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VirtualFlyBrain / VFB_json_schema

VFB json schema spec + code for rolling queries producing VFB json schema + related integration tests
Apache License 2.0
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Schema change in KB/PDB + edits to queries that need co-ordinating #44

Open dosumis opened 5 years ago

dosumis commented 5 years ago

Site IRIs and short_forms are currently a total hack

e.g.

"n.iri" "n.short_form" "n.link_base"
"http://flycircuit.tw" "VFBsite_FlyCircuit" "http://flycircuit.tw/modules.php?name=clearpage&op=detail_table&neuron="
"http://flweb.janelia.org/cgi-bin/flew.cgi" "VFBsite_FlyLight" "http://flweb.janelia.org/cgi-bin/view_flew_imagery.cgi?line="
"http://braintrap.inf.ed.ac.uk/braintrap/" "VFBsite_BrainTrap" "http://braintrap.inf.ed.ac.uk/braintrap/line/show?FBti="
"https://flybrain-ndb.virtualflybrain.org" "FlyBrain_NDB" "https://flybrain-ndb.virtualflybrain.org/neuronrec-"
"http://neuro.uni-konstanz.de/DoOR" "DoOR" "http://neuro.uni-konstanz.de/DoOR/content/receptor.php?OR="

short_forms have no relationship to IRIs. IRIs are being used to define site links. short_forms are being used as CURIE prefixes. These concerns need to be separated. Based on discussion with Nico, we propose:

  1. VFB should be minting its own IRIs for these resources. These could be numeric, but perhaps easier to have something like:
    http://virtualflybrain.org/site/DoOR ?
  2. We should have a separate field for Curie prefix
  3. We should have a separate field for homepage URL.

e.g. 

{
iri: "http://virtualflybrain.org/site/DoOR"
short_form: "DoOR"
prefix: "DoOR"
homepage: "http://neuro.uni-konstanz.de/DoOR"
link_base: "http://neuro.uni-konstanz.de/DoOR/content/receptor.php?OR="
}

A simpler option would be to continue the hack with the short_form but with VFB IRIs, however, this is non-standard and so less transparent to anyone who wants to use our site for linked data.

This will require updates to the xref query code, so we need to carefully co-ordinate.

We should probably do the same thing for licenses.

@matentzn @Robbie1977 - comments please.

matentzn commented 5 years ago

+10 on this suggestion! Love the readable VFB identifiers

Agree for licenses!

dosumis commented 5 years ago

Dependencies:

query code currently assumes homepage = iri. Best to do this in stages: