\n![](\"/assets/images/extid-wikidata-histogram.png\")
\nBar chart showing the number of compounds with a particular chemical identifier.\n\nI think Wikidata is a groundbreaking project, which will have a major impact on science. One of the\nreasons is the open license (CCZero), the very basic approach (Wikibase), and the superb community around\nit. For example, setting up your own Wikibase including a cool SPARQL endpoint, is\neasily done with Docker.
Wikidata has many sub projects, such as WikiCite, which captures the collective of primary literature.\nAnother one is the WikiProject Chemistry. The two nicely match\nup, I think, making a public database linking chemicals to literature (tho, very much needs to be done here), see my recent\nICCS 2018 poster (doi:10.6084/m9.figshare.6356027.v1, paper pending).
\n\nBut Wikidata is also a great resource for identifier mappings between chemical databases, something we need for\nour metabolism pathway research.\nThe mapping, as you may know, are used in the latter\nvia BridgeDb and we have been using Wikidata as one of three sources for some time now (the others being\nHMDB and ChEBI). WikiProject Chemistry has a related\nChemID effort, and while the wiki page does not show\nmuch recent activity, there is actually a lot of ongoing effort (see plot).\nAnd I’ve been adding my bits.
\n\nBut not each identifier in Wikidata has the same meaning. While they are all classified as ‘external-id’, the actual link may\nhave different meaning. This, of course, is the essence of scientific lenses, see this post\nand the papers cited therein. One reason here is the difference in what entries in the various databases mean.
\n\nWikidata has an extensive model, defined by the aforementioned WikiProject Chemistry. For example, it has different concepts\nfor chemical compounds (in fact, the hierarchy is pretty rich) and compound classes. And these are differently modeled. Furthermore,\nit has a model that formalizes that things with a different InChI are different, but even allows things with the same InChI to be\ndifferent, if need arises. It tries to accurately and precisely capture the certainty and uncertainty of the chemistry. As such,\nit is a powerful system to handle identifier mappings, because databases are not clear, and chemistry and biological in data is\neven less: we measure experimentally a characterization of chemicals, but what we put in databases and give names, are specific\nmodels (often chemical graphs).
\n\nThat model differs from what other (chemical) databases use, or seem to use, because not always do databases indicate what they\nactually have in a record. But I think this is a fair guess.
\n\nChEBI (and the matching ChEBI ID) has entries for chemical classes (e.g.\nfatty acid) and specific compounds (e.g.\nacetate).
\n\nThese three resources use the InChI as central asset. While they do not really have the concept of compound classes so much\n(though increasingly they have classifications), they do have entries where stereochemistry is undefined or unknown. Each\none has their own way to link to other databases themselves, which normally includes tons of structure normalization (see\ne.g. doi:10.1186/s13321-018-0293-8 and\ndoi:10.1186/s13321-015-0072-8).
\n\nHMDB (and the matching P2057) has a biological perspective; the entries\nreflect the biology of a chemical. Therefore, for most compounds, they focus on the neutral forms of compounds. This makes\nlinking to/from other databases where the compound is not neutral chemically less precise.
\n\nCAS (and the matching P231) is pretty unique itself, and has identifiers\nfor substances (see Q79529), much more than chemical compounds, and comes with a\nown set of unique features. For example, solutions of some compound, by design, have the same identifier. Previously,\nformaldehyde and formalin had different Wikipedia/Wikidata pages, both with the same CAS registry number.
\n\nNow, returning to our starting point: limitations in linking databases. If we want FAIR mappings, we need to be as precise\nas possible. Of course, that may mean we need more steps, but we can always simplify at will, but we never can have a\ncomputer make the links more complex (well, not without making assumptions, etc).
\n\nAnd that is why Wikidata is so suitable to link all these chemical databases: it can distinguish differences when needed,\nand make that explicit. It make mappings between the databases more FAIR.
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