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NIH Virtual Workshop on InChI, March 22-24, 2021, from 11 AM – ~3PM EST

  • 21 Mar 2021 11:59 PM
    Message # 10222642

    Note: The program of this workshop is given in its entity even not all presentation may be interested for the Group. Additional information would include some major approved documentation/publication related InChI projects, and additional information/publications to particular presentation of interest. -ab


    NIH Virtual Workshop on InChI, March 22-24, 2021

    A major theme emerging from the December 2020 NIH Workshop on Ultra Large Chemistry Databases  [see links to recording and presentations of this workshop-ab] is the essential role of the IUPAC International Chemical Identifier (InChI) in our ability to link and query across large and diverse chemistry data resources. Therefore, we now seek to bring the chemistry community together for an update on the development of the InChI and a discussion of its use in chemistry, biochemistry, and related research domains.

    Speakers will report on developments in the InChI field, usage of InChI in their organization, as well as challenges and areas not yet covered by InChI. The virtual workshop is scheduled for three half-days on March 22-24, from 11 AM – ~3PM EST and will include short talks and panel discussions


    Link to presentations



    Preliminary Agenda

    Day 1 – Monday, March 22, 2021


    11 -11:02 am Steve Heller NCBI/NLM/NIH/PubChem Housekeeping remarks 1
    11:02-11:17 am Ray Boucher InChI Trust/Wiley The IUPAC Chemical Structure Standard – Vision and Future 2
    11:17-11:25 Steve Heller NCBI/NLM/NIH/PubChem A Brief History of InChI 3
    11:45 - 12:05 pm  Marc Nicklaus   NCI/NIH Tautomers in InChI 5
    12:05 - 12:25 Jonathan Goodman University of Cambridge InChI with Markush Variations 6
    12:25 - 12:45 Evan Bolton NCBI/NLM/NIH PubChem Large Molecules 7
    12:45 - 1: 05 Gerd Blanke Structure Pendium Technologies GmbH Reaction InChI (RInChI) - What's Next? 8
    1:05 - 1:25 Bob Belford

    Univ of Arkansas at Little Rock

    InChI Open Education Resource (OER) 9
    1:25 - 1:45 Alex Clark Collaborative Drug Discovery Mixtures InChI: A Story of How Standards Drive Upstream Products 10
    1:45 - 2:05 Iseult Lynch University of Birmingham Towards an InChI for Nanomaterials 11
    2:05 - 2:25 Jeremy Frey University of Southampton Linking the Physical and Digital: QR Codes and the InChI 12
    2:25 - 2:45 Markus Sitzmann  FIZ Karlsruhe The InChI Resolver and its Protocol 13
    2:45 -3:05 Colin Batchelor RSC InChi, Organometallics and Inorganics 14

    Day 2 – Tuesday, March 23, 2021

    Time Speaker Affiliation Title
    11:00-11:25 am Yulia Borodina   FDA Usage of InChI in SPL Substance Indexing files 15
    11:25-11:50 Greg Landrum   ETH Zurich Using InChI, and bits of InChI, from within the RDKit 16
    11:50 - 12:15pm Roger Sayle NextMove Software InChI on Wikipedia: Why Many Compounds Have More Than One InChI n/a
    12:15 - 12:40 Tony Williams EPA The CompTox Chemicals Dashboard and Using InChI as a Mapping Identifier 18
    12:40 - 1:05 John Irwin UC San Francisco How ZINC Uses InChI 19
    1:05 - 1:30 István Őri ChemAxon Integrating InChI and RInChI Native Libraries into  Java Applications n/a
    1:30 - 1: 55 Peter Linstrom NIST Practical Applications of InChI 21
    1:55 - 2:20 Connor Coley MIT The Open Reaction Database (ORD) Initiative for  Standardizing and Sharing Organic Reaction Data 22
    2:20 - 2:45 Gunther Schadow  Pragmatic Data  QuinChi - A variation of InChi for expressing structure queries n/a

    Day 3 – Wednesday, March 24, 20244


    11:00-11:25 am Lutz Weber OntoChem GmbH Using InChI and RInChI for Registering Compound and Reactions Extracted from Literature 24
    11:25-11:50 John Mayfield   NextMove Software Data Compression of InChIKeys and 2D Coordinates 25
    11:50 - 12:15pm Patricia Bento EMBL-EBI InChI Applications in ChEMBL 26
    12:15 - 12:40 Mitch Miller NCATS Global Substance Registration System: Extending the Concept of InChiKey to Other Substances 27
    12:40 - 1:05 Egon Willihagen Maastricht University InChI and InChIKey in Wikidata and Scholia 28
    1:05 - 1:30 Richard Apodaca Metamolecular Running InChI Anywhere with WebAssembly 29
    1:30 - 1: 55 Stephen Schurer University of Miami Common errors and ignorance in small molecule chemical structure representation: Towards developing an Automated Molecular Identity Disambiguator (AutoMID) 30
    1:55 - 2:20 Trung Nguyen   NIH/NCATS Do Structurally Similar InChIs have Similar Hash Keys 31
    2:20 - 2:50 Open Discussion Jonathan Goodman - Chair, Evan Bolton, Richard Kidd, Gerd Blanke, Elena Herzog
    32

     Organizers:

    Steven Heller, Ph.D.
    Chemistry Group, Information Engineering Branch
    National Center for Biotechnology Information, NIH

    Marc Nicklaus, Ph.D.
    Computer-Aided Drug Design Group
    Center for Cancer Research, National Cancer Institute, NIH

    Evan Bolton, Ph.D.
    Chemistry Group, Information Engineering Branch
    National Center for Biotechnology Information, NIH

    Noel Southall, Ph.D.
    Division of Preclinical Innovation
    National Center for Advancing Translational Sciences, NIH

    +++++++++++++++++++++++++++++

    Additional information

    InChI = IUPAC International Chemical Identifier

    Information about InChi Project could be found at the website of  InChi Trust, LTd (https://www.inchi-trust.org/), which responsible for InChI maintenance and development and on web-pages web-pages of IUPAC Division VIII Chemical Nomenclature and Structure Representation which approves and funds particular IUPAC projects.


    Technical Dicumentation and publications:

    InChI (IUPAC International Chemical Identifier)

    Heller, S.R., McNaught, A., Pletnev, I., Stein, S., Tchekhovskoi, D., 2015. InChI, the IUPAC International Chemical Identifier. Journal of Cheminformatics 7, 23 (34 p.). https://doi.org/10.1186/s13321-015-0068-4

    Stein, S.E., Heller, S.R., Tchekhovskoi, D.V., Pletnev, I.V., 2011. IUPAC International Chemical Identifier (InChI). InChI version 1, software version 1.04 (2011), Technical Manual. National Institute of Standards and Technology . 89 p. https://www.inchi-trust.org/download/104/InChI_TechMan.pdf

    RIChi

    Grethe, G., Blanke, G., Kraut, H., Goodman, J.M., 2018. International chemical identifier for reactions (RInChI). Journal of Cheminformatics 10, 22 [9 p.]. https://doi.org/10.1186/s13321-018-0277-8

    Grethe, G., Goodman, J.M., Allen, C.H., 2013. International chemical identifier for reactions (RInChI). J Cheminform 5, 45 [9 p.]. https://doi.org/10.1186/1758-2946-5-45

    Blanke, G., 2017. International chemical identifier for reactions (RInChI) Version 1.00. Structure Pendium Technologies GmbH. 53 p. https://www.inchi-trust.org/download/RInChI/RInChI V1-00-0.pdf


    References/notes related to particular presentations:

    References/notes related to particular presentations:
    Notes to Day 1
    [1] See [3]
    [2] Boucher, R., Heller, S., McNaught, A., 2017. The Status of the IUPAC InChI Chemical Structure Standard – Today and the Future. Presented at IUPAC General Assembly, Sao Paulo, Brazil, July 13, 2017 44 p. http://www.hellers.com/steve/pub-talks/sao-paulo-7-17.pdf
    [3] Heller, S.(NIST & InChI Project Director). 2019. A Short History of the IUPAC InChI Algorithm. Presented at 257th American Chemical Society National Meeting, Orlando, FL, April 1, 2019. 54 p. http://www.hellers.com/steve/pub-talks/orlando-4-19.pdf (See particular pp.18-19)
    [4] n/a
    [5] Dhaked, D.K., Ihlenfeldt, W.-D., Patel, H., Delannée, V., Nicklaus, M.C., 2020. Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2. J. Chem. Inf. Model. 60, 1253–1275. https://doi.org/10.1021/acs.jcim.9b01080
    [6] See [8a] at p.22: Markush structures (Variable structures) in Reaction representation
    [7] Bolton, E., 2019. Large molecules, variability, and more... Presented at “Status and Future of the IUPAC InChI” Symposium, San Diego 23-24 August 2019, 28 p. Status and Future of the IUPAC InChI Symposium, https://www.inchi-trust.org/wp/wp-content/uploads/2019/12/12.-Large-Molecule-Evan.pdf;  IUPAC Project No.:  2013-010-1-800, Implementation of InChI for chemically modified large biomolecules
    [8] (a) Nicolaides, D., Blanke, G., Grethe, G., Kraut, H., Öri, I., Jensen, J.H., Goodman, J., 2019. What’s going on at the International Chemical Identifier for Reactions (RInChI): Proposed developments to incorporate into the next release of Reaction InChI, including process information in a machine-readable format, and atom mapping. Presented at ChemAxon User Meeting, Budapest, May 22, 2019 (Slides 22 p; video (14:53));
    -- (b)
    Nicolaides, D., Blanke, G., Grethe, G., Kraut, H., Öri, I., Jensen, J.H., Goodman, J., 2020. International Chemical Identifier for Reactions (RInChI): Present and Future. Presented at AI React 2020 (AI for Reaction Outcome & Synthetic Route Prediction 2020). Poster, https://drive.google.com/file/d/1pgmgWTWQMmCMURJouUQhmJzGKv9XvSms/view
    [9] (a) Belford, R.E., Bucholtz, E.C., Cornell, A.P., Cuadros, J., Scalfani, V., Walker, M.A., 2018. InChI Open Education Resource. Presented at Biennial Conference on Chemical Education (BCCE) at the University of Notre Dame, IN (29 July – 2 Aug 2018). Poster. https://iupac.org/wp-content/uploads/2018/08/2018BCCE_InChIOER_Poster_Final.pdf
    ---(b)
    Belford, R., 2019. InChI OER: Open Education Resource. Presented at ACS National Meeting, San Diego, Aug. 25-29, 2019. 45 p. https://www.inchi-trust.org/wp/wp-content/uploads/2019/12/7.-Belford_InChIOER_Talk-v2.pdf
    [10] (a) Clark, A.M., McEwen, L.R., Gedeck, P., Bunin, B.A., 2019. Capturing mixture composition: an open machine-readable format for representing mixed substances. Journal of Cheminformatics 11, 33 [17 p.]. https://doi.org/10.1186/s13321-019-0357-4
    -- (b) Clark, A.M., 2020. Online mixtures demo, with MInChI generator. Cheminformatics 2.0. URL https://cheminf20.org/2020/05/11/online-mixtures-demo-with-minchi-generator/ (accessed 3.21.2021).
    ---(c) [MInChI Demo]
    ---(d)
    McEven, L., Jacober, C., Clark, A., 2019. Capturing Mixtures — Bringing Informatics to the World of Practical Chemistry. CDD Vault Webinar. Dec. 19, 2019 (Presentation, 27 p., video, 55:28)
    ---(e McEwen, L., Clark, A.M., 2020. Mixtures: informatics for formulations and consumer products.Presented at RSC Interest Group Formulation Science & Technology (RSC FST) Formulation 4.1  Putting Digital into Formulation, Nov. 3, 2020. (Presentation, 27 p., video 28:05)
    ---(f) Clark, A.M., 2021. Mixtures InChI (MInChI): an open machine-readable format for representing mixed substances (Mixtures as first class citezens in the realm of cheminformatics). Presented at Cambridge Cheminformatics Network Meeting, Feb. 10, 2021, https://www.youtube.com/watch?v=0ILc0owuEzQ&t=3960s---(g)See John DiNatale (USPTO) comment in a Chart of 2021-03-22 at 13:38:51: “It seems like it might be a good idea to consult learnings from others by exploration of techniques of indexing of the mixtures in the new STN database of Chemical Compositions. I believe it is geared toward patent searching which is probably the bulk of searching for mixtures/compositions.”
    [11] Lynch, I.[University of Birmingham, UK], Afantitis, A., Exner, T, …
    Melagraki, G.[NovaMechanics Ltd., Cyprus]. 2020. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies? Nanomaterials 10, 2493 (44 p.). https://doi.org/10.3390/nano10122493 [Peer-Review Record]
    [12] Hartshorn, R. (Univ. of Canterbury_, 2019. QR Code InChI - IUPAC & InChITrust Project: Connecting Physical & Digital worlds. Presented at  Status and Future of the IUPAC InChI Symposium, San Diego 23-24 August 2019. 16 p. https://www.inchi-trust.org/wp/wp-content/uploads/2019/12/17.-InChI-QR-Code-RMH.pdf (See also IUPAC Project No.: 2015-019-2-800 [Identifying InChI Enhancements -- QR codes and Industry Applications])
     [13] (a)Markus Sitzmann. Chemical Identifier Resolver @NCI/CADD; Chemical Identifier Resolver documentation (See Standard InChIKeys; InChI/Standard InChI)
    ---(b) Markus Sitzmann. Home page of the InChI Resolver
    [14] See IUPAC Project No.: 2009-040-2-800 details: InChI Requirements for Representation of Organometallic and Coordination Compound Structures. Tabs: Description & Progress


    Notes to Day 2

    [15] Yulia Borodina, 2019. How InChI helps describe and identify biopharmaceuticals. Presented at InChI symposium Fall 2019 San Diego, CA, August 23 -24, 2019, 16 p. https://www.inchi-trust.org/wp/wp-content/uploads/2019/12/21.-Yulia_InChI_2019.pdf
    [16]
    Greg Landrum, 2017. Open file formats for chemical information. . Presented at InChI symposium San Diego, CA, August 23 -24, 2019, 21 p. https://www.inchi-trust.org/wp/wp-content/uploads/2017/11/26.-GregLandrumGL_InChI_OpenFileFormats.pdf
    [18] DSSTox Mapping File  The DSSTOX mapping file contains mappings between the DSSTox substance identifier (DTXSID) and the associated InChI String and InChI Key. See https://comptox.epa.gov/dashboard/downloads
    [19] Sterling, T., Irwin, J.J., 2015. ZINC 15 – Ligand Discovery for Everyone. J. Chem. Inf. Model. 55, 2324–2337. https://doi.org/10.1021/acs.jcim.5b00559 (CiteSeerX) See Chemical search in ZINC using InChI, InChIkey, p.2326-7
    [21]
    Linstrom, P.J. (NIST, Office of Data and Informatics). 2019. InChI and Data Management. Presented at InChI symposium San Diego, CA, August 23, 2019, 19 p. https://www.inchi-trust.org/wp/wp-content/uploads/2019/12/6.-inchi-san-diego-pjl-2019-08-23-NIST-.pdf
    [22] (a)
    Coley, C. (MIT), Kearnes, S.(Google), 2020. The Open Reaction Database. Presented at RDKit UGM, 7 October 2020. Presentation 32 p; video, (28:16)
    --- (b)
     Open Reaction Database Documentation

    Notes to Day 3

    [24] Weber, L.(OntoChem GmbH), 2019. Open access Web API registration and retrieval of ontology concepts. Presented at InChI Trust Symposium, Symposium, San Diego 23-24 August 2019. 17 p. https://www.inchi-trust.org/wp/wp-content/uploads/2019/12/4.-OntoChem-InChI_Trust_2019-08-23-v2-1.pdf
    [26] See ChEMBL Data Web Services [ising InChI (Substructure search or Similarity (80% cut off) for against ChEMBL using … InChI Key
    ; Get a single molecule by InChi; Get many compounds by a list of InChi Keys; Resolve InChi Key to Inchi using Unichem)
    [27] Peryea, T., Southall, N., Miller, M., et al. 2021. Global Substance Registration System: consistent scientific descriptions for substances related to health. Nucleic Acids Research 49, D1179–D1185. https://doi.org/10.1093/nar/gkaa962
    [28] Willighagen, E., 2019. Cheminformatics to improve Wikidata on chemical compounds. Presented at WikdiataCon 2019, Oct. 26, 2019 Berlin/DE. 27 p. https://upload.wikimedia.org/wikipedia/commons/e/ed/Cheminformatics_to_improve_Wikidata_on_chemical_compounds%2C_2019-10-26%2C_Egon_Willighagen.pdf (See p. 23 p.23 “ChemCuration example: InChIKeys”)
    [29] (a) Apodaca, R.L.(Metamolecular, LLC), 2019. Compiling InChI to WebAssembly Part 1: Hello InChI [WWW Document]. URL http://depth-first.com/articles/2019/05/15/compiling-inchi-to-webassembly-part-1/ (accessed 3.23.21).
    --- (b)Apodaca, R.L., 2021. Parsing InChI: It’s Complicated [WWW Document]. URL http://depth-first.com/articles/2021/03/10/parsing-inchi-its-complicated/ (accessed 3.23.21).
    [30] Kelley, T.T., Terryn, R., Koleti, A., Chung, C., Turner, J.P., Stathias, V., Vidović, D., Schürer, S., 2017. LINCS Small Molecules Standardization and Annotation to Improve Data Integration, Analysis, and Modeling. Presented at  BD2K-LINCS Data Science Symposium (DSS 2017) Cincinnati, OH on May 16-18, 2017. Poster. https://figshare.com/articles/poster/LINCS_Small_Molecules_Standardization_and_Annotation_to_Improve_Data_Integration_Analysis_and_Modeling/4962710/1
    [31] Tripod Development, 2013. Do structurally similar molecules have similar hash codes? Tripod Development. URL https://tripod.nih.gov/?p=522 (accessed 3.23.21).

    Update 3/31/2021 1:43: A link to the event web-page with available copies of presentations has been added.

    Update 4/1/2021 7:43:References to Note 10 has been amended

    Last modified: 01 Apr 2021 7:41 AM | Anonymous member

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