Talk:Main Page: Difference between revisions
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* [[Item:Q297]] and related | * [[Item:Q297]] and related | ||
* Instances of [[Item:Q657]] | * Instances of [[Item:Q657]] | ||
==Items that need some attention== | |||
* [[Item:Q388]] -- reference 10.1038/ismej.2010.40 describes more symbionts, only one is in DB? | |||
==Project maintenance to-dos== | ==Project maintenance to-dos== | ||
Chores: | Chores (have to periodically clear them): | ||
* Process backlog of new references | * Process backlog of new references | ||
* Add higher taxonomy (PR2 for eukaryotes | * Add higher taxonomy for newly added taxa that are not yet represented (PR2 for eukaryotes) | ||
* Add parent taxa for all taxon items | * 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 | * Ensure that all items have a class, check that class "placeholder taxon" is consistently used | ||
Ideas: | |||
* Link prokaryote names to LPSN? | |||
* Create reference items from DOIs in references and reconcile with Wikidata? | |||
* Add SILVA taxonomy for prokaryotes by mapping to NCBI taxon ID. Prefer SILVA to GTDB because more spp. represented by 16S, not just genomes | |||
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: | Modeling: | ||
Revision as of 23:36, 19 March 2024
NCBI taxon IDs requiring attention from NCBI Taxonomy team
Items that need some attention
- Item:Q388 -- reference 10.1038/ismej.2010.40 describes more symbionts, only one is in DB?
Project maintenance to-dos
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
Ideas:
- Link prokaryote names to LPSN?
- Create reference items from DOIs in references and reconcile with Wikidata?
- Add SILVA taxonomy for prokaryotes by mapping to NCBI taxon ID. Prefer SILVA to GTDB because more spp. represented by 16S, not just genomes
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?