Overwrite all Type/Attribute definitions with SEPIO defs.

[larrybabb]

@cbizon @bpow @tnavatar

I recall saying that we would use all the definitions that we worked on with MB (SEPIO) in place of our original definitions.

I will go through and update our Type/Attribute cells with the SEPIO defs but I'd like validation from @cbizon or @bpow. To be clear, I will only overwrite our original defs if there is a solid definition available in the SEPIO data.

[bpow]

That seems right to me. A lot of our original definitions were almost placeholders, and the ones worked out thorough the SEPIO collaboration are much more consistent and robust.

[cbizon]

Yes, this is correct.

[larrybabb]

As I am going through to incorporate the SEPIO and other definitions. I have hit quite a few (mostly attributes) that have no definition). Not sure if we should be doing this or if we should do it together with Matt B. I will put the text DEFINITION PENDING.

@bpow @cbizon I would like you guys to verify that we truly want to use these definitions because there are a number of attributes that are associated to a single IRI and therefore they all have a very ambiguous definition.

For example, the following attributes all share the IRI SEPIO:0000197 (asserted_conclusion) which has the definition

A relation that holds between an assertion (e.g. a variant interpretation or criterion assessment) and a term that summarizes its asserted conclusion.

These will all have that same definition in our documentation...

• VariantInterpretation.outcome
• CriterionAssessment.outcome
• BenignMissenseVariationRate.value
• LocusHeterogeneity.specificity
• ConditionMechanism.mechanism
• ConditionPenetrance.penetrance
• AlleleConservation.outcome
• IndividualAlleleInheritance.alleleInheritance
• FamilyCondition.familyHasCondition
• IndividualAllele.phase
• IndividualCondition.hasCondition
• InSilicoPrediction.categoricalPrediction
• MolecularConsequence.consequence
• NullAllele.annotation
• RegionAlleles.outcome
• RegionType.annotation
• ExcludedRegionType.annotation

[cbizon]

Thanks for making this clear. After viewing this list, I no longer thing we should document with the sepio definitions for these attributes.

[bpow]

Yeah, it sounds like we should refer to the sepio defs but have our own that are more domain specific.

[bpow]

@cbizon will fill out the 'description' column of the 'Type' table

[cbizon]

The description column is filled out, but now I need to make all the pages for DomainEntities

[cbizon]

I think that this is complete.