Applications of the InChI in cheminformatics with the CDK and Bioclipse

Journal of Cheminformatics

Volumn 5, Issue 3, 2013, Pages

  Spjuth, Ola ^a   Berg, Arvid ^a   Adams, Samuel ^b   Willighagen, Egon L ^c  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c MAASTRICHT UNIVERSITY   (Netherlands)

Author keywords

Bioclipse; Chemical structures; Databases; Decision support; InChI; InChIKey; JNI InChI; Linked data; OSGi; Semantic web; Tautomers; The Chemistry Development Kit

Indexed keywords

EID: 84879966950     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-5-14     Document Type: Article

References (34)

1. Heller S McNaught A Stein S Tchekhovskoi D Pletnev I: InChI - the worldwide chemical structure identifier standard. J Cheminform 2013 5(7).
2. O'Boyle NM Guha R Willighagen EL Adams SE Alvarsson J Bradley JC Filippov IV Hanson RM Hanwell MD Hutchison GR James CA Jeliazkova N Lang AS Langner KM Lonie DC Lowe DM Pansanel J Pavlov D Spjuth O Steinbeck C Tenderholt AL Theisen KJ Murray-Rust P: Open data open source and open standards in chemistry: The blue obelisk five years on. J Cheminform 2011 3(37).
3. Williams A: InChI connecting and navigating chemistry. J Cheminform 2012 4(33+).
4. Prlic A Yates A Bliven SE Rose PW Jacobsen J Troshin PV Chapman M Gao J Koh CH Foisy S Holland R Rimsa G Heuer ML Brandstatter-Muller H Bourne PE Willis S: BioJava: An open-source framework for bioinformatics in 2012. Bioinformatics 2012 28(20):2693-2695.
5. Wegner JK: Data Mining und Graph Mining auf molekularen Graphen - Cheminformatik und molekulare Kodierungen fur ADME/Tox QSAR Analysen. Logos Verlag Berlin GmbH; 2006.
6. Csizmadia F: JChem: Java applets and modules supporting chemical database handling from web browsers. J Chem Inf Comput Sci 2000 40(2):323-324.
7. Adams S: JNI-InChI. [http://jni-inchi.sf.net/]
8. OSGi. [http://www.osgi.org/]
9. Warr WA: Scientific workflow systems: Pipeline pilot and KNIME. J Comput AidedMol Des 2012 26(7):801-804.
10. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T: Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003 13(11):2498-2504.
11. Oinn T Addis M Ferris J Marvin D Senger M Greenwood M Carver T Glover K Pocock MR Wipat A Li P: Taverna: A tool for the composition and enactment of bioinformatics workflows. Bioinformatics 2004 20(17):3045-3054. (Pubitemid 39619196)
12. Truszkowski A Jayaseelan KV Neumann S Willighagen EL Zielesny A Steinbeck C: New developments on the cheminformatics open workflow environment CDK-Taverna. J Cheminform 2011 3(54).
13. Spjuth O Helmus T Willighagen EL Kuhn S Eklund M Wagener J Murray- Rust P Steinbeck C Wikberg JES: Bioclipse: An open source workbench for chemo- and bioinformatics. BMC Bioinformatics 2007 8(59).
14. Thalheim T Vollmer A Ebert RU Kuuhne R Schuurmann G: Tautomer identification and Tautomer structure generation based on the InChI code. J Chem Inf Model 2010 50(7):1223-1232.
15. Spjuth O Alvarsson J Berg A Eklund M Kuhn S Masak C Torrance G Wagener J Willighagen EL Steinbeck C Wikberg JES: Bioclipse 2: A scriptable integration platform for the life sciences. BMC Bioinformatics 2009 10(397).
16. Spjuth O Carlsson L Alvarsson J Georgiev V Willighagen E Eklund M: Open source drug discovery with Bioclipse. Curr TopMed Chem 2012 12(18):1980-1986.
17. Spjuth O Georgiev V Carlsson L Alvarsson J Berg A Willighagen E Wikberg J E S Eklund M: Bioclipse-R: integrating management and visualization of life science data with statistical analysis. Bioinformatics 2013 29(2):286-289.
18. Spjuth O Eklund M Ahlberg Helgee E Boyer S Carlsson L: Integrated decision support for assessing chemical liabilities. J Chem Inf Model 2011 51(8):1840-1847.
19. Fitzpatrick RB: CPDB: carcinogenic potency database. Med Ref Serv Q 2008 27(3):303-311.
20. Kazius J McGuire R Bursi R: Derivation and validation of toxicophores formutagenicity prediction. JMed Chem 2005 48:312-320. (Pubitemid 40105270)
21. Coles SJ Day NE Murray-Rust P Rzepa HS Zhang Y: Enhancement of the chemical semantic web through the use of InChI identifiers. Org Biomol Chem 2005 3(10):1832-1834. (Pubitemid 40751351)
22. Samwald M Jentzsch A Bouton C Kallesoe C Willighagen E Hajagos J Marshall M Prud'hommeaux E Hassanzadeh O Pichler E Stephens S: Linked open drug data for pharmaceutical research and development. J Cheminform 2011 3(19).
23. Willighagen E Alvarsson J Andersson A Eklund M Lampa S Lapins M Spjuth O Wikberg J: Linking the resource description framework to cheminformatics and proteochemometrics. J Biomed Sem 2011 2(Suppl 1):S6.
24. Guha RV Brickley D: RDF Vocabulary description language 1.0: RDF schema. W3C recommendationW3C 2004. [http://www.w3.org/TR/2004/ REC-rdf-schema-20040210/ ]
25. Bechhofer S Miles A: SKOS Simple Knowledge Organization System Reference. W3C recommendationW3C 2009. [http://www.w3.org/TR/ 2009/REC-skos-reference- 20090818/]
26. Graves M Constabaris A Brickley D: FOAF: Connecting People on the Semantic Web. Cataloging Classif Q 2007 43(3):191-202.
27. Adams N Cannon E Murray-Rust P: ChemAxiom - an ontological framework for chemistry in science. 2009. [http://dx.doi.org/10.1038/ npre.2009.3714.1]
28. Hastings J Chepelev L Willighagen E Adams N Steinbeck C Dumontier M: The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PLoS ONE 2011 6(10):e25513.
29. Belleau F Nolin MA Tourigny N Rigault P Morissette J: Bio2RDF Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform 2008 41(5):706-716.
30. Auer S Bizer C Kobilarov G Lehmann J Cyganiak R Ives Z: DBpedia A nucleus for a web of open data the semantic web. Edited by Aberer K Choi KS Noy N Allemang D Lee KI Nixon L Golbeck J Mika P Maynard D Mizoguchi R Schreiber G Cudre-Mauroux P. Berlin: Heidelberg: Springer; 2007:722-735. Lecture Notes in Computer Science.
31. Pence HE Williams A: ChemSpider An online chemical information resource. J Chem Educ 2010 87(11):1123-1124.
32. Kuhn M Campillos M Letunic I Jensen LJ Bork P: A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol 2010 6(343).
33. Rijnbeek M: Create tautomers based on InChI. 2011. [https://github. com/cdk/cdk/commit/68d21b76a0b73eeddf2b8234b74a73f7fa41a0c0]
34. Porter WR: Warfarin: history tautomerism and activity. J Comput Aided Mol Des 2010 24(6):553-573.