BioChemUDM: a unified data model for compounds and assays

References

[1] F. Agnetti, M. Bensch, H. Biller, M. Blapp, B. Cheikh, G. Blanke, J. Degen, B. Dienon, T. Doerner, G. Doernen, F. Farshchian, W. Gotzeina, P. Hilty, R. Horstmoeller, T. Jeker, B. Jones, M. Kappler, A. Momin, A. Regoli, D. Ribaud, B. Starck, D. Stoffler, K. Weymann, P. Udupa. Intuitive and integrated browsing of reactions, structures, and citations: The Roche experience. In 245th National Meeting of the American Chemical Society, New Orleans, LA, April 7–11, (2013), https://www.nextmovesoftware.com/news/KapplerPoster2013.pdf (accessed Sep 9, 2021).Search in Google Scholar

[2] R. Sayle, D. Lowe, N. O’Boyle, M. Kappler, A. Pelliccioli, N. Tomkinson, D. Stoffler. Extraction, analysis, atom mapping, classification and naming of reactions from pharmaceutical ELNs. 6th Joint Sheffield Conference on Cheminformatics, July 22–24, (2013), https://cisrg.shef.ac.uk/shef2013/showabstract.php?id=56 (accessed Oct 10, 2021).Search in Google Scholar

[3] Elsevier Press Release. Elsevier and Roche Collaborate to Integrate Proprietary Chemistry Data in Reaxys®, Elsevier GmbH, Frankfurt, Germany (2012), https://www.elsevier.com/about/press-releases/archive/science-and-technology/elsevier-and-roche-collaborate-to-integrate-proprietary-chemistry-data-in-reaxys. (accessed Apr 19, 2020).Search in Google Scholar

[4] T. Hoctor, M. Kappler. Making Dollars and Sense from Large Data, Global Drug Discovery Informatics Summit, Princeton, NJ (2013).Search in Google Scholar

[5] Elsevier Press Release. Elsevier Donates Unified Data Model to The Pistoia Alliance, Facilitating Data Sharing and Accelerating Research in the Life Sciences, Elsevier GmbH, Frankfurt, Germany (2017), https://www.elsevier.com/about/press-releases/archive/clinical-solutions/elsevier-donates-unified-data-model-to-the-pistoia-alliance,-facilitating-data-sharing-and-accelerating-research-in-the-life-sciences (accessed Oct 10, 2021).Search in Google Scholar

[6] XML 1.0 Specification. World Wide Web Consortium (2008), https://www.w3.org/TR/REC-xml/https://en.wikipedia.org/wiki/XML (accessed May 23, 2022). “The Extensible Markup Language is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable.” (accessed May 23, 2022).Search in Google Scholar

[7] CDXML Format. CDXML is the XML Analogue of the Binary CDX File Type used by CambridgeSoft Corporation’s ChemDraw Chemical Structure Application (2020), https://en.wikipedia.org/wiki/CDXML (accessed May 23, 2022).Search in Google Scholar

[8] JSON Format. JSON is an open standard file format and data interchange format that uses human-readable text to store and transmit data objects consisting of attribute–value pairs and arrays (or other serializable values) (2001), https://en.wikipedia.org/wiki/JSON (accessed May 23, 2022).Search in Google Scholar

[9] Pistoia Alliance News. The Pistoia Alliance announces major milestone in unified data model project to promote life sciences collaboration, The Pistoia Alliance is a Global Not-for-Profit Members’ Organization Collaborating to Lower Barriers to Innovation in Life Science and Healthcare R&D, Elsevier, Boston, MA (2018), https://www.pistoiaalliance.org/news/udm-release-v5/ (accessed Oct 10, 2021).Search in Google Scholar

[10] T. Struble, J. Alvarez, S. Brown, M. Chytil, J. Cisar, R. DesJarlais, O. Engkvist, S. Frank, D. Greve, D. Griffin, X. Hou, J. Johannes, C. Kreatsoulas, B. Lahue, M. Mathea, G. Mogk, C. Nicolaou, A. Palmer, D. Price, R. Robinson, S. Salentin, L. Xing, T. Jaakkola, W. Green, R. Barzilay, C. Coley, K. Jensen. J. Med. Chem. 63, 8667 (2020), https://doi.org/10.1021/acs.jmedchem.9b02120.Search in Google Scholar PubMed PubMed Central

[11] E. Cascade, C. Sears. Leveraging a Unified Data Model to Drive Collaboration and Clinical Trial Efficiency, Applied Clinical Trials (2018), https://www.appliedclinicaltrialsonline.com/view/leveraging-unified-data-model-drive-collaboration-and-clinical-trial-efficiency (accessed Oct 10, 2021).Search in Google Scholar

[12] J. Tomczak, E. Herzog, M. Fisher, J. Swienty-Busch, F. van den Broek, G. Whittick, M. Kappler, B. Jones, G. Blanke. UDM (Unified Data Model) for Chemical Reactions – Past, Present and Future, this issue.Search in Google Scholar

[13] A. Dalby, J. Nourse, W. Hounshell, A. Gushurst, D. Grier, B. Leland, J. Laufer. J. Chem. Inf. Comput. Sci. 32, 244 (1992), https://doi.org/10.1021/ci00007a012.Search in Google Scholar

[14] CTfile Formats, Elsevier (2005), http://c4.cabrillo.edu/404/ctfile.pdf (accessed Oct 10, 2021).Search in Google Scholar

[15] CTfile Formats. Dassault Systemes (2016), http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/direct/reference/ctfileformats2016.pdf (accessed Oct 10, 2021).Search in Google Scholar

[16] Y. Shafranovich. RFC 4180: Common Format and MIME Type for CSV Files, IETF (2005).Search in Google Scholar

[17] E. Martin, A. Monge, J.-A. Duret, F. Gualandi, M. Peitsch. J. Cheminform. 4, 11 (2012).10.1186/1758-2946-4-11Search in Google Scholar PubMed PubMed Central

[18] A. Hersey, J. Chambers, L. Bellis, A. Bento, A. Gaulton, J. Overington. Drug Discov. Today Technol. 14, 17 (2015).10.1016/j.ddtec.2015.01.005Search in Google Scholar PubMed PubMed Central

[19] R. Sayle. J. Comput. Aided Mol. Des. 24, 485 (2010).10.1007/s10822-010-9329-5Search in Google Scholar PubMed

[20] A. Gobbi, M.-L. Lee. J. Chem. Inf. Model. 52, 285 (2012), https://doi.org/10.1021/ci200330x.Search in Google Scholar PubMed

[21] L. Guasch, W. Yapamudiyansel, M. Peach, J. Kelley, J. JBachiJr, M. Nicklaus. J. Chem. Inf. Model. 56, 2149 (2016).10.1021/acs.jcim.6b00338Search in Google Scholar PubMed PubMed Central

[22] D. Dhaked, M. Nicklaus. Tautomeric conflicts in forty small-molecule databases (2021), ChemRxiv Cambridge Open Engage. This content is a working paper (preprint) and has not been peer-reviewed.10.26434/chemrxiv.14779254.v1Search in Google Scholar

[23] SMIRKS – A Reaction Transform Language. Daylight Theory Manual (1997), https://www.daylight.com/dayhtml/doc/theory/theory.smirks.html (accessed May 24, 2022).Search in Google Scholar

[24] W. Ihlenfeldt, Y. Takahashi, H. Abe, S. Sasaki. J. Chem. Inf. Comput. Sci. 34, 109 (1994).10.1021/ci00017a013Search in Google Scholar

[25] RDKit. Open-Source Cheminformatics, https://www.rdkit.org.Search in Google Scholar

[26] BIOVIA Pipeline Pilot. Release 21.2.0.2574, Dassault Systèmes, San Diego (2021).Search in Google Scholar

[27] C. Baker, N. Kidley, K. Papachristos, M. Hotson, R. Carson, D. Gravestock, M. Pouliot, J. Harrison, A. Dowling. J. Chem. Inf. Model. 60, 3781 (2020).10.1021/acs.jcim.0c00232Search in Google Scholar PubMed

[28] PerkinElmer Announcement. ChemDraw/ChemOffice+ Cloud v20.0 (2020), https://informatics.perkinelmer.com/Support/SupportNews/details/?SupportNews=290 (accessed Oct 10, 2021).Search in Google Scholar

[29] H. Morgan. J. Chem. Doc. 5, 107 (1965), https://doi.org/10.1021/c160017a018.Search in Google Scholar

[30] R. Cahn, C. Ingold, V. Prelog. Angew. Chem. Int. Ed. 5, 385 (1966), https://doi.org/10.1002/anie.196603851.Search in Google Scholar

[31] BIOVIA Pilotscript. Release 2016, Dassault Systèmes, San Diego (2016), http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/pipeline%20pilot/other/pilotscript.pdf (accessed Oct 10, 2021).Search in Google Scholar

[32] Scripting Integrations. KNIME Community (2019), https://www.knime.com/community/scripting (accessed Oct 10, 2021).Search in Google Scholar

[33] D. Bonchev. Chemical Graph Theory: Introduction and Fundamentals, Routledge (1991).Search in Google Scholar

[34] ChemAxon Documentation. ChemAxon Extended SMILES and SMARTS – CXSMILES and CXSMARTS, https://docs.chemaxon.com/display/docs/chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md (accessed Oct 10, 2021).Search in Google Scholar

[35] S. Heller, A. McNaught, I. Pletnev, S. Stein, D. Tchekhovskoi. Journal of Cheminformatics 7, 23 (2015), https://doi.org/10.1186/s13321-015-0068-4.Search in Google Scholar PubMed PubMed Central

[36] D. Dhaked, W. Ihlenfeldt, H. Patel, V. Delannee, M. Nicklaus. J. Chem. Inf. Model. 60, 1253 (2020).10.1021/acs.jcim.9b01080Search in Google Scholar PubMed PubMed Central

[37] W. DeGruyter. Chem. Int. 42, 1, 30 (2020).Search in Google Scholar

[38] USPTO Reg. No. 3,884,839, CDD Vault, registered December 7, 2010. https://tsdr.uspto.gov/documentviewer?caseId=sn77791158&docId=ORC20101207004753.Search in Google Scholar

[39] L. Fisher. CDD Support: Advanced Stereochemistry Registration: Atropisomers, Mixtures, Unknowns and Non-Tetrahedral Chirality, https://support.collaborativedrug.com/hc/en-us/articles/360020872171-Advanced-Stereochemistry-Registration-Atropisomers-Mixtures-Unknowns-and-Non-Tetrahedral-Chirality (accessed Oct 10, 2021).Search in Google Scholar

[40] M. Wilkinson, M. Dumontier, I. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. W. Boiten, L. da Silva Santos, P. Bourne, J. Bouwman, A. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C. Evelo, R. Finkers, A. Gonzalez-Beltran, A. Gray, P. Groth, C. Goble, J. Grethe, J. Heringa, P. Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S. Lusher, M. Martone, A. Mons, A. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S.-A. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, I. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, B. Mons. Sci. Data 3, 160018 (2016), https://doi.org/10.1038/sdata.2016.18.Search in Google Scholar PubMed PubMed Central

[41] AWS Lake Formation. What is a Data Lake? https://aws.amazon.com/big-data/datalakes-and-analytics/what-is-a-data-lake/ (accessed Oct 10, 2021).Search in Google Scholar