Difference between revisions of "Ontology Development progress report for March 2009 meetings"

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(New page: == Ontology Development Progress Report== ===Metrics=== ====GO term statistics==== '''October 15, 2008''' {| border="1" cellpadding="5" cellspacing="0" ! !!Current!!Defined!!Obsolete!!Tot...)
 
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! !!Current!!Defined!!Obsolete!!Total
 
! !!Current!!Defined!!Obsolete!!Total
 
|-
 
|-
|Function||n||n||n||n
+
|Function||8522||8272||780||9302
 
|-
 
|-
|Process||n||n||n||n
+
|Process||16207||16110||480||16687
 
|-
 
|-
|Component||n||n||n||n
+
|Component||2315||2315||117||2432
 
|-
 
|-
|'''All'''||'''n'''||'''n'''||'''n'''||'''n'''
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|'''All'''||'''27044'''||'''28074'''||'''1377'''||'''28421'''
 
|}
 
|}
  
  
 
====SourceForge statistics (Oct. 15, 2008 - March 27, 2009)====
 
====SourceForge statistics (Oct. 15, 2008 - March 27, 2009)====
*items opened: n
+
*items opened: 453
*items closed: n
+
*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)====
 
====SourceForge reports (on SF site)====
*[https://sourceforge.net/tracker/reporting/index.php?atid=440764&what=aging&span=12&period=month&group_id=36855| "Aging Report" for past year]
+
*[https://sourceforge.net/tracker/reporting/index.php?atid=440764&what=aging&span=&period=lifespan&group_id=36855 "Aging Report" for past year]
*[https://sourceforge.net/tracker/reporting/index.php?atid=440764&what=resolution&span=12&period=month&group_id=36855| "Distribution by Resolution" for past year]
+
*[https://sourceforge.net/tracker/reporting/index.php?atid=440764&what=resolution&span=&period=lifespan&group_id=36855 "Distribution by Resolution" for past year]
 +
 
 
===Ontology Quality Control===
 
===Ontology Quality Control===
 
We're continuing to use the [[Ontology_Quality_Control|ontology QC]] procedures we reported in [[Ontology_Development_progress_report_for_October_2008_meetings#Ontology_Quality_Control|October]]. These include:
 
We're continuing to use the [[Ontology_Quality_Control|ontology QC]] procedures we reported in [[Ontology_Development_progress_report_for_October_2008_meetings#Ontology_Quality_Control|October]]. These include:
Line 49: Line 51:
 
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 2008.
+
 
 
====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 07:55, 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