![\"\"](\"/assets/images/pfas_report.png\")
A recent report by the Dutch RIVM, PFAS in the blood of the Dutch population\n(doi:10.21945/RIVM-2025-0094), writes\nthat seven PFAS compounds are found in blood samples\nof all tested people. Another nine compounds are found in at least 1-in-10 people.\nBecause there is relevant data in the report on the 28 studied PFAS compound, I wanted to\nhave the report more FAIR than it is on the website. Why this report? Well, the chemistry and the\nhistory is fascinating and brutal (I like this Veritasium video).
\n\nThe history tells me that our society may sound woke and leftish, in reality it is a continous fight\nfor basic human rights. (Something that plenty have been saying for years.)\nIn this case, a healtht life is the human right.
\n\nSo, what can I do to make this report more FAIR?
\n\nSince this report has been mentioned in the news,\nit clearly is notable. The simplest thing to do is thus to just add it Wikidata.\nBecause the DOI of the report had not been recorded yet, I could not let Scholia\ndo it for me. But doing it manually is only a bit more work: Q135222054.\nThe provided metadata on the RIVM website\nis minimal.
\n\nBut we can do more. Particularly, because I want people to find this report when they look info knowledge\nabout the 28 studied chemicals, I added main subject annotation\nusing the information in Table 1 in the report. Using Scholia and the CAS registry number in the table,\nI crosscheck the information in Wikidata is consistent with the report (and visa versa). It was.\nI then added the Dutch name and acronym for most of them. Some already had the name as in the Table.\nThat gives us a nice “Topic scores” plot for the Scholia page of the report:
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The central PFAS bubble is also only one main subject but larger because many the specific PFAS compounds\nare subclassing PFAS. And you may also note many smaller bubbles. These actually come from main subject\nannotations of articles cited from the report. Because I added a few of them too. Not all, because many are\nnot in Wikidata (yet).
\n\nBut since 16 of these compounds are readily found in human blood samples, that is handy knowledge when\ndoing metabolomics (on blood samples). Or (and I leave that to later blog post), we can map the experimental\ndata for Dordrecht versus the rest of The Netherlands to the PFAS compounds. That is relevant to research\nby VHP4Safety. There are many ways to see if you have PFAS in your dataset,\nbut since we have many controlled lists of genes in metabolites, I added one for common PFAS in human\nblood samples. Well, the 16 common in Dutch blood samples:
\n\n![\"\"](\"/assets/images/pfas_wikipathways.png\")
Each metabolite here is annotated with their Wikidata identifier, allowing us to map experimental\ndata on top of it. And we get links out to other databases almost for free:
\n\n![\"\"](\"/assets/images/pfas_wikipathways_outlinks.png\")
And the link to Wikidata actually links to Scholia, so for the PFOA in the above example,\nwe can quickly see the boiling point, decomposition point, and melting point of this PFAS.\nAnd literature with undoubtedly even more knowledge about this PFAS:
\n\n![\"\"](\"/assets/images/pfas_scholia.png\")
Now, these two steps were mostly manual: drawing WP5579\nin WikiPathways and adding the report annotations (main subject and cites) in Wikidata.
\n\nAs part of the VHP4Safety project, I am collecting information on chemicals studied in the context\nof toxicology, safety, and risk assessment. Often specific collections of compounds studied as a whole.\nThis report is such a collection and provides experimental data on these compounds. So, I want this\nreport to be findable for the VHP4Safety Compound Wiki too.\nCreating the collection is a manual step: Q5145.
\n\nNow, because both Wikidata and our VHP4Safety Compound Wiki (a Wikibase instance) are semantic and support, I can use SPARQL\nto create instructions to link the 28 compounds to the new collection. Now, arguably, that can be\ndone manually too, and maybe faster, for larger collections this is harder. So, I dug up\nmy earlier notes and got some useful\nthings together.
\n\nThis query lists all 28 PFAS linked to the report in Wikidata:
\n\nSELECT ?pfas ?pfasLabel WHERE {\n wd:Q135222054 wdt:P921 ?pfas .\n ?pfas wdt:P31 wd:Q113145171 .\n SERVICE wikibase:label { bd:serviceParam wikibase:language \"[AUTO_LANGUAGE],mul,en\". }\n}\nUsing federation powers, I can use this for a SPARQL query,\nand return the results in QuickStatements that say this VHP compound is part of the VHP collection:
\n\nPREFIX wb: <https://compoundcloud.wikibase.cloud/entity/>\nPREFIX wbt: <https://compoundcloud.wikibase.cloud/prop/direct/>\n\nSELECT (SUBSTR(STR(?cmp),45) AS ?qid) ?P21 WHERE {\n ?cmp wbt:P5 ?wikidata .\n SERVICE <https://query.wikidata.org/sparql> {\n wd:Q135222054 wdt:P921 ?pfas .\n ?pfas wdt:P31 wd:Q113145171 .\n BIND (substr(str(?pfas),32) AS ?wikidata)\n }\n BIND (\"Q5145\" AS ?P21)\n}\nI actually had to add 5 PFAS compounds in the VHP4Safety Compound Wiki first. That follows the\nsame procedure for how I have been adding chemical compounds to Wikidata\n(see also this preprint).\nThe input cas.smi has the (missing) SMILES, Wikidata QID, and English label:
C(CS(=O)(=O)O)C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F Q27063662 6:2 Fluorotelomer sulfonate\nCN(CC(=O)O)S(=O)(=O)C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F Q126605979 MeFHxSAA\nCN(CC(=O)O)S(=O)(=O)C(C(C(C(F)(F)F)(F)F)(F)F)(F)F Q126682412 MeFBSAA\nC(=O)(C(C(F)(F)F)(F)OC(C(C(F)(F)F)(F)F)(F)F)O[H] Q29387971 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid\nC(C(C(=O)O)(F)F)(OC(C(C(OC(F)(F)F)(F)F)(F)F)(F)F)F Q81981675 4,8-Dioxa-3H-perfluorononanoic acid\nFor reference, this is the command line I used to create QuickStatement instructions:
\n\ngroovy createWDitemsFromSMILES.groovy -w compoundcloud.wikibase.cloud -c Q2368 -d P5 -l -i wikidata -a P11\nAre these 16 the only PFAS in our body? With 28 studied out of a potential seven million,\nI doubt it.
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