Habitat: map synonymous terms from different sources to one
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 77/100
Research direction
Start with inst/extdata/attribute_synonyms.tsv and attributes.tsv, then inspect how the synonym table is applied to TRUE rows and how the vocabulary test checks for unused terms. Confirm the four proposed source terms have no FALSE rows, add their mappings, and remove terms from attributes.tsv only when no rows still use them. Done when the mappings pass the vocabulary check and the marine water body term remains unchanged.
Written by the indexing model from the issue text.
Description
Habitat is a multistate-union attribute, so the states of different sources add up and never compete. Sources use different words for the same place, though, and a search on one word misses the rows under the other.
Rows per term and source in physiologies("habitat"), with the Wikipedia_2026 source (#296) included:
| Term | Source | Rows | Same place as | Rows |
|---|---|---|---|---|
| digestive system | ProTraits | 215 | gastrointestinal tract (Wikipedia_2026 268, ProTraits 1) | 269 |
| hydrothermal vents | ProTraits | 45 | hydrothermal vent (Wikipedia_2026 75, BacMap 5) | 80 |
| creosote contaminated soil | ProTraits | 3 | creosote-contaminated soil (BacMap) | 1 |
| human microflora | BacMap | 2 | human microbiome (ProTraits) | 115 |
| marine water body | ProTraits 71, BacMap 20 | 91 | sea water (Wikipedia_2026 625, BacMap 7) | 632 |
Proposed change
Add rows to inst/extdata/attribute_synonyms.tsv for the first four, mapping the left term to the right one. Then remove the left terms from attributes.tsv if nothing else uses them.
marine water body to sea water is less clear, since a marine water body also has sediment. I would leave it unless someone wants it.
Leave alone
These are a source's own categories and have no equivalent elsewhere: colonization of host (507), multiple (318) and specialized (144) in BacMap; free-living (1,280), environmental system (92) and secondary (57) in ProTraits; waste and sludge water (797) in MiDAS. Broader terms such as aquatic biome and terrestrial biome are parents of the specific ones, not synonyms, so they stay too.
Wikipedia habitats are written only with terms bugphyzz already had, so that source needs nothing.
Check
The synonym table applies to rows with Attribute_value TRUE only. Confirm that the four left terms have no FALSE rows, which would keep the old term and fail the vocabulary test.
Raised while adding the Wikipedia source (waldronlab/bugphyzzExports#105).
Written with Claude Code.
- Dominant language
- R
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- 6
- Forks
- 6
- Avg merge
- 3h 17m
- Merged PRs (30d)
- 20
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First steps
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