Mar2010 ontology report: Difference between revisions

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===I. Ontology Development===
===I. Ontology Development===
*SourceForge
====Tracker====
**Items opened: 127
**Items opened: 127
**Items closed: 128
**Items closed: 128
Line 9: Line 9:
***unassigned: 89
***unassigned: 89


*Completed content items
====Completed content items====
**[[Kidney_Development|Kidney development]] - the metanephros terms have been finished [Midori]
**Various SourceForge items
**Various SourceForge items


*Content items in progress
====Content items in progress===
**[[Signaling]]- working through the existing signaling terms to make them more consistent and fill in any gaps. Intracellular signaling terms, and regulation of signaling is on the agenda for the conference call next week. [Becky]
**[[Signaling]]- working through the existing signaling terms to make them more consistent and fill in any gaps. Intracellular signaling terms, and regulation of signaling is on the agenda for the conference call next week. [Becky]
**[[Chemical_terms_in_GO]] - continuing to edit the GOCHE ontology (chemicals in GO) [David, Tanya, Jane & Harold]
**[[Chemical_terms_in_GO]] - continuing to edit the GOCHE ontology (chemicals in GO) [David, Tanya, Jane & Harold]
**[[Kidney_Development|Kidney development]] - the metanephros terms have been finished [Midori]
**Further work in collaboration with with NIF (Neuroscience Information Framework) [Jane & Chris]
**Further work in collaboration with with NIF (Neuroscience Information Framework) [Jane & Chris]
**Review of bp x bp internal cross-product set, see [[CJM_EBI_Visit_June_2009#Status_overview_and_release_plan|plan to add internal cross-products]]. [David & Tanya]
**Review of bp x bp internal cross-product set, see [[CJM_EBI_Visit_June_2009#Status_overview_and_release_plan|plan to add internal cross-products]]. [David & Tanya]
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***Problematic regulates terms [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/regulates_xp_live/report-filtered.txt]](David, Tanya)
***Problematic regulates terms [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/regulates_xp_live/report-filtered.txt]](David, Tanya)


*Publications
====Publications====
**Manuscript on [[Taxon_Main_Page|Taxon triggers]] almost ready for submission to BMC Bioinformatics (Jen, Chris)
**New PAMGO paper "Unifying themes in microbial associations with animal and plant hosts described using the Gene Ontology" ready for submission to Microbiology and Molecular Biology Reviews
**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)
**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)
**Continued from November & December:
***Resuming work on manuscript on regulates relations (Jane, Midori, David, Chris, Tanya, maybe other annotators)


*Anything else
*Anything else
**Becky Foulger from UniProt is joining us until the May 14th 2010 
**Applications now closed for EBI GO curator position
**GO bibliography has 3164 entries
**GO bibliography has 3164 entries


Revision as of 06:02, 14 April 2010

Ontology Development Report - March 2010

I. Ontology Development

Tracker

    • Items opened: 127
    • Items closed: 128
    • Items still open: 239
      • assigned: 150
      • unassigned: 89

Completed content items

    • Kidney development - the metanephros terms have been finished [Midori]
    • Various SourceForge items

=Content items in progress

    • Signaling- working through the existing signaling terms to make them more consistent and fill in any gaps. Intracellular signaling terms, and regulation of signaling is on the agenda for the conference call next week. [Becky]
    • Chemical_terms_in_GO - continuing to edit the GOCHE ontology (chemicals in GO) [David, Tanya, Jane & Harold]
    • Further work in collaboration with with NIF (Neuroscience Information Framework) [Jane & Chris]
    • Review of bp x bp internal cross-product set, see plan to add internal cross-products. [David & Tanya]
    • Adding lots of transmembrane transport terms for Val's goslim mappings. [Becky]
    • Standardizing the GO terms that contain the word 'during'. [David & Tanya]
    • Quality control continues as usual - reports generated by Chris (cronjobs)
      • Reasoner-based implied links for new regulation terms - also see above (David, Tanya)
      • Multiple part_of parents (several GO curators, especially Tanya & David)
      • Abduced links [[1]](David, Tanya)
      • Problematic regulates terms [[2]](David, Tanya)

Publications

    • Case studies for publication on "revisability" of GO, proposed and coordinated by Sabina Leonelli - in progress (Midori, Jane, Alex, Karen C)
  • Anything else
    • Applications now closed for EBI GO curator position
    • GO bibliography has 3164 entries

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