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NCBI taxon IDs requiring attention from NCBI Taxonomy team
Items that need some attention
See: New studies to add
Taxonomic groups that need updates
- Euplotes symbionts
- Ciliate symbionts generally
Project maintenance to-dos
In progress:
- Add P42 statements "Method used to identify subject"
- Add environmental origin statements: P36, P38, P40
- Check for statements that should be moved from P19 to P41 "interacts experimentally with"
Chores (have to periodically clear them):
- Process backlog of new references
- Add higher taxonomy for newly added taxa that are not yet represented (PR2 for eukaryotes)
- Add parent taxa for all taxon items semi-automatically - try to match first word in taxon name to a genus name, remaining items have to be added manually
- Ensure that all items have a class, check that class "placeholder taxon" is consistently used
- Find references that have only DOIs and link them to reference items, or create new reference items for them by Wikidata lookup
Ideas:
- Decouple taxonomy from interaction partners? Class "interaction partner" that is independent of "taxon", though interaction partners are also instances of taxon. "taxon" can then have a new property "part of taxonomic system" with a "reference" item.
- Link prokaryote names to LPSN?
Add SILVA taxonomy for prokaryotes by mapping to NCBI taxon ID. Prefer SILVA to GTDB because more spp. represented by 16S, not just genomes- Better documentation of the data modeling, example workflow for adding a new entry based on information in a publication
- Interaction statement: Qualifier if identified in cultured strains (vs. in samples that were directly sampled from environment)
- Which environmental material is most appropriate for protists that are symbionts located in digestive tract environment?
- Copyright statement, privacy policy
NB: The taxonomy version (e.g. PR2 v5.0.0 for eukaryotes) is tagged by linking to a reference item for that particular taxonomy version to the 'parent taxon' statement in a 'stated in' reference. Ideally we should be able to specify which taxonomy version we want to use, if branches get moved around in the future...
Modeling:
- Sane way to model placeholder taxa and non-specific taxon statements? E.g. general statements like "all members of this family are associated with methanogens", without creating items for each individual?
- Modeling interactions: RO is insufficient?
- Add statements about metabolism ("phototroph", "nitrogen fixer") to symbiont items?
- Dummy taxon for "microbiome" to enable us to add references for microbiome studies?
Draft annotation guidelines:
- Reference items should always have DOI as an alias, so it that users can easily check with the search bar if it is already used somewhere in the database
- Environmental origin of the organisms using EnvO terms, use guidelines aligned to MIxS: https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5