terms used for mouse and human models by Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI). The anatomy resources designated for this study were the Adult Mouse Anatomy (MA) ontology and the set of anatomy concepts contained in the NCI Thesaurus (NCIt). Several methods and software tools were identified and evaluated, then used to conduct an in-depth comparative analysis of the anatomy ontologies. Matches between mouse and human anatomy terms were determined and validated, resulting in a highly curated set of mappings between the two ontologies that has been used by other resources. These mappings will enable linking of data from mouse and human. As the anatomy ontologies have been expanded and refined, the mappings have been updated accordingly. Insights are presented into the overall process of comparing and mapping between ontologies, which may prove useful for further comparative analyses and ontology mapping efforts, especially those involving anatomy ontologies. Finally, issues concerning further development of the ontologies, updates to the mapping files, and possible additional applications and significance were considered. DATABASE URL: http://obofoundry.org/cgi-bin/detail.cgi?id=ma2ncit.

CONCEPTION OF ONTOLOGY-BASED SECTOR EDUCATIONAL SPACE

Directory of Open Access Journals (Sweden)

V. I. Khabarov

2014-09-01

Full Text Available PurposeThe aim of the research is to demonstrate the need for the Conception of Ontology-based Sector Educational Space. This Conception could become the basis for the integration of transport sector university information resources into the open virtual network information resource and global educational space. Its content will be presented by standardized ontology-based knowledge packages for educational programs in Russian and English languages.MethodologyComplex-based, ontological, content-based approaches and scientific principles of interdisciplinarity and standardization of knowledge are suggested as the methodological basis of the research. ResultsThe Conception of Ontology-based Sector Educational Space (railway transport, the method of the development of knowledge packages as ontologies in Russian and English languages, the Russian-English Transport Glossary as a separate ontology are among the expected results of the project implementation.Practical implicationsThe Conception could become the basis for the open project to establish the common resource center for transport universities (railway transport. The Conception of ontology-based sector educational space (railway transport could be adapted to the activity of universities of other economic sectors.

History Matters: Incremental Ontology Reasoning Using Modules

Science.gov (United States)

Cuenca Grau, Bernardo; Halaschek-Wiener, Christian; Kazakov, Yevgeny

The development of ontologies involves continuous but relatively small modifications. Existing ontology reasoners, however, do not take advantage of the similarities between different versions of an ontology. In this paper, we propose a technique for incremental reasoning—that is, reasoning that reuses information obtained from previous versions of an ontology—based on the notion of a module. Our technique does not depend on a particular reasoning calculus and thus can be used in combination with any reasoner. We have applied our results to incremental classification of OWL DL ontologies and found significant improvement over regular classification time on a set of real-world ontologies.

An empirical analysis of ontology reuse in BioPortal.

Science.gov (United States)

Ochs, Christopher; Perl, Yehoshua; Geller, James; Arabandi, Sivaram; Tudorache, Tania; Musen, Mark A

2017-07-01

Biomedical ontologies often reuse content (i.e., classes and properties) from other ontologies. Content reuse enables a consistent representation of a domain and reusing content can save an ontology author significant time and effort. Prior studies have investigated the existence of reused terms among the ontologies in the NCBO BioPortal, but as of yet there has not been a study investigating how the ontologies in BioPortal utilize reused content in the modeling of their own content. In this study we investigate how 355 ontologies hosted in the NCBO BioPortal reuse content from other ontologies for the purposes of creating new ontology content. We identified 197 ontologies that reuse content. Among these ontologies, 108 utilize reused classes in the modeling of their own classes and 116 utilize reused properties in class restrictions. Current utilization of reuse and quality issues related to reuse are discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

A Mobile Army of Ontologies

DEFF Research Database (Denmark)

Juul, Jesper

2015-01-01

Presentation at the Ludo-ontologies panel. Do we need ludo-ontologies, and what are they? In this event several scholars of games and videogames discuss these questions from a variety of perspectives. What different game and videogame ontologies exist and could exist, and why they are important...... for game and videogame research? The round table is designed to promote ludo-ontological dialogue in order to make these questions visible and debated. A series of short presentations (approximately 10 minutes each) will be followed by an intense debate through freeform dialogue. After the industrial...... commercialization of games and videogames their study has shifted between approaches focused on players (ludic processes) and artifacts (ludic objects). Some attempts to analyze the relationship between the process and the object have occasionally been done in terms of ‘ontology’ (Zagal 2005; Leino 2010; Gualeni...

Gene Ontology and KEGG Enrichment Analyses of Genes Related to Age-Related Macular Degeneration

Directory of Open Access Journals (Sweden)

Jian Zhang

2014-01-01

Full Text Available Identifying disease genes is one of the most important topics in biomedicine and may facilitate studies on the mechanisms underlying disease. Age-related macular degeneration (AMD is a serious eye disease; it typically affects older adults and results in a loss of vision due to retina damage. In this study, we attempt to develop an effective method for distinguishing AMD-related genes. Gene ontology and KEGG enrichment analyses of known AMD-related genes were performed, and a classification system was established. In detail, each gene was encoded into a vector by extracting enrichment scores of the gene set, including it and its direct neighbors in STRING, and gene ontology terms or KEGG pathways. Then certain feature-selection methods, including minimum redundancy maximum relevance and incremental feature selection, were adopted to extract key features for the classification system. As a result, 720 GO terms and 11 KEGG pathways were deemed the most important factors for predicting AMD-related genes.

Ontology Versioning and Change Detection on the Web

NARCIS (Netherlands)

Klein, Michel; Fensel, Dieter; Kiryakov, Atanas; Ognyanov, Damyan

2002-01-01

To effectively use ontologies on the Web, it is essential that changes in ontologies are managed well. This paper analyzes the topic of ontology versioning in the context of the Web by looking at the characteristics of the version relation between ontologies and at the identification of online

Unintended consequences of existential quantifications in biomedical ontologies

Directory of Open Access Journals (Sweden)

Boeker Martin

2011-11-01

Full Text Available Abstract Background The Open Biomedical Ontologies (OBO Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL, which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors. Results We analyzed ontologies and ontology cross products available via the OBO Foundry site http://www.obofoundry.org for existential restrictions (someValuesFrom, from which we examined a random sample of 2,836 clauses. According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' κ = 0.78. We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (κ = 0.07. We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations. Conclusions The current OWL releases of OBO Foundry (and Foundry candidate ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.

Toward a general ontology for digital forensic disciplines.

Science.gov (United States)

Karie, Nickson M; Venter, Hein S

2014-09-01

Ontologies are widely used in different disciplines as a technique for representing and reasoning about domain knowledge. However, despite the widespread ontology-related research activities and applications in different disciplines, the development of ontologies and ontology research activities is still wanting in digital forensics. This paper therefore presents the case for establishing an ontology for digital forensic disciplines. Such an ontology would enable better categorization of the digital forensic disciplines, as well as assist in the development of methodologies and specifications that can offer direction in different areas of digital forensics. This includes such areas as professional specialization, certifications, development of digital forensic tools, curricula, and educational materials. In addition, the ontology presented in this paper can be used, for example, to better organize the digital forensic domain knowledge and explicitly describe the discipline's semantics in a common way. Finally, this paper is meant to spark discussions and further research on an internationally agreed ontological distinction of the digital forensic disciplines. Digital forensic disciplines ontology is a novel approach toward organizing the digital forensic domain knowledge and constitutes the main contribution of this paper. © 2014 American Academy of Forensic Sciences.

The MMI Device Ontology: Enabling Sensor Integration

Science.gov (United States)

Rueda, C.; Galbraith, N.; Morris, R. A.; Bermudez, L. E.; Graybeal, J.; Arko, R. A.; Mmi Device Ontology Working Group

2010-12-01

The Marine Metadata Interoperability (MMI) project has developed an ontology for devices to describe sensors and sensor networks. This ontology is implemented in the W3C Web Ontology Language (OWL) and provides an extensible conceptual model and controlled vocabularies for describing heterogeneous instrument types, with different data characteristics, and their attributes. It can help users populate metadata records for sensors; associate devices with their platforms, deployments, measurement capabilities and restrictions; aid in discovery of sensor data, both historic and real-time; and improve the interoperability of observational oceanographic data sets. We developed the MMI Device Ontology following a community-based approach. By building on and integrating other models and ontologies from related disciplines, we sought to facilitate semantic interoperability while avoiding duplication. Key concepts and insights from various communities, including the Open Geospatial Consortium (eg., SensorML and Observations and Measurements specifications), Semantic Web for Earth and Environmental Terminology (SWEET), and W3C Semantic Sensor Network Incubator Group, have significantly enriched the development of the ontology. Individuals ranging from instrument designers, science data producers and consumers to ontology specialists and other technologists contributed to the work. Applications of the MMI Device Ontology are underway for several community use cases. These include vessel-mounted multibeam mapping sonars for the Rolling Deck to Repository (R2R) program and description of diverse instruments on deepwater Ocean Reference Stations for the OceanSITES program. These trials involve creation of records completely describing instruments, either by individual instances or by manufacturer and model. Individual terms in the MMI Device Ontology can be referenced with their corresponding Uniform Resource Identifiers (URIs) in sensor-related metadata specifications (e

The Effects of Integrating LEGO Robotics into a Mathematics Curriculum to Promote the Development of Proportional Reasoning

Science.gov (United States)

Casler-Failing, Shelli L.

2017-01-01

This mixed methods, action research case study sought to investigate the effects of incorporating LEGO robotics into a seventh grade mathematics curriculum focused on the development of proportional reasoning through the lens of Social Constructivist Theory. Quantitative data was collected via pre- and post-tests from the mathematics class of six…

Matching biomedical ontologies based on formal concept analysis.

Science.gov (United States)

Zhao, Mengyi; Zhang, Songmao; Li, Weizhuo; Chen, Guowei

2018-03-19

The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign

Ontological realism: A methodology for coordinated evolution of scientific ontologies.

Science.gov (United States)

Smith, Barry; Ceusters, Werner

2010-11-15

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill's critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative.

Vaxvec: The first web-based recombinant vaccine vector database and its data analysis

Science.gov (United States)

Deng, Shunzhou; Martin, Carly; Patil, Rasika; Zhu, Felix; Zhao, Bin; Xiang, Zuoshuang; He, Yongqun

2015-01-01

A recombinant vector vaccine uses an attenuated virus, bacterium, or parasite as the carrier to express a heterologous antigen(s). Many recombinant vaccine vectors and related vaccines have been developed and extensively investigated. To compare and better understand recombinant vectors and vaccines, we have generated Vaxvec (http://www.violinet.org/vaxvec), the first web-based database that stores various recombinant vaccine vectors and those experimentally verified vaccines that use these vectors. Vaxvec has now included 59 vaccine vectors that have been used in 196 recombinant vector vaccines against 66 pathogens and cancers. These vectors are classified to 41 viral vectors, 15 bacterial vectors, 1 parasitic vector, and 1 fungal vector. The most commonly used viral vaccine vectors are double-stranded DNA viruses, including herpesviruses, adenoviruses, and poxviruses. For example, Vaxvec includes 63 poxvirus-based recombinant vaccines for over 20 pathogens and cancers. Vaxvec collects 30 recombinant vector influenza vaccines that use 17 recombinant vectors and were experimentally tested in 7 animal models. In addition, over 60 protective antigens used in recombinant vector vaccines are annotated and analyzed. User-friendly web-interfaces are available for querying various data in Vaxvec. To support data exchange, the information of vaccine vectors, vaccines, and related information is stored in the Vaccine Ontology (VO). Vaxvec is a timely and vital source of vaccine vector database and facilitates efficient vaccine vector research and development. PMID:26403370

The foundational ontology library ROMULUS

CSIR Research Space (South Africa)

Khan, ZC

2013-09-01

Full Text Available . We present here a basic step in that direction with the Repository of Ontologies for MULtiple USes, ROMULUS, which is the first online library of machine-processable, modularised, aligned, and logic-based merged foundational ontologies. In addition...

Tracking Changes during Ontology Evolution

NARCIS (Netherlands)

Noy, Natalya F.; Kunnatur, Sandhya; Klein, Michel; Musen, Mark A.

2004-01-01

As ontology development becomes a collaborative process, developers face the problem of maintaining versions of ontologies akin to maintaining versions of software code or versions of documents in large projects. Traditional versioning systems enable users to compare versions, examine changes, and

Using Lego robots to estimate cognitive ability in children who have severe physical disabilities.

Science.gov (United States)

Cook, Albert M; Adams, Kim; Volden, Joanne; Harbottle, Norma; Harbottle, Cheryl

2011-01-01

To determine whether low-cost robots provide a means by which children with severe disabilities can demonstrate understanding of cognitive concepts. Ten children, ages 4 to 10, diagnosed with cerebral palsy and related motor conditions, participated. Participants had widely variable motor, cognitive and receptive language skills, but all were non-speaking. A Lego Invention 'roverbot' was used to carry out a range of functional tasks from single-switch replay of pre-stored movements to total control of the movement in two dimensions. The level of sophistication achieved on hierarchically arranged play tasks was used to estimate cognitive skills. The 10 children performed at one of the six hierarchically arranged levels from 'no interaction' through 'simple cause and effect' to 'development and execution of a plan'. Teacher interviews revealed that children were interested in the robot, enjoyed interacting with it and demonstrated changes in behaviour and social and language skills following interaction. Children with severe physical disabilities can control a Lego robot to perform un-structured play tasks. In some cases, they were able to display more sophisticated cognitive skills through manipulating the robot than in traditional standardised tests. Success with the robot could be a proxy measure for children who have cognitive abilities but cannot demonstrate them in standard testing.

Ontological engineering versus metaphysics

Science.gov (United States)

Tataj, Emanuel; Tomanek, Roman; Mulawka, Jan

2011-10-01

It has been recognized that ontologies are a semantic version of world wide web and can be found in knowledge-based systems. A recent time survey of this field also suggest that practical artificial intelligence systems may be motivated by this research. Especially strong artificial intelligence as well as concept of homo computer can also benefit from their use. The main objective of this contribution is to present and review already created ontologies and identify the main advantages which derive such approach for knowledge management systems. We would like to present what ontological engineering borrows from metaphysics and what a feedback it can provide to natural language processing, simulations and modelling. The potential topics of further development from philosophical point of view is also underlined.

Nuclear Nonproliferation Ontology Assessment Team Final Report

Energy Technology Data Exchange (ETDEWEB)

Strasburg, Jana D.; Hohimer, Ryan E.

2012-01-01

Final Report for the NA22 Simulations, Algorithm and Modeling (SAM) Ontology Assessment Team's efforts from FY09-FY11. The Ontology Assessment Team began in May 2009 and concluded in September 2011. During this two-year time frame, the Ontology Assessment team had two objectives: (1) Assessing the utility of knowledge representation and semantic technologies for addressing nuclear nonproliferation challenges; and (2) Developing ontological support tools that would provide a framework for integrating across the Simulation, Algorithm and Modeling (SAM) program. The SAM Program was going through a large assessment and strategic planning effort during this time and as a result, the relative importance of these two objectives changed, altering the focus of the Ontology Assessment Team. In the end, the team conducted an assessment of the state of art, created an annotated bibliography, and developed a series of ontological support tools, demonstrations and presentations. A total of more than 35 individuals from 12 different research institutions participated in the Ontology Assessment Team. These included subject matter experts in several nuclear nonproliferation-related domains as well as experts in semantic technologies. Despite the diverse backgrounds and perspectives, the Ontology Assessment team functioned very well together and aspects could serve as a model for future inter-laboratory collaborations and working groups. While the team encountered several challenges and learned many lessons along the way, the Ontology Assessment effort was ultimately a success that led to several multi-lab research projects and opened up a new area of scientific exploration within the Office of Nuclear Nonproliferation and Verification.

Culture’s building blocks: Investigating cultural evolution in a LEGO construction task

DEFF Research Database (Denmark)

McGraw, John J.; Wallot, Sebastian; Mitkidis, Panagiotis

2014-01-01

to culture remains little more than a suggestive trope. Whereas the modern synthesis of evolutionary theory has provided an encompassing scientific framework for the selection and transmission of biological adaptations, a convincing theory of cultural evolution has yet to emerge. One of the greatest...... the ways people develop conventions in a series of LEGO construction tasks. The data revealed a surprising pattern in the selection of building bricks as well as features of car design across consecutive building sessions. Our findings support a novel methodology for studying the development...

A Knowledge Engineering Approach to Develop Domain Ontology

Science.gov (United States)

Yun, Hongyan; Xu, Jianliang; Xiong, Jing; Wei, Moji

2011-01-01

Ontologies are one of the most popular and widespread means of knowledge representation and reuse. A few research groups have proposed a series of methodologies for developing their own standard ontologies. However, because this ontological construction concerns special fields, there is no standard method to build domain ontology. In this paper,…

GFVO: the Genomic Feature and Variation Ontology

KAUST Repository

Baran, Joachim; Durgahee, Bibi Sehnaaz Begum; Eilbeck, Karen; Antezana, Erick; Hoehndorf, Robert; Dumontier, Michel

2015-01-01

Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

Using an ontology pattern stack to engineer a core ontology of Accounting Information Systems

NARCIS (Netherlands)

Blums, Ivar; Weigand, Hans

Although the field of Accounting Information Systems (AIS) has a long tradition, there is still a lack of a widely adopted conceptualization. In this paper, The UFO ontology patterns are regarded for application by analogy and extension in the engineering of a core ontology for AIS. The new IASB

Region-Based Image Retrieval Using an Object Ontology and Relevance Feedback

Directory of Open Access Journals (Sweden)

Kompatsiaris Ioannis

2004-01-01

Full Text Available An image retrieval methodology suited for search in large collections of heterogeneous images is presented. The proposed approach employs a fully unsupervised segmentation algorithm to divide images into regions and endow the indexing and retrieval system with content-based functionalities. Low-level descriptors for the color, position, size, and shape of each region are subsequently extracted. These arithmetic descriptors are automatically associated with appropriate qualitative intermediate-level descriptors, which form a simple vocabulary termed object ontology. The object ontology is used to allow the qualitative definition of the high-level concepts the user queries for (semantic objects, each represented by a keyword and their relations in a human-centered fashion. When querying for a specific semantic object (or objects, the intermediate-level descriptor values associated with both the semantic object and all image regions in the collection are initially compared, resulting in the rejection of most image regions as irrelevant. Following that, a relevance feedback mechanism, based on support vector machines and using the low-level descriptors, is invoked to rank the remaining potentially relevant image regions and produce the final query results. Experimental results and comparisons demonstrate, in practice, the effectiveness of our approach.

XML, Ontologies, and Their Clinical Applications.

Science.gov (United States)

Yu, Chunjiang; Shen, Bairong

2016-01-01

The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing. In particular, XML is very useful in the fields of data standardization, data exchange, and data integration. Moreover, ontologies have been attracting increased attention in various clinical fields in recent years. An ontology is the basic level of a knowledge representation scheme, and various ontology repositories have been developed, such as Gene Ontology and BioPortal. The creation of these standardized repositories greatly facilitates clinical research in related fields. In this chapter, we discuss the basic concepts of XML and ontologies, as well as their clinical applications.

Versioning System for Distributed Ontology Development

Science.gov (United States)

2016-03-15

Framework for Grid Computing and Semantic Web Services,” Trust Management, Springer Berlin Heidelberg (2004), pp. 16−26. [TIME] W3C, “Time Ontology in...Distributed Ontology Development S.K. Damodaran 15 March 2016 This material is based on work supported by the Assistant Secretary of Defense for...Distributed Ontology Development S.K. Damodaran Formerly Group 59 15 March 2016 Massachusetts Institute of Technology Lincoln Laboratory

Investigation of Self-assembly Structure and Properties of a Novel Designed Lego-type Peptide with Double Amphiphilic Surfaces

Energy Technology Data Exchange (ETDEWEB)

Wang, Liang [Sichuan University, Sichuan (China); Zhao, Xiao Jun [Massachusetts Institute of Technology, Cambridge (United States)

2010-12-15

A typically designed 'Peptide Lego' has two distinct surfaces: a hydrophilic side that contains the complete charge distribution and a hydrophobic side. In this article, we describe the fabrication of a unique lego-type peptide with the AEAEYAKAK sequence. The novel peptide with double amphiphilic surfaces is different from typical peptides due to special arrangement of the residues. The results of CD, FT-IR, AFM and DLS demonstrate that the peptide with the random coil characteristic was able to form stable nanostructures that were mediated by non-covalent interactions in an aqueous solution. The data further indicated that despite its different structure, the peptide was able to undergo self-assembly similar to a typical peptide. In addition, the use of hydrophobic pyrene as a model allowed the peptide to provide a new type of potential nanomaterial for drug delivery. These efforts collectively open up a new direction in the fabrication of nanomaterials that are more perfect and versatile.

Investigation of Self-assembly Structure and Properties of a Novel Designed Lego-type Peptide with Double Amphiphilic Surfaces

International Nuclear Information System (INIS)

Wang, Liang; Zhao, Xiao Jun

2010-01-01

A typically designed 'Peptide Lego' has two distinct surfaces: a hydrophilic side that contains the complete charge distribution and a hydrophobic side. In this article, we describe the fabrication of a unique lego-type peptide with the AEAEYAKAK sequence. The novel peptide with double amphiphilic surfaces is different from typical peptides due to special arrangement of the residues. The results of CD, FT-IR, AFM and DLS demonstrate that the peptide with the random coil characteristic was able to form stable nanostructures that were mediated by non-covalent interactions in an aqueous solution. The data further indicated that despite its different structure, the peptide was able to undergo self-assembly similar to a typical peptide. In addition, the use of hydrophobic pyrene as a model allowed the peptide to provide a new type of potential nanomaterial for drug delivery. These efforts collectively open up a new direction in the fabrication of nanomaterials that are more perfect and versatile

Development of an Ontology for Periodontitis.

Science.gov (United States)

Suzuki, Asami; Takai-Igarashi, Takako; Nakaya, Jun; Tanaka, Hiroshi

2015-01-01

In the clinical dentists and periodontal researchers' community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. A computer-readable representation of processes on disease development will give periodontal researchers opportunities to elucidate pathways and mechanisms of periodontitis. An ontology for periodontitis can be a model for integration of large variety of factors relating to a complex disease such as chronic inflammation in different organs accompanied by bone remodeling and immune system disorders, which has recently been referred to as osteoimmunology. Terms characteristic of descriptions related to the onset and progression of periodontitis were manually extracted from 194 review articles and PubMed abstracts by experts in periodontology. We specified all the relations between the extracted terms and constructed them into an ontology for periodontitis. We also investigated matching between classes of our ontology and that of Gene Ontology Biological Process. We developed an ontology for periodontitis called Periodontitis-Ontology (PeriO). The pathological progression of periodontitis is caused by complex, multi-factor interrelationships. PeriO consists of all the required concepts to represent the pathological progression and clinical treatment of periodontitis. The pathological processes were formalized with reference to Basic Formal Ontology and Relation Ontology, which accounts for participants in the processes realized by biological objects such as molecules and cells. We investigated the peculiarity of biological processes observed in pathological progression and medical treatments for the disease in comparison with Gene Ontology Biological Process (GO-BP) annotations. The results indicated that peculiarities of Perio existed in 1) granularity and context dependency of both the conceptualizations, and 2) causality intrinsic to the pathological processes

NanoParticle Ontology for Cancer Nanotechnology Research

Science.gov (United States)

Thomas, Dennis G.; Pappu, Rohit V.; Baker, Nathan A.

2010-01-01

Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. In this paper, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO was developed to represent knowledge underlying the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. Public releases of the NPO are available through BioPortal website, maintained by the National Center for Biomedical Ontology. Mechanisms for editorial and governance processes are being developed for the maintenance, review, and growth of the NPO. PMID:20211274

The Development of Ontology from Multiple Databases

Science.gov (United States)

Kasim, Shahreen; Aswa Omar, Nurul; Fudzee, Mohd Farhan Md; Azhar Ramli, Azizul; Aizi Salamat, Mohamad; Mahdin, Hairulnizam

2017-08-01

The area of halal industry is the fastest growing global business across the world. The halal food industry is thus crucial for Muslims all over the world as it serves to ensure them that the food items they consume daily are syariah compliant. Currently, ontology has been widely used in computer sciences area such as web on the heterogeneous information processing, semantic web, and information retrieval. However, ontology has still not been used widely in the halal industry. Today, Muslim community still have problem to verify halal status for products in the market especially foods consisting of E number. This research tried to solve problem in validating the halal status from various halal sources. There are various chemical ontology from multilple databases found to help this ontology development. The E numbers in this chemical ontology are codes for chemicals that can be used as food additives. With this E numbers ontology, Muslim community could identify and verify the halal status effectively for halal products in the market.

FOCIH: Form-Based Ontology Creation and Information Harvesting

Science.gov (United States)

Tao, Cui; Embley, David W.; Liddle, Stephen W.

Creating an ontology and populating it with data are both labor-intensive tasks requiring a high degree of expertise. Thus, scaling ontology creation and population to the size of the web in an effort to create a web of data—which some see as Web 3.0—is prohibitive. Can we find ways to streamline these tasks and lower the barrier enough to enable Web 3.0? Toward this end we offer a form-based approach to ontology creation that provides a way to create Web 3.0 ontologies without the need for specialized training. And we offer a way to semi-automatically harvest data from the current web of pages for a Web 3.0 ontology. In addition to harvesting information with respect to an ontology, the approach also annotates web pages and links facts in web pages to ontological concepts, resulting in a web of data superimposed over the web of pages. Experience with our prototype system shows that mappings between conceptual-model-based ontologies and forms are sufficient for creating the kind of ontologies needed for Web 3.0, and experiments with our prototype system show that automatic harvesting, automatic annotation, and automatic superimposition of a web of data over a web of pages work well.

Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

Science.gov (United States)

Amith, Muhammad; He, Zhe; Bian, Jiang; Lossio-Ventura, Juan Antonio; Tao, Cui

2018-04-01

With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications. Ontology evaluation is an integral part of ontology development and maintenance. In the biomedicine domain, ontology evaluation is often conducted by third parties as a quality assurance (or auditing) effort that focuses on identifying modeling errors and inconsistencies. In this work, we first organized four categorical schemes of ontology evaluation methods in the existing literature to create an integrated taxonomy. Further, to understand the ontology evaluation practice in the biomedicine domain, we reviewed a sample of 200 ontologies from the National Center for Biomedical Ontology (NCBO) BioPortal-the largest repository for biomedical ontologies-and observed that only 15 of these ontologies have documented evaluation in their corresponding inception papers. We then surveyed the recent quality assurance approaches for biomedical ontologies and their use. We also mapped these quality assurance approaches to the ontology evaluation criteria. It is our anticipation that ontology evaluation and quality assurance approaches will be more widely adopted in the development life cycle of biomedical ontologies. Copyright © 2018 Elsevier Inc. All rights reserved.

Ontology Based Model Transformation Infrastructure

NARCIS (Netherlands)

Göknil, Arda; Topaloglu, N.Y.

2005-01-01

Using MDA in ontology development has been investigated in several works recently. The mappings and transformations between the UML constructs and the OWL elements to develop ontologies are the main concern of these research projects. We propose another approach in order to achieve the collaboration

How the LEGO Group Is Embarking on Architectural Path Constitution to Transform Its Information Infrastructure into a Digital Platform

DEFF Research Database (Denmark)

Törmer, Robert Lorenz

2018-01-01

Traditional companies are increasingly turning towards platform strategies to gain speed in the development of digital value propositions and prepare for the challenges arising from digitalization. This paper reports on the digitalization journey of the LEGO Group to elaborate how brick-and-mortar...

One Song, Many Works: A Pluralist Ontology of Rock

Directory of Open Access Journals (Sweden)

Dan Burkett

2016-01-01

Full Text Available A number of attempts have been made to construct a plausible ontology of rock music. Each of these ontologies identifies a single type of ontological entity as the “work” in rock music. Yet, all the suggestions advanced to date fail to capture some important considerations about how we engage with music of this tradition. This prompted Lee Brown to advocate a healthy skepticism of higher-order musical ontologies. I argue here that we should instead embrace a pluralist ontology of rock, an ontology that recognizes more than one kind of entity as “the work” in rock music. I contend that this approach has a number of advantages over other ontologies of rock, including that of allowing us to make some comparisons across ontological kinds.

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Science.gov (United States)

Whetzel, Patricia L; Noy, Natalya F; Shah, Nigam H; Alexander, Paul R; Nyulas, Csongor; Tudorache, Tania; Musen, Mark A

2011-07-01

The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

Integrating phenotype ontologies with PhenomeNET

KAUST Repository

Rodriguez-Garcia, Miguel Angel

2017-12-19

Background Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies. While not applicable to matching arbitrary ontologies, PhenomeNET can be used to identify related phenotypes in different species, including human, mouse, zebrafish, nematode worm, fruit fly, and yeast. Results Here, we apply the PhenomeNET to identify related classes from two phenotype and two disease ontologies using automated reasoning. We demonstrate that we can identify a large number of mappings, some of which require automated reasoning and cannot easily be identified through lexical approaches alone. Combining automated reasoning with lexical matching further improves results in aligning ontologies. Conclusions PhenomeNET can be used to align and integrate phenotype ontologies. The results can be utilized for biomedical analyses in which phenomena observed in model organisms are used to identify causative genes and mutations underlying human disease.

Learning expressive ontologies

CERN Document Server

Völker, J

2009-01-01

This publication advances the state-of-the-art in ontology learning by presenting a set of novel approaches to the semi-automatic acquisition, refinement and evaluation of logically complex axiomatizations. It has been motivated by the fact that the realization of the semantic web envisioned by Tim Berners-Lee is still hampered by the lack of ontological resources, while at the same time more and more applications of semantic technologies emerge from fast-growing areas such as e-business or life sciences. Such knowledge-intensive applications, requiring large scale reasoning over complex domai

The current landscape of pitfalls in Ontologies

CSIR Research Space (South Africa)

Keet, CM

2013-09-01

Full Text Available 2Ontology Engineering Group, Departamento de Inteligencia Artificial, Universidad Polite´cnica de Madrid, Madrid, Spain keet@ukzn.ac.za, {mcsuarez,mpoveda}@fi.upm.es Keywords: Ontology Development : Ontology Quality : Pitfall Abstract: A growing... in Ontologies C. Maria Keet1, Mari Carmen Sua´rez-Figueroa2 and Marı´a Poveda-Villalo´n2 1School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, and UKZN/CSIR-Meraka Centre for Artificial Intelligence Research, Durban, South Africa...

Toward semantic interoperability with linked foundational ontologies in ROMULUS

CSIR Research Space (South Africa)

Khan, ZC

2013-06-01

Full Text Available A purpose of a foundational ontology is to solve interoperability issues among ontologies. Many foundational ontologies have been developed, reintroducing the ontology interoperability problem. We address this with the new online foundational...

ONTOLOGY-DRIVEN TOOL FOR UTILIZING PROGRAMMING STYLES

Directory of Open Access Journals (Sweden)

Nikolay Sidorov

2017-07-01

Full Text Available Activities of a programmer will be more effective and the software will be more understandable when within the process of software development, programming styles (standards are used, providing clarity of software texts. Purpose: In this research, we present the tool for the realization of new ontology-based methodology automated reasoning techniques for utilizing programming styles. In particular, we focus on representing programming styles in the form of formal ontologies, and study how description logic reasoner can assist programmers in utilizing programming standards. Our research hypothesis is as follows: ontological representation of programming styles can provide additional benefits over existing approaches in utilizing programmer of programming standards. Our research goal is to develop a tool to support the ontology-based utilizing programming styles. Methods: ontological representation of programming styles; object-oriented programming; ontology-driven utilizing of programming styles. Results: the architecture was obtained and the tool was developed in the Java language, which provide tool support of ontology-driven programming styles application method. On the example of naming of the Java programming language standard, features of implementation and application of the tool are provided. Discussion: application of programming styles in coding of program; lack of automated tools for the processes of programming standards application; tool based on new method of ontology-driven application of programming styles; an example of the implementation of tool architecture for naming rules of the Java language standard.

High School Students' Views on the PBL Activities Supported via Flipped Classroom and LEGO Practices

Science.gov (United States)

Cukurbasi, Baris; Kiyici, Mubin

2018-01-01

The purpose of this study was to investigate the high school students' views on instructions based on Flipped Classroom Model (FC) and LEGO applications. The case study, which is one of the qualitative research methods, was used within the scope of the study, the duration of which was 7 weeks. In order to choose the research group of the study,…

GOASVM: a subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition.

Science.gov (United States)

Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

2013-04-21

Prediction of protein subcellular localization is an important yet challenging problem. Recently, several computational methods based on Gene Ontology (GO) have been proposed to tackle this problem and have demonstrated superiority over methods based on other features. Existing GO-based methods, however, do not fully use the GO information. This paper proposes an efficient GO method called GOASVM that exploits the information from the GO term frequencies and distant homologs to represent a protein in the general form of Chou's pseudo-amino acid composition. The method first selects a subset of relevant GO terms to form a GO vector space. Then for each protein, the method uses the accession number (AC) of the protein or the ACs of its homologs to find the number of occurrences of the selected GO terms in the Gene Ontology annotation (GOA) database as a means to construct GO vectors for support vector machines (SVMs) classification. With the advantages of GO term frequencies and a new strategy to incorporate useful homologous information, GOASVM can achieve a prediction accuracy of 72.2% on a new independent test set comprising novel proteins that were added to Swiss-Prot six years later than the creation date of the training set. GOASVM and Supplementary materials are available online at http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer/GOASVM.html. Copyright © 2013 Elsevier Ltd. All rights reserved.

Crowdsourcing the verification of relationships in biomedical ontologies.

Science.gov (United States)

Mortensen, Jonathan M; Musen, Mark A; Noy, Natalya F

2013-01-01

Biomedical ontologies are often large and complex, making ontology development and maintenance a challenge. To address this challenge, scientists use automated techniques to alleviate the difficulty of ontology development. However, for many ontology-engineering tasks, human judgment is still necessary. Microtask crowdsourcing, wherein human workers receive remuneration to complete simple, short tasks, is one method to obtain contributions by humans at a large scale. Previously, we developed and refined an effective method to verify ontology hierarchy using microtask crowdsourcing. In this work, we report on applying this method to find errors in the SNOMED CT CORE subset. By using crowdsourcing via Amazon Mechanical Turk with a Bayesian inference model, we correctly verified 86% of the relations from the CORE subset of SNOMED CT in which Rector and colleagues previously identified errors via manual inspection. Our results demonstrate that an ontology developer could deploy this method in order to audit large-scale ontologies quickly and relatively cheaply.

Ontology Enabled Generation of Embedded Web Services

DEFF Research Database (Denmark)

Hansen, Klaus Marius; Zhang, Weishan; Soares, Goncalo Teofilo Afonso Pinheiro

2008-01-01

and software platforms, and of devices state and context changes. To address these challenges, we developed a Web service compiler, Limbo, in which Web Ontology Language (OWL) ontologies are used to make the Limbo compiler aware of its compilation context, such as targeted hardware and software. At the same...... time, knowledge on device details, platform dependencies, and resource/power consumption is built into the supporting ontologies, which are used to configure Limbo for generating resource efficient web service code. A state machine ontology is used to generate stub code to facilitate handling of state...

Product line based ontology development for semantic web service

DEFF Research Database (Denmark)

Zhang, Weishan; Kunz, Thomas

2006-01-01

Ontology is recognized as a key technology for the success of the Semantic Web. Building reusable and evolve-able ontologies in order to cope with ontology evolution and requirement changes is increasingly important. But the existing methodologies and tools fail to support effective ontology reuse...... will lead to the initial implementation of the meta-onotologies using design by reuse and with the objective of design for reuse. After that step new ontologies could be generated by reusing these meta-ontologies. We demonstrate our approach with a Semantic Web Service application to show how to build...

Facilities Management and Value Adding - The LEGO case

DEFF Research Database (Denmark)

Jensen, Per Anker; Katchamart, Akarapong

on the management model for FM included in the European FM standards, recent theories on added value of FM and real estate and the related concept of Value Management from building projects. The paper outlines a preliminary theoretical based management concept, which is investigated, tested and discussed based...... on a case study of LEGO. Results: The study shows that the management model for FM creates a relevant starting point but also that stakeholder and relationship management is an essential aspect of Value Adding Management. The case study confirms the relevance of the basic concept and provides an important...... example of how Value Adding Management can be implemented and added value measured. Practical Implications: The concept of Value Adding Management is expected to increase the awareness of the impacts and strategic importance of FM for organisations and can be a practical tool for facilities managers...

Learning Ontology from Object-Relational Database

Directory of Open Access Journals (Sweden)

Kaulins Andrejs

2015-12-01

Full Text Available This article describes a method of transformation of object-relational model into ontology. The offered method uses learning rules for such complex data types as object tables and collections – arrays of a variable size, as well as nested tables. Object types and their transformation into ontologies are insufficiently considered in scientific literature. This fact served as motivation for the authors to investigate this issue and to write the article on this matter. In the beginning, we acquaint the reader with complex data types and object-oriented databases. Then we describe an algorithm of transformation of complex data types into ontologies. At the end of the article, some examples of ontologies described in the OWL language are given.

Comparing Relational and Ontological Triple Stores in Healthcare Domain

Directory of Open Access Journals (Sweden)

Ozgu Can

2017-01-01

Full Text Available Today’s technological improvements have made ubiquitous healthcare systems that converge into smart healthcare applications in order to solve patients’ problems, to communicate effectively with patients, and to improve healthcare service quality. The first step of building a smart healthcare information system is representing the healthcare data as connected, reachable, and sharable. In order to achieve this representation, ontologies are used to describe the healthcare data. Combining ontological healthcare data with the used and obtained data can be maintained by storing the entire health domain data inside big data stores that support both relational and graph-based ontological data. There are several big data stores and different types of big data sets in the healthcare domain. The goal of this paper is to determine the most applicable ontology data store for storing the big healthcare data. For this purpose, AllegroGraph and Oracle 12c data stores are compared based on their infrastructural capacity, loading time, and query response times. Hence, healthcare ontologies (GENE Ontology, Gene Expression Ontology (GEXO, Regulation of Transcription Ontology (RETO, Regulation of Gene Expression Ontology (REXO are used to measure the ontology loading time. Thereafter, various queries are constructed and executed for GENE ontology in order to measure the capacity and query response times for the performance comparison between AllegroGraph and Oracle 12c triple stores.

Ontologies, Knowledge Bases and Knowledge Management

National Research Council Canada - National Science Library

Chalupsky, Hans

2002-01-01

...) an application called Strategy Development Assistant (SDA) that uses that ontology. The JFACC ontology served as a basis for knowledge sharing among several applications in the domain of air campaign planning...

A histological ontology of the human cardiovascular system.

Science.gov (United States)

Mazo, Claudia; Salazar, Liliana; Corcho, Oscar; Trujillo, Maria; Alegre, Enrique

2017-10-02

In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists. The histological ontology is developed following an existing methodology using Conceptual Models (CMs) and validated using OOPS!, expert evaluation with CMs, and how accurately the ontology can answer the Competency Questions (CQ). It is publicly available at http://bioportal.bioontology.org/ontologies/HO and https://w3id.org/def/System . The histological ontology is developed to support complex tasks, such as supporting teaching activities, medical practices, and bio-medical research or having natural language interactions.

An Iterative and Incremental Approach for E-Learning Ontology Engineering

Directory of Open Access Journals (Sweden)

Sudath Rohitha Heiyanthuduwage

2009-03-01

Full Text Available Abstract - There is a boost in the interest on ontology with the developments in Semantic Web technologies. Ontologies play a vital role in semantic web. Even though there is lot of work done on ontology, still a standard framework for ontology engineering has not been defined. Even though current ontology engineering methodologies are available they need improvements. The effort of our work is to integrate various methods, techniques, tools and etc to different stages of proposed ontology engineering life cycle to create a comprehensive framework for ontology engineering. Current methodologies discuss ontology engineering stages and collaborative environments with user collaboration. However, discussion on increasing effectiveness and correct inference has been given less attention. More over, these methodologies provide little discussion on usability of domain ontologies. We consider these aspects as more important in our work. Also, ontology engineering has been done for various domains and for various purposes. Our effort is to propose an iterative and incremental approach for ontology engineering especially for e-learning domain with the intention of achieving a higher usability and effectiveness of e-learning systems. This paper introduces different aspects of the proposed ontology engineering framework and evaluation of it.

The Effect on Pupils' Science Performance and Problem-Solving Ability through Lego: An Engineering Design-Based Modeling Approach

Science.gov (United States)

Li, Yanyan; Huang, Zhinan; Jiang, Menglu; Chang, Ting-Wen

2016-01-01

Incorporating scientific fundamentals via engineering through a design-based methodology has proven to be highly effective for STEM education. Engineering design can be instantiated for learning as they involve mental and physical stimulation and develop practical skills especially in solving problems. Lego bricks, as a set of toys based on design…

Biomedicine: an ontological dissection.

Science.gov (United States)

Baronov, David

2008-01-01

Though ubiquitous across the medical social sciences literature, the term "biomedicine" as an analytical concept remains remarkably slippery. It is argued here that this imprecision is due in part to the fact that biomedicine is comprised of three interrelated ontological spheres, each of which frames biomedicine as a distinct subject of investigation. This suggests that, depending upon one's ontological commitment, the meaning of biomedicine will shift. From an empirical perspective, biomedicine takes on the appearance of a scientific enterprise and is defined as a derivative category of Western science more generally. From an interpretive perspective, biomedicine represents a symbolic-cultural expression whose adherence to the principles of scientific objectivity conceals an ideological agenda. From a conceptual perspective, biomedicine represents an expression of social power that reflects structures of power and privilege within capitalist society. No one perspective exists in isolation and so the image of biomedicine from any one presents an incomplete understanding. It is the mutually-conditioning interrelations between these ontological spheres that account for biomedicine's ongoing development. Thus, the ontological dissection of biomedicine that follows, with particular emphasis on the period of its formal crystallization in the latter nineteenth and early twentieth century, is intended to deepen our understanding of biomedicine as an analytical concept across the medical social sciences literature.

Using Python to Program LEGO MINDSTORMS® Robots: The PyNXC Project

Directory of Open Access Journals (Sweden)

2010-04-01

Full Text Available

 

Construction of ontology augmented networks for protein complex prediction.

Science.gov (United States)

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

2013-01-01

Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

ONTOLOGY IN PHARMACY

Directory of Open Access Journals (Sweden)

L. Yu. Babintseva

2015-05-01

Full Text Available It’s considered ontological models for formalization of knowledge in pharmacy. There is emphasized the view that the possibility of rapid exchange of information in the pharmaceutical industry, it is necessary to create a single information space. This means not only the establishment of uniform standards for the presentation of information on pharmaceutical groups pharmacotherapeutic classifications, but also the creation of a unified and standardized system for the transfer and renewal of knowledge. It is the organization of information in the ontology helps quickly in the future to build expert systems and applications to work with data.

Semi-automated ontology generation and evolution

Science.gov (United States)

Stirtzinger, Anthony P.; Anken, Craig S.

2009-05-01

Extending the notion of data models or object models, ontology can provide rich semantic definition not only to the meta-data but also to the instance data of domain knowledge, making these semantic definitions available in machine readable form. However, the generation of an effective ontology is a difficult task involving considerable labor and skill. This paper discusses an Ontology Generation and Evolution Processor (OGEP) aimed at automating this process, only requesting user input when un-resolvable ambiguous situations occur. OGEP directly attacks the main barrier which prevents automated (or self learning) ontology generation: the ability to understand the meaning of artifacts and the relationships the artifacts have to the domain space. OGEP leverages existing lexical to ontological mappings in the form of WordNet, and Suggested Upper Merged Ontology (SUMO) integrated with a semantic pattern-based structure referred to as the Semantic Grounding Mechanism (SGM) and implemented as a Corpus Reasoner. The OGEP processing is initiated by a Corpus Parser performing a lexical analysis of the corpus, reading in a document (or corpus) and preparing it for processing by annotating words and phrases. After the Corpus Parser is done, the Corpus Reasoner uses the parts of speech output to determine the semantic meaning of a word or phrase. The Corpus Reasoner is the crux of the OGEP system, analyzing, extrapolating, and evolving data from free text into cohesive semantic relationships. The Semantic Grounding Mechanism provides a basis for identifying and mapping semantic relationships. By blending together the WordNet lexicon and SUMO ontological layout, the SGM is given breadth and depth in its ability to extrapolate semantic relationships between domain entities. The combination of all these components results in an innovative approach to user assisted semantic-based ontology generation. This paper will describe the OGEP technology in the context of the architectural

Finding the best visualization of an ontology

DEFF Research Database (Denmark)

Fabritius, Christina; Madsen, Nadia; Clausen, Jens

2006-01-01

An ontology is a classification model for a given domain.In information retrieval ontologies are used to perform broad searches.An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology....... One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version...

Finding the best visualization of an ontology

DEFF Research Database (Denmark)

Fabritius, Christina Valentin; Madsen, Nadia Lyngaa; Clausen, Jens

2004-01-01

An ontology is a classification model for a given domain. In information retrieval ontologies are used to perform broad searches. An ontology can be visualized as nodes and edges. Each node represents an element and each edge a relation between a parent and a child element. Working with an ontology....... One method uses a discrete location model to create an initial solution and we propose heuristic methods to further improve the visual result. We evaluate the visual results according to our success criteria and the feedback from users. Running times of the heuristic indicate that an improved version...

Manufacturing ontology through templates

Directory of Open Access Journals (Sweden)

Diciuc Vlad

2017-01-01

Full Text Available The manufacturing industry contains a high volume of knowhow and of high value, much of it being held by key persons in the company. The passing of this know-how is the basis of manufacturing ontology. Among other methods like advanced filtering and algorithm based decision making, one way of handling the manufacturing ontology is via templates. The current paper tackles this approach and highlights the advantages concluding with some recommendations.

Technique for designing a domain ontology

OpenAIRE

Palagin, A. V.; Petrenko, N. G.; Malakhov, K. S.

2018-01-01

The article describes the technique for designing a domain ontology, shows the flowchart of algorithm design and example of constructing a fragment of the ontology of the subject area of Computer Science is considered.

Ontology modeling in physical asset integrity management

CERN Document Server

Yacout, Soumaya

2015-01-01

This book presents cutting-edge applications of, and up-to-date research on, ontology engineering techniques in the physical asset integrity domain. Though a survey of state-of-the-art theory and methods on ontology engineering, the authors emphasize essential topics including data integration modeling, knowledge representation, and semantic interpretation. The book also reflects novel topics dealing with the advanced problems of physical asset integrity applications such as heterogeneity, data inconsistency, and interoperability existing in design and utilization. With a distinctive focus on applications relevant in heavy industry, Ontology Modeling in Physical Asset Integrity Management is ideal for practicing industrial and mechanical engineers working in the field, as well as researchers and graduate concerned with ontology engineering in physical systems life cycles. This book also: Introduces practicing engineers, research scientists, and graduate students to ontology engineering as a modeling techniqu...

3D printed Lego®-like modular microfluidic devices based on capillary driving.

Science.gov (United States)

Nie, Jing; Gao, Qing; Qiu, Jing-Jiang; Sun, Miao; Liu, An; Shao, Lei; Fu, Jian-Zhong; Zhao, Peng; He, Yong

2018-03-12

The field of how to rapidly assemble microfluidics with modular components continuously attracts researchers' attention, however, extra efforts must be devoted to solving the problems of leaking and aligning between individual modules. This paper presents a novel type of modular microfluidic device, driven by capillary force. There is no necessity for a strict seal or special alignment, and its open structures make it easy to integrate various stents and reactants. The key rationale for this method is to print different functional modules with a low-cost three-dimensional (3D) printer, then fill the channels with capillary materials and assemble them with plugs like Lego ® bricks. This rapidly reconstructed modular microfluidic device consists of a variety of common functional modules and other personalized modules, each module having a unified standard interface for easy assembly. As it can be printed by a desktop 3D printer, the manufacturing process is simple and efficient, with controllable regulation of the flow channel scale. Through diverse combinations of different modules, a variety of different functions can be achieved, without duplicating the manufacturing process. A single module can also be taken out for testing and analysis. What's more, combined with basic circuit components, it can serve as a low-cost Lego ® -like modular microfluidic circuits. As a proof of concept, the modular microfluidic device has been successfully demonstrated and used for stent degradation and cell cultures, revealing the potential use of this method in both chemical and biological research.

Mechatronics Education: From Paper Design to Product Prototype Using LEGO NXT Parts

Science.gov (United States)

Lofaro, Daniel M.; Le, Tony Truong Giang; Oh, Paul

The industrial design cycle starts with design then simulation, prototyping, and testing. When the tests do not match the design requirements the design process is started over again. It is important for students to experience this process before they leave their academic institution. The high cost of the prototype phase, due to CNC/Rapid Prototype machine costs, makes hands on study of this process expensive for students and the academic institutions. This document shows that the commercially available LEGO NXT Robot kit is a viable low cost surrogate to the expensive industrial CNC/Rapid Prototype portion of the industrial design cycle.

Methodology to build medical ontology from textual resources.

Science.gov (United States)

Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

2006-01-01

In the medical field, it is now established that the maintenance of unambiguous thesauri goes through ontologies. Our research task is to help pneumologists code acts and diagnoses with a software that represents medical knowledge through a domain ontology. In this paper, we describe our general methodology aimed at knowledge engineers in order to build various types of medical ontologies based on terminology extraction from texts. The hypothesis is to apply natural language processing tools to textual patient discharge summaries to develop the resources needed to build an ontology in pneumology. Results indicate that the joint use of distributional analysis and lexico-syntactic patterns performed satisfactorily for building such ontologies.

Building a Lego wall: Sequential action selection.

Science.gov (United States)

Arnold, Amy; Wing, Alan M; Rotshtein, Pia

2017-05-01

The present study draws together two distinct lines of enquiry into the selection and control of sequential action: motor sequence production and action selection in everyday tasks. Participants were asked to build 2 different Lego walls. The walls were designed to have hierarchical structures with shared and dissociated colors and spatial components. Participants built 1 wall at a time, under low and high load cognitive states. Selection times for correctly completed trials were measured using 3-dimensional motion tracking. The paradigm enabled precise measurement of the timing of actions, while using real objects to create an end product. The experiment demonstrated that action selection was slowed at decision boundary points, relative to boundaries where no between-wall decision was required. Decision points also affected selection time prior to the actual selection window. Dual-task conditions increased selection errors. Errors mostly occurred at boundaries between chunks and especially when these required decisions. The data support hierarchical control of sequenced behavior. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Markov Chain Ontology Analysis (MCOA).

Science.gov (United States)

Frost, H Robert; McCray, Alexa T

2012-02-03

Biomedical ontologies have become an increasingly critical lens through which researchers analyze the genomic, clinical and bibliographic data that fuels scientific research. Of particular relevance are methods, such as enrichment analysis, that quantify the importance of ontology classes relative to a collection of domain data. Current analytical techniques, however, remain limited in their ability to handle many important types of structural complexity encountered in real biological systems including class overlaps, continuously valued data, inter-instance relationships, non-hierarchical relationships between classes, semantic distance and sparse data. In this paper, we describe a methodology called Markov Chain Ontology Analysis (MCOA) and illustrate its use through a MCOA-based enrichment analysis application based on a generative model of gene activation. MCOA models the classes in an ontology, the instances from an associated dataset and all directional inter-class, class-to-instance and inter-instance relationships as a single finite ergodic Markov chain. The adjusted transition probability matrix for this Markov chain enables the calculation of eigenvector values that quantify the importance of each ontology class relative to other classes and the associated data set members. On both controlled Gene Ontology (GO) data sets created with Escherichia coli, Drosophila melanogaster and Homo sapiens annotations and real gene expression data extracted from the Gene Expression Omnibus (GEO), the MCOA enrichment analysis approach provides the best performance of comparable state-of-the-art methods. A methodology based on Markov chain models and network analytic metrics can help detect the relevant signal within large, highly interdependent and noisy data sets and, for applications such as enrichment analysis, has been shown to generate superior performance on both real and simulated data relative to existing state-of-the-art approaches.

Addressing issues in foundational ontology mediation

CSIR Research Space (South Africa)

Khan, ZC

2013-09-01

Full Text Available An approach in achieving semantic interoperability among heterogeneous systems is to offer infrastructure to assist with linking and integration using a foundational ontology. Due to the creation of multiple foundational ontologies, this also means...

Player-Specific Conflict Handling Ontology

Directory of Open Access Journals (Sweden)

Charline Hondrou

2014-09-01

Full Text Available This paper presents an ontology that leads the player of a serious game - regarding conflict handling - to the educative experience from which they will benefit the most. It provides a clearly defined tree of axioms that maps the player’s visually manifested affective cues and emotional stimuli from the serious game to conflict handling styles and proposes interventions. The importance of this ontology lies in the fact that it promotes natural interaction (non-invasive methods and at the same time makes the game as player-specific as it can be for its educational goal. It is an ontology that can be adapted to different educational theories and serve various educational purposes.

Ontology Matching with Semantic Verification.

Science.gov (United States)

Jean-Mary, Yves R; Shironoshita, E Patrick; Kabuka, Mansur R

2009-09-01

ASMOV (Automated Semantic Matching of Ontologies with Verification) is a novel algorithm that uses lexical and structural characteristics of two ontologies to iteratively calculate a similarity measure between them, derives an alignment, and then verifies it to ensure that it does not contain semantic inconsistencies. In this paper, we describe the ASMOV algorithm, and then present experimental results that measure its accuracy using the OAEI 2008 tests, and that evaluate its use with two different thesauri: WordNet, and the Unified Medical Language System (UMLS). These results show the increased accuracy obtained by combining lexical, structural and extensional matchers with semantic verification, and demonstrate the advantage of using a domain-specific thesaurus for the alignment of specialized ontologies.

The Electronic Notebook Ontology

OpenAIRE

Chalk, Stuart

2016-01-01

Science is rapidly being brought into the electronic realm and electronic laboratory notebooks (ELN) are a big part of this activity. The representation of the scientific process in the context of an ELN is an important component to making the data recorded in ELNs semantically integrated. This presentation will outline initial developments of an Electronic Notebook Ontology (ENO) that will help tie together the ExptML ontology, HCLS Community Profile data descriptions, and the VIVO-ISF ontol...

DeMO: An Ontology for Discrete-event Modeling and Simulation

Science.gov (United States)

Silver, Gregory A; Miller, John A; Hybinette, Maria; Baramidze, Gregory; York, William S

2011-01-01

Several fields have created ontologies for their subdomains. For example, the biological sciences have developed extensive ontologies such as the Gene Ontology, which is considered a great success. Ontologies could provide similar advantages to the Modeling and Simulation community. They provide a way to establish common vocabularies and capture knowledge about a particular domain with community-wide agreement. Ontologies can support significantly improved (semantic) search and browsing, integration of heterogeneous information sources, and improved knowledge discovery capabilities. This paper discusses the design and development of an ontology for Modeling and Simulation called the Discrete-event Modeling Ontology (DeMO), and it presents prototype applications that demonstrate various uses and benefits that such an ontology may provide to the Modeling and Simulation community. PMID:22919114

ContoExam: an ontology on context-aware examinations

NARCIS (Netherlands)

Brandt, P.; Basten, A.A.; Stuijk, S.

2014-01-01

Patient observations in health care, subjective surveys in social research or dyke sensor data in water management are all examples of measurements. Several ontologies already exist to express measurements, W3C's SSN ontology being a prominent example. However, these ontologies address quantities

On the ontological emergence from quantum regime

Energy Technology Data Exchange (ETDEWEB)

Luty, Damian [Adam Mickiewicz University, Poznan (Poland)

2014-07-01

There are several views on the relation between quantum physics and theory of relativity (especially General Relativity, GR). A popular perspective is this: GR with its macroscopic gravitational effects will turn out to be a limit of a more fundamental theory which should consider discrete physics and not deal with continuity (like theory of relativity). Thus, GR will emerge from a more basic theory, which should be quantum-like. One could call this an epistemic emergence view towards fundamental theories. The question is, given that scientific realism is valid: should emergence be a fundamental notion in our ontological view about the evolving, physical Universe? Is there an ontological emergence fully compatible with the notion of fundamentality? I argue that if we want to defend ontological emergence (from quantum to macroscopic regime) as something fundamental, we will arrive at the position of metaphysics of dispositions (and I argue, why this is undesirable), or conclude, that we cannot square fully fundamental ontology with the notion of emergence, and that we have to accept an ontological pluralism relativised to a certain scale. I defend the latter proposition, showing, that epistemic emergence doesn't entail (logically) ontological emergence.

Applications of the ACGT Master Ontology on Cancer

OpenAIRE

Brochhausen, Mathias; Weiler, Gabriele; Martín Martín, Luis; Cocos, Cristian; Stenzhorn, Holger; Graf, Norbert; Dörr, Martin; Tsiknakis, Manolis; Smith, Barry

2008-01-01

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the...

Semantics and metaphysics in informatics: toward an ontology of tasks.

Science.gov (United States)

Figdor, Carrie

2011-04-01

This article clarifies three principles that should guide the development of any cognitive ontology. First, that an adequate cognitive ontology depends essentially on an adequate task ontology; second, that the goal of developing a cognitive ontology is independent of the goal of finding neural implementations of the processes referred to in the ontology; and third, that cognitive ontologies are neutral regarding the metaphysical relationship between cognitive and neural processes. Copyright © 2011 Cognitive Science Society, Inc.

Improving the interoperability of biomedical ontologies with compound alignments.

Science.gov (United States)

Oliveira, Daniela; Pesquita, Catia

2018-01-09

Ontologies are commonly used to annotate and help process life sciences data. Although their original goal is to facilitate integration and interoperability among heterogeneous data sources, when these sources are annotated with distinct ontologies, bridging this gap can be challenging. In the last decade, ontology matching systems have been evolving and are now capable of producing high-quality mappings for life sciences ontologies, usually limited to the equivalence between two ontologies. However, life sciences research is becoming increasingly transdisciplinary and integrative, fostering the need to develop matching strategies that are able to handle multiple ontologies and more complex relations between their concepts. We have developed ontology matching algorithms that are able to find compound mappings between multiple biomedical ontologies, in the form of ternary mappings, finding for instance that "aortic valve stenosis"(HP:0001650) is equivalent to the intersection between "aortic valve"(FMA:7236) and "constricted" (PATO:0001847). The algorithms take advantage of search space filtering based on partial mappings between ontology pairs, to be able to handle the increased computational demands. The evaluation of the algorithms has shown that they are able to produce meaningful results, with precision in the range of 60-92% for new mappings. The algorithms were also applied to the potential extension of logical definitions of the OBO and the matching of several plant-related ontologies. This work is a first step towards finding more complex relations between multiple ontologies. The evaluation shows that the results produced are significant and that the algorithms could satisfy specific integration needs.

Ontology through a Mindfulness Process

Science.gov (United States)

Bearance, Deborah; Holmes, Kimberley

2015-01-01

Traditionally, when ontology is taught in a graduate studies course on social research, there is a tendency for this concept to be examined through the process of lectures and readings. Such an approach often leaves graduate students to grapple with a personal embodiment of this concept and to comprehend how ontology can ground their research.…

Development and Evaluation of an Ontology for Guiding Appropriate Antibiotic Prescribing

Science.gov (United States)

Furuya, E. Yoko; Kuperman, Gilad J.; Cimino, James J.; Bakken, Suzanne

2011-01-01

Objectives To develop and apply formal ontology creation methods to the domain of antimicrobial prescribing and to formally evaluate the resulting ontology through intrinsic and extrinsic evaluation studies. Methods We extended existing ontology development methods to create the ontology and implemented the ontology using Protégé-OWL. Correctness of the ontology was assessed using a set of ontology design principles and domain expert review via the laddering technique. We created three artifacts to support the extrinsic evaluation (set of prescribing rules, alerts and an ontology-driven alert module, and a patient database) and evaluated the usefulness of the ontology for performing knowledge management tasks to maintain the ontology and for generating alerts to guide antibiotic prescribing. Results The ontology includes 199 classes, 10 properties, and 1,636 description logic restrictions. Twenty-three Semantic Web Rule Language rules were written to generate three prescribing alerts: 1) antibiotic-microorganism mismatch alert; 2) medication-allergy alert; and 3) non-recommended empiric antibiotic therapy alert. The evaluation studies confirmed the correctness of the ontology, usefulness of the ontology for representing and maintaining antimicrobial treatment knowledge rules, and usefulness of the ontology for generating alerts to provide feedback to clinicians during antibiotic prescribing. Conclusions This study contributes to the understanding of ontology development and evaluation methods and addresses one knowledge gap related to using ontologies as a clinical decision support system component—a need for formal ontology evaluation methods to measure their quality from the perspective of their intrinsic characteristics and their usefulness for specific tasks. PMID:22019377

An Ontology for Description of Drug Discovery Investigations

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Qi Da

2010-12-01

Full Text Available The paper presents an ontology for the description of Drug Discovery Investigation (DDI. This has been developed through the use of a Robot Scientist “Eve”, and in consultation with industry. DDI aims to define the principle entities and the relations in the research and development phase of the drug discovery pipeline. DDI is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. This enables DDI to be integrated with such related ontologies as the Vaccine Ontology, the Advancing Clinico-Genomic Trials on Cancer Master Ontology, etc. DDI is available at http://purl.org/ddi/wikipedia or http://purl.org/ddi/home

Menthor Editor: An Ontology-Driven Conceptual Modeling Platform

NARCIS (Netherlands)

Moreira, João Luiz; Sales, Tiago Prince; Guerson, John; Braga, Bernardo F.B; Brasileiro, Freddy; Sobral, Vinicius

2016-01-01

The lack of well-founded constructs in ontology tools can lead to the construction of non-intended models. In this demonstration we present the Menthor Editor, an ontology-driven conceptual modelling platform which incorporates the theories of the Unified Foundational Ontology (UFO). We illustrate

Ontology-based intelligent fuzzy agent for diabetes application

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Acampora, G.; Lee, C.-S.; Wang, M.-H.; Hsu, C.-Y.; Loia, V.

2009-01-01

It is widely pointed out that classical ontologies are not sufficient to deal with imprecise and vague knowledge for some real world applications, but the fuzzy ontology can effectively solve data and knowledge with uncertainty. In this paper, an ontology-based intelligent fuzzy agent (OIFA),

War of ontology worlds: mathematics, computer code, or Esperanto?

Science.gov (United States)

Rzhetsky, Andrey; Evans, James A

2011-09-01

The use of structured knowledge representations-ontologies and terminologies-has become standard in biomedicine. Definitions of ontologies vary widely, as do the values and philosophies that underlie them. In seeking to make these views explicit, we conducted and summarized interviews with a dozen leading ontologists. Their views clustered into three broad perspectives that we summarize as mathematics, computer code, and Esperanto. Ontology as mathematics puts the ultimate premium on rigor and logic, symmetry and consistency of representation across scientific subfields, and the inclusion of only established, non-contradictory knowledge. Ontology as computer code focuses on utility and cultivates diversity, fitting ontologies to their purpose. Like computer languages C++, Prolog, and HTML, the code perspective holds that diverse applications warrant custom designed ontologies. Ontology as Esperanto focuses on facilitating cross-disciplinary communication, knowledge cross-referencing, and computation across datasets from diverse communities. We show how these views align with classical divides in science and suggest how a synthesis of their concerns could strengthen the next generation of biomedical ontologies.

St. Thomas and the hilemorfic ontology

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Lawrence Dewan, O.P.

2009-06-01

Full Text Available This article presents the relevancy of Aristotle’s hylemorphic ontology.Aristotle himself highlighted the importance and astonishing complexityof the problem of prime matter’s ontological status and he presenting thesolution in his doctrine of hylemorphism. As Saint Thomas Aquinasnoted, it is a crucial issue for philosophy because all four, hilemorfism,logic, physics and metaphysics, stand or fall depending on a correctunderstanding of the ontology of prime matter and of the kind of causalrelationship which exist between prime matter and substantial form ingenerable and corruptible substance.

Hierarchical Analysis of the Omega Ontology

Energy Technology Data Exchange (ETDEWEB)

Joslyn, Cliff A.; Paulson, Patrick R.

2009-12-01

Initial delivery for mathematical analysis of the Omega Ontology. We provide an analysis of the hierarchical structure of a version of the Omega Ontology currently in use within the US Government. After providing an initial statistical analysis of the distribution of all link types in the ontology, we then provide a detailed order theoretical analysis of each of the four main hierarchical links present. This order theoretical analysis includes the distribution of components and their properties, their parent/child and multiple inheritance structure, and the distribution of their vertical ranks.

The Effect of LEGO Training on Pupils' School Performance in Mathematics, Problem Solving Ability and Attitude: Swedish Data

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Hussain, Shakir; Lindh, Jorgen; Shukur, Ghazi

2006-01-01

The purpose of this study is to investigate the effect of one year of regular "LEGO" training on pupils' performances in schools. The underlying pedagogical perspective is the constructivist theory, where the main idea is that knowledge is constructed in the mind of the pupil by active learning. The investigation has been made in two…

DMTO: a realistic ontology for standard diabetes mellitus treatment.

Science.gov (United States)

El-Sappagh, Shaker; Kwak, Daehan; Ali, Farman; Kwak, Kyung-Sup

2018-02-06

Treatment of type 2 diabetes mellitus (T2DM) is a complex problem. A clinical decision support system (CDSS) based on massive and distributed electronic health record data can facilitate the automation of this process and enhance its accuracy. The most important component of any CDSS is its knowledge base. This knowledge base can be formulated using ontologies. The formal description logic of ontology supports the inference of hidden knowledge. Building a complete, coherent, consistent, interoperable, and sharable ontology is a challenge. This paper introduces the first version of the newly constructed Diabetes Mellitus Treatment Ontology (DMTO) as a basis for shared-semantics, domain-specific, standard, machine-readable, and interoperable knowledge relevant to T2DM treatment. It is a comprehensive ontology and provides the highest coverage and the most complete picture of coded knowledge about T2DM patients' current conditions, previous profiles, and T2DM-related aspects, including complications, symptoms, lab tests, interactions, treatment plan (TP) frameworks, and glucose-related diseases and medications. It adheres to the design principles recommended by the Open Biomedical Ontologies Foundry and is based on ontological realism that follows the principles of the Basic Formal Ontology and the Ontology for General Medical Science. DMTO is implemented under Protégé 5.0 in Web Ontology Language (OWL) 2 format and is publicly available through the National Center for Biomedical Ontology's BioPortal at http://bioportal.bioontology.org/ontologies/DMTO . The current version of DMTO includes more than 10,700 classes, 277 relations, 39,425 annotations, 214 semantic rules, and 62,974 axioms. We provide proof of concept for this approach to modeling TPs. The ontology is able to collect and analyze most features of T2DM as well as customize chronic TPs with the most appropriate drugs, foods, and physical exercises. DMTO is ready to be used as a knowledge base for

Fictions industrielles et apprentissage du temps : les jeux LEGO Bionicles

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Irène Langlet

2011-06-01

Full Text Available Il y a un paradoxe LEGO : venue tard aux nouveaux jouets médiatiques et numériques, la firme danoise a pourtant lancé l’un des phénomènes les plus exemplaires des années 2000 : la gamme Bionicle, qui mêle figurines, jeux de construction, fictions populaires multi-supports (imprimé, télévision, jeux vidéo, CD-Rom, cinéma, communautés de joueurs sur internet, univers partagé, et tous les produits non ludiques dérivés. Une description fine de la gamme Bionicle fait apparaître d’emblée, non seulement son adéquation étroite aux problématiques de porosité intermédiatique et d’exploitation de la fiction, mais son innovation majeure, étroitement liée à la nature des produits de la firme LEGO. Dans un processus de « médiatisation », la gamme accomplit, après la généralisation de séries thématiques favorisant l’imaginaire, le passage de LEGO à la narrativisation. On montrera en quoi l’introduction du narratif dans cette gamme a répondu à cet objectif-maître de l’industrie des biens de consommation en régime médiatique : consommer du média, c’est encore jouer au jeu-noyau. Mais on verra aussi en quoi ce cadre narratif peut suggérer des analyses qui vont au-delà de la théorie du marketing ou de la didactique du jouet, et qui ont trait aux usages contemporains de la fiction et à la psychologie du développement en matière de maîtrise de la temporalité.

Conflict Resolution in Partially Ordered OWL DL Ontologies

NARCIS (Netherlands)

Ji, Q.; Gao, Z.; Huang, Z.

2014-01-01

Inconsistency handling in OWL DL ontologies is an important problem because an ontology can easily be inconsistent when it is generated or modified. Current approaches to dealing with inconsistent ontologies often assume that there exists a total order over axioms and use such an order to select

An Ontology for Modeling Complex Inter-relational Organizations

Science.gov (United States)

Wautelet, Yves; Neysen, Nicolas; Kolp, Manuel

This paper presents an ontology for organizational modeling through multiple complementary aspects. The primary goal of the ontology is to dispose of an adequate set of related concepts for studying complex organizations involved in a lot of relationships at the same time. In this paper, we define complex organizations as networked organizations involved in a market eco-system that are playing several roles simultaneously. In such a context, traditional approaches focus on the macro analytic level of transactions; this is supplemented here with a micro analytic study of the actors' rationale. At first, the paper overviews enterprise ontologies literature to position our proposal and exposes its contributions and limitations. The ontology is then brought to an advanced level of formalization: a meta-model in the form of a UML class diagram allows to overview the ontology concepts and their relationships which are formally defined. Finally, the paper presents the case study on which the ontology has been validated.

Aber-OWL: a framework for ontology-based data access in biology

KAUST Repository

Hoehndorf, Robert

2015-01-28

Background: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning. Results: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://aber-owl.net. Conclusions: Aber-OWL provides a framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies. When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.

An Ontological Architecture for Orbital Debris Data

OpenAIRE

Rovetto, Robert J.

2017-01-01

The orbital debris problem presents an opportunity for inter-agency and international cooperation toward the mutually beneficial goals of debris prevention, mitigation, remediation, and improved space situational awareness (SSA). Achieving these goals requires sharing orbital debris and other SSA data. Toward this, I present an ontological architecture for the orbital debris domain, taking steps in the creation of an orbital debris ontology (ODO). The purpose of this ontological system is to ...

Integrating Ontology Debugging and Matching into the eXtreme Design Methodology

OpenAIRE

Dragisic, Zlatan; Lambrix, Patrick; Blomqvist, Eva

2015-01-01

Ontology design patterns (ODPs) and related ontology development methodologies were designed as ways of sharing and reusing best practices in ontology engineering. However, while the use of these reduces the number of issues in the resulting ontologies defects can still be introduced into the ontology due to improper use or misinterpretation of the patterns. Thus, the quality of the developed ontologies is still a major concern. In this paper we address this issue by describing how ontology d...

A LEGO Mindstorms NXT Approach for Teaching at Data Acquisition, Control Systems Engineering and Real-Time Systems Undergraduate Courses

Science.gov (United States)

Cruz-Martin, A.; Fernandez-Madrigal, J. A.; Galindo, C.; Gonzalez-Jimenez, J.; Stockmans-Daou, C.; Blanco-Claraco, J. L.

2012-01-01

LEGO Mindstorms NXT robots are being increasingly used in undergraduate courses, mostly in robotics-related subjects. But other engineering topics, like the ones found in data acquisition, control and real-time subjects, also have difficult concepts that can be well understood only with good lab exercises. Such exercises require physical…

MultiFarm: A Benchmark for Multilingual Ontology Matching

NARCIS (Netherlands)

Meilicke, C.; García-Castro, R.; Freitas, F.; van Hage, W.R.; Montiel-Ponsoda, E.; Ribeiro de Azevedo, R.; Stuckenschmidt, H.; Svab-Zamazal, O.; Svatek, V.; Tamalin, A.; Wang, S.

2012-01-01

In this paper we present the MultiFarm dataset, which has been designed as a benchmark for multilingual ontology matching. The MultiFarm dataset is composed of a set of ontologies translated in different languages and the corresponding alignments between these ontologies. It is based on the OntoFarm

Integrity and change in modular ontologies

NARCIS (Netherlands)

Stuckenschmidt, Heiner; Klein, Michel

2003-01-01

The benefits of modular representations arc well known from many areas of computer science. In this paper, we concentrate on the benefits of modular ontologies with respect to local containment of terminological reasoning. We define an architecture for modular ontologies that supports local

Collaborative ontology development for the geosciences

NARCIS (Netherlands)

Kalbasi Khoramdashti, R.; Janowicz, K.; Reitsma, F.; Boerboom, L.G.J.; Alasheikh, A.

2014-01-01

Ontology-based information publishing, retrieval, reuse, and integration have become popular research topics to address the challenges involved in exchanging data between heterogeneous sources. However, in most cases ontologies are still developed in a centralized top-down manner by a few knowledge

Building an Ontology of Tablewares using 'Legacy Data'

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Daniël van Helden

2018-05-01

Full Text Available This article aims to demonstrate how an ontology can be constructed to encompass many of the criteria needed for more consumption-orientated approaches to Roman tablewares. For this it demonstrates how a dataset in a relational database can be organised for the format and capabilities of an ontology, and then how these data are input into the ontology model. Finally it includes some sample analyses to show the effectiveness of such an ontology for types of analyses that are relevant to this network.

Ontology: ambiguity and accuracy

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Marcelo Schiessl

2012-08-01

Full Text Available Ambiguity is a major obstacle to information retrieval. It is source of several researches in Information Science. Ontologies have been studied in order to solve problems related to ambiguities. Paradoxically, “ontology” term is also ambiguous and it is understood according to the use by the community. Philosophy and Computer Science seems to have the most accentuated difference related to the term sense. The former holds undisputed tradition and authority. The latter, in despite of being quite recent, holds an informal sense, but pragmatic. Information Science acts ranging from philosophical to computational approaches so as to get organized collections based on balance between users’ necessities and available information. The semantic web requires informational cycle automation and demands studies related to ontologies. Consequently, revisiting relevant approaches for the study of ontologies plays a relevant role as a way to provide useful ideas to researchers maintaining philosophical rigor, and convenience provided by computers.

Application of neuroanatomical ontologies for neuroimaging data annotation

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Jessica A Turner

2010-06-01

Full Text Available The annotation of functional neuroimaging results for data sharing and reuse is particularly challenging, due to the diversity of terminologies of neuroanatomical structures and cortical parcellation schemes. To address this challenge, we extended the Foundational Model of Anatomy Ontology (FMA to include cytoarchitectural, Brodmann area labels, and a morphological cortical labeling scheme (e.g., the part of Brodmann area 6 in the left precentral gyrus. This representation was also used to augment the neuroanatomical axis of RadLex, the ontology for clinical imaging. The resulting neuroanatomical ontology contains explicit relationships indicating which brain regions are “part of” which other regions, across cytoarchitectural and morphological labeling schemas. We annotated a large functional neuroimaging dataset with terms from the ontology and applied a reasoning engine to analyze this dataset in conjunction with the ontology, and achieved successful inferences from the most specific level (e.g., how many subjects showed activation in a sub-part of the middle frontal gyrus to more general (how many activations were found in areas connected via a known white matter tract?. In summary, we have produced a neuroanatomical ontology that harmonizes several different terminologies of neuroanatomical structures and cortical parcellation schemes. This neuranatomical ontology is publicly available as a view of FMA at the Bioportal website at http://rest.bioontology.org/bioportal/ontologies/download/10005. The ontological encoding of anatomic knowledge can be exploited by computer reasoning engines to make inferences about neuroanatomical relationships described in imaging datasets using different terminologies. This approach could ultimately enable knowledge discovery from large, distributed fMRI studies or medical record mining.

HuPSON: the human physiology simulation ontology.

Science.gov (United States)

Gündel, Michaela; Younesi, Erfan; Malhotra, Ashutosh; Wang, Jiali; Li, Hui; Zhang, Bijun; de Bono, Bernard; Mevissen, Heinz-Theodor; Hofmann-Apitius, Martin

2013-11-22

Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. Hindering these initiatives is a lack of a comprehensive ontology that covers the essential concepts of the simulation domain. We propose a first version of a newly constructed ontology, HuPSON, as a basis for shared semantics and interoperability of simulations, of models, of algorithms and of other resources in this domain. The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles; the constructed ontology has been evaluated via structural features, competency questions and use case scenarios.The ontology is freely available at: http://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads.html (owl files) and http://bishop.scai.fraunhofer.de/scaiview/ (browser). HuPSON provides a framework for a) annotating simulation experiments, b) retrieving relevant information that are required for modelling, c) enabling interoperability of algorithmic approaches used in biomedical simulation, d) comparing simulation results and e) linking knowledge-based approaches to simulation-based approaches. It is meant to foster a more rapid uptake of semantic technologies in the modelling and simulation domain, with particular focus on the VPH domain.

Ontology alignment architecture for semantic sensor Web integration.

Science.gov (United States)

Fernandez, Susel; Marsa-Maestre, Ivan; Velasco, Juan R; Alarcos, Bernardo

2013-09-18

Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity). Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity's names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI) tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

Ontology Alignment Architecture for Semantic Sensor Web Integration

Directory of Open Access Journals (Sweden)

Bernardo Alarcos

2013-09-01

Full Text Available Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity. Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity’s names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

Development and Evaluation of an Adolescents' Depression Ontology for Analyzing Social Data.

Science.gov (United States)

Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min

2016-01-01

This study aims to develop and evaluate an ontology for adolescents' depression to be used for collecting and analyzing social data. The ontology was developed according to the 'ontology development 101' methodology. Concepts were extracted from clinical practice guidelines and related literatures. The ontology is composed of five sub-ontologies which represent risk factors, sign and symptoms, measurement, diagnostic result and management care. The ontology was evaluated in four different ways: First, we examined the frequency of ontology concept appeared in social data; Second, the content coverage of ontology was evaluated by comparing ontology concepts with concepts extracted from the youth depression counseling records; Third, the structural and representational layer of the ontology were evaluated by 5 ontology and psychiatric nursing experts; Fourth, the scope of the ontology was examined by answering 59 competency questions. The ontology was improved by adding new concepts and synonyms and revising the level of structure.

Expert2OWL: A Methodology for Pattern-Based Ontology Development.

Science.gov (United States)

Tahar, Kais; Xu, Jie; Herre, Heinrich

2017-01-01

The formalization of expert knowledge enables a broad spectrum of applications employing ontologies as underlying technology. These include eLearning, Semantic Web and expert systems. However, the manual construction of such ontologies is time-consuming and thus expensive. Moreover, experts are often unfamiliar with the syntax and semantics of formal ontology languages such as OWL and usually have no experience in developing formal ontologies. To overcome these barriers, we developed a new method and tool, called Expert2OWL that provides efficient features to support the construction of OWL ontologies using GFO (General Formal Ontology) as a top-level ontology. This method allows a close and effective collaboration between ontologists and domain experts. Essentially, this tool integrates Excel spreadsheets as part of a pattern-based ontology development and refinement process. Expert2OWL enables us to expedite the development process and modularize the resulting ontologies. We applied this method in the field of Chinese Herbal Medicine (CHM) and used Expert2OWL to automatically generate an accurate Chinese Herbology ontology (CHO). The expressivity of CHO was tested and evaluated using ontology query languages SPARQL and DL. CHO shows promising results and can generate answers to important scientific questions such as which Chinese herbal formulas contain which substances, which substances treat which diseases, and which ones are the most frequently used in CHM.

Ontology-based Metadata Portal for Unified Semantics

Data.gov (United States)

National Aeronautics and Space Administration — The Ontology-based Metadata Portal for Unified Semantics (OlyMPUS) will extend the prototype Ontology-Driven Interactive Search Environment for Earth Sciences...

Quantum physics and relational ontology

Energy Technology Data Exchange (ETDEWEB)

Cordovil, Joao [Center of Philosophy of Sciences of University of Lisbon (Portugal)

2013-07-01

The discovery of the quantum domain of reality put a serious ontological challenge, a challenge that is still well present in the recent developments of Quantum Physics. Physics was conceived from an atomistic conception of the world, reducing it, in all its diversity, to two types of entities: simple, individual and immutable entities (atoms, in metaphysical sense) and composite entities, resulting solely from combinations. Linear combinations, additive, indifferent to the structure or to the context. However, the discovery of wave-particle dualism and the developments in Quantum Field Theories and in Quantum Nonlinear Physical, showed that quantum entities are not, in metaphysical sense, neither simple, nor merely the result of linear (or additive) combinations. In other words, the ontological foundations of Physics revealed as inadequate to account for the nature of quantum entities. Then a fundamental challenge arises: How to think the ontic nature of these entities? In my view, this challenge appeals to a relational and dynamist ontology of physical entities. This is the central hypothesis of this communication. In this sense, this communication has two main intentions: 1) positively characterize this relational and dynamist ontology; 2) show some elements of its metaphysical suitability to contemporary Quantum Physics.

Knowledge Representation in Patient Safety Reporting: An Ontological Approach

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Liang Chen

2016-10-01

Full Text Available Purpose: The current development of patient safety reporting systems is criticized for loss of information and low data quality due to the lack of a uniformed domain knowledge base and text processing functionality. To improve patient safety reporting, the present paper suggests an ontological representation of patient safety knowledge. Design/methodology/approach: We propose a framework for constructing an ontological knowledge base of patient safety. The present paper describes our design, implementation, and evaluation of the ontology at its initial stage. Findings: We describe the design and initial outcomes of the ontology implementation. The evaluation results demonstrate the clinical validity of the ontology by a self-developed survey measurement. Research limitations: The proposed ontology was developed and evaluated using a small number of information sources. Presently, US data are used, but they are not essential for the ultimate structure of the ontology. Practical implications: The goal of improving patient safety can be aided through investigating patient safety reports and providing actionable knowledge to clinical practitioners. As such, constructing a domain specific ontology for patient safety reports serves as a cornerstone in information collection and text mining methods. Originality/value: The use of ontologies provides abstracted representation of semantic information and enables a wealth of applications in a reporting system. Therefore, constructing such a knowledge base is recognized as a high priority in health care.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

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Emanuel Santos

Full Text Available Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

Science.gov (United States)

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

Ontologies and Formation Spaces for Conceptual ReDesign of Systems

Directory of Open Access Journals (Sweden)

J. Bíla

2005-01-01

Full Text Available This paper discusses ontologies, methods for developing them and languages for representing them. A special ontology for computational support of the Conceptual ReDesign Process (CRDP is introduced with a simple illustrative example of an application. The ontology denoted as Global context (GLB combines features of general semantic networks and features of UML language. The ontology is task-oriented and domain-oriented, and contains three basic strata – GLBExpl(stratum of Explanation, GLBFAct (stratum of Fields of Activities and GLBEnv (stratum of Environment, with their sub-strata. The ontology has been developed to represent functions of systems and their components in CRDP. The main difference between this ontology and ontologies which have been developed to identify functions (the semantic details in those ontologies must be as deep as possible is in the style of the description of the functions. In the proposed ontology, Formation Spaces were used as lower semantic categories the semantic deepness of which is variable and depends on the actual solution approach of a specialised Conceptual Designer.

Mining rare associations between biological ontologies.

Science.gov (United States)

Benites, Fernando; Simon, Svenja; Sapozhnikova, Elena

2014-01-01

The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations.

Mining rare associations between biological ontologies.

Directory of Open Access Journals (Sweden)

Fernando Benites

Full Text Available The constantly increasing volume and complexity of available biological data requires new methods for their management and analysis. An important challenge is the integration of information from different sources in order to discover possible hidden relations between already known data. In this paper we introduce a data mining approach which relates biological ontologies by mining cross and intra-ontology pairwise generalized association rules. Its advantage is sensitivity to rare associations, for these are important for biologists. We propose a new class of interestingness measures designed for hierarchically organized rules. These measures allow one to select the most important rules and to take into account rare cases. They favor rules with an actual interestingness value that exceeds the expected value. The latter is calculated taking into account the parent rule. We demonstrate this approach by applying it to the analysis of data from Gene Ontology and GPCR databases. Our objective is to discover interesting relations between two different ontologies or parts of a single ontology. The association rules that are thus discovered can provide the user with new knowledge about underlying biological processes or help improve annotation consistency. The obtained results show that produced rules represent meaningful and quite reliable associations.

GFVO: the Genomic Feature and Variation Ontology

KAUST Repository

Baran, Joachim

2015-05-05

Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

The Cognitive Paradigm Ontology: Design and Application

Science.gov (United States)

Laird, Angela R.

2013-01-01

We present the basic structure of the Cognitive Paradigm Ontology (CogPO) for human behavioral experiments. While the experimental psychology and cognitive neuroscience literature may refer to certain behavioral tasks by name (e.g., the Stroop paradigm or the Sternberg paradigm) or by function (a working memory task, a visual attention task), these paradigms can vary tremendously in the stimuli that are presented to the subject, the response expected from the subject, and the instructions given to the subject. Drawing from the taxonomy developed and used by the BrainMap project (www.brainmap.org) for almost two decades to describe key components of published functional imaging results, we have developed an ontology capable of representing certain characteristics of the cognitive paradigms used in the fMRI and PET literature. The Cognitive Paradigm Ontology is being developed to be compliant with the Basic Formal Ontology (BFO), and to harmonize where possible with larger ontologies such as RadLex, NeuroLex, or the Ontology of Biomedical Investigations (OBI). The key components of CogPO include the representation of experimental conditions focused on the stimuli presented, the instructions given, and the responses requested. The use of alternate and even competitive terminologies can often impede scientific discoveries. Categorization of paradigms according to stimulus, response, and instruction has been shown to allow advanced data retrieval techniques by searching for similarities and contrasts across multiple paradigm levels. The goal of CogPO is to develop, evaluate, and distribute a domain ontology of cognitive paradigms for application and use in the functional neuroimaging community. PMID:21643732

Ontology Design of Influential People Identification Using Centrality

Science.gov (United States)

Maulana Awangga, Rolly; Yusril, Muhammad; Setyawan, Helmi

2018-04-01

Identifying influential people as a node in a graph theory commonly calculated by social network analysis. The social network data has the user as node and edge as relation forming a friend relation graph. This research is conducting different meaning of every nodes relation in the social network. Ontology was perfect match science to describe the social network data as conceptual and domain. Ontology gives essential relationship in a social network more than a current graph. Ontology proposed as a standard for knowledge representation for the semantic web by World Wide Web Consortium. The formal data representation use Resource Description Framework (RDF) and Web Ontology Language (OWL) which is strategic for Open Knowledge-Based website data. Ontology used in the semantic description for a relationship in the social network, it is open to developing semantic based relationship ontology by adding and modifying various and different relationship to have influential people as a conclusion. This research proposes a model using OWL and RDF for influential people identification in the social network. The study use degree centrality, between ness centrality, and closeness centrality measurement for data validation. As a conclusion, influential people identification in Facebook can use proposed Ontology model in the Group, Photos, Photo Tag, Friends, Events and Works data.

Self-supervised Chinese ontology learning from online encyclopedias.

Science.gov (United States)

Hu, Fanghuai; Shao, Zhiqing; Ruan, Tong

2014-01-01

Constructing ontology manually is a time-consuming, error-prone, and tedious task. We present SSCO, a self-supervised learning based chinese ontology, which contains about 255 thousand concepts, 5 million entities, and 40 million facts. We explore the three largest online Chinese encyclopedias for ontology learning and describe how to transfer the structured knowledge in encyclopedias, including article titles, category labels, redirection pages, taxonomy systems, and InfoBox modules, into ontological form. In order to avoid the errors in encyclopedias and enrich the learnt ontology, we also apply some machine learning based methods. First, we proof that the self-supervised machine learning method is practicable in Chinese relation extraction (at least for synonymy and hyponymy) statistically and experimentally and train some self-supervised models (SVMs and CRFs) for synonymy extraction, concept-subconcept relation extraction, and concept-instance relation extraction; the advantages of our methods are that all training examples are automatically generated from the structural information of encyclopedias and a few general heuristic rules. Finally, we evaluate SSCO in two aspects, scale and precision; manual evaluation results show that the ontology has excellent precision, and high coverage is concluded by comparing SSCO with other famous ontologies and knowledge bases; the experiment results also indicate that the self-supervised models obviously enrich SSCO.

BioPortal: An Open-Source Community-Based Ontology Repository

Science.gov (United States)

Noy, N.; NCBO Team

2011-12-01

Advances in computing power and new computational techniques have changed the way researchers approach science. In many fields, one of the most fruitful approaches has been to use semantically aware software to break down the barriers among disparate domains, systems, data sources, and technologies. Such software facilitates data aggregation, improves search, and ultimately allows the detection of new associations that were previously not detectable. Achieving these analyses requires software systems that take advantage of the semantics and that can intelligently negotiate domains and knowledge sources, identifying commonality across systems that use different and conflicting vocabularies, while understanding apparent differences that may be concealed by the use of superficially similar terms. An ontology, a semantically rich vocabulary for a domain of interest, is the cornerstone of software for bridging systems, domains, and resources. However, as ontologies become the foundation of all semantic technologies in e-science, we must develop an infrastructure for sharing ontologies, finding and evaluating them, integrating and mapping among them, and using ontologies in applications that help scientists process their data. BioPortal [1] is an open-source on-line community-based ontology repository that has been used as a critical component of semantic infrastructure in several domains, including biomedicine and bio-geochemical data. BioPortal, uses the social approaches in the Web 2.0 style to bring structure and order to the collection of biomedical ontologies. It enables users to provide and discuss a wide array of knowledge components, from submitting the ontologies themselves, to commenting on and discussing classes in the ontologies, to reviewing ontologies in the context of their own ontology-based projects, to creating mappings between overlapping ontologies and discussing and critiquing the mappings. Critically, it provides web-service access to all its

Interoperability between phenotype and anatomy ontologies.

Science.gov (United States)

Hoehndorf, Robert; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

2010-12-15

Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning. We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge. http://bioonto.de/pmwiki.php/Main/PheneOntology.

Ontological interpretation of biomedical database content.

Science.gov (United States)

Santana da Silva, Filipe; Jansen, Ludger; Freitas, Fred; Schulz, Stefan

2017-06-26

Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a database record is often ambiguous. We address this problem by grounding implicit and explicit database content in a formal-ontological framework. By using a typical extract from the databases UniProt and Ensembl, annotated with content from GO, PR, ChEBI and NCBI Taxonomy, we created four ontological models (in OWL), which generate explicit, distinct interpretations under the BioTopLite2 (BTL2) upper-level ontology. The first three models interpret database entries as individuals (IND), defined classes (SUBC), and classes with dispositions (DISP), respectively; the fourth model (HYBR) is a combination of SUBC and DISP. For the evaluation of these four models, we consider (i) database content retrieval, using ontologies as query vocabulary; (ii) information completeness; and, (iii) DL complexity and decidability. The models were tested under these criteria against four competency questions (CQs). IND does not raise any ontological claim, besides asserting the existence of sample individuals and relations among them. Modelling patterns have to be created for each type of annotation referent. SUBC is interpreted regarding maximally fine-grained defined subclasses under the classes referred to by the data. DISP attempts to extract truly ontological statements from the database records, claiming the existence of dispositions. HYBR is a hybrid of SUBC and DISP and is more parsimonious regarding expressiveness and query answering complexity. For each of the four models, the four CQs were submitted as DL queries. This shows the ability to retrieve individuals with IND, and classes in SUBC and HYBR. DISP does not retrieve anything because the axioms with disposition are embedded in General Class Inclusion (GCI) statements. Ambiguity of biological database content is

An ontology design pattern for surface water features

Science.gov (United States)

Sinha, Gaurav; Mark, David; Kolas, Dave; Varanka, Dalia; Romero, Boleslo E.; Feng, Chen-Chieh; Usery, E. Lynn; Liebermann, Joshua; Sorokine, Alexandre

2014-01-01

Surface water is a primary concept of human experience but concepts are captured in cultures and languages in many different ways. Still, many commonalities exist due to the physical basis of many of the properties and categories. An abstract ontology of surface water features based only on those physical properties of landscape features has the best potential for serving as a foundational domain ontology for other more context-dependent ontologies. The Surface Water ontology design pattern was developed both for domain knowledge distillation and to serve as a conceptual building-block for more complex or specialized surface water ontologies. A fundamental distinction is made in this ontology between landscape features that act as containers (e.g., stream channels, basins) and the bodies of water (e.g., rivers, lakes) that occupy those containers. Concave (container) landforms semantics are specified in a Dry module and the semantics of contained bodies of water in a Wet module. The pattern is implemented in OWL, but Description Logic axioms and a detailed explanation is provided in this paper. The OWL ontology will be an important contribution to Semantic Web vocabulary for annotating surface water feature datasets. Also provided is a discussion of why there is a need to complement the pattern with other ontologies, especially the previously developed Surface Network pattern. Finally, the practical value of the pattern in semantic querying of surface water datasets is illustrated through an annotated geospatial dataset and sample queries using the classes of the Surface Water pattern.

Constructing a Geology Ontology Using a Relational Database

Science.gov (United States)

Hou, W.; Yang, L.; Yin, S.; Ye, J.; Clarke, K.

2013-12-01

In geology community, the creation of a common geology ontology has become a useful means to solve problems of data integration, knowledge transformation and the interoperation of multi-source, heterogeneous and multiple scale geological data. Currently, human-computer interaction methods and relational database-based methods are the primary ontology construction methods. Some human-computer interaction methods such as the Geo-rule based method, the ontology life cycle method and the module design method have been proposed for applied geological ontologies. Essentially, the relational database-based method is a reverse engineering of abstracted semantic information from an existing database. The key is to construct rules for the transformation of database entities into the ontology. Relative to the human-computer interaction method, relational database-based methods can use existing resources and the stated semantic relationships among geological entities. However, two problems challenge the development and application. One is the transformation of multiple inheritances and nested relationships and their representation in an ontology. The other is that most of these methods do not measure the semantic retention of the transformation process. In this study, we focused on constructing a rule set to convert the semantics in a geological database into a geological ontology. According to the relational schema of a geological database, a conversion approach is presented to convert a geological spatial database to an OWL-based geological ontology, which is based on identifying semantics such as entities, relationships, inheritance relationships, nested relationships and cluster relationships. The semantic integrity of the transformation was verified using an inverse mapping process. In a geological ontology, an inheritance and union operations between superclass and subclass were used to present the nested relationship in a geochronology and the multiple inheritances

Two obvious intuitions : Ontology-mapping needs background knowledge and approximation

NARCIS (Netherlands)

Van Harmelen, Frank

2007-01-01

Ontology mapping (or: ontology alignment, or integration) is one of the most active areas the Semantic Web area. An increasing amount of ontologies are becoming available in recent years, and if the Semantic Web is to be taken seriously, the problem of ontology mapping must be solved. Numerous

Nuclear component design ontology building based on ASME codes

International Nuclear Information System (INIS)

Bao Shiyi; Zhou Yu; He Shuyan

2005-01-01

The adoption of ontology analysis in the study of concept knowledge acquisition and representation for the nuclear component design process based on computer-supported cooperative work (CSCW) makes it possible to share and reuse numerous concept knowledge of multi-disciplinary domains. A practical ontology building method is accordingly proposed based on Protege knowledge model in combination with both top-down and bottom-up approaches together with Formal Concept Analysis (FCA). FCA exhibits its advantages in the way it helps establish and improve taxonomic hierarchy of concepts and resolve concept conflict occurred in modeling multi-disciplinary domains. With Protege-3.0 as the ontology building tool, a nuclear component design ontology based ASME codes is developed by utilizing the ontology building method. The ontology serves as the basis to realize concept knowledge sharing and reusing of nuclear component design. (authors)

Where to search top-K biomedical ontologies?

Science.gov (United States)

Oliveira, Daniela; Butt, Anila Sahar; Haller, Armin; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

2018-03-20

Searching for precise terms and terminological definitions in the biomedical data space is problematic, as researchers find overlapping, closely related and even equivalent concepts in a single or multiple ontologies. Search engines that retrieve ontological resources often suggest an extensive list of search results for a given input term, which leads to the tedious task of selecting the best-fit ontological resource (class or property) for the input term and reduces user confidence in the retrieval engines. A systematic evaluation of these search engines is necessary to understand their strengths and weaknesses in different search requirements. We have implemented seven comparable Information Retrieval ranking algorithms to search through ontologies and compared them against four search engines for ontologies. Free-text queries have been performed, the outcomes have been judged by experts and the ranking algorithms and search engines have been evaluated against the expert-based ground truth (GT). In addition, we propose a probabilistic GT that is developed automatically to provide deeper insights and confidence to the expert-based GT as well as evaluating a broader range of search queries. The main outcome of this work is the identification of key search factors for biomedical ontologies together with search requirements and a set of recommendations that will help biomedical experts and ontology engineers to select the best-suited retrieval mechanism in their search scenarios. We expect that this evaluation will allow researchers and practitioners to apply the current search techniques more reliably and that it will help them to select the right solution for their daily work. The source code (of seven ranking algorithms), ground truths and experimental results are available at https://github.com/danielapoliveira/bioont-search-benchmark.

Ontology - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available gzip) consists of some directories (see the following table). Data file File name: ontology....tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/ontology.tar.gz File size: 9...he NCBI Taxonomy and INSDC ontology files were obtained from the DDBJ web site. O...ples Data item Description ontology/meo/meo.ttl An ontology for describing organismal habitats (especially focused on microbes). onto...logy/meo/meo_fma_mapping.ttl An ontology mapping files t

Quality control for terms and definitions in ontologies and taxonomies

Directory of Open Access Journals (Sweden)

Rüegg Alexander

2006-04-01

Full Text Available Abstract Background Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO, the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.

Ontology Enabled Generation of Embedded Web Services

DEFF Research Database (Denmark)

Hansen, Klaus Marius; Zhang, Weishan; Soares, Goncalo Teofilo Afonso Pinheiro

2008-01-01

Web services are increasingly adopted as a service provision mechanism in pervasive computing environments. Implementing web services on networked, embedded devices raises a number of challenges, for example efficiency of web services, handling of variability and dependencies of hardware...... and software platforms, and of devices state and context changes. To address these challenges, we developed a Web service compiler, Limbo, in which Web Ontology Language (OWL) ontologies are used to make the Limbo compiler aware of its compilation context, such as targeted hardware and software. At the same...... time, knowledge on device details, platform dependencies, and resource/power consumption is built into the supporting ontologies, which are used to configure Limbo for generating resource efficient web service code. A state machine ontology is used to generate stub code to facilitate handling of state...

Information Pre-Processing using Domain Meta-Ontology and Rule Learning System

Science.gov (United States)

Ranganathan, Girish R.; Biletskiy, Yevgen

Around the globe, extraordinary amounts of documents are being created by Enterprises and by users outside these Enterprises. The documents created in the Enterprises constitute the main focus of the present chapter. These documents are used to perform numerous amounts of machine processing. While using thesedocuments for machine processing, lack of semantics of the information in these documents may cause misinterpretation of the information, thereby inhibiting the productiveness of computer assisted analytical work. Hence, it would be profitable to the Enterprises if they use well defined domain ontologies which will serve as rich source(s) of semantics for the information in the documents. These domain ontologies can be created manually, semi-automatically or fully automatically. The focus of this chapter is to propose an intermediate solution which will enable relatively easy creation of these domain ontologies. The process of extracting and capturing domain ontologies from these voluminous documents requires extensive involvement of domain experts and application of methods of ontology learning that are substantially labor intensive; therefore, some intermediate solutions which would assist in capturing domain ontologies must be developed. This chapter proposes a solution in this direction which involves building a meta-ontology that will serve as an intermediate information source for the main domain ontology. This chapter proposes a solution in this direction which involves building a meta-ontology as a rapid approach in conceptualizing a domain of interest from huge amount of source documents. This meta-ontology can be populated by ontological concepts, attributes and relations from documents, and then refined in order to form better domain ontology either through automatic ontology learning methods or some other relevant ontology building approach.

Self-adaptation of Ontologies to Folksonomies in Semantic Web

OpenAIRE

Francisco Echarte; José Javier Astrain; Alberto Córdoba; Jesús Villadangos

2008-01-01

Ontologies and tagging systems are two different ways to organize the knowledge present in the current Web. In this paper we propose a simple method to model folksonomies, as tagging systems, with ontologies. We show the scalability of the method using real data sets. The modeling method is composed of a generic ontology that represents any folksonomy and an algorithm to transform the information contained in folksonomies to the generic ontology. The method allows representing folksonomies at...

Complex Topographic Feature Ontology Patterns

Science.gov (United States)

Varanka, Dalia E.; Jerris, Thomas J.

2015-01-01

Semantic ontologies are examined as effective data models for the representation of complex topographic feature types. Complex feature types are viewed as integrated relations between basic features for a basic purpose. In the context of topographic science, such component assemblages are supported by resource systems and found on the local landscape. Ontologies are organized within six thematic modules of a domain ontology called Topography that includes within its sphere basic feature types, resource systems, and landscape types. Context is constructed not only as a spatial and temporal setting, but a setting also based on environmental processes. Types of spatial relations that exist between components include location, generative processes, and description. An example is offered in a complex feature type ‘mine.’ The identification and extraction of complex feature types are an area for future research.

A document-centric approach for developing the tolAPC ontology.

Science.gov (United States)

Blfgeh, Aisha; Warrender, Jennifer; Hilkens, Catharien M U; Lord, Phillip

2017-11-28

There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different "formalisms" to represent and share their data - by the far most common, however, is the "office file" either in the form of a word-processor document or a spreadsheet. Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology. We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue. This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists.

Introduction to Semantic Web Ontology Languages

NARCIS (Netherlands)

Antoniou, Grigoris; Franconi, Enrico; Van Harmelen, Frank

2005-01-01

The aim of this chapter is to give a general introduction to some of the ontology languages that play a prominent role on the Semantic Web, and to discuss the formal foundations of these languages. Web ontology languages will be the main carriers of the information that we will want to share and

Inferring ontology graph structures using OWL reasoning

KAUST Repository

Rodriguez-Garcia, Miguel Angel; Hoehndorf, Robert

2018-01-01

' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies

Duelling Ontologies: Might Vitalism Offer Balance and Value?

Science.gov (United States)

Richards, Dennis; Emmanuel, Elizabeth; Grace, Sandra

This article is part of a project investigating chiropractors' beliefs on the role of vitalism in their philosophical and practice approaches and how that might contribute to addressing current epidemics of non-communicable diseases. It aims to present atomism, reductionism, materialism and mechanism as fundamental ontologies in biomedicine and to examine what role these might play in its struggle to deal with these epidemics; to present vitalism as a fundamental ontology existing in chiropractic along with these ontologies of biomedicine; and to discuss how imbalances in the use of these ontologies and practices stemming from them might be contributing to difficulties in addressing these epidemics. The use of more balanced approaches by chiropractors involving not only mechanistic biomedical ontologies but also an increased focus on vitalism might offer value in addressing these epidemics and should be investigated. Copyright © 2017 Elsevier Inc. All rights reserved.

OAE: The Ontology of Adverse Events.

Science.gov (United States)

He, Yongqun; Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Guo, Abra; Zhang, Shelley; Jagannathan, Desikan; Toldo, Luca; Tao, Cui; Smith, Barry

2014-01-01

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term 'adverse event' denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. For example, using the data extracted from the Vaccine Adverse Event Reporting System (VAERS), OAE was used to analyse vaccine adverse events associated with the administrations of different types of influenza vaccines. OAE has also been used to represent and classify the vaccine adverse events cited in package inserts of FDA-licensed human vaccines in the USA. OAE is a biomedical ontology that logically defines and classifies various adverse events occurring after medical interventions. OAE has successfully been applied in several adverse event studies. The OAE ontological framework provides a platform for systematic representation and analysis of adverse events and of the factors (e

A collaborative recommendation framework for ontology evaluation and reuse

OpenAIRE

Cantador, Iván; Fernández Sánchez, Miriam; Castells, Pablo

2006-01-01

This is an electronic version of the paper presented at the International Workshop on Recommender Systems, held in Riva del Garda on 2006 Ontology evaluation can be defined as assessing the quality and the adequacy of an ontology for being used in a spe-cific context, for a specific goal. Although ontology reuse is being extensively addressed by the Semantic Web community, the lack of appropriate support tools and automatic techniques for the evaluation of certain ontology features are oft...

Application of Ontologies for Big Earth Data

Science.gov (United States)

Huang, T.; Chang, G.; Armstrong, E. M.; Boening, C.

2014-12-01

Connected data is smarter data! Earth Science research infrastructure must do more than just being able to support temporal, geospatial discovery of satellite data. As the Earth Science data archives continue to expand across NASA data centers, the research communities are demanding smarter data services. A successful research infrastructure must be able to present researchers the complete picture, that is, datasets with linked citations, related interdisciplinary data, imageries, current events, social media discussions, and scientific data tools that are relevant to the particular dataset. The popular Semantic Web for Earth and Environmental Terminology (SWEET) ontologies is a collection of ontologies and concepts designed to improve discovery and application of Earth Science data. The SWEET ontologies collection was initially developed to capture the relationships between keywords in the NASA Global Change Master Directory (GCMD). Over the years this popular ontologies collection has expanded to cover over 200 ontologies and 6000 concepts to enable scalable classification of Earth system science concepts and Space science. This presentation discusses the semantic web technologies as the enabling technology for data-intensive science. We will discuss the application of the SWEET ontologies as a critical component in knowledge-driven research infrastructure for some of the recent projects, which include the DARPA Ontological System for Context Artifact and Resources (OSCAR), 2013 NASA ACCESS Virtual Quality Screening Service (VQSS), and the 2013 NASA Sea Level Change Portal (SLCP) projects. The presentation will also discuss the benefits in using semantic web technologies in developing research infrastructure for Big Earth Science Data in an attempt to "accommodate all domains and provide the necessary glue for information to be cross-linked, correlated, and discovered in a semantically rich manner." [1] [1] Savas Parastatidis: A platform for all that we know

Construction of Engineering Ontologies for Knowledge Sharing and Reuse

NARCIS (Netherlands)

Borst, Willem Nico; Borst, W.N.

1997-01-01

This thesis describes an investigation into the practical use of ontologies for the development of information systems. Ontologies are formal descriptions of shared knowledge in a domain. An ontology can be used as a specification of an information system because it specifies the knowledge that is

Towards Ontological Foundations for Agent Modeling Concepts using UFO

NARCIS (Netherlands)

Guizzardi, G.; Wagner, Gerd

Foundational ontologies provide the basic concepts upon which any domain-specific ontology is built. This paper presents a new foundational ontology, UFO, and shows how it can be used as a foundation of agent concepts and for evaluating agent-oriented modeling methods. UFO is derived from a

On Automatic Modeling and Use of Domain-specific Ontologies

DEFF Research Database (Denmark)

Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

2005-01-01

In this paper, we firstly introduce an approach to the modeling of a domain-specific ontology for use in connection with a given document collection. Secondly, we present a methodology for deriving conceptual similarity from the domain-specific ontology. Adopted for ontology representation is a s...

The Relationship between User Expertise and Structural Ontology Characteristics

Science.gov (United States)

Waldstein, Ilya Michael

2014-01-01

Ontologies are commonly used to support application tasks such as natural language processing, knowledge management, learning, browsing, and search. Literature recommends considering specific context during ontology design, and highlights that a different context is responsible for problems in ontology reuse. However, there is still no clear…

Examining Students' Proportional Reasoning Strategy Levels as Evidence of the Impact of an Integrated LEGO Robotics and Mathematics Learning Experience

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Martínez Ortiz, Araceli

2015-01-01

The presented study used a problem-solving experience in engineering design with LEGO robotics materials as the real-world mathematics-learning context. The goals of the study were (a) to determine if a short but intensive extracurricular learning experience would lead to significant student learning of a particular academic topic and (b) to…

Motivating programming students by Problem Based Learning and LEGO robots

DEFF Research Database (Denmark)

Lykke, Marianne; Coto Chotto, Mayela; Mora, Sonia

2014-01-01

. For this reason the school is focusing on different teaching methods to help their students master these skills. This paper introduces an experimental, controlled comparison study of three learning designs, involving a problem based learning (PBL) approach in connection with the use of LEGO Mindstorms to improve...... students programming skills and motivation for learning in an introductory programming course. The paper reports the results related with one of the components of the study - the experiential qualities of the three learning designs. The data were collected through a questionnaire survey with 229 students...... from three groups exposed to different learning designs and through six qualitative walk-alongs collecting data from these groups by informal interviews and observations. Findings from the three studies were discussed in three focus group interviews with 10 students from the three experimental groups....

GeoSciGraph: An Ontological Framework for EarthCube Semantic Infrastructure

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Gupta, A.; Schachne, A.; Condit, C.; Valentine, D.; Richard, S.; Zaslavsky, I.

2015-12-01

The CINERGI (Community Inventory of EarthCube Resources for Geosciences Interoperability) project compiles an inventory of a wide variety of earth science resources including documents, catalogs, vocabularies, data models, data services, process models, information repositories, domain-specific ontologies etc. developed by research groups and data practitioners. We have developed a multidisciplinary semantic framework called GeoSciGraph semantic ingration of earth science resources. An integrated ontology is constructed with Basic Formal Ontology (BFO) as its upper ontology and currently ingests multiple component ontologies including the SWEET ontology, GeoSciML's lithology ontology, Tematres controlled vocabulary server, GeoNames, GCMD vocabularies on equipment, platforms and institutions, software ontology, CUAHSI hydrology vocabulary, the environmental ontology (ENVO) and several more. These ontologies are connected through bridging axioms; GeoSciGraph identifies lexically close terms and creates equivalence class or subclass relationships between them after human verification. GeoSciGraph allows a community to create community-specific customizations of the integrated ontology. GeoSciGraph uses the Neo4J,a graph database that can hold several billion concepts and relationships. GeoSciGraph provides a number of REST services that can be called by other software modules like the CINERGI information augmentation pipeline. 1) Vocabulary services are used to find exact and approximate terms, term categories (community-provided clusters of terms e.g., measurement-related terms or environmental material related terms), synonyms, term definitions and annotations. 2) Lexical services are used for text parsing to find entities, which can then be included into the ontology by a domain expert. 3) Graph services provide the ability to perform traversal centric operations e.g., finding paths and neighborhoods which can be used to perform ontological operations like

Application of Alignment Methodologies to Spatial Ontologies in the Hydro Domain

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Lieberman, J. E.; Cheatham, M.; Varanka, D.

2015-12-01

Ontologies are playing an increasing role in facilitating mediation and translation between datasets representing diverse schemas, vocabularies, or knowledge communities. This role is relatively straightforward when there is one ontology comprising all relevant common concepts that can be mapped to entities in each dataset. Frequently, one common ontology has not been agreed to. Either each dataset is represented by a distinct ontology, or there are multiple candidates for commonality. Either the one most appropriate (expressive, relevant, correct) ontology must be chosen, or else concepts and relationships matched across multiple ontologies through an alignment process so that they may be used in concert to carry out mediation or other semantic operations. A resulting alignment can be effective to the extent that entities in in the ontologies represent differing terminology for comparable conceptual knowledge. In cases such as spatial ontologies, though, ontological entities may also represent disparate conceptualizations of space according to the discernment methods and application domains on which they are based. One ontology's wetland concept may overlap in space with another ontology's recharge zone or wildlife range or water feature. In order to evaluate alignment with respect to spatial ontologies, alignment has been applied to a series of ontologies pertaining to surface water that are used variously in hydrography (characterization of water features), hydrology (study of water cycling), and water quality (nutrient and contaminant transport) application domains. There is frequently a need to mediate between datasets in each domain in order to develop broader understanding of surface water systems, so there is a practical as well theoretical value in the alignment. From a domain expertise standpoint, the ontologies under consideration clearly contain some concepts that are spatially as well as conceptually identical and then others with less clear

LEGO Mindstorms NXT: Juego como Herramienta de Aprendizaje de Programación

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Leidy Diana Jiménez-Pinzón

2014-06-01

Full Text Available LEGO Mindstorms es un juego que se usa como herramienta para el aprendizaje de distintas áreas de conocimiento. Una persona puede aprender acerca de programación mediante distintos lenguajes y aplicaciones para compilar el código de la solución planteada y resolver una situación particular. Sin embargo, la enseñanza de programación es sólo un fundamento teórico y poco práctico. Por estas razones, se pretende enseñar a programar mediante un lenguaje sencillo y una plataforma que permita visualizar el código gráficamente y validarlo específicamente con las instrucciones programadas sobre un robot.

Towards Self-managed Pervasive Middleware using OWL/SWRL ontologies

DEFF Research Database (Denmark)

Zhang, Weishan; Hansen, Klaus Marius

2008-01-01

Self-management for pervasive middleware is important to realize the Ambient Intelligence vision. In this paper, we present an OWL/SWRL context ontologies based self-management approach for pervasive middleware where OWL ontology is used as means for context modeling. The context ontologies....../SWRL context ontologies based self-management approach with the self-diagnosis in Hydra middleware, using device state machine and other dynamic context information, for example web service calls. The evaluations in terms of extensibility, performance and scalability show that this approach is effective...

Fuzzy knowledge bases integration based on ontology

OpenAIRE

Ternovoy, Maksym; Shtogrina, Olena

2012-01-01

the paper describes the approach for fuzzy knowledge bases integration with the usage of ontology. This approach is based on metadata-base usage for integration of different knowledge bases with common ontology. The design process of metadata-base is described.

ExO: An Ontology for Exposure Science

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An ontology is a formal representation of knowledge within a domain and typically consists of classes, the properties of those classes, and the relationships between them. Ontologies are critically important for specifying data of interest in a consistent manner, thereby enablin...

TrhOnt: building an ontology to assist rehabilitation processes.

Science.gov (United States)

Berges, Idoia; Antón, David; Bermúdez, Jesús; Goñi, Alfredo; Illarramendi, Arantza

2016-10-04

One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, information such as the physiotherapy record of a patient or treatment protocols for specific disorders must be adequately modeled, because they play a relevant role in the management of the evolutionary recovery process of a patient. In this scenario, we introduce TRHONT, an application ontology that can assist physiotherapists in the management of the patients' evolution via reasoning supported by semantic technology. The ontology was developed following the NeOn Methodology. It integrates knowledge from ontological (e.g. FMA ontology) and non-ontological resources (e.g. a database of movements, exercises and treatment protocols) as well as additional physiotherapy-related knowledge. We demonstrate how the ontology fulfills the purpose of providing a reference model for the representation of the physiotherapy-related information that is needed for the whole physiotherapy treatment of patients, since they step for the first time into the physiotherapist's office, until they are discharged. More specifically, we present the results for each of the intended uses of the ontology listed in the document that specifies its requirements, and show how TRHONT can answer the competency questions defined within that document. Moreover, we detail the main steps of the process followed to build the TRHONT ontology in order to facilitate its reproducibility in a similar context. Finally, we show an evaluation of the ontology from different perspectives. TRHONT has achieved the purpose of allowing for a reasoning process that changes over time according to the patient's state and performance.

Geographic Ontologies, Gazetteers and Multilingualism

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Robert Laurini

2015-01-01

Full Text Available Different languages imply different visions of space, so that terminologies are different in geographic ontologies. In addition to their geometric shapes, geographic features have names, sometimes different in diverse languages. In addition, the role of gazetteers, as dictionaries of place names (toponyms, is to maintain relations between place names and location. The scope of geographic information retrieval is to search for geographic information not against a database, but against the whole Internet: but the Internet stores information in different languages, and it is of paramount importance not to remain stuck to a unique language. In this paper, our first step is to clarify the links between geographic objects as computer representations of geographic features, ontologies and gazetteers designed in various languages. Then, we propose some inference rules for matching not only types, but also relations in geographic ontologies with the assistance of gazetteers.

A four stage approach for ontology-based health information system design.

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Kuziemsky, Craig E; Lau, Francis

2010-11-01

To describe and illustrate a four stage methodological approach to capture user knowledge in a biomedical domain area, use that knowledge to design an ontology, and then implement and evaluate the ontology as a health information system (HIS). A hybrid participatory design-grounded theory (GT-PD) method was used to obtain data and code them for ontology development. Prototyping was used to implement the ontology as a computer-based tool. Usability testing evaluated the computer-based tool. An empirically derived domain ontology and set of three problem-solving approaches were developed as a formalized model of the concepts and categories from the GT coding. The ontology and problem-solving approaches were used to design and implement a HIS that tested favorably in usability testing. The four stage approach illustrated in this paper is useful for designing and implementing an ontology as the basis for a HIS. The approach extends existing ontology development methodologies by providing an empirical basis for theory incorporated into ontology design. Copyright © 2010 Elsevier B.V. All rights reserved.

Operational Plan Ontology Model for Interconnection and Interoperability

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Long, F.; Sun, Y. K.; Shi, H. Q.

2017-03-01

Aiming at the assistant decision-making system’s bottleneck of processing the operational plan data and information, this paper starts from the analysis of the problem of traditional expression and the technical advantage of ontology, and then it defines the elements of the operational plan ontology model and determines the basis of construction. Later, it builds up a semi-knowledge-level operational plan ontology model. Finally, it probes into the operational plan expression based on the operational plan ontology model and the usage of the application software. Thus, this paper has the theoretical significance and application value in the improvement of interconnection and interoperability of the operational plan among assistant decision-making systems.

Unsupervised Ontology Generation from Unstructured Text. CRESST Report 827

Science.gov (United States)

Mousavi, Hamid; Kerr, Deirdre; Iseli, Markus R.

2013-01-01

Ontologies are a vital component of most knowledge acquisition systems, and recently there has been a huge demand for generating ontologies automatically since manual or supervised techniques are not scalable. In this paper, we introduce "OntoMiner", a rule-based, iterative method to extract and populate ontologies from unstructured or…

Gene ontology based transfer learning for protein subcellular localization

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Zhou Shuigeng

2011-02-01

Full Text Available Abstract Background Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting multi-aspect protein feature information. Gene ontology, hereinafter referred to as GO, uses a controlled vocabulary to depict biological molecules or gene products in terms of biological process, molecular function and cellular component. With the rapid expansion of annotated protein sequences, gene ontology has become a general protein feature that can be used to construct predictive models in computational biology. Existing models generally either concatenated the GO terms into a flat binary vector or applied majority-vote based ensemble learning for protein subcellular localization, both of which can not estimate the individual discriminative abilities of the three aspects of gene ontology. Results In this paper, we propose a Gene Ontology Based Transfer Learning Model (GO-TLM for large-scale protein subcellular localization. The model transfers the signature-based homologous GO terms to the target proteins, and further constructs a reliable learning system to reduce the adverse affect of the potential false GO terms that are resulted from evolutionary divergence. We derive three GO kernels from the three aspects of gene ontology to measure the GO similarity of two proteins, and derive two other spectrum kernels to measure the similarity of two protein sequences. We use simple non-parametric cross validation to explicitly weigh the discriminative abilities of the five kernels, such that the time & space computational complexities are greatly reduced when compared to the complicated semi-definite programming and semi-indefinite linear programming. The five kernels are then linearly merged into one single kernel for

Benchmarking the Applicability of Ontology in Geographic Object-Based Image Analysis

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Sachit Rajbhandari

2017-11-01

Full Text Available In Geographic Object-based Image Analysis (GEOBIA, identification of image objects is normally achieved using rule-based classification techniques supported by appropriate domain knowledge. However, GEOBIA currently lacks a systematic method to formalise the domain knowledge required for image object identification. Ontology provides a representation vocabulary for characterising domain-specific classes. This study proposes an ontological framework that conceptualises domain knowledge in order to support the application of rule-based classifications. The proposed ontological framework is tested with a landslide case study. The Web Ontology Language (OWL is used to construct an ontology in the landslide domain. The segmented image objects with extracted features are incorporated into the ontology as instances. The classification rules are written in Semantic Web Rule Language (SWRL and executed using a semantic reasoner to assign instances to appropriate landslide classes. Machine learning techniques are used to predict new threshold values for feature attributes in the rules. Our framework is compared with published work on landslide detection where ontology was not used for the image classification. Our results demonstrate that a classification derived from the ontological framework accords with non-ontological methods. This study benchmarks the ontological method providing an alternative approach for image classification in the case study of landslides.

A unified anatomy ontology of the vertebrate skeletal system.

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Wasila M Dahdul

Full Text Available The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO, to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish and multispecies (teleost, amphibian vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages, and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO, Gene Ontology (GO, Uberon, and Cell Ontology (CL, and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

A unified anatomy ontology of the vertebrate skeletal system.

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Dahdul, Wasila M; Balhoff, James P; Blackburn, David C; Diehl, Alexander D; Haendel, Melissa A; Hall, Brian K; Lapp, Hilmar; Lundberg, John G; Mungall, Christopher J; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E; Vickaryous, Matthew K; Westerfield, Monte; Mabee, Paula M

2012-01-01

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

A Unified Anatomy Ontology of the Vertebrate Skeletal System

Science.gov (United States)

Dahdul, Wasila M.; Balhoff, James P.; Blackburn, David C.; Diehl, Alexander D.; Haendel, Melissa A.; Hall, Brian K.; Lapp, Hilmar; Lundberg, John G.; Mungall, Christopher J.; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E.; Vickaryous, Matthew K.; Westerfield, Monte; Mabee, Paula M.

2012-01-01

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity. PMID:23251424

NeOn Methodology for Building Ontology Networks: Specification, Scheduling and Reuse

OpenAIRE

Suárez-Figueroa, Mari Carmen

2010-01-01

A new ontology development paradigm has started; its emphasis lies on the reuse and possible subsequent reengineering of knowledge resources, on the collaborative and argumentative ontology development, and on the building of ontology networks; this new trend is the opposite of building new ontologies from scratch. To help ontology developers in this new paradigm, it is important to provide strong methodological support. This thesis presents some contributions to the methodological area of...

Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

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He, Yongqun

2014-07-01

While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including Vaccine Ontology, Ontology of Adverse Events and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network ('OneNet') Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms.

An Ontology Design Pattern for Surface Water Features

Energy Technology Data Exchange (ETDEWEB)

Sinha, Gaurav [Ohio University; Mark, David [University at Buffalo (SUNY); Kolas, Dave [Raytheon BBN Technologies; Varanka, Dalia [U.S. Geological Survey, Rolla, MO; Romero, Boleslo E [University of California, Santa Barbara; Feng, Chen-Chieh [National University of Singapore; Usery, Lynn [U.S. Geological Survey, Rolla, MO; Liebermann, Joshua [Tumbling Walls, LLC; Sorokine, Alexandre [ORNL

2014-01-01

Surface water is a primary concept of human experience but concepts are captured in cultures and languages in many different ways. Still, many commonalities can be found due to the physical basis of many of the properties and categories. An abstract ontology of surface water features based only on those physical properties of landscape features has the best potential for serving as a foundational domain ontology. It can then be used to systematically incor-porate concepts that are specific to a culture, language, or scientific domain. The Surface Water ontology design pattern was developed both for domain knowledge distillation and to serve as a conceptual building-block for more complex surface water ontologies. A fundamental distinction is made in this on-tology between landscape features that act as containers (e.g., stream channels, basins) and the bodies of water (e.g., rivers, lakes) that occupy those containers. Concave (container) landforms semantics are specified in a Dry module and the semantics of contained bodies of water in a Wet module. The pattern is imple-mented in OWL, but Description Logic axioms and a detailed explanation is provided. The OWL ontology will be an important contribution to Semantic Web vocabulary for annotating surface water feature datasets. A discussion about why there is a need to complement the pattern with other ontologies, es-pecially the previously developed Surface Network pattern is also provided. Fi-nally, the practical value of the pattern in semantic querying of surface water datasets is illustrated through a few queries and annotated geospatial datasets.

Towards ontology based search and knowledgesharing using domain ontologies

DEFF Research Database (Denmark)

Zambach, Sine

verbs for relations in the ontology modeling. For this work we use frequency lists from a biomedical text corpus of different genres as well as a study of the relations used in other biomedical text mining tools. In addition, we discuss how these relations can be used in broarder perspective....

SWARMs Ontology: A Common Information Model for the Cooperation of Underwater Robots

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Li, Xin; Bilbao, Sonia; Martín-Wanton, Tamara; Bastos, Joaquim; Rodriguez, Jonathan

2017-01-01

In order to facilitate cooperation between underwater robots, it is a must for robots to exchange information with unambiguous meaning. However, heterogeneity, existing in information pertaining to different robots, is a major obstruction. Therefore, this paper presents a networked ontology, named the Smart and Networking Underwater Robots in Cooperation Meshes (SWARMs) ontology, to address information heterogeneity and enable robots to have the same understanding of exchanged information. The SWARMs ontology uses a core ontology to interrelate a set of domain-specific ontologies, including the mission and planning, the robotic vehicle, the communication and networking, and the environment recognition and sensing ontology. In addition, the SWARMs ontology utilizes ontology constructs defined in the PR-OWL ontology to annotate context uncertainty based on the Multi-Entity Bayesian Network (MEBN) theory. Thus, the SWARMs ontology can provide both a formal specification for information that is necessarily exchanged between robots and a command and control entity, and also support for uncertainty reasoning. A scenario on chemical pollution monitoring is described and used to showcase how the SWARMs ontology can be instantiated, be extended, represent context uncertainty, and support uncertainty reasoning. PMID:28287468

Developing Learning Materials Using an Ontology of Mathematical Logic

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Boyatt, Russell; Joy, Mike

2012-01-01

Ontologies describe a body of knowledge and give formal structure to a domain by describing concepts and their relationships. The construction of an ontology provides an opportunity to develop a shared understanding and a consistent vocabulary to be used for a given activity. This paper describes the construction of an ontology for an area of…

Uberon, an integrative multi-species anatomy ontology

Science.gov (United States)

2012-01-01

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org PMID:22293552

Annotating breast cancer microarray samples using ontologies

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Liu, Hongfang; Li, Xin; Yoon, Victoria; Clarke, Robert

2008-01-01

As the most common cancer among women, breast cancer results from the accumulation of mutations in essential genes. Recent advance in high-throughput gene expression microarray technology has inspired researchers to use the technology to assist breast cancer diagnosis, prognosis, and treatment prediction. However, the high dimensionality of microarray experiments and public access of data from many experiments have caused inconsistencies which initiated the development of controlled terminologies and ontologies for annotating microarray experiments, such as the standard microarray Gene Expression Data (MGED) ontology (MO). In this paper, we developed BCM-CO, an ontology tailored specifically for indexing clinical annotations of breast cancer microarray samples from the NCI Thesaurus. Our research showed that the coverage of NCI Thesaurus is very limited with respect to i) terms used by researchers to describe breast cancer histology (covering 22 out of 48 histology terms); ii) breast cancer cell lines (covering one out of 12 cell lines); and iii) classes corresponding to the breast cancer grading and staging. By incorporating a wider range of those terms into BCM-CO, we were able to indexed breast cancer microarray samples from GEO using BCM-CO and MGED ontology and developed a prototype system with web interface that allows the retrieval of microarray data based on the ontology annotations. PMID:18999108

Ontology-centric integration and navigation of the dengue literature.

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Rajapakse, Menaka; Kanagasabai, Rajaraman; Ang, Wee Tiong; Veeramani, Anitha; Schreiber, Mark J; Baker, Christopher J O

2008-10-01

Uninhibited access to the unstructured information distributed across the web and in scientific literature databases continues to be beyond the reach of scientists and health professionals. To address this challenge we have developed a literature driven, ontology-centric navigation infrastructure consisting of a content acquisition engine, a domain-specific ontology (in OWL-DL) and an ontology instantiation pipeline delivering sentences derived by domain-specific text mining. A visual query tool for reasoning over A-box instances in the populated ontology is presented and used to build conceptual queries that can be issued to the knowledgebase. We have deployed this generic infrastructure to facilitate data integration and knowledge sharing in the domain of dengue, which is one of the most prevalent viral diseases that continue to infect millions of people in the tropical and subtropical regions annually. Using our unique methodology we illustrate simplified search and discovery on dengue information derived from distributed resources and aggregated according to dengue ontology. Furthermore we apply data mining to the instantiated ontology to elucidate trends in the mentions of dengue serotypes in scientific abstracts since 1974.

Løgstrup’s Ontological Ethics

DEFF Research Database (Denmark)

Rabjerg, Bjørn

2017-01-01

aim is to provide a coherent exposition of Løgstrup’s ethics. However, the result is not a normative ethics upon which we may act, but rather a descriptive diagnosis of interdependence as the basic ontological condition of human social life, where the sovereign expressions of life may enable us to act.......The article explores K. E. Løgstrup’s ontological ethics, understood as an ethics rooted in interdependence. Interdependence, the fact that human beings always hold power over each other, has two very different aspects, which I will call negative and positive, each of them in turn leading...... to different aspects of ontological ethics. By negative and positive I mean the two opposing possibilities of all human interaction that we can either destroy the other person’s life (to a greater or smaller degree) or cause the other person’s life to flourish. We can either be a blessing in the other person’s...

Modelamiento y programación de un juego de legos en un entorno de realidad virtual

OpenAIRE

Arboleda, Freddy; Laica, Ricardo; Loor, Magdalena; García, Sixto

2011-01-01

This project seeks by the use of the techn Lego blocks, in order to check the applicability of the concepts learned throughout the topic specifies the general ideas on the model blocks. First, we focus in the creation of the 3D objects and scenes, which are going to constitute the virtual environment. Later, we are going to detail the different positioning and control algorithms created to help us in the precision and the logic en the movements of the virtu and disadvantages...

Ontology for cell-based geographic information

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Zheng, Bin; Huang, Lina; Lu, Xinhai

2009-10-01

Inter-operability is a key notion in geographic information science (GIS) for the sharing of geographic information (GI). That requires a seamless translation among different information sources. Ontology is enrolled in GI discovery to settle the semantic conflicts for its natural language appearance and logical hierarchy structure, which are considered to be able to provide better context for both human understanding and machine cognition in describing the location and relationships in the geographic world. However, for the current, most studies on field ontology are deduced from philosophical theme and not applicable for the raster expression in GIS-which is a kind of field-like phenomenon but does not physically coincide to the general concept of philosophical field (mostly comes from the physics concepts). That's why we specifically discuss the cell-based GI ontology in this paper. The discussion starts at the investigation of the physical characteristics of cell-based raster GI. Then, a unified cell-based GI ontology framework for the recognition of the raster objects is introduced, from which a conceptual interface for the connection of the human epistemology and the computer world so called "endurant-occurrant window" is developed for the better raster GI discovery and sharing.

Semi Automatic Ontology Instantiation in the domain of Risk Management

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Makki, Jawad; Alquier, Anne-Marie; Prince, Violaine

One of the challenging tasks in the context of Ontological Engineering is to automatically or semi-automatically support the process of Ontology Learning and Ontology Population from semi-structured documents (texts). In this paper we describe a Semi-Automatic Ontology Instantiation method from natural language text, in the domain of Risk Management. This method is composed from three steps 1 ) Annotation with part-of-speech tags, 2) Semantic Relation Instances Extraction, 3) Ontology instantiation process. It's based on combined NLP techniques using human intervention between steps 2 and 3 for control and validation. Since it heavily relies on linguistic knowledge it is not domain dependent which is a good feature for portability between the different fields of risk management application. The proposed methodology uses the ontology of the PRIMA1 project (supported by the European community) as a Generic Domain Ontology and populates it via an available corpus. A first validation of the approach is done through an experiment with Chemical Fact Sheets from Environmental Protection Agency2.

OntoPop: An Ontology Population System for the Semantic Web

Science.gov (United States)

Thongkrau, Theerayut; Lalitrojwong, Pattarachai

The development of ontology at the instance level requires the extraction of the terms defining the instances from various data sources. These instances then are linked to the concepts of the ontology, and relationships are created between these instances for the next step. However, before establishing links among data, ontology engineers must classify terms or instances from a web document into an ontology concept. The tool for help ontology engineer in this task is called ontology population. The present research is not suitable for ontology development applications, such as long time processing or analyzing large or noisy data sets. OntoPop system introduces a methodology to solve these problems, which comprises two parts. First, we select meaningful features from syntactic relations, which can produce more significant features than any other method. Second, we differentiate feature meaning and reduce noise based on latent semantic analysis. Experimental evaluation demonstrates that the OntoPop works well, significantly out-performing the accuracy of 49.64%, a learning accuracy of 76.93%, and executes time of 5.46 second/instance.

Ontology Language to Support Description of Experiment Control System Semantics, Collaborative Knowledge-Base Design and Ontology Reuse

International Nuclear Information System (INIS)

Gyurjyan, Vardan; Abbott, D.; Heyes, G.; Jastrzembski, E.; Moffit, B.; Timmer, C.; Wolin, E.

2009-01-01

In this paper we discuss the control domain specific ontology that is built on top of the domain-neutral Resource Definition Framework (RDF). Specifically, we will discuss the relevant set of ontology concepts along with the relationships among them in order to describe experiment control components and generic event-based state machines. Control Oriented Ontology Language (COOL) is a meta-data modeling language that provides generic means for representation of physics experiment control processes and components, and their relationships, rules and axioms. It provides a semantic reference frame that is useful for automating the communication of information for configuration, deployment and operation. COOL has been successfully used to develop a complete and dynamic knowledge-base for experiment control systems, developed using the AFECS framework.

CRAVE: a database, middleware and visualization system for phenotype ontologies.

Science.gov (United States)

Gkoutos, Georgios V; Green, Eain C J; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M

2005-04-01

A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

SSDOnt: An Ontology for Representing Single-Subject Design Studies.

Science.gov (United States)

Berges, Idoia; Bermúdez, Jesus; Illarramendi, Arantza

2018-02-01

Single-Subject Design is used in several areas such as education and biomedicine. However, no suited formal vocabulary exists for annotating the detailed configuration and the results of this type of research studies with the appropriate granularity for looking for information about them. Therefore, the search for those study designs relies heavily on a syntactical search on the abstract, keywords or full text of the publications about the study, which entails some limitations. To present SSDOnt, a specific purpose ontology for describing and annotating single-subject design studies, so that complex questions can be asked about them afterwards. The ontology was developed following the NeOn methodology. Once the requirements of the ontology were defined, a formal model was described in a Description Logic and later implemented in the ontology language OWL 2 DL. We show how the ontology provides a reference model with a suitable terminology for the annotation and searching of single-subject design studies and their main components, such as the phases, the intervention types, the outcomes and the results. Some mappings with terms of related ontologies have been established. We show as proof-of-concept that classes in the ontology can be easily extended to annotate more precise information about specific interventions and outcomes such as those related to autism. Moreover, we provide examples of some types of queries that can be posed to the ontology. SSDOnt has achieved the purpose of covering the descriptions of the domain of single-subject research studies. Schattauer GmbH.

Ontological Choices and the Value-Free Ideal

NARCIS (Netherlands)

Ludwig, D.J.

2015-01-01

The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species,

Ontological Choices and the Value-Free Ideal

NARCIS (Netherlands)

Ludwig, David

2016-01-01

The aim of this article is to argue that ontological choices in scientific practice undermine common formulations of the value-free ideal in science. First, I argue that the truth values of scientific statements depend on ontological choices. For example, statements about entities such as species,

In search of a primitive ontology for relativistic quantum field theory

Energy Technology Data Exchange (ETDEWEB)

Lam, Vincent [University of Lausanne, CH-1015 Lausanne (Switzerland)

2014-07-01

There is a recently much discussed approach to the ontology of quantum mechanics according to which the theory is ultimately about entities in 3-dimensional space and their temporal evolution. Such an ontology postulating from the start matter localized in usual physical space or spacetime, by contrast to an abstract high-dimensional space such as the configuration space of wave function realism, is called primitive ontology in the recent literature on the topic and finds its roots in Bell's notion of local beables. The main motivation for a primitive ontology lies in its explanatory power: the primitive ontology allows for a direct account of the behaviour and properties of familiar macroscopic objects. In this context, it is natural to look for a primitive ontology for relativistic quantum field theory (RQFT). The aim of this talk is to critically discuss this interpretative move within RQFT, in particular with respect to the foundational issue of the existence of unitarily inequivalent representations. Indeed the proposed primitive ontologies for RQFT rely either on a Fock space representation or a wave functional representation, which are strictly speaking only unambiguously available for free systems in flat spacetime. As a consequence, it is argued that these primitive ontologies constitute only effective ontologies and are hardly satisfying as a fundamental ontology for RQFT.

Metadata and Ontologies in Learning Resources Design

Science.gov (United States)

Vidal C., Christian; Segura Navarrete, Alejandra; Menéndez D., Víctor; Zapata Gonzalez, Alfredo; Prieto M., Manuel

Resource design and development requires knowledge about educational goals, instructional context and information about learner's characteristics among other. An important information source about this knowledge are metadata. However, metadata by themselves do not foresee all necessary information related to resource design. Here we argue the need to use different data and knowledge models to improve understanding the complex processes related to e-learning resources and their management. This paper presents the use of semantic web technologies, as ontologies, supporting the search and selection of resources used in design. Classification is done, based on instructional criteria derived from a knowledge acquisition process, using information provided by IEEE-LOM metadata standard. The knowledge obtained is represented in an ontology using OWL and SWRL. In this work we give evidence of the implementation of a Learning Object Classifier based on ontology. We demonstrate that the use of ontologies can support the design activities in e-learning.

Towards a Consistent and Scientifically Accurate Drug Ontology.

Science.gov (United States)

Hogan, William R; Hanna, Josh; Joseph, Eric; Brochhausen, Mathias

2013-01-01

Our use case for comparative effectiveness research requires an ontology of drugs that enables querying National Drug Codes (NDCs) by active ingredient, mechanism of action, physiological effect, and therapeutic class of the drug products they represent. We conducted an ontological analysis of drugs from the realist perspective, and evaluated existing drug terminology, ontology, and database artifacts from (1) the technical perspective, (2) the perspective of pharmacology and medical science (3) the perspective of description logic semantics (if they were available in Web Ontology Language or OWL), and (4) the perspective of our realism-based analysis of the domain. No existing resource was sufficient. Therefore, we built the Drug Ontology (DrOn) in OWL, which we populated with NDCs and other classes from RxNorm using only content created by the National Library of Medicine. We also built an application that uses DrOn to query for NDCs as outlined above, available at: http://ingarden.uams.edu/ingredients. The application uses an OWL-based description logic reasoner to execute end-user queries. DrOn is available at http://code.google.com/p/dr-on.

Kernel Methods for Mining Instance Data in Ontologies

Science.gov (United States)

Bloehdorn, Stephan; Sure, York

The amount of ontologies and meta data available on the Web is constantly growing. The successful application of machine learning techniques for learning of ontologies from textual data, i.e. mining for the Semantic Web, contributes to this trend. However, no principal approaches exist so far for mining from the Semantic Web. We investigate how machine learning algorithms can be made amenable for directly taking advantage of the rich knowledge expressed in ontologies and associated instance data. Kernel methods have been successfully employed in various learning tasks and provide a clean framework for interfacing between non-vectorial data and machine learning algorithms. In this spirit, we express the problem of mining instances in ontologies as the problem of defining valid corresponding kernels. We present a principled framework for designing such kernels by means of decomposing the kernel computation into specialized kernels for selected characteristics of an ontology which can be flexibly assembled and tuned. Initial experiments on real world Semantic Web data enjoy promising results and show the usefulness of our approach.

Platonic wholes and quantum ontology

CERN Document Server

Woszczek, Marek

2015-01-01

The subject of the book is a reconsideration of the internalistic model of composition of the Platonic type, more radical than traditional, post-Aristotelian externalistic compositionism, and its application in the field of the ontology of quantum theory. At the centre of quantum ontology is nonseparability. Quantum wholes are atemporal wholes governed by internalistic logic and they are primitive, global physical entities, requiring an extreme relativization of the fundamental notions of mechanics. That ensures quantum theory to be fully consistent with the relativistic causal structure, with

Root justifications for ontology repair

CSIR Research Space (South Africa)

Moodley, K

2011-08-01

Full Text Available stream_source_info Moodley_2011.pdf.txt stream_content_type text/plain stream_size 32328 Content-Encoding ISO-8859-1 stream_name Moodley_2011.pdf.txt Content-Type text/plain; charset=ISO-8859-1 Root Justi cations... the ontology, based on the no- tion of root justi cations [8, 9]. In Section 5, we discuss the implementation of a Prot eg e3 plugin which demonstrates our approach to ontology repair. In this section we also discuss some experimental results comparing...

Experiences with Aber-OWL, an Ontology Repository with OWL EL Reasoning