The use of concept maps during knowledge elicitation in ontology development processes - The nutrigenomics use case

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Castro, Alexander Garcia ^a,b   Rocca Serra, Philippe ^a   Stevens, Robert ^c   Taylor, Chris ^a   Nashar, Karim ^c   Ragan, Mark A ^b   Sansone, Susanna Assunta ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-ONTOLOGIES; BIOLOGICAL DOMAIN; CONCEPTUAL MAPS; DESIGN PROCESS; DOMAIN EXPERTS; ONTOLOGY DEVELOPMENT; SEMANTIC INTEGRATION; UNIFIED METHODOLOGY;

LIFE CYCLE; SEMANTICS;

KNOWLEDGE ACQUISITION;

ACCURACY; ARTICLE; COMPUTER PROGRAM; CONCEPT MAPPING; CONTROLLED STUDY; FEASIBILITY STUDY; GEOGRAPHIC DISTRIBUTION; INTERMETHOD COMPARISON; LIFE CYCLE; METHODOLOGY; NOMENCLATURE; NUTRIGENOMICS; PROCESS DESIGN; ALGORITHM; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; COMPUTER SIMULATION; FACTUAL DATABASE; GENOMICS; NATURAL LANGUAGE PROCESSING; NUTRITION; PROCEDURES;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; DATABASES, FACTUAL; GENOMICS; MODELS, BIOLOGICAL; NATURAL LANGUAGE PROCESSING; NUTRITIONAL PHYSIOLOGICAL PHENOMENA; TERMINOLOGY AS TOPIC;

EID: 33746752066     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-267     Document Type: Article

References (39)

1. Quackenbush J: Data standards for 'omic' science. Nature Biotechnology 2004, 22:613-614.
2. Field D, Sansone SA: A special issue on data standards. OMICS 2006, 2(10):84-93.
3. Blake J: Bio-ontologies - fast and furious. Nature Biotechnology 2004, 22:773-774.
4. Garcia C, Chen YP, Ragan AM: Information integration in molecular bioscience: a review. Applied Bioinformatics 2005, 4(3):157-173.
5. Corcho O, Fernandez-Lopez M, Gomez-Perez A: Methodologies, tools, and languages for building ontologies. Where is their meeting point? Data and Knowledge Engineering 2002, 46(1):41-64.
6. Smith B, Rosse C: The Role of Foundational Relations in the Alignment of Biomedical Ontologles. Amsterdam: IOS press; 2004.
7. Rosse C, Kumar A, Mejino J, Cook D, Detwiler L, Smith B: A Strategy for Improving and Integrating Biomedical Ontologies. In American Medical Informatics Association 2005 Symposium: 2005 Washington DC; 2005:639-643.
8. Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C: Relations in Biomedical Ontologies. Genome Biology 2005, 6(5):R46.
9. Lopez F, Perez G, Sierra J, Pazos S: Building a Chemical Ontology Using Methontology and the Ontology Design Environment. IEEE Intelligent Systems & Their Applications 1999, 14(1):37-46.
10. Cmap Tools [http://cmap.ihmc.us/]
11. Uschold M, King M: Towards Methodology for Building Ontologies. In Workshop on Basic Ontological Issues in Knowledge Sharing, held in conjunction with IJCAI-95: 1995 Cambridge, UK; 1995.
12. Fox M: The TOVE Project: A Common-sense Model of the Enterprise Systems. In Industrial and Engineering Applications of Artificial Intelligence and Expert 1992 Springer-Verlag; 1992:25-34.
13. Gruninger M, Fox MS: The Design and Evaluation of Ontologies for Enterprise Modelling. In Workshop on Implemented Ontologies, European Workshop on Artificial Intelligence. 1994 Amsterdam, NL; 1994.
14. Uschold M: Building Ontologies: Towards a Unified Methodology. In 16th Annual Conf of British Computer Society Specialist Group on Expert Systems,: 1996 Cambridge, UK; 1996.
15. Uschold M, Gruninger M: Ontologies: Principles, methods and applications. Knowledge Engineering Review 1996, 11(2):93-136.
16. Vrandecic D, Pinto H, Sure Y, Tempich C: The DILIGENT Knowledge Processes. Journal of Knowledge Management 2005, 9(5):85-96.
17. Fernandéz M, Gómez-Pérez A, Juristo N: METHONTOLOGY: From Ontological Art to Ontological Engineering. In Workshop on Ontological Engineering Spring Symposium Series AAA/97: 1997 Stanford; 1997.
18. Beck H, Pinto HS: Overview of Approach, Methodologies, Standards, and Tools for Ontologles. The Agricultural Ontology Service (UN FAO) 2003.
19. Hayes P, Eskridge CT, Saavedra R, Reichherzer T, Mehrotra M, Bobrovnikoff D: Collaborative Knowledge Capture in Ontologies. In K-CAP 05:2005 Banff, Canada; 2005.
20. Berners-Lee T: Weaving the Web. HarperCollins 1999.
21. Pinto H, Staab S, Tempich C: Diligent: towards a fine-grained methodology for Distributed, Loosely-controiled and evolving engineering of ontologies. In European conference on Artificial Intelligence: 2004 Valencia, Spain; 2004:393-397.
22. Bada M, Stevens R, Goble C, Gil Y, Ashbourner M, Blake J, Cherry J, Harris M, Lewis S: A short study on the success of the GeneOntology. Journal of Web Semantics 2004, 1:235-240.
23. Canas A, Leake DB, Wilson DC: Managing, Mapping and Manipulating Conceptual Knowledge. In AAAI Workshop Technical Report WS-99-10: Exploring the Synergies of Knowledge Management & Case-Based Reasoning Menlo California: AAAI Press; 1999.
24. European Nutrigenomics Organisation [http://www.nugo.org]
25. Sansone SA, Rocca-Serra P, Tong W, Fostel J, Morrison N: A strategy capitalizing on synergies - The Reporting Structure for Biological Investigation (RSBI) working group. OMICS 2006, 2(10):164-171.
26. Whetzel P, Brinkman RR, Causton HC, Fan L, Fostel J, Fragoso G, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert C, Taylor C, White J. members of the communities collaborating in the FuGO project: Development of FuGO: an Ontology for Functional Genomics Investigations. OMICS 2006, 2(10):199-204.
27. Whetzel P, Parkinson H, Causton HC, Fan L, Fostell J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr: The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 2006, 22(7):866-873.
28. Open Biomedical Ontologies [http://obo.sourceforge.net/]
29. Rubin D, Lewis S, Mungall C, Misra S, Westerfield M, Ashburner M, Sim I, Chute C, Solbrig H, Storey M, Smith B, Day-Richter J, Noy NF, Musen M: The National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge. OMICS 2006, 2(10):185-198.
30. Noy N, Fergerson R, Musen M: The knowledge model of Protege-2000: Combining interoperability and flexibility. In 2th International Conference on Knowledge Engineering and Knowledge Management (EKAW'2000): 2000 Juan-Ies-Pins, France; 2000.
31. Briggs G, Shamma DA, Cañas AJ, Carff R, Scaargle J, Novak JD: Concept Maps Applied to Mars Exploration Public Outreach. In Proceedings of the First International Conference on Concept Mapping: 2004 Pamplona, Spain; 2004.
32. WEBEX [http://www.webex.com/]
33. Hayes P, Saavedra R, Reichherzer T: A collaborative development environment for ontologies. Semantic Integration Workshop. 2003, Sanibel Island, Florida, USA 2003.
34. Seipel D, Baumeister J: Declarative Methods for the Evaluation of Ontologies. Künstliche Intelligenz 2004:51-57.
35. Haarslev V, Möller R: Racer: A Core Inference Engine for the Semantic Web. Proceedings of the 2nd International Workshop on Evaluation of Ontology-based Tools (EON2003): Sanibel Island, Florida, USA 2003:27-36. October 20 2003
36. Tempich C, Pinto H, Sure Y, Staab S: An Argumentation Ontology for Distributed, Loosely-controlled and evolvinG Eningeering processes of oNTologies (DILIGENT). Second European Semantic Web Conference. 2005 Greece 2005:241-256.
37. GMS Ontology [http://cropwiki.irri.org/icis/index.php/GermplasmOntology]
38. GMS Ontology [http://cropwiki.irri.org/icis/index.php/GermplasmOntology]
39. Diaz A, Baldo G: Co-Protege: A Groupware Tool for Supporting Collaborative Ontology Design with Divergence. 8th International Protege Conference 2005 Madrid, Spain 2005:32-32.