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1.

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.

2.

Self-organizing ontology of biochemically relevant small molecules.

Chepelev LL, Hastings J, Ennis M, Steinbeck C, Dumontier M.

BMC Bioinformatics. 2012 Jan 6;13:3. doi: 10.1186/1471-2105-13-3.

3.

Semantic Web integration of Cheminformatics resources with the SADI framework.

Chepelev LL, Dumontier M.

J Cheminform. 2011 May 16;3:16. doi: 10.1186/1758-2946-3-16.

4.

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.

5.

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.

6.

The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions.

Vandervalk B, McCarthy EL, Cruz-Toledo J, Klein A, Baker CJ, Dumontier M, Wilkinson MD.

JMIR Res Protoc. 2013 Apr 5;2(1):e14. doi: 10.2196/resprot.2315.

7.

SADI, SHARE, and the in silico scientific method.

Wilkinson MD, McCarthy L, Vandervalk B, Withers D, Kawas E, Samadian S.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S7. doi: 10.1186/1471-2105-11-S12-S7.

8.

Towards ontology-driven navigation of the lipid bibliosphere.

Baker CJ, Kanagasabai R, Ang WT, Veeramani A, Low HS, Wenk MR.

BMC Bioinformatics. 2008;9 Suppl 1:S5. doi: 10.1186/1471-2105-9-S1-S5.

9.

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.

10.

Algorithms and semantic infrastructure for mutation impact extraction and grounding.

Laurila JB, Naderi N, Witte R, Riazanov A, Kouznetsov A, Baker CJ.

BMC Genomics. 2010 Dec 2;11 Suppl 4:S24. doi: 10.1186/1471-2164-11-S4-S24.

11.

LMSD: LIPID MAPS structure database.

Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR, Russell DW, Subramaniam S.

Nucleic Acids Res. 2007 Jan;35(Database issue):D527-32. Epub 2006 Nov 10.

12.

Semantics-enabled service discovery framework in the SIMDAT pharma grid.

Qu C, Zimmermann F, Kumpf K, Kamuzinzi R, Ledent V, Herzog R.

IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):182-90. doi: 10.1109/TITB.2007.907987. Review.

PMID:
18348948
13.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

Wollbrett J, Larmande P, de Lamotte F, Ruiz M.

BMC Bioinformatics. 2013 Apr 15;14:126. doi: 10.1186/1471-2105-14-126.

14.
15.

Update of the LIPID MAPS comprehensive classification system for lipids.

Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CR, Shimizu T, Spener F, van Meer G, Wakelam MJ, Dennis EA.

J Lipid Res. 2009 Apr;50 Suppl:S9-14. doi: 10.1194/jlr.R800095-JLR200. Epub 2008 Dec 19. Review.

16.

A relation based measure of semantic similarity for Gene Ontology annotations.

Sheehan B, Quigley A, Gaudin B, Dobson S.

BMC Bioinformatics. 2008 Nov 4;9:468. doi: 10.1186/1471-2105-9-468.

17.

Annotation of SBML models through rule-based semantic integration.

Lister AL, Lord P, Pocock M, Wipat A.

J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S3. doi: 10.1186/2041-1480-1-S1-S3.

18.

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63. doi: 10.1093/nar/gks1146. Epub 2012 Nov 24.

19.

Discovering gene annotations in biomedical text databases.

Cakmak A, Ozsoyoglu G.

BMC Bioinformatics. 2008 Mar 6;9:143. doi: 10.1186/1471-2105-9-143.

20.

Open semantic annotation of scientific publications using DOMEO.

Ciccarese P, Ocana M, Clark T.

J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S1. doi: 10.1186/2041-1480-3-S1-S1.

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