Wikidata as a semantic framework for the gene Wiki initiative

Database

Volumn 2016, Issue , 2016, Pages

  Burgstaller Muehlbacher, Sebastian ^a   Waagmeester, Andra ^b   Mitraka, Elvira ^c   Turner, Julia ^a   Putman, Tim ^a   Leong, Justin ^d   Naik, Chinmay ^e   Pavlidis, Paul ^d   Schriml, Lynn ^c   Good, Benjamin M ^a   Su, Andrew I ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b Miceliobe ^*  (Belgium)

^c UNIVERSITY OF MARYLAND   (United States)

^d UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^e BANGALORE INSTITUTE OF TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; HUMAN; MOUSE; NUCLEIC ACID DATABASE; SEARCH ENGINE; SEMANTICS; THEORETICAL MODEL;

ANIMALS; DATABASES, NUCLEIC ACID; HUMANS; MICE; MODELS, THEORETICAL; SEARCH ENGINE; SEMANTICS;

EID: 84964891019     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/baw015     Document Type: Article

References (24)

1. Daub, J., Gardner, P. P., Tate, J. et al. (2008) The RNA WikiProject: community annotation of RNA families. RNA, 14, 2462-2464.
2. Huss, J. W. 3rd, Orozco, C., Goodale, J. et al. (2008) A gene wiki for community annotation of gene function. PLoS Biol., 6, e175.
3. Huss, J. W. 3rd, Lindenbaum, P., Martone, M. et al. (2010) The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Res., 38, D633-D639.
4. Good, B. M., Clarke, E. L., De Alfaro, L. et al. (2012) The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res., 40, D1255-D1261.
5. Ashburner, M., Ball, C. A., Blake, J. A. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet, 25, 25-29.
6. Berman, H. M., Westbrook, J., Feng, Z. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
7. Su, A. I., Wiltshire, T., Batalov, S. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA, 101, 6062-6067.
8. Good, B. M., Clarke, E. L., Loguercio, S. et al. (2012) Building a biomedical semantic network in Wikipedia with Semantic Wiki Links. Database, 2012, bar060.
9. Krötzsch, M., Vrandećić, D., Völkel, M. et al. (2007) Semantic Wikipedia. Web Semantics: Science, Services and Agents on the WorldWideWeb, 5, 251-261.
10. Vrandećić, D. and Krötzsch, M. (2014) Wikidata. A free collaborative knowledgebase. Commun. ACM, 57, 78-85.
11. NCBI Resource Coordinators (2015) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 43, D6-17.
12. Cunningham, F., Amode, M. R., Barrell, D. et al. (2015) Ensembl 2015. Nucleic Acids Res., 43, D662-D669.
13. Eppig, J. T., Blake, J. A., Bult, C. J. et al. Mouse Genome Database Group (2015) The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res., 43, D726-D736.
14. Southan, C., Sharman, J. L., Benson, H. E. et al. NC-IUPHAR (2015) The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. Nucleic Acids Res.
15. Bragin, E., Chatzimichali, E. A., Wright, C. F. et al. (2014) DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res., 42, D993-D1000.
16. Forbes, S. A., Beare, D., Gunasekaran, P. et al. (2015) COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res., 43, D805-D811.
17. Yang, H. and Wang, K. (2015) Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat. Protoc., 10, 1556-1566.
18. Belleau, F., Nolin, M. A., Tourigny, N. et al. (2008) Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inform., 41, 706-716.
19. Dumontier, M., Baker, C. J., Baran, J. et al. (2014) The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J. Biomed. Semantics, 5, 14
20. Galperin, M. Y., Rigden, D. J. and Fernàndez-Suàrez, X. M. (2015) The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. Nucleic Acids Res., 43, D1-D5.
21. Cariaso, M. and Lennon, G. (2012) SNPedia: a wiki supporting personal genome annotation, interpretation and analysis. Nucleic Acids Res., 40, D1308-D1312.
22. Good, B. M., Clarke, E. L., Loguercio, S. et al. (2012) Linking genes to diseases with a SNPedia-Gene Wiki mashup. J. Biomed. Semantics, 3, S6.
23. Mons, B., Ashburner, M., Chichester, C. et al. (2008) Calling on a million minds for community annotation in WikiProteins. Genome Biol., 9, R89.
24. Gray, K. A., Yates, B., Seal, R. L. et al. (2015) Genenames.org: the HGNC resources in 2015. Nucleic Acids Res., 43, D1079-D1085.