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NCBI taxon IDs requiring attention from NCBI Taxonomy team

• Item:Q251
• Item:Q297 and related
• Instances of Item:Q657

Items that need some attention

• Item:Q448 - should be split to two entries
• Item:Q1156 - check that examples in their Discussion are incldued in DB
• Add other Phycorickettsia hosts mentioned in Item:Q1090, in addition to Trachydiscus minutus
• New item for Psalteriomonas vulgaris, based on this ref: Item:Q1055

To add:

• Pelomyxa spp. described in Item:Q1742

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
• 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
• 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?

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?