Two week ago I uploaded a paper that has been in the works for some time. In fact, I first mention it as conference paper\nfor the special issue of the 11th International Conference on Chemical Structures,\nyou know, the meeting held in 2018, of which the 13th edition starts in 7 days. I had a\nposter at that conference which I described in\nthis blog post.
\n\nIn turn, that poster described work of at least three years, going back to\nadding identifiers in 2015\nand chemical structures in early 2016.\nI started using scripts two months later.\nThis helped a lot with migrating pKa data\nfrom a custom Semantic MediaWiki installation to Wikidata and with adding thousands of EPA CompTox\nidentifiers in 2017.
\n\nBut that 2018 conference paper never happened. Because Scholia did.\nAnd even on the ICCS poster, Scholia was used to visualize chemistry data in Wikidata. To be honest, not just that,\nof course. About a year ago I had a serious go at finishing the paper, and it was sent around to co-authors.\nBut I realized at the time, that the paper was lacking some good suggestions how the peer review our\nactual contributions to Wikidata. I could hardly expect readers of the paper browse the individual\nhistories of all, by then, 1.3 million chemical compounds. And during the holidays I collected a few\ntools, which I had lined up to add to the manuscript.
\n\nHowever, another thing happened, the COVID-19 pandemic. While all the experience helped a lot with getting\nknowledge together around SARS-CoV-2, it also made something else clear: the software behind Wikidata\ndoes not scale well (enough). This lead to plans to split the RDF graph representation into two\nseparate SPARQL endpoints. And that breaks many, if not most, of Scholia’s SPARQL queries, including\nthose for the chemistry aspects. The situation in Summer 2024 was that there was a significant\nchance Scholia would not survive the split. And the Scholia Chemistry paper had to wait. You\ncannot publish an article of which the website is gone before it is formally accepted.
\n\nLet me make clear, this graph split is not solved and the risk is not gone. But a serious of unfunded,\nweekend hackathons allows us to refactor Scholia to give us a chance. It started with\nmaking Scholia more configurable.\nWe had the first hackathons in October and November, and I had\nfour more hackathon weekends\nthis April.
\n\nThe graph split into a main graph and a scholarly graph happened on May 9.\nCurrently, we have been granted extra time and can use a legacy server with the full graph, but a lot\nless hardware, so slower. A final patch, merged in last week, allows us to define which SPARQL endpoint a query\nshould run. So, each time we port a SPARQL query, we can directly update Scholia, making the migration\nsomewhat more manageable.
\n\nBut, with those uncertainties out of the way, it was time to finish the Scholia Chemistry paper!
\n\nThe preprint (doi:10.26434/chemrxiv-2025-53n0w) brings\n10 years of research together, and describes details of the used methods not formally peer-reviewed before.\nWe describe in detail how chemical structures are added, the choices of Wikidata on how to\nrepresent chemical structures, how we curate the quality, and how we visualize chemical structures\nand data with Scholia. As you can expect, the Chemistry Development Kit has an important role,\nalong with the InChI.
\n\nThe paper introduces three new Scholia aspects for chemicals, chemical classes, and elements.\nEach aspect is a template for a page with information about molecular entities and chemical substances,\ncompound classes (like fatty acids), and elements (like carbon). Each template provides relevant\ninformation. Of course, any compound, class, or element can also still be opened in the Scholia\n“topic” aspect, listing relevant literature.
\n\nWith this paper we aim to show that Wikidata is a innovative platform that meets the needs for\na chemical structure database, with detailed data provenance, and scalable community curation.
\n\nI welcome your strongest peer review on the preprint. I don’t liking settling for anything less.\nHere’s the abstract:
\n\n\n\n\nSharing knowledge on chemicals in the digital age has been the playground of databases such\nas the Chemical Abstract Services and PubChem. Wikipedia complements this field by providing\ncontext to chemicals aimed at a broad audience, but is not easily read by machines. Wikidata\nwas started as a database service to improve the machine readability of the knowledge captured\nin Wikipedia. Wikidata has an open license, application programming interfaces, and a strong\nprovenance model. Scholia uses the features to provide access to chemical knowledge. This\nstudy reviews the chemistry in Wikidata, shows how thousands of new chemicals were added,\nextends Wikidata with new properties for chemical representation and external links to\nadditional databases, and shows how we extended Scholia to represent the chemistry in Wikidata.
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Thanks to Finn, Denise, Daniel, and Adriano!
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