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Items: 1 to 20 of 93

1.

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery.

Dumontier M, Baker CJ, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, Del Rio NR, Duck G, Furlong LI, Keath N, Klassen D, McCusker JP, Queralt-Rosinach N, Samwald M, Villanueva-Rosales N, Wilkinson MD, Hoehndorf R.

J Biomed Semantics. 2014 Mar 6;5(1):14. doi: 10.1186/2041-1480-5-14.

2.

Ontology-Based Querying with Bio2RDF's Linked Open Data.

Callahan A, Cruz-Toledo J, Dumontier M.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S1. doi: 10.1186/2041-1480-4-S1-S1. Epub 2013 Apr 15.

3.

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

Wilkinson MD, Vandervalk B, McCarthy L.

J Biomed Semantics. 2011 Oct 24;2(1):8. doi: 10.1186/2041-1480-2-8.

4.

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R.

J Biomed Semantics. 2014 Jun 2;5:25. doi: 10.1186/2041-1480-5-25. eCollection 2014.

5.

A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL.

Mutowo P, Bento AP, Dedman N, Gaulton A, Hersey A, Lomax J, Overington JP.

J Biomed Semantics. 2016 Sep 27;7(1):59.

6.

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside.

Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK, Domarew C, Gambet T, Harland L, Jentzsch A, Kashyap V, Kos P, Kozlovsky J, Lebo T, Marshall SM, McCusker JP, McGuinness DL, Ogbuji C, Pichler E, Powers RL, Prud'hommeaux E, Samwald M, Schriml L, Tonellato PJ, Whetzel PL, Zhao J, Stephens S, Dumontier M.

J Biomed Semantics. 2011 May 17;2 Suppl 2:S1. doi: 10.1186/2041-1480-2-S2-S1.

7.

Bio2RDF: towards a mashup to build bioinformatics knowledge systems.

Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J.

J Biomed Inform. 2008 Oct;41(5):706-16. doi: 10.1016/j.jbi.2008.03.004. Epub 2008 Mar 21.

8.

Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics.

Chepelev LL, Riazanov A, Kouznetsov A, Low HS, Dumontier M, Baker CJ.

BMC Bioinformatics. 2011 Jul 26;12:303. doi: 10.1186/1471-2105-12-303.

9.

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.

Fu G, Batchelor C, Dumontier M, Hastings J, Willighagen E, Bolton E.

J Cheminform. 2015 Jul 14;7:34. doi: 10.1186/s13321-015-0084-4. eCollection 2015.

10.

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, Ennis M, Foulger RE, Harris MA, Hastings J, Kale NS, de Matos P, Mungall CJ, Owen G, Roncaglia P, Steinbeck C, Turner S, Lomax J.

BMC Genomics. 2013 Jul 29;14:513. doi: 10.1186/1471-2164-14-513.

11.

The Orthology Ontology: development and applications.

Fernández-Breis JT, Chiba H, Legaz-García Mdel C, Uchiyama I.

J Biomed Semantics. 2016 Jun 4;7(1):34. doi: 10.1186/s13326-016-0077-x.

12.

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M.

PLoS One. 2011;6(10):e25513. doi: 10.1371/journal.pone.0025513. Epub 2011 Oct 3.

13.

The use of web ontology languages and other semantic web tools in drug discovery.

Chen H, Xie G.

Expert Opin Drug Discov. 2010 May;5(5):413-23. doi: 10.1517/17460441003762709. Epub 2010 Apr 19.

PMID:
22823127
14.

Generation of open biomedical datasets through ontology-driven transformation and integration processes.

Carmen Legaz-García MD, Miñarro-Giménez JA, Menárguez-Tortosa M, Fernández-Breis JT.

J Biomed Semantics. 2016 Jun 3;7:32. doi: 10.1186/s13326-016-0075-z.

15.

PREDOSE: a semantic web platform for drug abuse epidemiology using social media.

Cameron D, Smith GA, Daniulaityte R, Sheth AP, Dave D, Chen L, Anand G, Carlson R, Watkins KZ, Falck R.

J Biomed Inform. 2013 Dec;46(6):985-97. doi: 10.1016/j.jbi.2013.07.007. Epub 2013 Jul 25.

16.

KaBOB: ontology-based semantic integration of biomedical databases.

Livingston KM, Bada M, Baumgartner WA Jr, Hunter LE.

BMC Bioinformatics. 2015 Apr 23;16:126. doi: 10.1186/s12859-015-0559-3.

17.

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.

Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P.

Bioinformatics. 2013 May 15;29(10):1325-32. doi: 10.1093/bioinformatics/btt113. Epub 2013 Mar 11.

18.

Automatically exposing OpenLifeData via SADI semantic Web Services.

González AR, Callahan A, Cruz-Toledo J, Garcia A, Egaña Aranguren M, Dumontier M, Wilkinson MD.

J Biomed Semantics. 2014 Nov 19;5:46. doi: 10.1186/2041-1480-5-46. eCollection 2014.

19.

Deploying mutation impact text-mining software with the SADI Semantic Web Services framework.

Riazanov A, Laurila JB, Baker CJ.

BMC Bioinformatics. 2011;12 Suppl 4:S6. doi: 10.1186/1471-2105-12-S4-S6. Epub 2011 Jul 5.

20.

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

Blank CE, Cui H, Moore LR, Walls RL.

J Biomed Semantics. 2016 Apr 12;7:18. doi: 10.1186/s13326-016-0060-6. eCollection 2016.

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