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* 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. | * 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? | * 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 | * <s>Add SILVA taxonomy for prokaryotes by mapping to NCBI taxon ID. Prefer SILVA to GTDB because more spp. represented by 16S, not just genomes</s> | ||
* Better documentation of the data modeling, example workflow for adding a new entry based on information in a publication | * 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) | * 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? | * 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... | 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... | ||
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* Add statements about metabolism ("phototroph", "nitrogen fixer") to symbiont items? | * Add statements about metabolism ("phototroph", "nitrogen fixer") to symbiont items? | ||
* Dummy taxon for "microbiome" to enable us to add references for microbiome studies? | * 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 | |||