Ontology Development progress report for March 2009 meetings: Difference between revisions

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The ontology development group (including "core" members and ad hoc participants) has made a great deal of progress in several areas.
The ontology development group (including "core" members and ad hoc participants) has made a great deal of progress in several areas.
====Lung development====
====Lung development====
*A content meeting on [[Lung_Development|lung development]] was held in December 2007.
** Met with experts in Boston; who did not want anatomical terms in the lung development in the ontology. So David made two files, one with and one without anatomical structures.
** Until last week, lung development only had one child, and Dimitry (MGI)  has been requesting new terms; interestingly those include anatomical terms
** This also leads to the expansion of the 'morphogenesis of a branching structure' branch of the GO
** Chris asks whether the lung development is being analyzed from the mouse/mammalian point of view: David says, for lung development, yes, but for branching morphogenesis he is trying to capture different organs and species
** Alex: makes the point that this is analogous to the mitochondrial/cytoplasmic translation issue: all those branching types of development are different to some level, so we might need to add much more terms to describe this?
**David: we've asked this question since the beginning of GO
**Judy: we need to provide the information that researchers need


====Signal transduction====
====Signal transduction====
*The overhaul of [[Signaling|functions and processes involved in signal transduction]] has continued, with plans for a content meeting in the works.
*The overhaul of [[Signaling|functions and processes involved in signal transduction]] has continued, with plans for a content meeting in the works.
(Jennifer)
* This wiki new will be linked from the comments field of the ontology, so that the users can easily give feedback
* New mailing list : signaling @genome
* This is just starting; look for feedback from as many people as possible and members of the community
====Cellular component organization====
====Cellular component organization====
*We have done a lot of work to reorganize terms representing [[Cellular_component_processes|Processes affecting cellular components]], including defining "organization" and "biogenesis" in the context of CCs. Progress and the tasks remaining to be completed will be presented.
*We have done a lot of work to reorganize terms representing [[Cellular_component_processes|Processes affecting cellular components]], including defining "organization" and "biogenesis" in the context of CCs. Progress and the tasks remaining to be completed will be presented.
====Internal cross-products====
====Internal cross-products====
*We have done extensive work on [[:Category:Internal_Cross_Products|cross-products within GO]], vetting autogenerated cross-products and estabilshing a [[Editors_cross-product_implementation_plan|plan]] for releasing them in the "extended" GO OBO file.
*We have done extensive work on [[:Category:Internal_Cross_Products|cross-products within GO]], vetting autogenerated cross-products and estabilshing a [[Editors_cross-product_implementation_plan|plan]] for releasing them in the "extended" GO OBO file.
* David and Tanya: working on on regulates
====MF-BP links====
====MF-BP links====
*There is a new proposal to add process-specific MF terms to support part_of links between MF and BP.
*There is a new proposal to add process-specific MF terms to support part_of links between MF and BP.
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*Work on [[Transcription|transcription and transcription factors]] continues.
*Work on [[Transcription|transcription and transcription factors]] continues.
*Plans are being made for a small content meeting on electron transport in prokaryotes, organized by Rob Gunsalus at UCLA.
*Plans are being made for a small content meeting on electron transport in prokaryotes, organized by Rob Gunsalus at UCLA.
[[Category:Reports]]

Latest revision as of 11:55, 20 August 2009

Ontology Development Progress Report

Metrics

GO term statistics

October 15, 2008

Current Defined Obsolete Total
Function 8421 8116 765 9186
Process 15565 15436 479 16044
Component 2226 2226 117 2343
All 26212 27139 1361 27573

March 27, 2009

Current Defined Obsolete Total
Function 8522 8272 780 9302
Process 16207 16110 480 16687
Component 2315 2315 117 2432
All 27044 28074 1377 28421


SourceForge statistics (Oct. 15, 2008 - March 27, 2009)

  • items opened: 453
  • items closed: more than 335 (new SF tracker has lost the feature that made counting straightforward; estimate about 420-430)

SourceForge reports (on SF site)

Ontology Quality Control

We're continuing to use the ontology QC procedures we reported in October. These include:

Progress is summarized on the Ontology_QC_Metrics page.

Completed work

Work in progress

The ontology development group (including "core" members and ad hoc participants) has made a great deal of progress in several areas.

Lung development

Signal transduction

(Jennifer)

  • This wiki new will be linked from the comments field of the ontology, so that the users can easily give feedback
  • New mailing list : signaling @genome
  • This is just starting; look for feedback from as many people as possible and members of the community

Cellular component organization

  • We have done a lot of work to reorganize terms representing Processes affecting cellular components, including defining "organization" and "biogenesis" in the context of CCs. Progress and the tasks remaining to be completed will be presented.

Internal cross-products

  • We have done extensive work on cross-products within GO, vetting autogenerated cross-products and estabilshing a plan for releasing them in the "extended" GO OBO file.
  • David and Tanya: working on on regulates

MF-BP links

  • There is a new proposal to add process-specific MF terms to support part_of links between MF and BP.
  • MF-BP link items reported in October remain relevant:

Other work in progress