Avoid example.com justification for conceptwiki

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ConceptWiki void has justifications like

www_uniprot_org_uniprot-gene.ttl:   dul:expresses <http://example.com/ConceptWikiGene> ;
www_uniprot_org_uniprot-protein.ttl:    dul:expresses <http://example.com/ConceptWikiProtein> ;

These should be replaced with proper justifications. Even if this remains special, terms should be minted in the bridgedb or openphacts namespace.

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Used for Protein-Gene mapping - particularly for looking up labels which could be for both genes or proteins.

The two lenses

http://heater.cs.man.ac.uk:3004/QueryExpander/Lens?lensGroup=gene

opts between http://example.com/ConceptWikiGene and http://example.com/ConceptWikiProtein

Related to SQL hack for different direction?

Tricky to fix properly in time for Open PHACTS 2.0

[ianwdunlop]

Maybe someone could explain what the page at http://heater.cs.man.ac.uk:3004/QueryExpander/Lens?lensGroup=gene is actually trying to tell me. Why do we have justifications which use the example.com domain?

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Excerpts from Ian Dunlop's message of 2015-10-14 13:34:27 +0100:

Maybe someone could explain what the page at http://heater.cs.man.ac.uk:3004/QueryExpander/Lens?lensGroup=gene is actually trying to tell me. Why do we have justifications which use the example.com domain?

As far as Daniela explained, the http://example.com/ConceptWikiGene and
http://example.com/ConceptWikiProtein are custom justifications just for
ConceptWiki linksets for protein and gene (and in particular just the links to
Uniprot).

There are two different lenses so when you ask for labels for say a uniprot
identifier, you can ask if you want the gene name or the protein name.

There's also the related gene-to-protein but not protein-to-gene issue.

Now even if we are to keep a special justification for conceptwiki, then
it shouldn't use example.com, but be part of some openphacts or conceptwiki
namespace.

Stian Soiland-Reyes, eScience Lab
School of Computer Science
The University of Manchester
http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718

[ianwdunlop]

Thanks for that explanation but I'm not sure I could figure that out from the web page. For example, the description "The lens used to Add ConcepWiki Gene URIs into the Open PHACTS Discovery Platform" doesn't seem to tell me that if I use this ConceptWikiGene Lens then I will get the gene name rather than the protein name. As another example, what are the assumptions behind the Default Lens. Justifications using a collection of URIs are fine for machines but not so good for humans. Anyway, apologies for hijacking the thread.