Table 2. Example of a basic sequence of beacon queries to discover knowledge about a human disease.
| Step | Endpoint | Beaconsa | Query | Result | ||
|---|---|---|---|---|---|---|
| Type | Identifier | Description | ||||
| 1 | /concepts | SEMMEDB, HMDB | keywords = "Progressive Supranuclear Palsy" | Concept | UMLS:C008868 | Progressive Supranuclear Palsy (disease or phenotypic feature) |
| 2 | /statements | HMDB | s = UMLS:C008868 | Statement | S1.1 | HMDB:HMDB000742 (Homocysteine)—related to -> Progressive Supranuclear Palsy |
| 3 | /statements/details | HMDB | S1.1 | Evidence | PMID:20606437 | Levin J, et al. 2010: Elevated levels of. . . homocysteine in. . . progressive supranuclear palsy. Dement Geriatr Cogn Disord. 29(6):553–9 |
| 4 | /concepts | SEMMEDB | keywords = "hyperhomocysteinemia" | Concept | UMLS:C0598608 | Hyperhomocysteinemia (disease or phenotypic feature) |
| 5 | /statements | SEMMEDB | edge_label = treats & t = UMLS:C0598608 | Statement | S2.1.. S2.n | subject[1..n]—treats -> HMDB:HMDB000742 (Homocysteine) |
| 6 | /statements/details | SEMMEDB | S2.x | Evidence | ? | ? |
a Beacons used in this example: SEMMEDDB: Semantic Medline Database, HMDB: Human Metabolome Database