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VirtualFlyBrain / VFB_reporting

Scripts for reporting on the state of VFB content and pipeline
https://github.com/VirtualFlyBrain/VFB_reporting_results
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Extend expression_pipelist with CATMAID papers #28

Open dosumis opened 4 years ago

dosumis commented 4 years ago

Looks like we could use

get_catmaid_papers.gen_cat_paper_report

Some refactoring needed - as import will run main, but still:

gen_cat_paper_report("https://l1em.catmaid.virtualflybrain.org", 1, "papers", ...: "L1EM")

=>

id name
21218996 Andrade et al. 2019
19711421 Berck, Khandelwal et al. 2016
19862922 Burgos et al 2018
20522905 Carreira-Rosario, Arzan Zarin, Clark et al. 2018

etc

dosumis commented 4 years ago

Hi @Clare72 - IIRC we have some additional scripts that find FBrfs in KB for papers from CATMAID (if present). Did these ever get completed? It would be good to have a report of all CATMAID papers with mappings from DB wherever possible & a mechanism for adding mappings for new papers as the come through.

dosumis commented 4 years ago

In latest schema - this can be used to map paper/dataset accession in CATMAID to FlyBase FBrf (if in KB)

MATCH (p:pub)-[]-(ds:DataSet)-[r]->(api:API) 
RETURN p.short_form, ds.short_form, r.accession, api.short_form

=>

p.short_form ds.short_form r.accession api.short_form
"FBrf0232785" "Berck2016" 19711421 "l1em_catmaid_api"
"FBrf0228257" "Ohyama2015" 19712046 "l1em_catmaid_api"
"FBrf0233076" "Zwart2016" 19496665 "l1em_catmaid_api"
"FBrf0238464" "Burgos2018" 19862922 "l1em_catmaid_api"

...

dosumis commented 4 years ago

Fix: Extend query here to pull pub.short_form:

https://github.com/VirtualFlyBrain/VFB_reporting/blob/master/src/comparison.py#L42

Integrate this as VFB pub ID into comparison tsv reports (e.g. https://github.com/VirtualFlyBrain/VFB_reporting_results/blob/master/L1EM_comparison.tsv)