Habitat: map synonymous terms from different sources to one

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Evaluación

Dificultad
3/5
Tiempo estimado
1-2 días
Aptitud para principiantes
77/100
Tipo de issue
Nueva funcionalidad
Claridad
Bien especificado
Estado de actividad
Activo
Stack tecnológico
r
Área
data

Línea de trabajo

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.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

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.

Lenguaje dominante
R
Estrellas
6
Forks
6
Merge medio
3 h 17 min
PR fusionados (30 d)
20

Preparar el entorno

Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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