ELIXIR Europe

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformati...

Funders and data producers need to know not just which databases are cited in the literature, but whether a cited accession actually exists and how it was used. Making that reuse visible is itself an incentive for the wider research community to deposit data, by giving concrete, attributable evidence that public deposits are genuinely reused and contribute to science. We report on a pipeline, built during the DBCLS BioHackathon 2026, that extracts database identifiers from PMC full text, verifies each one against source-of-truth APIs (TogoID/RDF Portal, NCBI E-utilities, EBI Search), and classifies confirmed accessions into one of five credit/provenance classes. On a working slice of 10,896 PMC documents, the pipeline confirms 19,786 (paper, accession) links across 1,352 papers and 18,159 distinct accessions, though a single namespace (insdc) accounts for roughly 70% of that volume. An independent comparison against Europe PMC’s own accession annotations over the same slice shows 74.6% agreement at the individual-citation level, with a bimodal split at the per-document level: 64% of documents that either system found anything in agree at 90-100%, while 16% agree at only 0-10%, a pattern that needs manual citation and analysis. The pipeline, its Europe PMC comparison, and a static, backend-free dashboard reporting the results are complete and reproducible for this slice. A reference-role (generated/used/mentioned) classifier and a 221-item human gold standard evaluating it were also completed, reaching 0.80 macro-F1 with a near-zero generated-vs-used confusion; extending coverage and running against the full corpus are left as future work. ## Figures Pipeline architecture: PMC full text to a verified, entry-level data-reuse dashboard, in five stages. Database-namespace coverage: Europe PMC’s TextMinedTerms vs. this pipeline’s TogoID-derived pattern set. Data Reuse Dashboard: database usage drill-down These figures come from the source repository of the preprint; their captions are also in the PDF.

Preprints for BioHackathons

Are you interested in joining this year’s BioHackathon Europe, but can’t face the long haul flights? You should join the Australian Outpost team who will gather in Melbourne, while checking in regularly with our international colleagues.

Preprints for BioHackathons

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformati...