Project:Main: Difference between revisions

From Protist-Prokaryote Symbiosis Database
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* [[Item:Q297]] and related
* [[Item:Q297]] and related
* Instances of [[Item:Q657]]
* Instances of [[Item:Q657]]
* [[Item:Q557]] name is misspelled in NCBI Taxonomy database


=== Items that need some attention ===
=== Items that need some attention ===

Revision as of 20:51, 11 June 2024

Lists of pages

Project pages

EntitySchema pages

MediaWiki pages

Software

  • ppsdb-utils -- Python scripts for various maintenance task (private GitHub repo)


To do lists

NCBI taxon IDs requiring attention from NCBI Taxonomy team

Items that need some attention

  • Item:Q448 - should be split to two entries
  • Item:Q994 - check that all listed host species included

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
  • Link taxon items to Wikidata by their NCBI taxon IDs
  • Find (prokaryote) taxon items that have NCBI taxon ID and a LPSN record, but which are not in Wikidata, and export them to Wikidata

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: