{ "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/2015/04/10/getting-cas-registry-numbers-out-of.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/10.59350/2cfqr-fwe26", "url": "https://chem-bla-ics.linkedchemistry.info/2015/04/10/getting-cas-registry-numbers-out-of.html", "title": "Getting CAS registry numbers out of WikiData", "content_html": "

I have promised my Twitter followers the SPARQL query you have all been waiting\nfor. Sadly, you had to wait for it for more than two months. I’m sorry about that. But, here it is:

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PREFIX wd: <http://www.wikidata.org/entity/>\n\nSELECT ?compound ?id WHERE {\n  ?compound wd:P231s [ wd:P231v ?id ] .\n}\n
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What this query does is ask for all things (let’s call whatever is behind the identifier is a “compound”; of course, it can\nbe mixtures, ill-defined chemicals, nanomaterials, etc) that have a CAS registry identifier. This query results in a nice\ntable of Wikidata identifiers (e.g. Q47512 is acetic acid)\nand matching CAS numbers, 16298 of them.

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Because Wikidata is not specific to the English Wikipedia, CAS numbers from other origin will show up too. For example, the\nCAS number for N-benzylacrylamide (Q10334928) is provided by the Portuguese Wikipedia:

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\"\"

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I used Peter Ertl’s cheminfo.org (doi:10.1186/s13321-015-0061-y)\nto confirm this compound indeed does not have an English page, which is somewhat surprising.

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The SPARQL query uses a predicate specifically for the CAS registry number (P231).\nOther identifiers have similar predicates, like for PubChem compound (P662) and\nChemspider (P661). That means, Wikidata can become a community crowdsource of\nidentifier mappings, which is one of the things Daniel Mietchen, me, and a few others proposed in this H2020 grant application\n(doi:10.5281/zenodo.13906). The SPARQL query is run by the\nLinked Data Fragments platform, which you should really check out too, using the\nBioclipse manager I wrote around that.

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The full Bioclipse script looks like:

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wikidataldf = ldf.createStore(\n  \"http://data.wikidataldf.com/wikidata\"\n)\n\n// P231 CAS\nidentifier = \"P231\"\ntype = \"cas\"\n\nsparql = \"\"\"\nPREFIX wd:\n\nSELECT ?compound ?id WHERE {\n  ?compound wd:${identifier}s [ wd:${identifier}v ?id ] .\n}\n\"\"\"\nmappings = rdf.sparql(wikidataldf, sparql)\n\n// recreate an empty output file\noutFilename = \"/Wikidata/${type}2wikidata.csv\"\nif (ui.fileExists(outFilename)) {\n  ui.remove(outFilename)\n  ui.newFile(outFilename)\n}\n\n// safe to a file\nfor (i=1; i<=mappings.rowCount; i++) {\n  wdID = mappings.get(i, \"compound\").substring(3)\n  ui.append(\n    outFilename,\n    wdID + \",\" + mappings.get(i, \"id\") + \"\\n\"\n  )\n}\n
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BTW, of course, all this depends on work by many others including the core RDF generation\nwith the Wikidata Toolkit. See also the paper by Erxleben et al.\n(PDF).

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References

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Ertl, P., Patiny, L., Sander, T., Rufener, C., & Zasso, M. (2015). Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia. Journal of Cheminformatics, 7(1). https://doi.org/10.1186/s13321-015-0061-y CrossRef Scholia
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Erxleben, F., Günther, M., Krötzsch, M., Mendez, J., & Vrandečić, D. (2014). Introducing Wikidata to the Linked Data Web. In Lecture Notes in Computer Science (pp. 50–65). Springer International Publishing. https://doi.org/10.1007/978-3-319-11964-9_4 CrossRef Scholia
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Mietchen, D., Hagedorn, G., Willighagen, E., Rico, M., Gomez-Perez, A., Aibar, E., Rafes, K., Germain, C., Dunning, A., Pintscher, L., Kinzler, D., & Anonymous. (2015). Enabling Open Science: Wikidata For Research. Zenodo. https://doi.org/10.5281/ZENODO.13906 CrossRef Scholia
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", "summary": "I have promised my Twitter followers the SPARQL query you have all been waiting for. Sadly, you had to wait for it for more than two months. I’m sorry about that. But, here it is:", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/casPT.png", "date_published": "2015-04-10T00:00:00+00:00", "date_modified": "2015-04-10T00:00:00+00:00", "tags": ["wikidata","chemistry","cas","ldf"], "_references": [ { "url": "https://doi.org/10.1186/s13321-015-0061-y", "doi": "10.1186/s13321-015-0061-y" } , { "url": "https://doi.org/10.5281/ZENODO.13906", "doi": "10.5281/ZENODO.13906" } , { "url": "https://doi.org/10.1007/978-3-319-11964-9_4", "doi": "10.1007/978-3-319-11964-9_4" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }