amigo

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Annotation filter GO class (direct) not working

4

To reproduce: https://amigo.geneontology.org/amigo/term/GO:0008746 click on GO class (direct) shows Total annotations: 103 (89) NAD(P)+ transhydrogenase activity (9) NAD(P)+ transhydrogenase (AB-specific) activity (5) NAD(P)+ transhydrogenase (B-specific) activity click on any line...

raymond91125

Remove stats page from AmiGO

5

GO has 2 pages with statistics with partially overlapping content: Home page https://www.geneontology.org/stats.html See section changes in the GO resource over time Number of annotations by evidence Amigo https://amigo.geneontology.org/amigo/base_statistics Also,...

ValWood

Taxon info displays "none" when there are constraints

24

AmiGO displays no taxon info: https://amigo.geneontology.org/amigo/term/GO:0007117 But QuickGO shows the expected constraints: https://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0007117#term=history Shouldn't AmiGO be loading these too?

suzialeksander

DNA binding transcription factors. MAJOR ISSUE

29

When I try to search for all DNA-binding transcription factors this annotation is the first in the list URS00001B341F_9606 | Homo sapiens (human) hsa-miR-27a-5p |   | negative regulation of NF-kappaB...

ValWood

Closure should be used when querying the genes biotype

2

If I select "ncRNA" in amigo it should also include the subtypes of ncRNA, however, it doesn't use the closure (low priority as the type hierarchy is basically flat other...

cmungall

searching on gene name

2

Historically I used to search on gene name for pombe and I always used to find the entity. These days, as more species are added I never can, because it's...

ValWood

Support node > 8

1

Currently the Dockerfile & installation scripts appear to be compatible with node 8.x and npm 3.x (both long since EOL), currently installed on ubuntu:18.04 (also EOL) in the docker/Dockerfile, but...

nathanweeks

Removes JXON use for native DOMParser for Pubmed abstract parsing

4

fixes #655 First time touching this codebase so tried to keep changes as minimal as possible. Line indentation looks a bit off as it appears there was a previous mix...

AlexanderNull

Remove link to GOnuts

2

Hi @kltm the link to GOnuts in fact links back to the AmiGO page, See for example this page: https://amigo.geneontology.org/amigo/term/GO:0006807#display-lineage-tab, under Mappings:  Can these links be removed? Thanks, Pascale

pgaudet

Display logical definitions and reaction participants in AmiGO

15

This is something that would be useful for GO curators that are not using Protégé; could this information be added in the AmiGO pages?

pgaudet