Eric Deutsch

One concern is if BioLink entities must have identifiers? Arbitrary sets of proteins won't have identifiers. Is that a problem? Sure, you could consider a pathway as a set of...

In our usage, is_set is only used in the QueryGraph QNodes. In the KnowledgeGraph the Nodes are all individual (because one node may belong to multiple sets). The sets are...

FWIW, here's an example of how ARAX is using it: https://arax.rtx.ai/beta/?m=2648 This is a query that is basically (DOID:14330)---(protein,is_set=true)---(chemical_substance) This basically means that we're looking for chemical_substances that share *sets*...

not necessarily, you can have a set of one protein. But sets with more members are ranked higher in our algorithm.

and stated another way, if protein has is_set=false, then the results are all possible paths through the knowledge_graph, rather than the non-redundant set of chemical_substances with the sets of proteins...

Okay, thank you, @dosumis how can we address these issues?

I think you captured this very well. The attribute_type_id conveys to the reader that the value will be primary_knowledge_source (which is_a knowledge_source). So all the reader then needs to know...

yes, thank you all!

Great! I'm surprised! I just did a query for pathways and got this: https://arax.ncats.io/?r=40441 and see publications associated with a non-SemMedDB edge, so this is great! 

This is a good example. KEGG has this: https://www.genome.jp/dbget-bin/www_bget?pathway:map05323 The Node Synonymizer shows this at https://arax.ncats.io/?term=KEGG:05323  which I think means that KG2pre has a node KEGG:05323 which is considered...