Taxon-GO Implementation April 2009 onwards
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.
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.
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
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.
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".