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
SourceLabel / pathAssertionsUnit
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
TaxonSourceRankPoolCorroborated
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.

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. NCIT:C15189 'Biopsy Procedure' kept as an xref. 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.