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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?

Latest revision as of 08:03, 23 April 2024

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