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First implementation meeting:
Technology: webex and skype.
Personnel:
Personnel:
* Chris Mungall  
* Chris Mungall  
* Jane Lomax
* Tanya Berardini 
* Amelia Ireland
* David Hill  
* David Hill  
* John Day-Richter  
* John Day-Richter
* Jane Lomax
 
'''TIMELINE'''
 
* January
** Documentation of creating regulates DONE
*** investigate how to create regulates terms in the future (use test file in scratch directory)
** Review some cases from part_of relationships that exist in BP to test 'regulation is transitive over part_of' rule DONE
** Go through the No_target lines from Chris' QC report DONE
** Begin on the No_parse list DONE
*** Chris needs to whittle down the no_parse list to get rid of the ones we already looked at
 
* February
** Finish No_parse list DONE
* March
** Review Second error report: scratch/regulation-unimplied-links.txt where the regulates hierarchy doesn't parallel the process hierarchy. DONE
** Training session for ontology editors on how to create new 'regulation' terms, likely Tues. 3/11 during OEWG webex meeting DONE
 
The new layout will be phased in from March 18-25 2007.
 
This will be tied in with the introduction of the regulates relation
 
# Midnight Pacific time March 18 (8 am, 3/19 Jen's time) : Begin freeze. DONE
#* Jen merges electron transport changes into gene_ontology_edit.obo, then let's Chris know that he can start file conversion DONE
#* This marks the last ever manual edit to gene_ontology_edit.obo DONE
# March 19: Add regulates relations - keep in scratch/ then cp to gene_ontology_write DONE
# March 20: Switch edit files: gene_ontology_write.obo open for business. DONE
#* Editors (David, Tanya, Jen only) can edit new file for QC purposes only. However, new changes remain largely invisible to general public DONE
# March 20-25: Switch script to use gene_ontology_write as source. See software TODO below
# Freeze period will last until March 25th, x am Pacific when Chris puts up gene_ontology_write.obo as editor's file. Chris will email go list to say that new file is available for editing. DONE
# March 26+: Announce changes to community
 
*March/April
** Finish pre-release generated QC report, NO_TARGET and UNEXPECTED are done, NP are still pending
** Review report that lists non-regulation processes that are parts of other processes to see if we can find examples of regulates not being transitive over part-of. IN PROGRESS
** Review and begin to fix problems in BP ontology that have to do with multiple part_of parentage of certain terms, file to look at is mp-asserted.txt (email from cjm, 1-17-08)  [[transitive over part_of documentation]]
** Review third report: scratch/regulation-newlinks.txt in which the transitivity over part_of has been implemented.
** Work on terms starting with 'maintenance' or 'establishment'
** Testing: is regulates transitive over regulates?  Only in BP?
** Metrics
** Metabolism, missing rungs in the ladder problem
 
 
 
The new layout will be phased in from March 18-25 2007.
 
This will be tied in with the introduction of the regulates relation
 
# Midnight Pacific time March 18 (8 am, 3/19 Jen's time) : Begin freeze. DONE
#* Jen merges electron transport changes into gene_ontology_edit.obo, then let's Chris know that he can start file conversion DONE
#* This marks the last ever manual edit to gene_ontology_edit.obo DONE
# March 19: Add regulates relations - keep in scratch/ then cp to gene_ontology_write DONE
# March 20: Switch edit files: gene_ontology_write.obo open for business. DONE
#* Editors (David, Tanya, Jen only) can edit new file for QC purposes only. However, new changes remain largely invisible to general public DONE
# March 20-25: Switch script to use gene_ontology_write as source. See software TODO below
# Freeze period will last until March 25th, x am Pacific when Chris puts up gene_ontology_write.obo as editor's file. Chris will email go list to say that new file is available for editing. DONE
# March 26+: Announce changes to community
 
[[Regulation Implementation Plan]]
 
[[Regulates- Meeting Minutes]]
 
[[Regulation cross-products]]
 
[[Regulation metrics]]


Implementation plan:
[[Regulates_Documentation]]


* Enable reasoner to create implied links. (Chris Mungall and John Day-Richter)
[[Image:Regulates_talk.ppt]]
** Sort regulation cross-products:  
*** Molecular function
*** Biological process
*** Biological quality
*** Unassignable
**** Chris has run the reasoner and there is a report in the go/scratch directory that list all of the 'regulation of...' terms where the target of the regulation is not a valid biological process. ftp://ftp.geneontology.org/pub/go/scratch/regulation-of-non-process.txt
* Biologists categorize unassignable (David Hill, Amelia Ireland, Jane Lomax)
** David has gone through this list and noted the following.
*** Terms where the 'regulation of...' is a regulation of a molecular function. RoMF
*** Terms where the 'regulation of...' is a regulation of a biological quality.RoBQ
*** Terms where the 'regulation of...' is a valid subtype of another 'regulation of...' term and we probably do not want to make subtypes of the original BP term. Terms like 'regulation of transcription involved in....' are examples of this. The transcription is basically the same, but it is the regulation that differs.
*** Terms where the 'regulation of...' and the BP parent need to be made univocal or there is a missing BP type.
*** Terms that are still questionable. I have noted suggestions about what to do with these.
** The file with David's notes and questions can be found here. [[Regulation Worksheet]]
** Outstanding questions/thoughts
*** For biological qualities, it makes sense to have positive and negative regulation be a part of the parent regulation term, but does this make sense with biological processes?
*** Should we make relationships between the RoMF terms and the processes in which the execution of the functions take part? For example, should 'regulation of epidermal growth factor receptor activity' relate to the eipdermal growth factor receptor signaling pathway? If so, how?
*** In some cases, a regulation process can be a bona-fide part of another process, or be a bona-fide type of another process. We need to be careful about which part-ofs are replaced by regulates.
*** Do we want to instantiate all of the implied regulates relationships that are generated by legitimate 'regulation of ...' subtypes?
* Rerun reasoner
* Export to instantiate implied links.
* Remove redundant links (Requires OBO-Edit feature, John Day-Richter)
* Add Chris Mungall's logical definitions to gene_ontology_edit.obo file.


*[[Regulation cross-products]]
[[Category:Regulation]]

Revision as of 11:59, 5 May 2014

Personnel:

  • Chris Mungall
  • Tanya Berardini
  • David Hill
  • John Day-Richter
  • Jane Lomax

TIMELINE

  • January
    • Documentation of creating regulates DONE
      • investigate how to create regulates terms in the future (use test file in scratch directory)
    • Review some cases from part_of relationships that exist in BP to test 'regulation is transitive over part_of' rule DONE
    • Go through the No_target lines from Chris' QC report DONE
    • Begin on the No_parse list DONE
      • Chris needs to whittle down the no_parse list to get rid of the ones we already looked at
  • February
    • Finish No_parse list DONE
  • March
    • Review Second error report: scratch/regulation-unimplied-links.txt where the regulates hierarchy doesn't parallel the process hierarchy. DONE
    • Training session for ontology editors on how to create new 'regulation' terms, likely Tues. 3/11 during OEWG webex meeting DONE

The new layout will be phased in from March 18-25 2007.

This will be tied in with the introduction of the regulates relation

  1. Midnight Pacific time March 18 (8 am, 3/19 Jen's time) : Begin freeze. DONE
    • Jen merges electron transport changes into gene_ontology_edit.obo, then let's Chris know that he can start file conversion DONE
    • This marks the last ever manual edit to gene_ontology_edit.obo DONE
  2. March 19: Add regulates relations - keep in scratch/ then cp to gene_ontology_write DONE
  3. March 20: Switch edit files: gene_ontology_write.obo open for business. DONE
    • Editors (David, Tanya, Jen only) can edit new file for QC purposes only. However, new changes remain largely invisible to general public DONE
  4. March 20-25: Switch script to use gene_ontology_write as source. See software TODO below
  5. Freeze period will last until March 25th, x am Pacific when Chris puts up gene_ontology_write.obo as editor's file. Chris will email go list to say that new file is available for editing. DONE
  6. March 26+: Announce changes to community
  • March/April
    • Finish pre-release generated QC report, NO_TARGET and UNEXPECTED are done, NP are still pending
    • Review report that lists non-regulation processes that are parts of other processes to see if we can find examples of regulates not being transitive over part-of. IN PROGRESS
    • Review and begin to fix problems in BP ontology that have to do with multiple part_of parentage of certain terms, file to look at is mp-asserted.txt (email from cjm, 1-17-08) transitive over part_of documentation
    • Review third report: scratch/regulation-newlinks.txt in which the transitivity over part_of has been implemented.
    • Work on terms starting with 'maintenance' or 'establishment'
    • Testing: is regulates transitive over regulates? Only in BP?
    • Metrics
    • Metabolism, missing rungs in the ladder problem


The new layout will be phased in from March 18-25 2007.

This will be tied in with the introduction of the regulates relation

  1. Midnight Pacific time March 18 (8 am, 3/19 Jen's time) : Begin freeze. DONE
    • Jen merges electron transport changes into gene_ontology_edit.obo, then let's Chris know that he can start file conversion DONE
    • This marks the last ever manual edit to gene_ontology_edit.obo DONE
  2. March 19: Add regulates relations - keep in scratch/ then cp to gene_ontology_write DONE
  3. March 20: Switch edit files: gene_ontology_write.obo open for business. DONE
    • Editors (David, Tanya, Jen only) can edit new file for QC purposes only. However, new changes remain largely invisible to general public DONE
  4. March 20-25: Switch script to use gene_ontology_write as source. See software TODO below
  5. Freeze period will last until March 25th, x am Pacific when Chris puts up gene_ontology_write.obo as editor's file. Chris will email go list to say that new file is available for editing. DONE
  6. March 26+: Announce changes to community

Regulation Implementation Plan

Regulates- Meeting Minutes

Regulation cross-products

Regulation metrics

Regulates_Documentation

File:Regulates talk.ppt