Antimicrobial chemical structures, harmonized — ChEBI’s antimicrobial role hierarchy merged with CARD’s Antibiotic Resistance Ontology onto one identity per structure, with the mechanism layer a compound list does not carry.
Every compound in the corpus, searchable, with its class, grounding status and review state.
Antibacterial, antifungal, antiviral and the rest — the class a record’s activity places it in, not its structural family.
All 2909 records placed by chiral molecular fingerprint alone — no labels, mechanisms or prose in the coordinates. Search a compound and inspect its nearest structural neighbours.
LinkML-validated YAML under data/antibiotics/. Schema,
curation history and the seeding pipeline all live in the repository.
One AntibioticRecord is one chemical structure — a compound with a
defined connectivity (an InChIKey), not a drug class. "Macrolide antibiotic" is a
structural class and appears as structural_class on the records it
covers; erythromycin A is a record. AntibioticMech merges ChEBI's antimicrobial
role hierarchy with CARD's Antibiotic Resistance Ontology (ARO) molecule list onto
one identity per structure, and layers on the mechanism a compound list does not
carry: molecular target, mode of action, and resistance route.
| Class | Records | Share |
|---|---|---|
| Antibacterial | 1091 | |
| Antimycobacterial | 78 | |
| Antifungal | 594 | |
| Antiprotozoal | 248 | |
| Antiviral | 473 | |
| Biocide | 31 | |
| Unspecified | 472 |
Every record's identity is either an ontology term asserted by ChEBI or ARO
themselves, or — when no defensible term exists — a content-hashed
antibioticmech: CURIE minted at seed time. Grounding is a fact about
the identifier, kept separately from curator review.
| Status | Records | Meaning |
|---|---|---|
| EXACT | 2669 | The identifier is an ontology term asserted by ChEBI or ARO themselves. |
| MINTED | 240 | No defensible ontology identity; the record keeps a content-hashed antibioticmech: CURIE. |
ChEBI and ARO supply identity, structure and cross-references for every record. The mechanism fields below are what curation adds on top, one record at a time — most are still empty, which is the honest state of an incrementally curated corpus.
| Field | Records | Share |
|---|---|---|
| Molecular targets | 245 | 8.4% |
| Resistance mechanisms | 281 | 9.7% |
| Mode of action | 417 | 14.3% |
| Causal graphs | 16 | 0.6% |
| Activity spectrum | 0 | 0.0% |
| Producer organisms | 3 | 0.1% |
| Discussions | 4 | 0.1% |
| Datasets | 0 | 0.0% |
This corpus is machine-generated. 2909 of 2909 records (100.0%) have had no human review — their identity, structure and resistance/target links come straight from ChEBI's and CARD's own data. A database assertion is not a primary citation; treat SEEDED records as a starting point for curation, not a reviewed claim.