Databases and Provenance

PHU database downloads are scientific inputs. Record the backend, local manifest, release identifier, and checksum with every analysis. The development registry currently exposes pfam, kofam, dbcan, and avg.

Backend matrix

Backend	Purpose	Upstream source in current build	Local files/indexes	Readiness	Provenance status
pfam	Resolve PFAM accessions and search protein-family HMMs	Pfam current release	Pfam-A.hmm.gz, Pfam-A.hmm, offsets.json, optional models/, manifest.json	HMM and byte-offset index available	The source is a floating current_release; pinning, upstream release ID, license, size, and expected checksum are not yet recorded as a stable PHU contract.
kofam	Resolve KO models and apply KOfam thresholds	Zenodo record 19503464: ko_list.gz, kofam.hmm.xz	ko_list.gz, ko_list, kofam.hmm.xz, kofam.hmm, ko_metadata.json, offsets.json, optional models/, manifest.json	HMM, KO metadata, and byte-offset index available	The Zenodo record is pinned in code, but per-file checksums, license, size, and citation metadata are not yet exposed as a stable PHU contract.
dbcan	Resolve CAZyme families and PUL signatures	dbCAN HMM V15 and current PUL workbook	Raw HMM/workbook, family_offsets.json, pul_rules.json, optional models/, manifest.json	HMM family and PUL indexes available	Manifest records source URLs, retrieval time, hashes, schema version, and counts.
avg	Provide AVG/APG/AReG reference tables and scores	CheckAMG-derived reference source configured by the backend	normalized score, positive, and filter tables plus manifest.json	Reference tables and manifest available	The current code reports release v1.1.1; upstream URL, checksum policy, license, size, and immutable source identity require a stable provenance contract.

Lifecycle

Inspect status before using a backend:

phu dbs list
phu dbs status pfam kofam avg

Prepare an explicitly named backend. Omitting names currently selects all supported backends, which may download substantial data:

phu dbs prepare pfam

Use refresh to validate or repair local state and remove --yes to delete a backend. An indexed state is not applicable to every backend; for table-based backends, readiness means that the validated normalized table and manifest are available.

Reporting requirements

A reproducible run should record the backend key, local root, manifest path, release or snapshot identifier, upstream URL, SHA-256 values, database files, and preparation timestamp. Do not describe pfam's floating current_release source as immutable. Do not treat a local readiness result as evidence that the upstream scientific release is permanently identified.

The current development build does not yet guarantee a complete provenance record for every backend.