Write query to cover current FlyBase->VFB transgene linkouts

[dosumis]

The following query produces a standard FLyBase linkout table with 1-2 links per FB construct.

MATCH (f:Feature)<-[]-(ep:Class)-[dbx:hasDbXref]->(s:Site { short_form: 'FlyLight'})
WITH f, ep MATCH (ep)<-[:INSTANCEOF]-(i:Individual)
<-[]-(channel:Individual)-[irw:in_register_with]->(t:Individual) 
WITH distinct f.short_form AS `#FlyBase ID`, collect(i.short_form)[0] AS DBID, 
t.label as template
 RETURN `#FlyBase ID`, 'VFB' as DBNAME, DBID ORDER BY `#FlyBase ID`

=>

#FlyBase ID	DBNAME	DBID
"FBtp0057296"	"VFB"	"VFB_00020468"
"FBtp0057297"	"VFB"	"VFB_00023198"
"FBtp0057299"	"VFB"	"VFB_00020592"
...

Link recipe:
https://virtualflybrain.org/reports/VFB_00068899

Thumbnail link recipe:
https://virtualflybrain.org/reports/VFB_00068899/thumbnail.png

[dosumis]

From: https://wiki.flybase.org/wiki/FlyBase:Links_to_and_from_FlyBase

• Column 1
  • FlyBase ID: A valid FlyBase ID matching this regular expression: '^FB\w\w\d+\t'
• Column 2
  • DBNAME: Some unique/standard name for external database. Alpha-numeric only 'A-z0-9'. If you are submitting more than one linking table you need to ensure that the DBNAME is unique to each file. Reusing a DbName once it is used in another linking table is not permitted.
  • For example, if a group named "FLYLAB" wanted to establish links between FlyBase gene reports and 2 different types of analysis on their web site they could use "FLYLAB_EX1" and "FLYLAB_EX2" for the DbName column in their linkout files.
• Column 3 - DBID
  • External database object id. This field can either be an ID or a short phrase (e.g. name of a pathway/reaction). Spaces are allowed, but tabs are not. This field cannot exceed 255 characters.
• Column 4 - DBURL
  • Relative link to external database web report. This is the text that will be appended to the base URL parameter that is defined in the database information file.

Notes: Use 4 for key and Column 3 for text to link on.

[dosumis]

Take2:

MATCH (f:Feature)<-[]-(ep:Class)-[dbx:hasDbXref]->(s:Site { short_form: 'FlyLight'})
WITH f, ep MATCH (ep)<-[:INSTANCEOF]-(i:Individual)
<-[]-(channel:Individual)-[irw:in_register_with]->(t:Individual) 
WITH distinct f.short_form AS `#FlyBase ID`, 
collect(i.short_form)[0] AS DBURL, ep.label AS DBID, t.label as template
 RETURN `#FlyBase ID`, 'VFB' as DBNAME, DBID, DBURL ORDER BY `#FlyBase ID`

#FlyBase ID	DBNAME	DBID	DBURL
"FBtp0057296"	"VFB"	"P{GMR10A06-GAL4} expression pattern"	"VFB_00020468"
"FBtp0057297"	"VFB"	"P{GMR10A07-GAL4} expression pattern"	"VFB_00023198"

Query could be optimised(?)

Or use individual name ?

[dosumis]

Latest:

MATCH (f:Feature)<-[]-(ep:Class)-[dbx:hasDbXref]->(s:Site)
WHERE (s.short_form = 'FlyLight') OR (s.short_form = 'FlyLightSplit')
WITH f, ep MATCH (ep)<-[:INSTANCEOF]-(i:Individual)
<-[]-(channel:Individual)-[irw:in_register_with]->(t:Individual)
WITH distinct f.short_form AS `#FlyBase ID`,
collect(i.short_form)[0] AS DBURL, ep.label AS epl, t.label as template
RETURN `#FlyBase ID`, DBURL, 'VFB' AS DBNAME,
       epl + ' in ' + replace(
        replace(template, ' template - Court2018_c', ''),
       'JFRC2_template_c',
       'adult brain') + ' on Virtual Fly Brain' AS DBID ORDER BY `#FlyBase ID`

Note replace hack is necessary for template because a longer match pattern bridging to template:anatomy classification does not complete.

=>

#FlyBase ID	DBURL	DBID
"FBtp0057296"	"VFB_00020468"	"P{GMR10A06-GAL4} expression pattern in adult brain on Virtual Fly Brain"
"FBtp0057297"	"VFB_00023198"	"P{GMR10A07-GAL4} expression pattern in adult brain on Virtual Fly Brain"
"FBtp0057299"	"VFB_00020592"	"P{GMR10A09-GAL4} expression pattern in adult brain on Virtual Fly Brain"

One query => Image linkout for transgene expression patterns & splits, adult brain & VNS, conforming to linkout spec. Single, arbitrary image is chosen for each.

Ways we might improve:

• Add Janelia split names from synonyms where these are available
• ...

[dosumis]

Script for generating linkout.tsv https://gist.github.com/dosumis/9e2551acd3daa2f2343c6ee169ee71a7