PubChemRDF: Towards the semantic annotation of PubChem compound and substance databases

Journal of Cheminformatics

Volumn 7, Issue 1, 2015, Pages

  Fu, Gang ^a   Batchelor, Colin ^b   Dumontier, Michel ^c   Hastings, Janna ^d   Willighagen, Egon ^e   Bolton, Evan ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b ROYAL SOCIETY OF CHEMISTRY   (United Kingdom)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Italy)

^e MAASTRICHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84937200100     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/s13321-015-0084-4     Document Type: Article

References (57)

1. PubChem. http://pubchem.ncbi.nlm.nih.gov. Accessed 8 July 2015
2. Bolton EE, Wang Y, Thiessen PA, Bryant SH (2008) Chapter 12 PubChem: integrated platform of small molecules and biological activities. In: Ralph AW, David CS (eds) Annual reports in computational chemistry, vol 4. Elsevier, USA, pp 217-241
3. Bolton EE, Kim S, Geer LY, Yu B, Bryant SH, He J PubChem synonym filtering process using crowdsourcing. In preparation
4. Bolton E, Kim S, Bryant S (2011) PubChem3D: conformer generation. J Cheminform 3(1):4
5. Cheng T, Zhao Y, Li X, Lin F, Xu Y, Zhang X et al (2007) Computation of octanol-water partition coefficients by guiding an additive model with knowledge. J Chem Inf Model 47(6):2140-2148
6. Heller S, McNaught A, Stein S, Tchekhovskoi D, Pletnev I (2013) InChI - the worldwide chemical structure identifier standard. J Cheminform 5(1):7
7. OEChem Toolkit for SMILES. http://www.eyesopen.com/docs/toolkits/current/html/OEChem-TK-c++/SMILES.html. Accessed 8 July 2015
8. James CA (2012) OpenSMILES specification. http://www.opensmiles.org/opensmiles.html. Accessed 8 July 2015
9. Lexichem ToolKit for IUPAC. http://www.eyesopen.com/docs/toolkits/current/html/Lexichem-TK-c++/index.html. Accessed 8 July 2015
10. Phadungsukanan W, Kraft M, Townsend JA, Murray-Rust P (2012) The semantics of Chemical Markup Language (CML) for computational chemistry: CompChem. J Cheminform 4(1):15
11. Chepelev LL, Dumontier M (2011) Chemical entity semantic specification: knowledge representation for efficient semantic cheminformatics and facile data integration. J Cheminform 3(1):20
12. W3C Linkeddata. http://www.w3.org/wiki/LinkedData. Accessed 8 July 2015
13. W3C Semantic Web. http://www.w3.org/2001/sw/. Accessed 8 July 2015
14. Wild DJ, Ding Y, Sheth AP, Harland L, Gifford EM, Lajiness MS (2012) Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research. Drug Discov Today 17(9-10):469-474
15. Luciano JS, Andersson B, Batchelor C, Bodenreider O, Clark T, Denney CK et al (2011) The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. J Biomed Semantics 2(Suppl 2):S1
16. Yu L (2011) A developers guide to the semantic web: Springer Publishing Company, Incorporated
17. ontop: a platform to query databases as Virtual RDF Graphs using SPARQL. http://ontop.inf.unibz.it/. Accessed 8 July 2015
18. D2R: Accessing relational databases as virtual RDF graphs. http://d2rq.org/. Accessed 8 July 2015
19. Virtuoso. http://virtuoso.openlinksw.com/. Accessed 8 July 2015
20. OWLIM. http://www.ontotext.com/owlim. Accessed 8 July 2015
21. Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L et al (2014) The EBI RDF platform: linked open data for the life sciences. Bioinformatics 30(9):1338-1339
22. Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J (2008) Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 41(5):706-716
23. Callahan A, Cruz-Toledo J, Ansell P, Dumontier M (2013) Bio2RDF Release 2: improved coverage, interoperability and provenance of life science linked data. In: Cimiano P, Corcho O, Presutti V, Hollink L, Rudolph S (eds) The semantic web: semantics and big data, vol 7882. Springer Berlin Heidelberg, pp 200-212
24. Samwald M, Jentzsch A, Bouton C, Kallesoe CS, Willighagen E, Hajagos J et al (2011) Linked open drug data for pharmaceutical research and development. J Cheminform 3(1):19
25. Chen B, Dong X, Jiao D, Wang H, Zhu Q, Ding Y et al (2010) Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data. BMC Bioinformatics 11:255
26. Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, Willighagen EL et al (2012) Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today 17(21-22):1188-1198
27. Willighagen EL, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V et al (2013) The ChEMBL database as linked open data. J Cheminform 5(1):23
28. Brenninkmeijer C, Evelo C, Goble C, Gray AJG, Groth P, Pettifer S et al (2012) Scientific lenses over linked data: an approach to support task specific views of the data. A vision. In: Proceedings of 2nd international workshop on linked science 2012 - Tackling Big Data
29. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A et al (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 36(Database issue):D344-D350
30. de Matos P, Alcantara R, Dekker A, Ennis M, Hastings J, Haug K et al (2010) Chemical entities of biological interest: an update. Nucleic Acids Res 38(Database issue):D249-D254
31. Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N et al (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41(Database issue):D456-D463
32. Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M (2011) The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PLoS One 6(10):e25513
33. Semanticscience Integrated Ontology (SIO). http://code.google.com/p/semanticscience/wiki/SIO. Accessed 8 July 2015
34. Gkoutos GV, Schofield PN, Hoehndorf R (2012) The units ontology: a tool for integrating units of measurement in science. Database (Oxford) 2012:bas033
35. DCMI (2012) DCMI terms. In: DCMI recommendation. http://dublincore.org/documents/dcmi-terms/. Accessed 8 July 2015
36. Shotton D (2010) CiTO, the citation typing ontology. J Biomed Semantics 1(Suppl 1):S6
37. Miles A, Bechhofer S (2009) SKOS simple knowledge organization system In: W3C recommendation. http://www.w3.org/TR/skos-reference/. Accessed 8 July 2015
38. Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T et al (2011) BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res 39(Web Server issue):W541-W545
39. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W et al (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25(11):1251-1255
40. Beckett D, Berners-Lee T (2011) Turtle - Terse RDF Triple Language. In: W3C team submission. http://www.w3.org/TeamSubmission/turtle/. Accessed 8 July 2015
41. Berners-Lee T. Uniform resource identifier (URI): generic syntax. In: Request for Comments: 3986. http://www.ietf.org/rfc/rfc3986.txt. Accessed 8 July 2015
42. Cool URIs for the semantic web. http://www.w3.org/TR/cooluris/#solutions. Accessed 8 July 2015
43. Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A et al (2014) MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res 42(Database issue):D297-D303
44. Bolton EE, Kim S, Bryant SH (2011) PubChem3D: similar conformers. J Cheminform 3:13
45. PubChem Fingerprints. ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem-fingerprints.txt. Accessed 8 July 2015
46. Bolton EE, Chen J, Kim S, Han L, He S, Shi W et al (2011) PubChem3D: a new resource for scientists. J Cheminform 3(1):32
47. Nanopub. http://nanopub.org/wordpress/. Accessed 8 July 2015
48. Biron PV, Permanente K, Malhotra A (2004) XML schema part 2: datatypes second edition. In: W3C recommendation. http://www.w3.org/TR/xmlschema-2/
49. Substance categorization classification. http://pubchem.ncbi.nlm.nih.gov/docs/subcmpd-summary-page-help.html#ClassificationSubstanceCategorization. Accessed 8 July 2015
50. Chepelev LL, Dumontier M (2011) Semantic web integration of cheminformatics resources with the SADI framework. J Cheminform 3:16
51. Wilkinson M, Vandervalk B, McCarthy L (2011) The semantic automated discovery and integration (SADI) web service design-pattern, API and reference implementation. J Biomed Semantics 2(1):8
52. Groth P, Gibson A, Velterop J (2010) The anatomy of a nanopublication. Inform Serv Use 30(1):51-56
53. Bio2RDF Dataset Provenance. https://github.com/bio2rdf/bio2rdf-scripts/wiki/Bio2RDF-Dataset-Provenance. Accessed 8 July 2015
54. Willighagen E (2012) Dataset descriptions for the open pharmacological space. In: Open PHACTS Recommendations. http://www.openphacts.org/specs/2012/WD-datadesc-20121019/. Accessed 8 July 2015
55. Brickley D, Guha RV (2004) RDF schema. In: W3C Recommendation. http://www.w3.org/TR/rdf-schema/. Accessed 8 July 2015
56. Malona F, Miller E (2004) RDF primer. In: W3C recommendation. http://www.w3.org/TR/2004/REC-rdf-primer-20040210/. Accessed 8 July 2015
57. Sperberg-McQueen CM, Thompson H (2000) XML schema. In: W3C recommendation. http://www.w3.org/XML/Schema. Accessed 8 July 2015