Hello,
Currently, I have been working as part of an effort to add new concept terms into our own localhost branch of ATLAS, as well as their relationships. These concepts, however, are generally not standard (i.e. not standard vocabulary like SNOMED) and tend to be in vocabularies such as DIDEO, CHEBI, and so on (more examples of vocabularies and concepts we have inserted can be seen here: http://www.ontobee.org/).
So with these concepts and new vocabularies, we are interested in visualizing the hierarchical relationships between the terms we add in the “Hierarchy” tab of ATLAS. For instance, in this example concept for the term “CHO Cell”, we can see the parents and children for “CHO Cell”. All of such parents and children have been added, along with “CHO Cell” into our concept table, and the relationships have been added into the “concept_relationship” and “concept_ancestor” table accordingly. The relationship_id “Subsumes” is being used in the “concept_relationship table” for the children and “Is a” for the parents of a term. In the “concept_ancestor” table, the max and min levels of separation are both 1 for the immediate parents and children.
While the concepts that we insert into the “concepts” table show up in ATLAS, and the “Related Concepts” tab also is populated as expected for these concepts in ATLAS based on what we put in the “concept_relationship” table, we are, however, having trouble getting the “Hierarchy” tab to display the parents or children for the concepts we insert.
What we have tried:
We have experimented by adjusting some “Vocabulary” and “Concept class” pairings in some of the concepts we inserted. We noticed that if we changed a concept’s “Vocabulary” and “Concept Class” to, for example, “SNOMED” and “Clinical Finding” respectively, the “Hierarchy” would work correctly.
We then understood that the “metatrix” property within Atlas/js/app.js::499-690 appears to be constructing the “Hierarchy” tab based on the Vocabulary / Concept class pairings, along with relationship id and levels of separation. So after searching this forum for previous posts related to our issue and finding threads such as this related forum post, we then added our own customization of the “SNOMED”.“Clinical Finding” snippet of code seen in Atlas/js/app.js::670-679, replacing ‘SNOMED.Clinical Finding’ with a vocabulary / concept class pairing used for our own set of concepts, such as ‘CHEBI.Domain’.
'CHEBI.Domain': {
childRelationships: [{
name: 'Has descendant of',
range: [0, 1]
}],
parentRelationships: [{
name: 'Has ancestor of',
range: [0, 1]
}]
},
This Github issue and its fix appeared to suggest that this modification would allow us to show parent/child concepts in hierarchy view for concepts with vocabulary id “CHEBI” and concept class “Domain”. However, the hierarchy view still did not change.
We also tried the opposite, by commenting out the “SNOMED” lines in the above app.js snippets to see if the SNOMED concept hierarchies that have been already functioning would no longer work. Still, this change to app.js did not alter anything in our ATLAS’shierarchy.
So, with this information, we were wondering if the community here had any further ideas on how to get the hierarchy tab to function for the concepts we insert. Please feel free to ask any about any further questions or clarifications, and any help or feedback would be greatly appreciated.
Thank you!
-Eric Chou
