amigo

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GO Xrefs are not updating in align with db-xref.yaml

12

Hello, The page: http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/ links to http://amigo.geneontology.org/xrefs (under 'DB (column 1)'). However http://amigo.geneontology.org/xrefs is out of date compared with the YAML file - for example Wormbase is not in the...

pgaudet

Replace software page with link to GO Tools page

8

Can the AmiGO link to 'Tools' link to http://geneontology.org/docs/tools-overview/ so it's the same as on the geneontology.org website ?

pgaudet

Hello, ZDB-GENE-081105-93 is annotated to 'protein binding' with extension 'occurs in neuron projection'; the extension is repeated over 1000 times in AmiGO. Thanks, Pascale

pgaudet

Add IEA filter to Matrix tool

5

Hi @kltm Would it be possible to add an IEA filter to the matrix tool? I'm sorting out the paper and checking the rules. It's very time-consuming to do the...

ValWood

Some AspGD taxon data appears without a label

12

there is something amiss with the way AspDB annotations appear in AmiGO. Tha taxon isn't parsed correctly so they are not available in the organsim filter, E.g. http://amigo.geneontology.org/amigo/gene_product/AspGD:Aspfo1_0204585

ValWood

Decommission GOOSE

1

As the database production is being halted (part of #312), GOOSE can no longer be considered a publicly usable resource. It already has the following prominent warning message from some...

kltm

We currently have a set of files in external/ that are used for testing and used to be used more seriously in installation. The naming of these files can lead...

kltm

Synonyms and alternate IDs as legitimate input

6

From http://jira.geneontology.org/browse/GO-374 --- I open the Visualization form: http://amigo.geneontology.org/amigo/visualize I put the GO term "GO:0001589" into the search field, nothing else. I click "visualize". Then the error appears. The URL...

kltm

Which version of GO do we have in AmiGO?

4

Hello, The term label for GO:0008283 was changed in Dec 2018 according to the QuickGO log (https://www.ebi.ac.uk/QuickGO/term/GO:0008283), from 'cell proliferation' to 'cell population proliferation'; however in AmiGO we still have...

pgaudet

Hello, In QuickGO P12872 (a human protein) has 2 IEAs form InterPro * UniProtKB:P12872 | MLN | enables | GO:0005179 hormone activity | ECO:0000256 IEA | GO_REF:0000002 | InterPro:IPR006737 more......

pgaudet