Open Biomedical Knowledge Graphs at Scale: Construction, Federation, and AI Agent Access with Samyama Graph Database
-cross Abstract: Biomedical knowledge is fragmented across siloed databases---Reactome, STRING, Gene Ontology, ClinicalTrials.gov, DrugBank, DGIdb,…
Why am I seeing this Ranked on source trust — arXiv
It ranks mainly on source trust: arXiv is the most reliable outlet we track on this subject, and is the only one on the story so far.
Link-outLink-out, because it did not clear the bar for a write-up. Link-out means we point at the publisher and say nothing of our own.
| Factor | Weight | Score | Contribution | Where it came from |
|---|---|---|---|---|
| Corroboration | 0.35 | 0.39 | +0.135 25% | 1 independent org on the story. Tier-3 aggregators never corroborate — they can show something is circulating, never that it is true. |
| Source trustleads | 0.25 | 0.85 | +0.212 39% | arXiv is the highest-trust source on this story and is first-party — the organisation announcing its own news. Trust is taken from the best source, not averaged. |
| Pickup rate | 0.20 | 0.00 | +0.000 0% | One counted organisation, so there is no spread to measure — nothing has picked this up to set a rate. |
| Freshness | 0.20 | 0.99 | +0.198 36% | Halves every 10 hours from the newest item on the story. This is the only factor that rewards a story for nothing more than being recent. |
Corroboration counts distinct organisations, once each, and only from tiers 1 and 2. Freshness halves every 10 hours, so this ranking is a snapshot and will differ at the next build.
What happened
-cross Abstract: Biomedical knowledge is fragmented across siloed databases---Reactome, STRING, Gene Ontology, ClinicalTrials.gov, DrugBank, DGIdb, SIDER, PubMed, ClinVar, ChEMBL, OpenTargets, and more. We present an open, reproducible biomedical knowledge graph ecosystem built on Samyama, a Rust-native graph database: three foundational graphs detailed end-to-end---Pathways KG (118,686 nodes, 834,785 edges), Clinical Trials KG (7,774,446 nodes, 26,973,997 edges), and Drug Interactions KG (32,726 nodes, 191,970 edges)---and their expansion into a 22-graph, 2-cohort merged biomedical store (328,130,739 nodes and 1,441,425,733 imported edges, including 295,000 synthetic OMOP CDM patients from Synthea).
How this story arrived
Ordered by when each source was first observed, which is what the velocity figure is computed from. Publishers backdate; observed order does not.
- 01 Arxivfirst-party first seen Open Biomedical Knowledge Graphs at Scale: Construction, Federation, and AI Agent Access wit
Overclock clusters coverage from independent sources and grades it automatically. The figures above are computed, not editorial. This page summarises and links to reporting by the outlets named — follow the links for the original work.