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VirtualFlyBrain / VFB_owl

A repository for VFB owl files and the code that generates them
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OLS: Specify linkouts to VFB (& FlyBase) #39

Open dosumis opened 6 years ago

dosumis commented 6 years ago

In OLS it is possible to specify linkouts from xrefs and to display reference images. We should take advantage of this to get links to VFB and to supply reference images to OLS.

e.g. liver has xrefs to MA and EMAPA:

image

And an image of a liver: image

Expansion of the xrefs into hyperlinks is driven by the GOdb-xrefs.yaml doc. Although OLS could take additional docs for this. We should investigate extending this yaml to allow specification of a logo PNG for linking ( CC @cmungall ).

This provides one route for specifying linkouts as we already roll these to drive linkouts from FlyBase: image

These xrefs are added to nervous system terms as part of the release pipeline (@temjones do you know if this still happens?) and are used to provide linkouts from FlyBase to VFB.

A simpler mechanism would be to use the short_form or OBO ID (curie) to drive linkouts to the same term in OLS on a range of alternative browsers (for GO this could be Amigo & QuickGO). The obvious place to specify this would be in the obofoundry spec: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/ontology/fbbt.md. This already has generic browser links. It would be great if these could be turned into link recipes to allow linking on specific terms (CC @cmungall would this be overloading? )

temjones commented 6 years ago

@dosumis My understanding is that the VFB xrefs are added manually upon creation of new anatomy terms, in OBO the line:

xref: VFB:FBbt_xxxxxxxx

would be added to the term stanza.

dosumis commented 6 years ago

@dosumis My understanding is that the VFB xrefs are added manually upon creation of new anatomy terms, in OBO the line:

Hmmm - that's slightly terrifying. Some will undoubtedly fall through the cracks. I'm sure I had this automated at some point and we should be able to do so again.

mmc46 commented 6 years ago

I don’t remember this being automated, but yes, it would be better if so. What we show in VFB (and wanted linkouts from) has also changed though: we use to only show neural terms, and I think now the queries are not restricted. I think I’d made a ticket about this a couple of months ago (I don’t know where this now).

On 18 Dec 2017, at 14:34, David Osumi-Sutherland notifications@github.com wrote:

@dosumis https://github.com/dosumis My understanding is that the VFB xrefs are added manually upon creation of new anatomy terms, in OBO the line:

Hmmm - that's slightly terrifying. Some will undoubtedly fall through the cracks. I'm sure I had this automated at some point and we should be able to do so again.

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