Add reference pseudo-documents into AmiGO, add references into general index

[ValWood]

I was going to tell our users to check this out, http://amigo.geneontology.org/amigo/reference/PMID:25411334
but currently you can't search on PMID. Do you plan to add? if so will wait.

[kltm]

I think what you're looking for would be on:
http://amigo.geneontology.org/amigo/software_list
Entering PMID:10508172 would take you to:
http://amigo.geneontology.org/amigo/reference/PMID:10508172
There is currently no separate PMID document type and PMIDs are not separately indexed, so searching in the general interfaces do not return much of interest.

[kltm]

For reference, there is the similar #285 .
As a workaround for now, there is also just searching for the local part of the PMID in the annotation search; e.g.:
http://amigo.geneontology.org/amigo/search/annotation?q=10508172*&sfq=document_category:%22annotation%22

[kltm]

After discussion with @cmungall, we'll work towards making the current "hacked" /reference/ path into a more proper page, which could then be referenced by a general index entity (id).

The page would render as it does now for PMIDs, and basically just display the ID and faceted search display for other references (although that can be expanded in the future fairly easily).

Before this is done, the owltools loader will need to collect references and add them to general. Given how little information we currently have about references internally (essentially just the ID), we may even be be able to clobber repeats in place.

Once in general, additional routing will need to be added to the perl and js to have /reference/ to be another (almost) top-level entity (even though it does not have a corresponding document type). Should mostly be the linker code, for which we'll need another NPM release.