QSAR DataBank repository: Open and linked qualitative and quantitative structure-activity relationship models

Journal of Cheminformatics

Volumn 7, Issue 1, 2015, Pages

  Ruusmann, V ^a   Sild, S ^a   Maran, U ^a  

^a UNIVERSITY OF TARTU   (Estonia)

Author keywords

Digital object identifier; Digital repository; DSpace; ODOSOS; Predictive model; QDB; QSAR; QsarDB; QSPR; QSTR

Indexed keywords

EID: 84933530233     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/s13321-015-0082-6     Document Type: Article

References (43)

1. Worth AP, Van Leeuwen CJ, Hartung T (2004) The prospects for using (Q)SARs in a changing political environment-high expectations and a key role for the european commission's joint research centre. SAR QSAR Environ Res 15:331-343
2. QSAR DataBank repository. http://qsardb.org. Accessed 12 June 2015
3. Ruusmann V, Sild S, Maran U (2014) QSAR DataBank - an approach for the digital organization and archiving of QSAR model information. J Cheminf 6:25
4. DSpace System. http://www.dspace.org/. Accessed 12 June 2015
5. European Commission JRC-IHCP QSAR Model Reporting Format Inventory. http://qsardb.jrc.ec.europa.eu/qmrf/. Accessed 12 June 2015
6. (Q)SAR Model Reporting Format (QMRF). https://eurl-ecvam.jrc.ec.europa.eu/databases/jrc-qsar-model-database-and-qsar-model-reporting-formats. Accessed 12 June 2015
7. Example QSAR-s from JRC-IHCP QSAR Model Inventory at QsarDB. http://hdl.handle.net/10967/109. Accessed 12 June 2015
8. Sushko I, Novotarskyi S, Körner R, Pandey AK, Rupp M, Teetz W et al (2011) Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J Comput Aided Mol Des 25:533-554
9. Walker T, Grulke CM, Pozefsky D, Tropsha A (2010) Chembench: a cheminformatics workbench. Bioinformatics 26:3000-3001
10. Jeliazkova N, Jeliazkov V (2011) AMBIT RESTful web services: an implementation of the OpenTox application programming interface. J Cheminf 3:18
11. Chemical Activity Predictor - GUSAR. http://cactus.nci.nih.gov/chemical/apps/cap. Accessed 12 June 2015
12. US EPA (2014) Estimation Programs Interface Suite™ for Microsoft® Windows, v 4.11. United States Environmental Protection Agency, Washington, DC
13. EPI Suite™ v4.11. http://www.epa.gov/oppt/exposure/pubs/episuitedl.htm. Accessed 12 June 2015
14. 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 ChemInf Model 47:2140-2148
15. VEGA platform. http://www.vega-qsar.eu/. Accessed 12 June 2015
16. UFZ Department of Ecological Chemistry 2014. ChemProp 6.1. http://www.ufz.de/index.php?en=6738. Accessed 12 June 2015
17. Patlewicz G, Jeliazkova N, Safford RJ, Worth AP, Aleksiev B (2008) An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. SAR QSAR Environ Res 19:495-524
18. EC-JRC Predictive Toxicology - ToxTree. https://eurl-ecvam.jrc.ec.europa.eu/laboratories-research/predictive-toxicology/qsar-tools/toxtree. Accessed 12 June 2015
19. Toxtree site. http://toxtree.sourceforge.net. Accessed 12 June 2015
20. Gramatica P, Cassani S, Chirico N (2014) QSARINS-Chem: insubria datasets and new QSAR/QSPR models for environmental pollutants in QSARINS. J Comput Chem 35:1036-1044
21. OECD QSAR Toolbox. http://www.qsartoolbox.org. Accessed 12 June 2015
22. Open Archives Initiative. http://www.openarchives.org/. Accessed 12 June 2015
23. DSpace User Registry. http://registry.duraspace.org/registry/dspace. Accessed 12 June 2015
24. QsarDB Java Reference Implementation. http://github.com/qsardb/qsardb. Accessed 12 June 2015
25. QsarDB middleware libraries. http://github.com/qsardb/qsardb-common. Accessed 12 June 2015
26. DSpace Functional Overview. https://wiki.duraspace.org/display/DSDOC4x/Functional+Overview. Accessed 12 June 2015
27. Handle System. http://www.handle.net. Accessed 12 June 2015
28. Corporation for National Research Initiatives®. http://www.cnri.reston.va.us/. Accessed 12 June 2015
29. Digital Object Identifier System. http://www.doi.org/index.html. Accessed 12 June 2015
30. Neumann J, Brase J (2014) DataCite and DOI names for research data. J Comput Aided Mol Des 28:1035-1041
31. International Data Citation Initiative. http://www.datacite.org/. Accessed 12 June 2015
32. ONSchallenge, Predictive Solubility. http://onschallenge.wikispaces.com/Predictive+Solubility. Accessed 12 June 2015
33. The Dublin Core® Metadata Initiative. http://dublincore.org/. Accessed 12 June 2015
34. Dodd JS, Solla L, Bérard PM (2006) References. In: Coghill AM, Garson LR (eds) The ACS style guide: effective communication of scientific informationa, chap 14. American Chemical Society, Washington, pp 287-341
35. Patashnik O (1988) BIBTEXing
36. Gramatica P, Cassani S, Roy PP, Kovarich S, Yap CW, Papa E (2012) QSAR modeling is not "push a button and find a correlation": a case study of toxicity of (benzo-)triazoles on algae. Mol Inf 31:817-835
37. Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E (2003) The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics. J Chem Inf Comput Sci 43:493-500
38. QsarDB web service API. http://qsardb.org/docs/api. Accessed 12 June 2015
39. Ruusmann V, Maran U (2013) From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions. J Comput Aided Mol Des 27:583-603
40. TETRATOX primary publications. http://hdl.handle.net/10967/7. Accessed 12 June 2015
41. Collection of Open Notebook Science models at QsarDB. http://hdl.handle.net/10967/2. Accessed 12 June 2015
42. Open Notebook Science original research models at QsarDB. http://hdl.handle.net/10967/5. Accessed 12 June 2015
43. Open Notebook Science Challenge. http://en.wikipedia.org/wiki/Open-Notebook-Science-Challenge. Accessed 12 June 2015