Delete incorrectly imported ontologies

[Hannah-Doerpholz]

I have looked at the ontologies that are currently included in our ontology lookup service (using both swate and the Ontology DB API - v2).

Below you can see a screenshot of the swate advanced search. When I want to select a specific ontology to look through I can see that there are several suggestions that are not actually ontologies but individual terms.

According to GitHub we have the following ontologies included: chebi, credit, dpbo, efo, envo, go, miappe, mod (PSI-MS), ms (psi-ms; not importing Typedefs, those are faulty anyways: label was used as ID), ncbitaxon, ncit, nfdi4pso (obsolete), obi, pato, peco, po, PPEO (can't be imported due to faulty file, will in the future be removed from the GitHub and is replaced by the miappe ontology), ro, to, uo (unit). When I check swate, I can choose the following ADDITIONAL "ontologies": apollo_sv, bao, bao_0000875, bao_0000925, bfo, biological_material, bto, caro, ccredit, chmo, cl, clo, country, credit_00000000, credit_00000001, credit_00000002, credit_00000003, credit_00000004, credit_00000005, credit_00000006, credit_00000007, credit_00000008, credit_00000009, credit_00000010, credit_00000011, credit_00000012, credit_00000013, credit_00000014, data, data_file, dc, doid, edam, ehdaa2, environment, environment_parameter, eo, ero, event, experimental_design, factor, factor_value, fao, fbbt, fbdv, fma, foodon, gaz, genepio, gps_location, growth_facility, hancestro, hp, http, https, iao, ido, institution, investigation, location, ma, material_source, method, mondo, mp, mpath, named_location, oba, observation, observation_level, observation_level_hierarchy, observation_unit, observed_variable, obsoleteclass, ogms, ome, omiabis, omit, omrse, ontology, orphanet, pco, peff, person, pr, pso, reo, role, sample, scale, sctid, sio, so, south, spatial_coordinate, spatial_distribution, spatial_distribution_type, stato, study, subset, trait, uberon, united, upheno, vo, wbls, xsd, zea, zfa. I get them from the API as well.

The database should be checked for terms that have been (incorrectly) imported but cannot be found through the actively included ontologies (those listed in the GitHub folder as .obo files and within the ext_ontologies.include file) and be removed from the database.

[Zerskk]

Ontologies imported from the repository are marked in the database with the property "generated". With this scheme other ontologies can be hidden so that they are not shown in the list in SWATE. This feature is also be used at the Swobup status page to show only the main ontologies. Considering this, this function should be adjusted in the client (SWATE).

For the rest, further checks need to be done

[Zerskk]

Most of the ontologies are imported from PPEO, so this ontology needs to be adjusted.

[kdumschott]

We have removed PPEO from the ontology list but the problem is still persisting. We think it could be to do with imported terms within the included external ontologies and would have to be handled by how Swate or Swobup parses those (as we cannot see how these options are generated from our end). Is this something that can be looked into @Zerskk @Freymaurer ?

[Freymaurer]

This function is not yet restored for swate alpha and can be designed in any way desired.

[Hannah-Doerpholz]

I think the best would be if we would just show the namespaces of all ontologies that are explicitly included. This should entail the following:

• DPBO
• CRO
• NCBITaxon
• ENVO
• MS
• CHEBI
• GO
• OBI
• PATO
• PECO
• PO
• RO
• TO
• UO
• MOD
• EFO
• NCIT
• OMP
• ARC

We also discussed that it would be nice to display additional information for each ontology regarding its scope. We could provide a yml file for the ontologies describing each scope, so that the users know, for example, if they do a phenotyping experiment, MIAPPE would be a good fit for them.