Project:Main
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Lists of pages
Project pages
- Project:Main -- This page
- Project:Curation workflow -- Workflow guidelines for adding new entries and annotations
- Project:New studies to add -- List of papers with potentially relevant information for the database
- Project:SPARQL/examples -- Example SPARQL queries added here will appear in the examples list in the Query Service interface
- Project:Cradle -- Cradle templates (not really used at the moment, prefer to define EntitySchema)
EntitySchema pages
- EntitySchema:E1 -- Taxon
MediaWiki pages
- MediaWiki:Wikibase-SortedProperties -- Set the order in which statements are displayed on item 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
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