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.
Midori had added a new only_in_taxon link to a union_of term that did not exist. I have made the union_of stanza and added it to the file. I should check with Midori that she knows all the ins and outs of the editing of these files. I did not know she had started.
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.