Specimens

Use ehitk specimens to inspect host and specimen metadata.

Query specimens

ehitk specimens query --host-species "Podarcis muralis"
ehitk specimens query --host-taxid 8509
ehitk specimens query --host-lineage Mammalia --sex Female
ehitk specimens query --weight-min 8 --weight-max 9 --length-min 40 --length-max 41
ehitk specimens query --specimen-id SD00508 --columns specimen_id,host_species,sex

Filters

--specimen-id: Exact specimen ID.
--host-taxid: NCBI host taxon ID. Catalog descendants are included, so higher-level identifiers such as 8509 match descendant host species.
--host-species: Exact host species name.
--host-lineage: Exact term matched against host_species, host_genus, host_family, host_order, and host_class.
--sex: Exact sex label.
--weight-min and --weight-max: Minimum and maximum recorded specimen weight.
--length-min and --length-max: Minimum and maximum recorded specimen length.

The catalog may store multiple recorded weight or length values per specimen. Range filters match when any recorded value falls inside the requested range.

Summarize specimens

ehitk specimens stats --host-lineage Reptilia
ehitk specimens fields
ehitk specimens values --field host_order
ehitk specimens values --field sex --csv --output-file specimen-sex-values.csv

Available query columns

specimen_id, host_taxid, host_species, host_genus, host_family, host_order, host_class, weight, length, and sex.