Feature Request for Pathways Interactions byEntity

[RyAMiller]

One thing Peter pointed out when testing was that when specifically looking at the Interactions/byEntity calls was that we should also use the 'type' of interaction it is. Getting information about what sort of interaction it is is useful when looking for places to stop (for example: an inhibition event). Adding the type should be easy enough, it is already in the RDF and only requires an additional one line to the query used in the call. Something along the lines of ' a ?type ' and then use ?type as a variable.

[stain]

Could you give example of which API calls should add which types? I can't find any additional types beyond DirectedInteraction and Interaction on the example call

[stain]

These are the interaction types I can find:

http://vocabularies.wikipathways.org/wp#Binding http://vocabularies.wikipathways.org/wp#ComplexBinding http://vocabularies.wikipathways.org/wp#Interaction http://vocabularies.wikipathways.org/wp#DirectedInteraction http://vocabularies.wikipathways.org/wp#TranscriptionTranslation http://vocabularies.wikipathways.org/wp#Conversion http://vocabularies.wikipathways.org/wp#Catalysis http://vocabularies.wikipathways.org/wp#Inhibition http://vocabularies.wikipathways.org/wp#Stimulation

[stain]

So say in interactions with ENSBTAG00000048213 you would want to include:

<http://rdf.wikipathways.org/Pathway/WP1065_r80781/WP/Interaction/b23fd> rdf:type ns0:DirectedInteraction, ns0:Inhibition ;
      ns1:source <http://identifiers.org/ensembl/ENSBTAG00000048213> ;
      ns1:target <http://identifiers.org/ensembl/ENSBTAG00000005359> .

?

[stain]

Now added on ops2 - please check and then we can squeeze it in for 2.1.

note that this means that the for the interaction sometimes is an array in JSON or nested in XML:

<item href="http://rdf.wikipathways.org/Pathway/WP1065_r80781/WP/Interaction/d28eb">
    <type>
        <item href="http://vocabularies.wikipathways.org/wp#Inhibition"/>
        <item href="http://vocabularies.wikipathways.org/wp#DirectedInteraction"/></type>
        <target href="http://identifiers.org/ensembl/ENSBTAG00000010671">
           <type>
              <item href="http://vocabularies.wikipathways.org/wp#GeneProduct"/>
              <item href="http://vocabularies.wikipathways.org/wp#Protein"/>
           </type>
(..)

(but as you see this was already the case with the source and target types)

[stain]

Probably needs to be added to the swagger file documentation to indicate the optional array of ?types in orange background

[PeterWoollard]

Thanks Stain, that looks good to me. This adds a lot of value. Yes it would be great if this can be squeezed into the 2.1 release. Any concerns Ryan?

[stain]

Thanks, then I think we can deploy this.

@ghard - could you do a git pull on the 2.1 branch on the API? That should deploy this change.