Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[go-friends] Obsoletion of 'cell part' terms and upper level reorganization

Pascale Gaudet pascale.gaudet at sib.swiss
Thu Sep 5 23:06:42 PDT 2019


Two terms were omitted form the previous announcement: 
'intracellular organelle part' and 'growth cone part’ (no annotations, no mappings). 

They will be obsoleted in this pull request: https://github.com/geneontology/go-ontology/pull/17800

Thanks, Pascale


> On 29 Aug 2019, at 12:08, Pascale Gaudet <pascale.gaudet at sib.swiss> wrote:
> 
> Dear all, 
> 
> GO is reorganizing some of the top level terms in the Cellular Component branch to better fit future annotation requirements. (see also [1])
> 
> We have created a new term, 'cellular anatomical entity', that groups all cellular components that are not protein-containing complexes or whole cells. Now the CC aspect of the ontology will have the following main branches: 
> 
> - cell
> - 'cellular anatomical entity'
> - intracellular (see [2])
> - 'other organism part'
> - 'protein-containing complex'
> - virion
> - 'virion part'
> 
> As a part of this reorganization we are obsoleting 'x part' terms such as 'nuclear part'. Instead, parts will be asserted directly in the ontology. For example, a term x that is a nuclear part will have the relationship x part_of nucleus. 
> 
> The following terms will be obsoleted: 
> 
> GO:0033267 axon part
> GO:0044447 axoneme part
> GO:0097312 bacterial biofilm matrix component
> GO:0044461 bacterial-type flagellum part
> GO:0044448 cell cortex part
> GO:0032155 cell division site part
> GO:0044464 cell part - mapped to NIF_Subcellular:sao628508602
> GO:0044463 cell projection part
> GO:0044457 cell septum part
> GO:0044426 cell wall part
> GO:0044434 chloroplast part
> GO:0044427 chromosomal part
> GO:0044441 ciliary part
> GO:0060103 collagen and cuticulin-based cuticle extracellular matrix part
> GO:0044449 contractile fiber part
> GO:0044444 cytoplasmic part
> GO:0044433 cytoplasmic vesicle part
> GO:0044430 cytoskeletal part
> GO:0044445 cytosolic part
> GO:0044432 endoplasmic reticulum part
> GO:0044440 endosomal part
> GO:0044462 external encapsulating structure part
> GO:0044420 extracellular matrix component
> GO:0044421 extracellular region part
> GO:0044431 Golgi apparatus part
> GO:0044424 intracellular part
> GO:0110144 magnetosome part
> GO:0044425 membrane part
> GO:0044438 microbody part
> GO:0044450 microtubule organizing center part
> GO:0044455 mitochondrial membrane part
> GO:0044429 mitochondrial part
> GO:0097458 neuron part
> GO:0044454 nuclear chromosome part
> GO:0044453 nuclear membrane part
> GO:0044428 nuclear part - mapped to NIF_Subcellular:  sao1499850686
> GO:0044452 nucleolar part
> GO:0044451 nucleoplasm part
> GO:0044422 organelle part
> GO:0044439 peroxisomal part
> GO:0044443 pilus part
> GO:0120038 plasma membrane bounded cell projection part
> GO:0044459 plasma membrane part
> GO:0044435 plastid part
> GO:0097425 smooth endoplasmic reticulum part - mapped to NIF_Subcellular:sao184202831
> GO:0097223 sperm part
> GO:0044456 synapse part - mapped to NIF_Subcellular:sao1784069613
> GO:0044436 thylakoid part
> GO:0044437 vacuolar part
> 
> 
> **goslim-pir:** 
> GO:0044464 cell part
> 
> **go-slim-flybase-ribbon**
> GO:0097458 neuron part
> 
> There are a few annotations to those terms: 
> https://github.com/geneontology/go-annotation/issues/2632
> 
> affecting the folowing groups: 
> AspGD : 1 annotation
> CGD : 2 
> GeneDB : 1
> GR : 2
> JCVI : 1
> MGI : 13
> SGN : 7 
> 
> Any comments can be added to the issue: https://github.com/geneontology/go-ontology/issues/17778
> 
> We are opening a comment period for this proposed obsoletion. We’d like to proceed and obsolete this term on September 4th, 2019. Unless objections are received by September 4th, 2019 we will assume that you agree to this change. 
> 
> Thanks, Pascale
> 
> [1] https://github.com/geneontology/go-ontology/issues/17696
> [2] https://github.com/geneontology/go-ontology/issues/17776



More information about the go-friends mailing list