Pathway browser
Filter and search the published collection by pathway class, organism, protein grounding, or identifier.
Browse pathway recordsMicrobial pathway knowledge base
PathwayMech
Explore microbial pathways, their molecular participants, and the evidence behind their mechanistic connections.
- Pathway records
- 271
- Taxa represented
- 105
- Mechanistic edges
- 14,393
- Distinct references
- 5,875
Explore PathwayMech
Find a pathway, explore embedding spaces, follow its evidence, or contribute a record.
Corpus text embedding map
Interactive 2D PaCMAP projection of BAAI/bge-large-en-v1.5 embeddings across all 271 pathway records.
Explore text embedding mapSequence map (ESM-2 pLM)
Explore protein language model (ESM-2 650M) representations for UniProt-grounded pathway proteins and centroids.
Explore pLM sequence mapSource records & curation
Inspect the underlying YAML records and learn how to attach mechanistic evidence to individual pathway edges.
Explore source recordsDownloads, schema & complete pathway graph
KGX TSV exports from the same 271 pathway records shown here: All nodes (TSV), All edges (TSV), Pathway index (JSON), and Version, row counts and file checksums.
LinkML Schema & Data Model:
PathwayMech LinkML schema (pathwaymech.yaml) ·
Shared X-Mech primitives (mech_shared.yaml) ·
Curation history schema (history.yaml) ·
Source authority registry (sources.yaml) ·
Corpus text embedding coordinates (JSON) ·
ESM-2 sequence embedding coordinates (JSON).
Graph version: cc835e3d26bd1f2e940216d5f5a0c977e09aa2d3900337dc8d22c4f2baf1ea60.
Data: CC BY 4.0;
upstream source terms still apply.