Integration and publication of heterogeneous text-mined relationships on the Semantic Web

Journal of Biomedical Semantics

Volumn 2, Issue 2, 2011, Pages

  Coulet, Adrien ^a,b,c   Garten, Yael ^b,c   Dumontier, Michel ^d   Altman, Russ B ^b,c,e   Musen, Mark A ^b   Shah, Nigam H ^b  

^a INRIA   (France)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c STANFORD UNIVERSITY   (United States)

^d CARLETON UNIVERSITY   (Canada)

^e Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 82755183234     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-2-S2-S10     Document Type: Article

References (26)

1. Groth P, Gibson A, Velterop J: The anatomy of a nanopublication. Information Services and Use. 2010, 30 (1-2): 51-56.
2. Klein T, Chang J, Cho M, Easton K, Fergerson K, Hewett M, Lin Z, Liu Y, Liu S, Oliver D, Rubin D, Shafa F, Stuart J, Altman RB: Integrating genotype and phenotype information: An overview of the PharmGKB project. The Pharmacogenomics Journal. 2001, 1 (3): 167-170. 10.1038/sj.tpj.6500035.
3. Garten Y, Coulet A, Altman R: Recent progress in automatically extracting information from the pharmacogenomic literature. Pharmacogenomics. 2010, 11 (10): 1467-1489. 10.2217/pgs.10.136.
4. Hunter L, Lu Z, Firby J, Baumgartner WA, Johnson HL, Ogren P, Cohen K: OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics. 2008, 9: 78-10.1186/1471-2105-9-78.
5. Friedman C, Kra P, Yu H, Krauthammer M, Rzhetsky A: Genies: a natural-language processing system for the extraction of molecular pathways from journal articles. Bioinformatics. 2001, 17 (suppl 1): S74-S82. 10.1093/bioinformatics/17.suppl_1.S74.
6. Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P: Extraction of regulatory gene/protein networks from medline. Bioinformatics. 2006, 22 (6): 645-650. 10.1093/bioinformatics/bti597.
7. Ciaramita M, Gangemi A, Ratsch E, Saric J, Rojas I: Unsupervised learning of semantic relations between concepts of a molecular biology ontology. IJCAI. 2005, 659-664.
8. Ramakrishnan C, Mendes P, Wang S, Sheth A: Unsupervised Discovery of Compound Entities for Relationship Extraction. EKAW. 2008, 146-155.
9. Tari L, Answar S, Liang S, Cai J, Baral C: Discovering drug interactions: a text-mining and reasoning approach based on properties of drug metabolism. Bioinformatics. 2010, 26 (18): i547-i553. 10.1093/bioinformatics/btq382.
10. Manning CD, Schütze H: Foundations of Statistical Natural Language Processing. 1999, Cambridge, MS, The MIT Press
11. Coulet A, Shah NH, Garten Y, Musen MA, Altman RB: Using Text to Build Semantic Networks for Pharmacogenomics. Journal of Biomedical Informatics. 2010, 43 (6): 1009-19. 10.1016/j.jbi.2010.08.005.
12. Agichtein E, Gravano L: Snowball: extracting relations from large plain text collections. ACM DL. 2000, 85-94.
13. Xu R, Supekar K, Morgan A, Das A, Garber A: Unsupervised method for automatic construction of a disease dictionary from a large free text collection. AMIA. 2008, 820-824.
14. PharmGKB VIP genes. [ http://www.pharmgkb.org/search/annotatedGene ]
15. de Marneffe MC, Manning CD: The Stanford typed dependencies representation. COLING Workshop on Cross-framework and Cross-domain Parser Evaluation. 2008
16. Feebaum C: WordNet, An Electronic Lexical Database. 1998, Cambridge, MS, The MIT Press
17. Cytoscape website. [ http://www.cytoscape.org/ ]
18. 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: R46-10.1186/gb-2005-6-5-r46.
19. Linking Open Data Community Project. [ http://esw.w3.org/SweoIG/TaskForces/CommunityProjects/LinkingOpenData ]
20. Mission of the Concept Web Alliance. [ http://conceptweblog.wordpress.com/declaration/ ]
21. Life Science Identifier resolution project. [ http://lsids.sourceforge.net/ ]
22. Shared Name project. [ http://sharedname.org/ ]
23. Relation Ontology and TAIR Relations. [ http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations ]
24. Ciccarese P, Ocana M, Castro LJG, Das S, Clark T: An Open Annotation Ontology for Science on the Web. J Biomed Semantics. 2011, 2 (Suppl 2): S4-10.1186/2041-1480-2-S2-S4.
25. HUGO Gene Nomenclature. [ http://www.genenames.org/ ]
26. Garten Y: Text mining the scientific literature to identify pharmacogenomic interactions. PhD Thesis in Biomedical Informatics. 2010, Stanford University