Using ChEMBL web services for building applications and data processing workflows relevant to drug discovery

References

• Gaulton A, Hersey A, Nowotka M, et al. The ChEMBL database in 2017. Nucleic Acids Res. 2017;45(D1):D945–D954.
   PubMed Web of Science ®Google Scholar
• Mok NY, Brenk R. Mining the ChEMBL database: an efficient chemoinformatics workflow for assembling an ion channel-focused screening library. J Chem Inf Model. 2011 Oct 24;51(10):2449–2454.
   PubMed Web of Science ®Google Scholar
• Klimenko K, Marcou G, Horvath D. Chemical space mapping and structure-activity analysis of the ChEMBL antiviral compound set. J Chem Inf Model. 2016;56(8):1438–1454. DOI:10.1021/acs.jcim.6b00192
   PubMed Web of Science ®Google Scholar
• Hu Y, Lounkine E, Bajorath J. Many approved drugs have bioactive analogs with different target annotations. AAPS J. 2014;16(4):847–859. DOI:10.1208/s12248-014-9621-8
   PubMed Web of Science ®Google Scholar
• Mervin LH, Afzal AM, Drakakis G, et al. Target prediction utilising negative bioactivity data covering large chemical space. J Cheminform. 2015;7:51. DOI:10.1186/s13321-015-0098-y
   PubMed Web of Science ®Google Scholar
• Hu Y, De La Vega De León A, Zhang B, et al. Matched molecular pair-based data sets for computer-aided medicinal chemistry. Version 2. F1000Res. 2014;3:36. DOI:10.12688/f1000research.3-36.v2
   PubMedGoogle Scholar
• Resource Description Framework (RDF) Model and Syntax Specification. Available from: https://www.w3.org/TR/PR-rdf-syntax/
   Google Scholar
• Davies M, Nowotka M, Papadatos G, et al. ChEMBL web services: streamlining access to drug discovery data and utilities. Nucleic Acids Res. 43(W1):W612–W620.
   PubMed Web of Science ®Google Scholar
• Creative Commons Attribution-ShareAlike 3.0 Unported license terms and conditions, [cited 2017 May 12]. Available from https://creativecommons.org/licenses/by-sa/3.0/legalcode
   Google Scholar
• Source code of the ChEMBL web services, cited 2017 May 12. Available from https://github.com/chembl/chembl_webservices_2
   Google Scholar
• Apache License Version 2.0 terms and conditions, cited 2017 May 12. Available from https://www.apache.org/licenses/LICENSE-2.0
   Google Scholar
• Davies M, Nowotka M, Papadatos G, et al. MyChEMBL: a virtual platform for distributing cheminformatics tools and open data. Challenges. 2014;5:334–337.
   Google Scholar
• Fielding, Roy Thomas (2000). Architectural styles and the design of network-based software architectures. Doctoral dissertation, University of California, Irvine.
   Google Scholar
• ChEMBL web services live documentation, cited 2017 May 12. Available from https://www.ebi.ac.uk/chembl/api/data/docs
   Google Scholar
• ChEMBL API manual, cited 2017 May 12. Available from https://www.ebi.ac.uk/chembl/ws
   Google Scholar
• Tastypie documentation section about the concept of throttling, cited 2017 May 12. Available from http://django-tastypie.readthedocs.io/en/latest/throttling.html
   Google Scholar
• Official Python client for accessing ChEMBL API, cited 2017 May 12. Available from https://github.com/chembl/chembl_webresource_client
   Google Scholar
• The Python Package Index, cited 2017 May 12. Available from https://pypi.python.org/pypi,
   Google Scholar
• Jupyter Notebook with ChEMBL API usage examples, cited 2017 May 12. Available from https://github.com/chembl/mychembl/blob/master/ipython_notebooks/09_myChEMBL_web_services.ipynb
   Google Scholar
• Anderson E, Veith GD, Weininger D (1987). SMILES: A line notation and computerized interpreter for chemical structures. Duluth, MN: U.S. EPA, Environmental Research Laboratory-Duluth. Report No. EPA/600/M-87/021.
   Google Scholar
• Maximum URL length is 2,083 characters in Internet Explorer, cited 2017 May 12. Available from https://support.microsoft.com/en-us/kb/208427
   Google Scholar
• Slack - team communication for the 21st century, cited 2017 May 12. Available from https://slack.com/.
   Google Scholar
• Perkel JM. How scientists use Slack. Nature. 2017;541:123–124. DOI:10.1038/541123a
   Web of Science ®Google Scholar
• Legacy custom integrations, Slack documentation, cited 2017 May 12. Available from https://api.slack.com/custom-integrations
   Google Scholar
• Slash Commands, Slack documentation, cited 2017 May 12. https://api.slack.com/slash-commands
   Google Scholar
• Chambers J, Davies M, Gaulton A, et al. . UniChem: a unified chemical structure cross-referencing and identifier tracking system. J Cheminform. 2013;5(January 2013):3. DOI:10.1186/1758-2946-5-3 .
   PubMed Web of Science ®Google Scholar
• ChEMBL Slack integration source code, cited 2017 May 12. Available from https://github.com/chembl/chembl-slack
   Google Scholar
• Berthold MR, Cebron N, Dill F, et al. KNIME: the Konstanz information miner. studies in classification, data analysis, and knowledge organization. 2007.
   Google Scholar
• The new REST nodes: Get Request, cited 2017 May 12. Available from http://www.dataminingreporting.com/blog/the-new-rest-nodes-get-request
   Google Scholar
• Example KNIME worklow retrieving activities for target using ChEMBL API, cited 2017 May 12. Available from https://github.com/chembl/KNIME_REST_example/blob/master/Activities_for_Target.knwf?raw=true
   Google Scholar
• ETL - What it is and why it matters, cited 2017 May 12. Available from
   Google Scholar
• Nowotka M, Davies M, Papadatos G, et al. ChEMBL beaker: a lightweight web framework providing robust and extensible cheminformatics services. Challenges. 2014;5:444–449.
   Google Scholar
• ChEMBL Beaker live documentation, cited 2017 May 12. Available from https://www.ebi.ac.uk/chembl/api/utils/docs
   Google Scholar
• Filippov IV, Nicklaus MC. Optical structure recognition software to recover chemical information: OSRA — an open source solution. J Chem Inf Model. 2009;49(3):740–743.
   PubMed Web of Science ®Google Scholar
• Luigi library documentation, cited 2017 May 12. Available from https://luigi.readthedocs.io/en/latest/.
   Google Scholar
• Example of using Luigi with ChEMBL API, cited 2017 May 12. Available from https://gist.github.com/mnowotka/b7df2253f31f0f2a4f88ab1747665fa0
   Google Scholar
• Comparison of different SQL implementations, cited 2017 May 12. Available from http://troels.arvin.dk/db/rdbms/
   Google Scholar
• Dragoni N, Giallorenzo S, Lafuente AL, et al. (2017). Microservices: yesterday, today, and tomorrow, Available from https://arxiv.org/pdf/1606.04036v2.pdf
   Google Scholar
• What is the Document Object Model? cited 2017 May 12. Available from https://www.w3.org/TR/DOM-Level-2-Core/introduction.html
   Google Scholar
• SASS, CSS with superpowers, cited 2017 May 12. Available from http://sass-lang.com/
   Google Scholar
• Ajax: A New Approach to Web Applications, cited 2017 May 12. Available from http://adaptivepath.org/ideas/ajax-new-approach-web-applications/
   Google Scholar
• Google Polymer Project, cited 2017 May 12. Available from https://www.polymer-project.org/
   Google Scholar
• Yandex BEM Technology, cited 2017 May 12. Available from https://tech.yandex.com/bem/
   Google Scholar
• Papadatos G, Gaulton A, Hersey A, et al. Activity, assay and target data curation and quality in the ChEMBL database. J Comput Aided Mol Des. 2015;29:885.10.1007/s10822-015-9860-5 .
   PubMed Web of Science ®Google Scholar
• Williams AJ, Harland L, Groth P, et al. Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today. 2012;17(21–22):1188–1198. DOI:10.1016/j.drudis.2012.05.016
   PubMed Web of Science ®Google Scholar
• Nguyen DT, Mathias S, Bologa C, et al. Pharos: collating protein information to shed light on the druggable genome. Nucleic Acids Res. 2017;45(D1):D995–D1002. DOI:10.1093/nar/gkw1072
   PubMed Web of Science ®Google Scholar
• Koscielny G, An P, Carvalho-Silva D, et al. Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 2017;45(D1):D985–D994. DOI:10.1093/nar/gkw1055
   PubMed Web of Science ®Google Scholar
• The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45(D1): D158–D169. DOI:10.1093/nar/gkw1099
   PubMed Web of Science ®Google Scholar
• Kutmon M, Riutta A, Nunes N, et al. WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Res. 2016;44(D1):D488–94. DOI:10.1093/nar/gkv1024
   PubMed Web of Science ®Google Scholar
• Hastings J, Owen G, Dekker A, et al. ChEBI in 2016: improved services and an expanding collection of metabolites. Nucleic Acids Res. 2016;44(D1):D1214–D1219. DOI:10.1093/nar/gkv1031
   PubMed Web of Science ®Google Scholar
• Piñero J, Bravo À, Queralt-Rosinach N, et al. DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res. 2017;45(D1):D833–D839. DOI:10.1093/nar/gkw943
   PubMed Web of Science ®Google Scholar
• Papadatos G, Davies M, Dedman N, et al. SureChEMBL: a large-scale, chemically annotated patent document database. Nucleic Acids Res. 2016;44(D1):D1220–D1228. DOI:10.1093/nar/gkv1253
   PubMed Web of Science ®Google Scholar
• Batchelor C, Brenninkmeijer CYA, Chichester C, et al. Scientific lenses to support multiple views over linked chemistry data. The Semantic Web–ISWC; Cham:Springer International Publishing. 2014. 98–113.
   Google Scholar
• Wang Y, Bryant SH, Cheng T, et al. PubChem BioAssay: 2017 update. Nucleic Acids Res. 2017;45(D1):D955–D963.
   PubMed Web of Science ®Google Scholar
• Gilson MK, Liu T, Baitaluk M, et al. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology. Nucleic Acids Res. 2016;44(D1):D1045–D1053. DOI:10.1093/nar/gkv1072
   PubMed Web of Science ®Google Scholar
• Southan C, Sharman JL, Benson HE, et al. The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands. Nucleic Acids Res. 2016;44(D1):D1054–D1068. DOI:10.1093/nar/gkv1037
   PubMed Web of Science ®Google Scholar
• PubChem Power User Gateway documentation, cited 2017 May 12. Available fromhttps://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html
   Google Scholar
• BindingDB Web Services documentation, cited 2017 May 12. Available from https://www.bindingdb.org/bind/BindingDBRESTfulAPI.jsp
   Google Scholar
• Guide to Pharmacology API documentation, cited 2017 May 12. Available from http://www.guidetopharmacology.org/webServices.jsp
   Google Scholar
• Kim S, Thiessen PA, Bolton EE, et al. PubChem substance and compound databases. Nucleic Acids Res. 2016;44(D1):D1202–D1213. DOI:10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• DailyMed API documentation, cited 2017 May 12. Available from https://dailymed.nlm.nih.gov/dailymed/app-support-web-services.cfm
   Google Scholar
• OpenFDA API documentation, cited 2017 May 12. Available from https://open.fda.gov/api/
   Google Scholar
• Wishart DS, Knox C, Guo AC, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006;34(supp_1):D668–72. DOI:10.1093/nar/gkj067
   PubMed Web of Science ®Google Scholar
• DrugBank API documentation, cited 2017 May 12. Available from https://docs.drugbankplus.com/v1/
   Google Scholar
• Cactus Chemical Identifier Resolver documentation, cited 2017 May 12. Available from https://cactus.nci.nih.gov/chemical/structure
   Google Scholar
• Open PHACTS API documentation, cited 2017 May 12. Available from https://dev.openphacts.org/docs/2.1
   Google Scholar
• ChemSpider Webservices Overview, cited 2017 May 12. Available from http://www.chemspider.com/AboutServices.aspx?
   Google Scholar
• Chambers J, Davies M, Gaulton A, et al. UniChem: extension of InChI-based compound mapping to salt, connectivity and stereochemistry layers. J Cheminform. 2014;6:43. DOI:10.1186/s13321-014-0043-5
   PubMed Web of Science ®Google Scholar
• Uniprot mapping database identifiers example from programmatic access documentation, cited 2017 May 12. Available from http://www.uniprot.org/help/programmatic_access#id_mapping_examples
   Google Scholar
• The Principle of Least Power, cited 2017 May 12. Available from https://blog.codinghorror.com/the-principle-of-least-power/.
   Google Scholar
• Marvin JS, cited 2017 May 12. Available from https://www.chemaxon.com/products/marvin/marvin-js/
   Google Scholar
• Jiang C, Jin X, Dong Y, et al. Kekule.js: an open source javascript chemoinformatics toolkit. J Chem Inf Model. 2016;56(6). DOI:10.1021/acs.jcim.6b00167
   Web of Science ®Google Scholar
• Emscripten project cited 2017 May 12. Available from http://kripken.github.io/emscripten-site/
   Google Scholar
• Ertl P, Patiny L, Sander T, et al. Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia. J Cheminform. 2015;7:10. DOI:10.1186/s13321-015-0061-y
   PubMed Web of Science ®Google Scholar
• Searching ChEMBL in the browser, cited 2017 May 12. Available from https://nextmovesoftware.com/blog/2017/01/05/searching-chembl-in-the-browser/
   Google Scholar
• Newman S. Building microservices. O’Reilly Media. ISBN 978-14919. O'Reilly Media. 2015.280.
   Google Scholar