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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
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Slim needed for AGR ribbon view #13013

Closed selewis closed 7 years ago

selewis commented 7 years ago

Consisting of these terms (will be using closure) GO:0003824 catalysis OK GO:0004872 receptor OK GO:0005102 receptor binding OK GO:0005215 transporter OK GO:0005198 structural molecule OK GO:0008092 cytoskeleton binding OK GO:0003677 DNA binding OK GO:0003723 RNA binding OK GO:0008134 transcription factor -> This is tx factor binding -> used "GO:0001071 nucleic acid binding transcription factor activity" instead OK GO:0036094 small molecule binding OK GO:0046872 metal ion binding OK GO:0030246 carbohydrate binding OK

GO:0008283 cell proliferation OK GO:0071840 cellular organization/biogenesis OK GO:0051179 cellular transport/localization OK GO:0032502 development OK GO:0000003 reproduction OK GO:0002376 immune system OK GO:0050877 neurological OK GO:0007610 behavior OK GO:0050896 response to stimulus OK GO:0023052 signaling OK GO:0010467 gene expression OK GO:0019538 protein metabolism OK GO:0006259 DNA metabolism OK GO:0044281 small molecule metabolism OK GO:0050789 regulation OK

GO:0005576 extracellular OK GO:0005829 cytosol OK GO:0005856 cytoskeleton OK GO:0005739 mitochondrion OK GO:0005634 nucleus OK GO:0005694 chromosome OK GO:0016020 membrane OK GO:0071944 cell periphery OK GO:0030054 cell junction OK GO:0042995 cell projection OK GO:0032991 macromolecular complex OK

ukemi commented 7 years ago

This will provide a nice example of creating slims for next week's workshop.

pgaudet commented 7 years ago

Merge request is here: https://github.com/geneontology/go-ontology/pull/13117

judyblake commented 7 years ago

I would like to have us do analysis of all 5 major model organism groups as to distribution of annotations. I post a slide deck that shows how we developed this approach at MGI. Mary Dolan is working on the analysis now.

judyblake commented 7 years ago

I had left comments on AGR UI site, but understanding this working group didn't see

ukemi commented 7 years ago

@mdolanme can you do this?

mdolanme commented 7 years ago

Here is a graphical comparison of the MGI slim and the AGR slim and the analysis of MGI annotations using the two slims: compareGOslims.pdf

pgaudet commented 7 years ago

hello,

This is still assigned to me, let me know if I need to do anything (and what!)

Thanks, Pascale