Use UBERON IDs for body-site terms in attributes.tsv

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Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
68/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Active
Tech stack
r
Domain
data

Research direction

Start with inst/extdata/attributes.tsv and inspect the ontology column for the habitat and isolation-site groups. Check whether code reads that column, then update the listed body-site terms to their proposed UBERON IDs and merge the duplicate rows with empty ontology values. Done means only the intended ontology entries and duplicate rows change, while attribute names stay the same.

Written by the indexing model from the issue text.

Description

The body-site terms of the habitat and isolation-site groups in inst/extdata/attributes.tsv carry IDs from seven ontologies (NCIT, FMA, EHDAA2, MCO, ZFA, SPD, UBERON), and some have none. BugSigDB records body sites with UBERON, so UBERON IDs would let bugphyzz habitats be matched to BugSigDB body sites. UBERON covers body sites only; environments stay on ENVO and hosts on NCBITaxon.

Proposed IDs

Labels were checked against OLS on 2026-11-11.

bugphyzz term Now UBERON UBERON label
gastrointestinal tract FMA:71132 UBERON:0001555 digestive tract
large intestine NCIT:C12379 UBERON:0000059 large intestine
vagina NCIT:C12407 UBERON:0000996 vagina
nasopharyngeal cavity EHDAA2:0004555 UBERON:0001728 nasopharynx
respiratory system NCIT:C12779 UBERON:0001004 respiratory system
human urine MCO:0000662 UBERON:0001088 urine
oral none UBERON:0000165 mouth
skin NCIT:C12470 UBERON:0002097 skin of body
cerebral spinal fluid ZFA:0001626 UBERON:0001359 cerebrospinal fluid
circulatory system SPD:0000611 UBERON:0001009 circulatory system
feces FMA:64183 UBERON:0001988 feces
rumen NCIT:C98778 UBERON:0007365 rumen
sputum NCIT:C13278 UBERON:0007311 sputum

blood (UBERON:0000178) and foregut (UBERON:0001041) already have UBERON IDs. digestive system would go away if #300 is done; otherwise it needs one as well.

Notes

  • Only the ontology column changes. The attribute names stay, so no data or export changes.
  • Several of these terms have a second row in attributes.tsv with no ontology (rumen, blood, cerebral spinal fluid, circulatory system, digestive system, foregut, intestinal microflora). Merging the duplicates belongs in the same change.
  • I have not checked whether any code reads the ontology column.
  • EFO imports most of these UBERON terms but not feces, rumen, sputum or foregut. That matters only if someone matches through EFO and not UBERON directly.

Raised while adding the Wikipedia source (waldronlab/bugphyzzExports#105).

Written with Claude Code.

Dominant language
R
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6
Forks
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Avg merge
3h 17m
Merged PRs (30d)
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