Aug2010 ontology report: Difference between revisions

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Ontology Development Report - July 2010
Ontology Development Report - August 2010


===I. Ontology Development===
===I. Ontology Development===
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**unassigned: 94
**unassigned: 94


====Completed content items====
====Completed items====
*Updated GO to match the latest MetaCyc mappings [Amelia]
*[[Kidney_Development|Kidney development]]: mesonephros terms are done [David and Yasmin]
*A new set of interaction between organism terms added for PAMGO, including several cc terms [Jane]  
*BPxBP (BP involved_in BP) clean-up for parsing is done [David and Tanya]
*Resolved issues regarding [[Cognition_and_Sensory_perception|cognition and sensory processing]] [David and Tanya]
*[http://www.berkeleybop.org/obo/quickterm/GO TermGenie] up and running.  Commits going in on a regular basis.  Can request terms for regulation of existing MF and BP terms. [Chris, Seth, David, Jane, Tanya]
*Various SourceForge items [all]
*Various SourceForge items [all]


====Content items in progress====
====Content items in progress====
*[[Transcription|Overhaul of transcription]] proposal complete, and has been sent out to GOC for comments. Almost ready to proceed with edits [David & Karen]
*Lots of enzyme-related stuff; added various new terms, filled in missing defs or EC / other xrefs for some undefined or poorly defined terms [Amelia]
* Final stages of checking the BP-BP cross-products. Clean-up done (all 'during' terms fixed), now need to look at the reasoner results and fix up the details [David & Tanya]
*First commit of the [[Transcription|transcription]] overhaul was made. [Karen and David]
*[[Chemical_terms_in_GO|Chemicals in GO project]]: we had a successful [[Chemical_terms_in_GO#Meeting_with_CHEBI.2C_Carnegie_July_22-25.2C_2010|GOCHE meeting]], with CHEBI, 22-25 July. Next steps are to add missing GOCHE terms to CHEBI, make some fixes to GO and CHEBI then make CHEBI xps in GO. [David, Tanya, Jane & Harold]
*Started submitting missing GOCHE terms to CHEBI [Jane]
* Ready to commit mesonephros terms for kidney project [David]
* Automatic [[cross product term submission tool]] almost ready to release to wider group (regulates terms only) [Chris, Seth, Jane, David, Tanya, Amelia]
* F-P links for transporters complete. Beginning work on catalytic activity [David, Tanya]
 
*Quality control continues as usual - reports generated by Chris (cronjobs)
*Quality control continues as usual - reports generated by Chris (cronjobs)
**Reasoner-based implied links for new regulation terms - also see above (David, Tanya)
**Abduced links [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF-abduced-links.txt]][David, Tanya]
**Abduced links [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF-abduced-links.txt]](David, Tanya)


====Publications====
====Publications====
* GOCHE paper draft is up and being circulated [David, Chris, Tanya, Jane, Harold, Midori and others]
* Heart development paper is in the draft stage [David, Varsha]
* Heart development paper is in the draft stage [David, Varsha]
* GOCHE paper manuscript started [David, Tanya, Jane & Harold]
*Case studies for publication on "revisability" of GO, proposed and coordinated by [http://huss.exeter.ac.uk/sociology/staff/leonelli/index.php Sabina Leonelli] - submitted to BMC Bioinformatics [Midori, Jane, Alex, Karen C]
*"Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology" accepted by Microbiology and Molecular Biology Reviews [Jane, Michelle, PAMGO consortium]
*Case studies for publication on "revisability" of GO, proposed and coordinated by [http://huss.exeter.ac.uk/sociology/staff/leonelli/index.php Sabina Leonelli] - in progress [Midori, Jane, Alex, Karen C]


====Anything else====
====Anything else====

Latest revision as of 09:58, 16 September 2010

Ontology Development Report - August 2010

I. Ontology Development

Tracker

  • Items opened: 102
  • Items closed: 88
  • Items still open: 325
    • assigned: 231
    • unassigned: 94

Completed items

  • Kidney development: mesonephros terms are done [David and Yasmin]
  • BPxBP (BP involved_in BP) clean-up for parsing is done [David and Tanya]
  • Resolved issues regarding cognition and sensory processing [David and Tanya]
  • TermGenie up and running. Commits going in on a regular basis. Can request terms for regulation of existing MF and BP terms. [Chris, Seth, David, Jane, Tanya]
  • Various SourceForge items [all]

Content items in progress

  • Lots of enzyme-related stuff; added various new terms, filled in missing defs or EC / other xrefs for some undefined or poorly defined terms [Amelia]
  • First commit of the transcription overhaul was made. [Karen and David]
  • Started submitting missing GOCHE terms to CHEBI [Jane]
  • Quality control continues as usual - reports generated by Chris (cronjobs)
    • Abduced links [[1]][David, Tanya]

Publications

  • GOCHE paper draft is up and being circulated [David, Chris, Tanya, Jane, Harold, Midori and others]
  • Heart development paper is in the draft stage [David, Varsha]
  • Case studies for publication on "revisability" of GO, proposed and coordinated by Sabina Leonelli - submitted to BMC Bioinformatics [Midori, Jane, Alex, Karen C]

Anything else

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