Enhance the way OntoPortal displays changes between ontologies

[jonquet]

Is your feature request related to a problem? Please describe. We need advanced user interfaces to "see" the differences between ontologie versions and overall evolution of the content of the ontologies through out time.

Describe the solution you'd like We need to display diagrams showing the evolution of the metrics as well as a better diff tool that will provide a useful content and possibly a UI showing it. @naouelkaram To refines the needs

Technical steps

• [ ] Add the metrics "deprecatedObjects" to store the number of deprecated (owl:deprecated=true) objects (class, property or individual)
• [ ] Add the metrics "mod:numberOfLabels" to store the number of labels (pref or synonym) for objects (class, property or individual).
• [ ] Consolidate the metrics for all the previous submissions including for the 2 new properties
• [ ] Create a diagram view that will show evolution of the metrics through time (at least : classes, properties, individuals, classesWithNoDefinition, deprecatedObjects and labels)
• [ ] Create a new view to display the content of the diff files generated with Bubastis => another issue
• [ ] Enhance the Bubastis third party tool to address new needs => another issue

[jonquet]

An exemple of possible diagrams from OLS:

When one clicked on the graph, it displayed the list of all changes and if you clicked a concept, it displayed more details:

http://www.ebi.ac.uk/efo/EFO_0000618 2019-01-16 Add Synonym synonym: neurological problem 2019-01-16 Add Synonym synonym: neurological disorder

http://www.ebi.ac.uk/efo/EFO_1001128 2019-01-16 ADD LABEL label: Rickettsiaceae infectious disease 2019-01-16 Add Synonym synonym: primary Rickettsiaceae infectious disease 2019-01-16 DELETE LABEL label: primary Rickettsiaceae infectious disease

[jonquet]

@naouelkaram IS there any other metrics you would like to see? (I have added "numberOfDeprecated" to MOD2 (numberOfLabels was already there: https://github.com/sifrproject/MOD-Ontology/blob/master/mod-v2.0_profile.ttl#L2748

[graybeal]

that's a lovely OLS graph, would be cool to have that!

wanted to note this for the record: if you have the historical copies of the ontologies in the triple store (as BioPortal seems to, judging from some content lists I've seen), and you use AllegroGraph as your triple store, it has a tool that does a pretty impressive 'view over time' of the ontology graphs. (Can't remember if the tool is part of Gruff or separate.) Maybe something that would add value in this case.

[naouelkaram]

@jonquet the information we need for now can be extacted from the bubabtis tool's output + the extension we made for including annotation properties information (added/deleted labels/synonyms). We plan to follow the proposal of KGCL to represent and store the changes. Should we create a new issue for the detailed view and link it? @graybeal the OLS representation of the changes was definitely nice! One could also select a single concept and follow it changes through releases. I don't know what happened with the implementation, the tab just disappeared from OLS all together. Concerning Allegrograph, I would be very interested in seeing their approach, are the historical versions of an ontology all kept in the triple store? From what I understood only metadata info are kept and the files are archived.

[graybeal]

You can see the Allegrograph Time Bar feature here, it starts out slowly but gets more entertaining as it goes along. In that case they are dealing with an ontology that embeds time annotations about each event/class within it—I think AG embeds that information with ontologies as metadata on the fly, but it's been a while since I talked to them about it so ymmv.

[alexskr]

I don’t think AG Time Bar feature has anything to do with displaying changes between versions of ontologies. I might be wrong about it but it looks like all information about dates/time is embedded in a single graph and the tool just pulls that out based on pre-defined predicates.

[naouelkaram]

I think you are right @alexskr, the tool displays the temporal relations from the graph that fall into the selected time period while moving the bar. It seems to me that the temporal information is stored only at the ABox level through reification.