InChI Tag: Google Sheet

2 posts

Molecule2PubChemLCSS

English Google Sheet Graduate Researcher safety Spreadsheet

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


IUPAC Name2PubChem

Audience Content type Curricular Material File Type Google Sheet Graduate InChI Algorithm and Description Researcher Resolvers Spreadsheet Undergraduate video

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.