Regulation Main Page

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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