search

geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
BSD 3-Clause "New" or "Revised" License
34 stars 10 forks source link

Matrix: cohesion case study (tim-1) #2528

Closed ValWood closed 5 years ago

ValWood commented 5 years ago

tim-1 |   | colocalizes_with | mitotic cohesin complex |   | WB | Caenorhabditis elegans | IPI | WB:WBGene00001860 |   | gene |   | PMID:12827206WB_REF:WBPaper00005919 | 2008033

comes up in the cohesin intersection, should this removed? (I think we are obsoleting ~contributes to~ colocalizes_with?)

ValWood commented 5 years ago

Although wiht the above fix, the matrix issue is resolved I would question all of the following from the same paper

tim-1 |   |   | regulation of sister chromatid cohesion |   | WB | Caenorhabditis elegans | IGI | WB:WBGene00001860 |   | gene |   | PMID:12827206WB_REF:WBPaper00005919 | 20080331

  | tim-1 |   |   | regulation of sister chromatid cohesion |   | WB | Caenorhabditis elegans | IMP | WB:WBVar00249136 |   | gene |   | PMID:12827206WB_REF:WBPaper00005919 | 20080331

  | tim-1 |   |   | mitotic sister chromatid cohesion |   | WB | Caenorhabditis elegans | IGI | WB:WBGene00001860 |   | gene |   | PMID:12827206WB_REF:WBPaper00005919 | 20080331

  | tim-1 |   |   | mitotic sister chromatid cohesion |   | WB | Caenorhabditis elegans | IMP |   |   | gene |   | PMID:12827206WB_REF:WBPaper00005919 | 20080331

tim-1 |   |   | meiotic sister chromatid cohesion |   | WB | Caenorhabditis elegans | IMP | WB:WBVar00249136 |   | gene |   | PMID:12827206WB_REF:WBPaper00005919 | 20080331

Because this is a well studied replication fork protection complex subunit. I'll have a quick glance at this paper

ValWood commented 5 years ago

These are OK, there is a connection between a DNA checkpoint complex and cohesin. It might be quite indirect, but it is related to cohesin establishment.

So it's just the "complex" term here.

vanaukenk commented 5 years ago

@ValWood - the 'complex' annotation was deleted a while back, but it hasn't yet trickled down to our latest production GAF. I'll go ahead and close this ticket.