Record browser
Browse every compound by antimicrobial class, with its grounding and curation status. Each class has an identifier and name filter.
By antimicrobial class
Antibacterial, antifungal, antiviral and the rest — the class a record’s activity places it in, not its structural family.
Chemical & text maps
All 2939 records placed by chiral molecular fingerprint alone — no labels, mechanisms or prose in the coordinates. Search a compound and inspect its nearest structural neighbours.
Protein sequence map (pLM)
2D PaCMAP projection of ESM-2 (esm2_t33_650M_UR50D) embeddings
for curated target and resistance determinant proteins.
Source, schema & downloads
LinkML-validated YAML under data/antibiotics/. Schema,
bulk JSON exports, 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.
Browse by class
| Class | Records | Share |
|---|---|---|
| Antibacterial | 1121 | |
| Antimycobacterial | 78 | |
| Antifungal | 594 | |
| Antiprotozoal | 248 | |
| Antiviral | 473 | |
| Biocide | 31 | |
| Unspecified | 472 |
Identity grounding
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 | 270 | No defensible ontology identity; the record keeps a content-hashed antibioticmech: CURIE. |
What the mechanism layer holds so far
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 | 282 | 9.6% |
| Resistance mechanisms | 321 | 10.9% |
| Mode of action | 454 | 15.4% |
| Causal graphs | 16 | 0.5% |
| Activity spectrum | 60 | 2.0% |
| Producer organisms | 61 | 2.1% |
| Discussions | 9 | 0.3% |
| Datasets | 0 | 0.0% |
SEEDED and REVIEWED describe recorded curation workflow states. Curation may be agent-assisted; these counts do not establish human review. Consult each record’s curation history for the actor and method.
This corpus is machine-generated. 2829 of 2939 records (96.3%) have the SEEDED workflow status — 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.