HabitatMech

Biopsy

habitatmech:BACDIVE.3d4fdc29fb ·CLINICAL ·UNGROUNDED REVIEWED

Source attestations

Each upstream vocabulary's own account of this habitat. Assertion counts are per-source units and are not comparable across sources — GOLD counts organisms, BacDive strains, PREGO taxa.

What each upstream vocabulary says about this habitat

Source	Label / path	Assertions	Unit
BACDIVE	Biopsy	95	STRAIN

Associated taxa

Taxa reported from this habitat, which is weaker than being characteristic of it. rank is out of pool: a high rank in a pool of thousands of near-tied scores is a weak claim. Entries corroborated by a second, independent source are listed first.

Taxa reported from this habitat

Taxon	Source	Rank	Pool	Corroborated
Helicobacter pylori NCBITaxon:210	BACDIVE	1	73
Eggerthella lenta NCBITaxon:84112	BACDIVE	2	73
Granulicatella adiacens NCBITaxon:46124	BACDIVE	3	73
Campylobacter concisus NCBITaxon:199	BACDIVE	4	73
Prevotella jejuni NCBITaxon:1177574	BACDIVE	5	73
Clostridium sp. NCBITaxon:1506	BACDIVE	6	73
Cutibacterium acnes NCBITaxon:1747	BACDIVE	7	73
Campylobacter jejuni subsp. doylei NCBITaxon:32021	BACDIVE	8	73
Helicobacter pylori NCTC 11637 = CCUG 17874 = ATCC 43504 = JCM 12093 NCBITaxon:102618	BACDIVE	9	73
Campylobacter hyointestinalis subsp. lawsonii CCUG 27631 NCBITaxon:1031752	BACDIVE	10	73
Mycobacterium heckeshornense NCBITaxon:110505	BACDIVE	11	73
Nocardia kruczakiae NBRC 101016 NCBITaxon:1210078	BACDIVE	12	73
Nocardia niwae NBRC 108934 = DSM 45340 NCBITaxon:1223489	BACDIVE	13	73
Pediococcus acidilactici NCBITaxon:1254	BACDIVE	14	73
Mycobacterium arosiense ATCC BAA-1401 = DSM 45069 NCBITaxon:1265311	BACDIVE	15	73
Streptococcus gordonii NCBITaxon:1302	BACDIVE	16	73
Streptococcus sp. NCBITaxon:1306	BACDIVE	17	73
Schaalia turicensis NCBITaxon:131111	BACDIVE	18	73
Nocardia veterana NCBITaxon:132249	BACDIVE	19	73
Corynebacterium freneyi NCBITaxon:134034	BACDIVE	20	73
Kroppenstedtia pulmonis NCBITaxon:1380685	BACDIVE	21	73
Mycobacterium lentiflavum NCBITaxon:141349	BACDIVE	22	73
Limosilactobacillus gastricus DSM 16045 NCBITaxon:1423749	BACDIVE	23	73
Lactobacillus kalixensis DSM 16043 NCBITaxon:1423763	BACDIVE	24	73
Mycobacterium decipiens NCBITaxon:1430326	BACDIVE	25	73

Related terms

Terms a source linked to this concept without this record claiming to be one of them, or to be narrower than one. A cross-reference, not a grounding.

• Biopsy Procedure NCIT:C15189

Curation

What a curator decided about this record, and why. A record built from several source concepts can carry one decision per concept.

1. CONFIRM_UNGROUNDED 2026-08-16 · claude-opus-5

   Confirmed UNGROUNDED: no ontology term fits this concept. Nearest broader term NCIT:C15189 'Biopsy Procedure' attached as a parent. CLOSE-grounding review (#12): the seeder made NCIT:C15189 'Biopsy Procedure' the identity of BacDive's 'Biopsy' category, 95 strains. A procedure is not a habitat — it is the act of taking the sample, not the place the organism lived, the same category error as grounding a record to an organism or a quality. The habitat is whichever tissue was biopsied, which BacDive does not say, so no term fits. The procedure term is kept as an xref (#99) to record what upstream matched without this repo asserting the record is a procedure. The record was CLINICAL while it carried the NCIT term and would fall to OTHER without one, because the category is inferred from the grounding; a biopsy is a clinical source whether or not a term fits, so the category is pinned rather than lost with the grounding. (source concept habitatmech:BACDIVE.3d4fdc29fb)

Provenance

Generated by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record.