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VirtualFlyBrain / VFB

Virtual Fly Brain
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Fixing confusing type column in Display table #703

Open dosumis opened 9 years ago

dosumis commented 9 years ago

The name column display table in VFB 1.5 is a mix of individuals and classes. The type column is a mix of types (for individuals) and parent classes (for classes). e.g.

screen shot 2015-09-11 at 3 00 34 pm

Gad1-F-200073 is an individual (to simplify the interface, perhaps better referred to an image?). Its type is 'adult antennal lobe projection neuron DL1 adPN'. Lateral horn is a class. Its parent class is 'synaptic neuropil domain.

This is confusing. An all round better solution would be to treat painted domains as individuals. Here's a suggestion for an improved table using this solution:

screen shot 2015-09-11 at 3 04 03 pm

I've generated individuals for all painted domains on the JFRC2 template (I haven't bothered to create separate individuals for left and right domains.). I can do the same for the Ito half brain. Linking these to thumbnails as for other registered images should allow image display to slot into the existing system (e.g. showing up at the bottom of TermInfo pages.

I've been puzzling over how to fill in data source fields and fields used to create links. There are a couple of issues:

  1. The current system is designed for serving external links. This doesn't play nicely with internal links (where we want to change the base URI to fit test servers). Any suggestions for how to cope with this?
  2. It makes sense to use the same reference as we have on the site for the JFRC standard brain. I'm wondering whether we should change this to reference the GAL4 driver line paper http://www.cell.com/action/showImagesData?pii=S2211-1247%2812%2900292-6 - Adding a note about subsequent modifications by Jenett and Shinomiya to fit with BrainName standard.
dosumis commented 9 years ago

Background layer should be individual too.

Robbie1977 commented 9 years ago

with links just use the main site address and the deployment scripts already change the base urls for test servers.

Robbie1977 commented 9 years ago

@mmc46 would be better to discuss the types as she has been using the system; the current values are just what was available so am happy to change.

dosumis commented 9 years ago

No confusion about how to type things. Have made individuals. Now need to associate with images.

dosumis commented 9 years ago

Thumbnail Images for painted domains would need to be stored by vfb ID as for any other. Table to follow shortly.

dosumis commented 9 years ago

Related: Type column seems to have been dropped: #697

dosumis commented 9 years ago

Thinking about this proposal: Need to work out how this plays with the stack browser/tree. Right now there is a direct association between class (of neuropil) and domain on the stack/node on the browser. With proposed mode, it might make more sense for the association to be to the individual. But perhaps this obfuscates selection on stack - where it would probably be clearer to see name of the type, as we've always had.

e.g. showing 'LH - painted domain JFRC2' when clicking (or floating over) stack is less clear than showing 'lateral horn'.

mmc46 commented 9 years ago

I'd prefer if the domains kept displayed their names, and not the individual name. It's much clearer to have a name than to have an acronym.

Robbie1977 commented 9 years ago

the type column is still there just hidden as it took so long to resolve without solr but you may spot it reappearing after a while thanks to a bug in datatables

dosumis commented 9 years ago

I'd prefer if the domains kept displayed their names, and not the individual name. It's much clearer to have a name than to have an acronym.

Agree re any text displayed on stack. But with my proposal, the class names will appear in the type column of the display table - just as they do (or did until very recently) for all other individuals. Might want to make sure this column is adjacent to the thumbnail image column though to make sure the association is clear.

I could also change the names of the individuals. e.g. this might work: lateral horn (JFRC2)

dosumis commented 9 years ago

the type column is still there just hidden as it took so long to resolve without solr but you may spot it reappearing after a while thanks to a bug in datatables

OK. Hopefully solved by move to SOLR in near future, as this should be in the latest SOLR release (it's appearing for individuals on the OLS GUI test server).

Robbie1977 commented 8 years ago

Notes

Class query works http://vfbdev.inf.ec.ac.uk/search/select?fl=label,short_form&sort=score+desc&wt=json&rows=5&q=child_iri:*FBbt_00007401

Still need an individuals version

dosumis commented 8 years ago

SOLR?

Should use Neo4J. Relevant queries all working there. Need to work on getting Jenkins jobs working for build. Will make ticket. On 19 Feb 2016, at 18:25, Rob Court notifications@github.com wrote:

Notes

Class query works http://vfbdev.inf.ec.ac.uk/search/select?fl=label,short_form&sort=score+desc&wt=json&rows=5&q=child_iri:*FBbt_00007401

Still need an individuals version

— Reply to this email directly or view it on GitHub.

Robbie1977 commented 8 years ago

Just optimising the existing site till the new backend is ready On Fri, 19 Feb 2016 at 19:18, David Osumi-Sutherland < notifications@github.com> wrote:

SOLR? On 19 Feb 2016, at 18:25, Rob Court notifications@github.com wrote:

Notes

Class query works http://vfbdev.inf.ec.ac.uk/search/select?fl=label,short_form&sort=score+desc&wt=json&rows=5&q=child_iri:*FBbt_00007401

Still need an individuals version

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/VirtualFlyBrain/VFB/issues/703#issuecomment-186366477 .