PubChem: Advancing chemical information through InChI
Evan Bolton InChI in the Wild: Celebrating Over 20 years of InChI Development in Memory of InChI Developer Igor Pletnev
Fall 2022 ACS National Meeting
2022-08-21
Abstract: The PubChem project (https://pubchem.ncbi.nlm.nih.gov) has been a long time user and contributor to the InChI project. The impact of the InChI project on chemical information and chemical informatics cannot be understated. Professor Igor Pletnev was a key interface for InChI almost from the beginning with many interactions with the PubChem team. This talk will show some of the ways InChI is being used by the PubChem team to improve chemical information quality. In addition, some of the key interactions and contributions made by Igor to the InChI project will be highlighted.
Chris Jakober, Leah McEwen and Alex Clark
Slides and Video Available at CDD VAULT
Webinar Summary
Our industry has been using cheminformatics to support drug discovery for decades, leveraging formats for describing organic molecules, such as Molfile, SMILES, and InChI. These are idealized concepts rather than a description of the laboratory reality: it is rare that a substance can be accurately described with a single molecule.
Almost every sample has an impurity level, or is dissolved in solvent, or exists as an adduct, or is explicitly combined with other substances. Mixtures often combine certainty and uncertainty within the same description: some components can be well-defined molecules with an accurately measured molar concentration, while others are estimated portions, or amorphous adjuncts.
The cheminformatics community has yet to select a standard format for describing mixtures in a machine-readable, standardized, and interoperable way, and most publications fall back to using a text description. Electronic lab notebooks and inventory databases are forced to choose between using text, proprietary formats, or ignoring mixture composition altogether.
We will describe our work toward two new data structures: Mixfile and MInChI, which are intended to fill roles that are analogous to Molfile and InChI, respectively. We will describe the ways in which we expect that mixtures-based informatics tools will affect all industries that intersect with chemistry.
Join our expert panelists as we discuss the future of mixture representation, including:
IUPAC Standards Online is a database built from IUPAC’s (The International Union of Pure and Applied Chemistry) standards and recommendations, which are extracted from the journal Pure and Applied Chemistry (PAC).
The International Union of Pure and Applied Chemistry (IUPAC) is the organization responsible for setting the standards in chemistry that are internationally binding for scientists in industry and academia, patent lawyers, toxicologists, environmental scientists, legislation, etc. “Standards” are definitions of terms, standard values, procedures, rules for naming compounds and materials, names and properties of elements in the periodic table, and many more.
The database will be the only product that provides for the quick and easy search and retrieval of IUPAC’s standards and recommendations which until now have remained unsorted within the huge Pure and Applied Chemistry archive.
Covered topics:
Analytical Chemistry
Biochemistry
Chemical Safety
Data Management
Education
Environmental Chemistry
Inorganic Chemistry
Materials
Medicinal Chemistry
Nomenclature and Terminology
Nuclear Chemistry
Organic Chemistry
Physical Chemistry
Theoretical & Computational Chemistry
Toxicology
This presentation is a part of Google Tech Talks which was added to the GoogleTalksArchive on August 22, 2006. The original presentation date took place on November 2, 2006.
ABSTRACT (Imported From YouTube Source)
The central token of information in Chemistry is a chemical substance, an entity that can often be represented as a well-defined chemical structure. With InChI we have a means of representing this entity as a unique string of characters, which is otherwise represented by various of 2-D and 3-D chemical drawings, ‘connection tables’ and synonyms. InChI therefore represents a discrete physical entity, to which is associated as array of chemical properties and data. NIST has long been involved in disseminating chemical reference data associated with such discrete substances. A InChI is therefore the key index to this data. Many other types of data and information are also naturally tied to it, including biological information, commercial availability, toxicity, drug effectiveness and so forth. Because of the diversity of properties and interactions of a chemical substance, effective location of chemical information generally requires further qualifiers, which may be represented coarsely as a key word, but more precisely using a controlled vocabulary. There are no simple separations between information sought by difference disciplines and for different objectives. However, reference data may be organized according the disciplines most directly involved in making the measurements: -isolated substance – mass, infrared, NMR, spectra; physical properties -substance in the context of others – solubility, affinity, .. -properties of a mixture containing the substance The desired data can be a number, vector or image, usually associated with dimensions and links to source information. In some cases, this information is typically converted to a curve or diagram for use by an expert and may be further processed by specialized software. In other cases, a single numerical values is the target. Also, some complexities of structure that must be dealt with in practical search is represented in InChI, but must be decoded for use in searching.
2012 San Diego ACS presentation: Registration system of mcule: InChI is the key
Mcule provides virtual screening services on the web to help identifying novel drug candidates by screening different databases. For these databases, it is essential to have a robust molecule registration system not depending on different drawing conventions, tautomeric states, etc. It is critical to assure that the same compounds get the same IDs and, most importantly, different compounds never get the same ID. To the best of our knowledge, InChI provides the best solution for this problem. In this presentation we would like to summarize how InChI is implemented into the mcule registration system and how it is used effectively with our vendor database and open registration services.
This submission shows you how to create a smart spreadsheet with Google Sheets that links an IUPAC name to a chemical’s PubChem landing page. You may click here to get a copy of this sheet. This particular sheet uses the Centre for Molecular Informatics OPSIN (Open Parser for Systematic IUPAC nomenclature) web service to convert the name to an InChI key, which is then appended to a hyperlink to PubChem. You will note that some of the names do not work and this is because those names in the sample sheet are incorrect names. If you paste those names directly into the OPSIN web service, it will tell you were an error in parsing the name occurred.
The following video shows you how to create this Google Sheet and below it is the instructions and code needed. This application takes advantage of the canonical nature of the InChI and its key, and the fact that the key allows you to communicate over the web.
Step 1: Paste your IUPAC names into a column of your spread sheet
Step 2: Convert IUPAC name to Standard InChI key
type the following script into the top cell of the column you want to place your keys into, and hit enter”
=IMPORTDATA(“http://opsin.ch.cam.ac.uk/opsin/”&[SPREADSHEET CELL WITH IUPAC NAME]&“.stdinchikey”)
the ampersand(&)concatenates the cell content to the URL
the ampersand must be surrounded by quotation marks
the URL must be in quotation marks
Click on the black box in the bottom right corner of cell and drag down, converting the entire column of names to keys.
Step 3: Hyperlink the key to PubChem Type the following script into the top cell of the column you want to place your links into, and hit enter”n
=HYPERLINK(“https://pubchem.ncbi.nlm.nih.gov/compound/”&[SPREADSHEET CELL WITH INCHIKEY]&“”)
the ampersand (&) concatenates the cell content to the URL
the ampersand must be surrounded by quotation marks
the URL must be in quotation marks
NOTE, these are dynamic cells – And will be recalculated everytime you open the page, or change the chemical name. If you want them to be static, you can copy the block of cells, and paste to another location as text.
You can also download the sheet as an Excel Spreadsheet, but the downloaded sheet will not be dynamic. It will be linked, but will not change if you change the IUPAC name.
