{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2016/01/27/adding-chemical-compound-to-wikidata.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/q5a38-51n24", "url": "https://chem-bla-ics.linkedchemistry.info/2016/01/27/adding-chemical-compound-to-wikidata.html", "title": "Adding chemical compounds to Wikidata", "content_html": "

Adding chemical compounds to Wikidata is not difficult. You can store the chemical formula\n(P274), (canonical) SMILES\n(P233), InChIKey (P235) (and InChI\n(P234), of course), as well various database identifiers (see what I wrote about that\nhere ]). It also allows storing of the provenance, and has predicates\nfor that too.

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So, to enter a new structure for a compound, you should enter the compound information to Wikidata. Of course, make sure to create the needed accounts,\nparticularly one for Wikidata (create account)\n(not sure if the next steps needs a more general Wikimedia account too).

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Entering the research paper:
\nMagnus Manske pointed me to\nthis helper tool. If you have the DOI of the paper, it is easy to add a new paper. This is what the tool shows\nfor doi:10.1128/AAC.01148-08 (but no longer when you try!):

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You need permission to run this script and the tool will alert you about that, and give the instructions how to get permission. After\nI clicked the Open in QuickStatements I get this output, showing me an entry in Wikidata was created for this paper:

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Later, I can use the new Q-code (Q22309806) to use as source for statements about the compound (formula, etc).

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Draw your compound and get an InChIKey:
\nThe next step is to draw a compound and get an InChIKey. This can be done with many tools, including\nBioclipse. Rajarshi opted for alternatives:

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Then check if the compound is not already in Wikidata. You can use this SPARQL query for that using the InChIKey of the compound (it’s for acetic acid, so it will be found):

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For convenience, here the copy/pastable SPARQL:

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PREFIX wdt:\nSELECT ?compound WHERE {\n  ?compound wdt:P235 \"QTBSBXVTEAMEQO-UHFFFAOYSA-N\" .\n}\n
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Entering the compound:
\nSo, the compound is not already in Wikidata, so time to add it. The minimal information you should provide is the following:

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The first step is to create a new Wikidata entry. The Create new item menu in the left side panel can be used, showing a page like this:

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As a label you can use the name used in the paper for the compound, even if a code, and as description ‘chemical compound’ will do for now; it can be changed later.

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Feel free to add as much information about the compound as you can find. There are some chemically rich entries in Wikidata, such as that for acetic acid\n(Q47512).

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References

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Wang, Q.-Y., Patel, S. J., Vangrevelinghe, E., Xu, H. Y., Rao, R., Jaber, D., Schul, W., Gu, F., Heudi, O., Ma, N. L., Poh, M. K., Phong, W. Y., Keller, T. H., Jacoby, E., & Vasudevan, S. G. (2009). A Small-Molecule Dengue Virus Entry Inhibitor. Antimicrobial Agents and Chemotherapy, 53(5), 1823–1831. https://doi.org/10.1128/aac.01148-08 CrossRef Scholia
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", "summary": "Adding chemical compounds to Wikidata is not difficult. You can store the chemical formula (P274), (canonical) SMILES (P233), InChIKey (P235) (and InChI (P234), of course), as well various database identifiers (see what I wrote about that here ]). It also allows storing of the provenance, and has predicates for that too.", "date_published": "2016-01-27T00:00:00+00:00", "date_modified": "2025-05-25T00:00:00+00:00", "tags": ["wikidata","chemistry","bioclipse"], "_references": [ { "url": "https://doi.org/10.1128/AAC.01148-08", "doi": "10.1128/AAC.01148-08" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }