Using SPARQL to query bioportal ontologies and metadata

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7650 LNCS, Issue PART 2, 2012, Pages 180-195

  Salvadores, Manuel ^a   Horridge, Matthew ^a   Alexander, Paul R ^a   Fergerson, Ray W ^a   Musen, Mark A ^a   Noy, Natalya F ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Biomedical; Linked Data; Ontologies; RDF; SPARQL

Indexed keywords

LINKED DATA; MEDICINE; METADATA; ONTOLOGY; TERMINOLOGY;

BIOMEDICAL; BIOMEDICAL DOMAIN; MEDICAL TERMINOLOGIES; NATIONAL LIBRARY OF MEDICINES; SPARQL; USAGE SCENARIOS;

SEMANTIC WEB;

EID: 84868590003     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-35173-0_12     Document Type: Conference Paper

References (22)

1. Arenas, M., Conca, S., Perez, J.: Counting beyond a Yottabyte, or how SPARQL 1.1 property paths will prevent adoption of the standard. In: WWW, pp. 629-638 (2012)
2. Cyganiak, R., Wood, D.: RDF 1.1 concepts and abstract syntax, http://www.w3.org/TR/2012/WD-rdf11-concepts-20120605/
3. Day-Richter, J., Harris, M.A., Haendel, M.: Gene Ontology OBO-Edit Working Group, Lewis, S.: OBO-Edit-an ontology editor for biologists. Bioinformatics 23(16), 2198-2200 (2007), http://dx.doi.org/10.1093/ bioinformatics/btm112
4. Gene Ontology Consortium: The Gene Ontology (GO) project. Nucleic Acids Research 34(suppl. 1), D322-D326 (2006)
5. Harris, S., Lamb, N., Shadbolt, N.: 4store: The Design and Implementation of a Clustered RDF Store. In: Scalable Semantic Web Knowledge Base Systems, SSWS 2009, pp. 94-109 (2009)
6. Horridge, M., Bechhofer, S.: The OWL API: A Java API for OWL ontologies. Semantic Web 2(1), 11-21 (2011)
7. Jonquet, C., LePendu, P., Falconer, S.M., Coulet, A., Noy, N.F., Musen, M.A., Shah, N.H.: NCBO Resource Index: Ontology-based search and mining of biomedical resources. Journal of Web Semantics (JWS) 9(3) (2011)
8. Lindberg, C.: The Unified Medical Language System (UMLS) of the National Library of Medicine. Journal of American Medical Record Association 61(5), 40-42 (1990)
9. Motik, B., Patel-Schneider, P.F., Parsia, B.: Owl 2 web ontology language structural specification and functional-style syntax, http://www.w3.org/TR/ 2009/REC-owl2-syntax-20091027/
10. Munoz, S., Perez, J., Gutierrez, C.: Simple and efficient minimal RDFS. Web Semant 7, 220-234 (2009)
11. Noy, N.F., Shah, N.H., Whetzel, P.L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D.L., Storey, M.A., Chute, C.G., Musen, M.A.: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research 37(suppl. 2), W170-W173 (2009), http://dx.doi.org/10.1093/nar/gkp440
12. Noy, N.F., Griffith, N., Musen, M.A.: Collecting Community-Based Mappings in an Ontology Repository. In: Sheth, A.P., Staab, S., Dean, M., Paolucci, M., Maynard, D., Finin, T., Thirunarayan, K. (eds.) ISWC 2008. LNCS, vol. 5318, pp. 371-386. Springer, Heidelberg (2008)
13. Patel-Schneider, P.F., Motik, B.: OWL 2 Web Ontology Language Mapping to RDF Graphs, http://www.w3.org/TR/owl2-mapping-to-rdf/
14. Price, C., Spackman, K.: SNOMED clinical terms. British Journal of Healthcare Computing & Information Management 17(3), 27-31 (2000)
15. Project, N.: The BioPortal Metadata Ontology (2012), http://purl. bioontology.org/ontology/BPMetadata
16. Salvadores, M.: UMLS2RDF Unified Medical Language System (UMLS) into RDF (2012), https://github.com/ncbo/umls2rdf
17. Salvadores, M., Alexander, P.R., Musen, M.A., Noy, N.F.: Bioportal as a dataset of linked biomedical ontologies and terminologies in RDF. Semantic Web Journal. IOS Press Journal (under review)
18. Salvadores, M., Alexander, P.R., Musen, M.A., Noy, N.F.: The quad economy of a semantic web ontology repository. In: The 7th International Workshop on Scalable Semantic Web Knowledge Base Systems, SSWS 2011 (2011)
19. Salvadores, M., Correndo, G., Harris, S., Gibbins, N., Shadbolt, N.: The Design and Implementation of Minimal RDFS Backward Reasoning in 4store. In: Antoniou, G., Grobelnik, M., Simperl, E., Parsia, B., Plexousakis, D., De Leenheer, P., Pan, J. (eds.) ESWC 2011, Part II. LNCS, vol. 6644, pp. 139-153. Springer, Heidelberg (2011)
20. Seaborne, A.: SPARQL 1.1 property paths, http://www.w3.org/TR/2010/WD- sparql11-property-paths-20100126/
21. Shah, N.H., Jonquet, C., Chiang, A.P., Butte, A.J., Chen, R., Musen, M.A.: Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics 10 (suppl. 2), S1 (2009)
22. Tirmizi, S.H., Aitken, S., Moreira, D.A., Mungall, C., Sequeda, J., Shah, N.H., Miranker, D.P.: OBO & OWL: Roundtrip ontology transformations. In: SWAT4LS (2009)