Regulation Main Page: Difference between revisions
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Personnel: | Personnel: | ||
* Chris Mungall | * Chris Mungall | ||
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* Jane Lomax | * Jane Lomax | ||
[[Implementation Plan]] | '''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]] | [[Regulates- Meeting Minutes]] | ||
[[Regulation cross-products]] | |||
[[Regulation metrics]] | |||
[[Regulates_Documentation]] | |||
[[Image:Regulates_talk.ppt]] | |||
[[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
- Documentation of creating regulates DONE
- 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