Composition Relations via Properties

[everbeek]

The word on the street is that some time in September, a new REST call will be available to fetch properties in a way that will tell us whether a property is a relation that we can render. Keep an ear to the ground. This supplements the part_of relation, and replaces the SNOMED specific has_part relation that I have hard coded.

[everbeek]

They are here: http://data.bioontology.org/ontologies/UBERON/properties?apikey=efcfb6e1-bcf8-4a5d-a46a-3ae8867241a1

Testing: http://127.0.0.1:8888/conceptPathToRoot.html?gwt.codesvr=127.0.0.1:9997&initial_vis=term_neighborhood&ontology_acronym=UBERON&full_concept_id=http://purl.obolibrary.org/obo/UBERON_0002407&restURLPrefix=data.bioontology.org

Note that my fave ontology, SNOMEDCT, has no properties at this time.

See what Peggy and Ray think about this multitude of properties being included in expansions.

[everbeek]

I have it set up, but I am having trouble finding UBERON concepts that actually make use of the properties. Inspecting to see if I am misinterpreting something...

This one has "immediate transformation of" but I searched via "develops_from": http://bioportal.bioontology.org/ontologies/UBERON?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0006591

[found via search http://bioportal.bioontology.org/search?q=develops_from&ontologies=&include_properties=true&include_views=false&includeObsolete=false&require_definition=false&exact_match=false&categories=] [use the UBERON properties in the search box...but not ids!]

http://127.0.0.1:8888/conceptPathToRoot.html?gwt.codesvr=127.0.0.1:9997&initial_vis=term_neighborhood&ontology_acronym=UBERON&full_concept_id=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0006591&restURLPrefix=data.bioontology.org

Confirmed that the id "http://purl.obolibrary.org/obo/RO_0002495" for "immediate transformation of" appears in the properties of the class. It is not showing up in the visualization yet, but now I have a positive test case.

[everbeek]

1) Test with layouts -layouts seem ok. Trees work well, force, circles. The radial layout is always sort of hard to see as optimal or suboptimal. It is probably fine.

2) Get the new arc types added to the "Edge Types Displayed" menu. -have the entries updating when nodes are added and removed. Sorted the non-property ones to the top.

3) Decide on arc color and style, but I have it as dotted red for now. -I feel like keeping the dotted is good, but that the color needs to match the ontology. We'll see what people say.

[everbeek]

I must change the default arc colors so they are not going to be stomped on by relation property ontology-inherited colors. Basically, is_a, has_part, and map_to cannot be confusable with any of the possible ontology colors. Ontology colors are finite, currently set to 20 colors that get cycled through in nextNodeColor() function. To see them easily, load the ontology overview, and set the range to 1-21 (in the menu). You will see the first repeated color, and the way the cycle looks.

http://127.0.0.1:8888/ontologyMappingOverview.html?ontology_acronym=RCD

It is this color pallet: https://github.com/mbostock/d3/wiki/Ordinal-Scales#category20