search

geneontology / paint

This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
Other
4 stars 4 forks source link

annotation in "Annotations" tab but not in "Annotation Matrix #3

Closed krchristie closed 8 years ago

krchristie commented 9 years ago

When I load PTHR12858 (either New or Open from my saved files) there is one annotation I need isn’t showing up in PAINT-b14 correctly. For S. cerevisiae TSR1, there are three experimental CC annotations (from SGD's Manual Annotations section) listed in the “Annotations” tab:

However, in the “Annotation Matrix”, only two direct annotations show up, those for “nucleolus” (1st column) and “cytoplasm” (3rd column).

The "preribosome, small subunit precursor" annotation is IDA and is listed in SGD’s “Manually Curated” section, NOT in the HTP section. In contrast, the term "90S preribosome" which is listed only in SGD's "HTP" section does not show up in the "Annotations" tab: http://www.yeastgenome.org/locus/S000002218/go

I’ve tried loading this family a couple different times, and even after relaunching PAINT, I still get this problem and can’t propagate the "preribosome, small subunit precursor” because it isn’t in the annotation matrix.

krchristie commented 9 years ago

It looks to me like the experimental GOCN annotations from P2GO are mostly being treated as already propagated, as if they were GOCN (aka GO_Central) annotations made by PAINT, though I have no suggestion for why a few of the P2GO GOCN annotations fail to show up in the annotation matrix.

I am also having this issue in PTHR23105, which is also blocking my ability to finish annotating the family. Specifically, the "90S preribosome" annotation by IDA for S. cerevisiae UTP30 is not present in the Annotation Matrix.

selewis commented 8 years ago

These are all showing up in both the annotations table and the matrix for TSR1: cytoplasm, nucleolus, nucleus, preribosome, small subunit precursor, and 90S preribosome in PAINTv2.

Pascale is testing this now, and it should be release soon.