Reposted by WikiPathways
"DBCLS BioHackathon 2026 report: Extending TogoMCP beyond RDF Portal while making its schema guides check their own answers" doi.org/10.37044/osf.io/t25ng_v1
#biohackathon #mcp #rdf #BH26JP #qlever
"In the first six days of the event we published eleven releases (v2.12.2 to v2.20.0) […]
fediscience.org
Original post on fediscience.org
![Figure 5: Metabolite cross-reference coverage: direct BridgeDb mapping complements InChIKey federation. (A) How the 4,577 wp:Metabolite nodes resolve to external chemical databases: 3,198 (69.9%) carry ≥1 BridgeDb-materialised cross-reference and are resolvable directly in the graph without federation; 1,207 (26.4%) carry only an InChIKey and remain reachable through query-time federation to Wikidata (wdt:P235) and other InChIKey-indexed resources; 172 (3.8%) have neither. (B) Cross reference coverage per database, comparing the single PlantCyc source identifier each metabolite carries with the BridgeDb-added wp:bdb* cross-references. [..]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:tkpuxuh62gao5msdnrcfauzb/bafkreidf36xpebq45jwnoqg2vgcnzqa4xs22cxntdd4xzfe4qw6nfwguv4)
![Screenshot of the linked BioHackrXiv preprint, showing the top half of a preprint PDF page, showing the BioHackrXiv logo from the template, a table at the top listing a Arabidopsis thaliana pathway, and below that part of Figure 1 showing a "[p]athway diagram for for Caffeine synthesis inCoffea arabica. This diagram is already published in WikiPathways at https://www.wikipathways.org/pathways/WP5586.html".](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:qnlzf7v57j4fqwgx6nm2xd6r/bafkreicu3yju7lslnbmgkqa5jbcparc5kvhlwipwnxsoufbd6ngdjtangi)
![WP5579 shows two lists of PFAS, one found in all sampled humans, the second list in 10-99% of the sampled humans. The description of the pathway writes: "A recent study by the Dutch RIVM found that across The Netherlands seven PFAS are found in every tested human, with an additional nine found in at least 10% of the population. Three of these PFAS were found to be associated to cancer. PFOS, PFHxS, and PFOA were found to be significantly positively associated with testicular germ cell tumors (TGCT) among U.S. Air Force servicemen [PMID:37458713 ]. Data from a 2-year bioassay study on rats did not support a PFOS-related effect on testicular tumors, while serum PFOS concentrations were much higher in magnitude compared to levels reported in the former study [PMID:37751326]. ..."](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:tkpuxuh62gao5msdnrcfauzb/bafkreicldkvzlapuk424svrosonxl4csivuin2zeg5jizdxotdvq25uma4)
