Identifier namespaces

EHItk keeps identifier columns in the same namespace used by the bundled EHI catalog or by the external authority that minted the identifier. The table below lists the identifier fields that can appear in query output or be used in filters, together with their namespace and a manual resolution route.

Field	Namespace	Meaning	Manual resolution
`specimen_id`	EHI specimen catalog	EHI specimen metadata identifier, for example `SD00508`.	Resolve inside the EHItk catalog with `ehitk specimens query --specimen-id SD00508`.
`hologenome_id`	EHI hologenome catalog	EHI shotgun metagenomic dataset identifier, for example `EHI00001`.	Resolve inside the EHItk catalog with `ehitk hologenomes query --hologenome-id EHI00001`.
`mag_id`	EHI MAG catalog	EHI metagenome-assembled genome identifier, for example `EHM00001`.	Resolve inside the EHItk catalog with `ehitk mags query --mag-id EHM00001`.
`host_taxid`	NCBI Taxonomy	NCBI taxon identifier for the host organism, for example `8509`.	Resolve at `https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=8509`.
`biome_envo_id`	Environment Ontology (ENVO)	ENVO class identifier for the sampled biome, for example `ENVO:01000175`.	Resolve at `https://purl.obolibrary.org/obo/ENVO_01000175`.
`release` and `hologenome_release`	EHI data release labels	EHI catalog release labels used to group records.	Resolve inside EHItk with `--release` filters or by pinning the corresponding versioned SQLite catalog.
`url`, `url1`, and `url2`	Absolute download URLs	MAG FASTA or paired-end read download locations.	Resolve directly with the URL. Hologenome read URLs commonly include the sequencing run accession in the path.

Catalog-local identifiers

specimen_id, hologenome_id, and mag_id are EHI catalog identifiers. They are stable within a versioned EHItk database artifact, and can be resolved by querying that catalog with the matching resource command. They are not NCBI, ENA, BioSample, BioProject, SRA, or INSDC accessions unless a separate output field explicitly provides such an accession.

External ontology and taxonomy identifiers

host_taxid values are NCBI Taxonomy identifiers. biome_envo_id values are ENVO CURIEs. EHItk expands these filters to include descendants present in the bundled catalog, so a higher-level NCBI or ENVO identifier may match records whose stored value is a descendant identifier.

Taxonomy names

Fields such as host_species, host_genus, mag_genus, and mag_species are names or labels, not identifier fields. MAG taxonomy labels come from GTDB-style MAG assignments; EHItk normalizes g__ and s__ prefixes in query output and filters, but it does not infer NCBI taxon identifiers for MAG taxa.