Molecule2PubChemLCSS
by Jordi Cuadros This Google spreadsheet will allow anyone to connect a list of up to 1,000 chemical names to safety chemical information available in PubChem LCSS. To obtain the spreadsheet you click the content link, which directs you to Google Docs and allows you to make your own copy of the sheet. It comes preloaded with 10 items on the sheet, after a few seconds redundant items became grayed out, unique chemicals are converted to black pring and non chemicals stay red. If you click the “OrderedStockroom” tab you will see a table listing the number of chemicals, their PubChem ID, their alphabetically ordered IUPAC name and a link to the PubChem LCSS.
PubChem aggregates chemical safety data from a variety of databases and models the Laboratory Chemical Safety Summaries of the National Research Councils Prudent Practices in the Laboratory. The provenance of all data is maintained and this spreadsheet thus connects a database to updated and evolving chemical safety information, with a direct link to the original source
This is an application that uses InChI in identifying unique chemicals and in communicating with the database, and was developed by Jordi Cuadros of Universitat Ramon Llull. The followind youtube shows how to use and access this resource
This post consist of a simple spreadsheet that takes that splits an InChI in its layers to facilitate its conceptualisation and its teaching. It considers the six layers currently detailed in the InChI TechnicalFAQ, https://www.inchi-trust.org/wp/technical-faq-2/#4.3.
The spreadsheet also facilitates looking up an InChI by entering the molecule name or its SMILES representation.
Common tools for conversions, including some spreadsheet-based options included in this site, are hard to use for hundred or thousands of compounds we may want to use in cheminformatics projects. This resource includes a diferent approach to the conversion. By using the PubChem Power User Gateway it allows converting hundreds of chemical identifiers on a single call the a webservice.
Two files are included in this OER: an Excel file, that includes two UDF functions for doing the conversions, documentation and examples; and a VBA module that can be imported to any Excel file to include this functions to any existing spreadsheet.
This resource is a simple spreadsheet in Excel that provides a handy interconversion between different chemical identifiers, namely name, InChI, InChIKey and SMILES. It uses some web services to do translations, i.e. PubChem PUG REST and NCI/CADD Chemical Identifier Resolver.
This workbook does not uses macros but makes use of the WEBSERVICE function added to Excel for Windows in Excel 2013.
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.
