Difference between revisions of "Taxon-GO Implementation April 2009 onwards"

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N.B. The dosage compensation terms do not need a taxon link even though they have a sensu synonym.  
 
N.B. The dosage compensation terms do not need a taxon link even though they have a sensu synonym.  
  
Michelle Gwinn-Giglio has requested the following change in the live file:
+
TODO: Michelle Gwinn-Giglio has requested the following change in the live file:
  
 
  I'd say that the following terms should all have "flagellin-based" changed to
 
  I'd say that the following terms should all have "flagellin-based" changed to

Revision as of 07:22, 1 May 2009

1st April 2009

This work has been on hold for a while as we were waiting for more sophisticated filtering in OBO-Edit to let all editor edit the file while doing normal live file editing. However Chris has asked that we push on without the filtering for a while.

Today:

Loaded the files in OE2 and found some file problems. The UnionTerm stanzas were a bit messed up, but were fixed by adding a Typedef for the the union_of relationship, and removing the top term.

Other file errors found and fixed:

Two entire taxa had gone missing from the taxon slim, and we had also lost a union_of term from the UnionTerms file. I do not know how that happened but I have replaced them.

I have recommitted the edited source files and also saved out and recommitted the all_files_mid_edit.obo file. I did not make any edits so the perl scripts do not need to be run.

Fixed this misformed tag 'name: synonym: "synonym: "synonym: "'in both edit file and source.

Set up WinXP laptop to run the perl scripts to generate the tab delimited file that the users need to act on these links.

TODO: There are a bunch of terms that currently have two only_in_taxon links and they mess up the converstion to tab-delimited. Need to resolve these relationships. Have deleted them from the file for now. This is the list:

GO:0048494	chromatophore ribulose bisphosphate carboxylase complex
GO:0030075	plasma membrane-derived thylakoid
GO:0030094	plasma membrane-derived photosystem I
GO:0030096	plasma membrane-derived thylakoid photosystem II
GO:0031676	plasma membrane-derived thylakoid membrane
GO:0031979	plasma membrane-derived thylakoid lumen
GO:0048493	plasma membrane-derived thylakoid ribulose bisphosphate carboxylase complex
GO:0009521	photosystem
GO:0030077	plasma membrane light-harvesting complex
GO:0042716	chromatophore
GO:0009760	C4 photosynthesis
GO:0009761	CAM photosynthesis
GO:0016168	chlorophyll binding
GO:0030093	chloroplast photosystem I
GO:0030095	chloroplast photosystem II
GO:0030089	phycobilisome

I am wondering what the violations.txt file is in cvs. There is a readme but it is a dead end when you follow the urls.


9th April 2009

Looked through the rest of Michelle's taxon spreadsheet and sent a few questions to her before doing the final edits:


> 2.  regarding "flagellin-based flagella...." terms - I left these as prok,
> but Archaeal flagella have "flagellin-based" flagella too, but the
> flagellins are different than bacterial flagellins ­ and also they have
> different overall flagellar structures.  Therefore, the "flagellin-based"
> terms do not provide a way to distinguish between the Arch and Bact types.
> These will likely need to be revised.

Oh that's good to know. So for now I should make these prokaryote,
but later we might like to make child terms then?

> 3.  Archaea do not have peptidoglycan, but they have other cell wall
> materials that are similar ­ we don¹t have terms to cover those.

Good to know. So I'll leave these as Bacterial for now and we can add Archaeal terms later.

> 4.  I notice that there are terms like ³plant-type cell wall² and
> ³fungal-type cell wall².  Can¹t we then have ³Bacterial-type cell wall² and
> ³Archaeal-type cell wall²?  Or even "bacterial-type flagella" and
> "archaeal-type flagella"?  That would be more clear I think.

Yes that would be fine. Which ones would you like me to add? If you
put a column in the attached spreadsheet and write the names in I can do the edits.


27th/28th April

The prokaryotic terms are now finished and a list of questions has been sent to SGD for the fungal terms.

A plan has been formed to finished the sensu terms and release the file in time to submit a paper to this conference:

IEEE International Conference
on Bioinformatics and Biomedicine (BIBM09)
Washington DC, USA, Nov. 1-4, 2009
http://www.ittc.ku.edu/bioinformatics/BIBM09
Electronic submission of full papers: July 10, 2009

I sent this list to Kimberly to get feedback:

GO:0060111 alae of collagen and cuticulin-based cuticle extracellular matrix
GO:0060110 basal layer of collagen and cuticulin-based cuticle extracellular matrix
GO:0060102 collagen and cuticulin-based cuticle extracellular matrix
GO:0060106 cortical layer of collagen and cuticulin-based cuticle extracellular matrix
GO:0042715 dosage compensation complex assembly during dosage compensation by hypoactivation of X chromosome
GO:0042464  dosage compensation, by hypoactivation of X chromosome
GO:0060105 epicuticle of collagen and cuticulin-based cuticle extracellular matrix
GO:0060104 surface coat of collagen and cuticulin-based cuticle extracellular matrix 

This list was sent to Eurie to get feedback:

Sensu Fungi terms	
	
GO:0000754	adaptation to pheromone during conjugation with cellular fusion
GO:0007569	cell aging
GO:0030466	chromatin silencing at silent mating-type cassette
GO:0000747	conjugation with cellular fusion
GO:0000755	cytogamy
GO:0030473	nuclear migration along microtubule
GO:0000750	pheromone-dependent signal transduction during conjugation with cellular fusion
GO:0034306	regulation of sexual sporulation
GO:0000749	response to pheromone during conjugation with cellular fusion
GO:0009847	spore germination 

Sensu Saccharomyces terms	 

GO:0000754	adaptation to pheromone during conjugation with cellular fusion
GO:0007571	age-dependent general metabolic decline
GO:0000752	agglutination during conjugation with cellular fusion
GO:0007569	cell aging
GO:0000751	cell cycle arrest in response to pheromone
GO:0030466	chromatin silencing at silent mating-type cassette
GO:0000747	conjugation with cellular fusion
GO:0000501	flocculation via cell wall protein-carbohydrate interaction
GO:0001403	invasive growth in response to glucose limitation
GO:0030473	nuclear migration along microtubule
GO:0007576	nucleolar fragmentation
GO:0007323	peptide pheromone maturation
GO:0000750	pheromone-dependent signal transduction during conjugation with cellular fusion
GO:0030163	protein catabolic process
GO:0000321	re-entry into mitotic cell cycle after pheromone arrest
GO:0000749	response to pheromone during conjugation with cellular fusion

The current up to date version is in the edit file.


1st May 2008

Finished Nematode terms

TODO: return to dosage compensation terms and put a note in the def e.g. 'for example in Nematodes'. Do the same for the other terms. These terms need a taxon note so people know which one is which, but they are not suitable to be restricted on what can be annotated to them. This needs to be done in the live file. The taxon links are sorted out.

N.B. The dosage compensation terms do not need a taxon link even though they have a sensu synonym.

TODO: Michelle Gwinn-Giglio has requested the following change in the live file:

I'd say that the following terms should all have "flagellin-based" changed to
"bacterial-type":
 
flagellin-based flagellum
flagellin-based flagellum filament
flagellin-based flagellum filament cap
flagellin-based flagellum hook-filament junction
flagellin-based flagellum hook
flagellin-based flagellum basal body
flagellin-based flagellum basal body, distal rod
flagellin-based flagellum basal body, distal rod, L ring
flagellin-based flagellum basal body, distal rod, P ring
flagellin-based flagellum basal body, proximal rod
flagellin-based flagellum basal body, MS ring
flagellin-based flagellum basal body, C ring
flagellin-based flagellum basal body, rod
flagellin-based flagellum part

We could add the phrase "as found in bacteria" [to the def] - would that work?

Then we should add a term "archaeal-type flagellum".