Enhance the portal to support SKOS

[syphax-bouazzouni]

Requirements :

• Enhance SKOS parsing and handling in BioPortal / AgroPortal #20
• Short term hierarchy enhancement for SKOS vocabularies including multiple Concept Schemes #258
• Handling multiple Concept Scheme in SKOS resource #259

Schemes part

Todo :

• Add skos:ConceptScheme model (+ tests)
• Add SKOS schemes and skos roots by scheme ontoportal-lirmm/ontologies_linked_data#27
• Shows all concept schemes if on a SKOS resource ontoportal-lirmm/bioportal_web_ui#81
• Shows all concept schemes of an ontology ontoportal-lirmm/ontologies_linked_data#24
• Filter a submission roots by a concepts scheme ontoportal-lirmm/ontologies_linked_data#22
• Filter tree view roots by concepts scheme
• In the UI tree view add a select field to choose what concepts scheme to show
• Changes "Classes" tab name to "Concepts" when browsing SKOS vocabularies ontoportal-lirmm/bioportal_web_ui#73 (comment)
• Remove the "Instances" tabs when browsing SKOS vocabularies ontoportal-lirmm/bioportal_web_ui#72
• Print the "missing roots" error log for the users ontoportal-lirmm/bioportal_web_ui#84
• order alphabetically the schemes in the scheme selector ontoportal-lirmm/bioportal_web_ui#83
• add :inScheme and :isInScheme attributes ontoportal-lirmm/ontologies_linked_data#43
• Extract tree code into a module
• update the path_to_root of a concept methods to use custom roots ontoportal-lirmm/ontologies_linked_data#44
• Add SKOS scheme model to the ontologies_api client
• handle concept tree if the concept is not found in a scheme ontoportal-lirmm/ontologies_linked_data#46
• Handle resources that didn't define the main concept scheme ontoportal-lirmm/ontologies_linked_data#49
• Fix in UI tree when expanding a concept children getting muted (grey color) by default
• Add SKOS concepts to the api client ontoportal-lirmm/ontologies_api_ruby_client#6
• Add SKOS links ontoportal-lirmm/ontologies_linked_data#51
• Show the type of object in the details views ontoportal-lirmm/bioportal_web_ui#112
• handle empty schemes ontoportal-lirmm/bioportal_web_ui#113

Collections part

Todo :

• Add the skos:Collection class to the model (+ tests)
• add the Collections endpoints ontoportal-lirmm/ontologies_api#20
• Add the Collection filter to Concepts endpoint (will be the endpoint :collection/members)
• Add a tab for Collections in the UI
• Add UI to filter concepts by Collection
• Add SKOS collection model to the ontologies_api client
• In the UI factorize the similar code between schemes, collections and concepts
• Add :inCollection and :isInActiveCollection attributes ontoportal-lirmm/ontologies_linked_data#45
• Add a filter in the tree view for collections (done with the attribute :isInActiveCollection)
• Add in the concepts tree view in UI a collection filter with a system of tagged colors ontoportal-lirmm/bioportal_web_ui#98
• Add icons in the concepts browsers (a tree icon for the hierarchy, and a list for the list)
• Do a dropdown modal for the filters (schemes + collections) ontoportal-lirmm/bioportal_web_ui#103
• show inCollection when we display=all for a concept
• Hande resources that do not have collections
• Add SKOS concepts to the api client ontoportal-lirmm/ontologies_api_ruby_client#6
• Add SKOS links ontoportal-lirmm/ontologies_linked_data#51
• Show the type of object in the details views ontoportal-lirmm/bioportal_web_ui#112
• Use unskos:memberOf unstead of our local inCollection attribute ontoportal-lirmm/ontologies_linked_data#54

SKOS-XL labels part

• add skos-xl model ontoportal-lirmm/ontologies_linked_data#47
• Add the properties skosxl:prefLabel, skosxl:altLabel, sksoxl:hiddenLabel to the class model ontoportal-lirmm/ontologies_linked_data#48
• Add the Labels endpoint (add skos-xl model ontoportal-lirmm/ontologies_linked_data#47)
• Add a UI component to display Label properties in the details tab especially skosxl:literalForm
• Fix a bug in the link buttons (the ontology acronym is duplicated)
• Add SKOS concepts to the api client ontoportal-lirmm/ontologies_api_ruby_client#6
• Add SKOS links ontoportal-lirmm/ontologies_linked_data#51
• Show the type of object in the details views ontoportal-lirmm/bioportal_web_ui#112

Concept date sort

• Add attributes dct:created and dct:modified to the Classes/Concept model ontoportal-lirmm/ontologies_linked_data#50
• Add an endpoint /classes/sorted_by_date to show the classes ordered by dct:modified (desc) and dct:created (desc) ontoportal-lirmm/ontologies_api#21
• Bug in the paginated concepts sorted by date, that is empty after page 200 ontoportal-lirmm/ontologies_api#25
• Add a UI that will list the class grouped by month of creation or modification ontoportal-lirmm/bioportal_web_ui#111
• ID concepts does't show for some concepts ontoportal-lirmm/bioportal_web_ui#115

use topConceptOf if no hasTopConcept found

• use topConceptOf to fetch roots if hasTopConcept not found ontoportal-lirmm/ontologies_linked_data#34

Metadata part

• extract metdata from the main scheme if no owl:ontology found ontoportal-lirmm/ontologies_linked_data#33

[jonquet]

Note for later : when working on Collection we nend to remember that there are actually 2 type

[jonquet]

Little addition to this SKOS wish list :

• A view to see the "news" based on the concept dates.
• A revised SKOS specific metrics in the Summary page.

[syphax-bouazzouni]

For next iterations

• extract metdata from the main scheme if no owl:ontology found ontoportal-lirmm/ontologies_linked_data#33
• Isolate the two models Concept (skos) and Class (owl) ontoportal-lirmm/ontologies_linked_data#52
• revised SKOS-specific metrics in the Summary page
• Add the option to choose the Date property to use
• Bug in the paginated concepts sorted by date, that is empty after page 200 ontoportal-lirmm/ontologies_api#25
• handle concept tree if the concept is not found in a scheme ontoportal-lirmm/ontologies_linked_data#46