Difference between revisions of "WormBase-Caltech Weekly Calls"
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Mock Upload | Mock Upload | ||
− | *Everything OK | + | *Everything was OK |
*Wen will leave files in the same directories, so curators will need to overwrite or replace if you want a new file | *Wen will leave files in the same directories, so curators will need to overwrite or replace if you want a new file | ||
*Ghost objects? Allele-phenotype didn't have correct life stages; fixed | *Ghost objects? Allele-phenotype didn't have correct life stages; fixed | ||
Line 66: | Line 66: | ||
*Paper-anatomy term associations in Citace Minus; Raymond will take care of them | *Paper-anatomy term associations in Citace Minus; Raymond will take care of them | ||
*Kimberly uses legacy data for anatomy term associations to papers | *Kimberly uses legacy data for anatomy term associations to papers | ||
+ | *Cell/Cell-Group issues | ||
Interaction OA | Interaction OA | ||
+ | *Interaction OA and dumper script essentially finished | ||
+ | *Curators should check the OA on the sandbox once more before we make it live | ||
*Interaction summary vs. Remark | *Interaction summary vs. Remark | ||
+ | **Interaction summary is for biological info/summary | ||
+ | **Remark is more for technical details | ||
+ | **We will ask Juancarlos if Remark data from old Interaction objects can be transferred to Interaction_summary field/table | ||
*Make Interaction type unique (single ontology field) | *Make Interaction type unique (single ontology field) | ||
*Move the "Phenotype" field to the first TAB | *Move the "Phenotype" field to the first TAB | ||
*Error checks | *Error checks | ||
− | **5 Fatal errors (Interaction does not get dumped) | + | **5 Fatal errors (Interaction does not get dumped) if the following are not satisfied |
***1) There are at least two interactors | ***1) There are at least two interactors | ||
− | ***2) There is a | + | ***2) There is a reference |
***3) The Interactor types are compatible | ***3) The Interactor types are compatible | ||
***4) There is an Interaction ID | ***4) There is an Interaction ID | ||
***5) There is an Interaction type | ***5) There is an Interaction type | ||
**1 Non-fatal error (Interaction gets dumped but error is reported in error file on dump) | **1 Non-fatal error (Interaction gets dumped but error is reported in error file on dump) | ||
− | + | ***Interaction type and directionality of interactors | |
− | * | + | *Additional error check for Karen - duplicate interactions on multiple rows |
+ | *"Check Data" button, what is it doing now? Can it do all the same checks as the dumper? |
Revision as of 18:37, 14 June 2012
2012 Meetings
June 7, 2012
Midbuild
- Wen needs all .ace files ready to test the midbuild
- Chris will send modified WS232 models.wrm to Wen
- Chris will add all model changes proposed for WS233
- ?Interaction model "Rearrangement" tag needs an XREF and ?Rearrangement model needs an "Interactor" tag
New Interaction OA
- Curators should take a look at the new Interaction OA on the sandbox (mangolassi) and notify Juancarlos, Chris, and/or Xiaodong of any problems
- All interactions, including Yeast-Two-Hybrid and Yeast-One-Hybrid experiments, are in the new OA
Paper pipeline for other species
- Kimberly will update pipeline to include papers from other species
- Papers can go through data tagging pipeline (SVM etc.)
- Images could be captured from cooperating journals
- Are PDFs available?
- ~1600 papers for Brugia malayi, for example
- Mapping to genomes will be an issue (e.g. RNAi)
- We would want an automated curation mechanism in place for non-core species
June 14, 2012
Mock Upload
- Everything was OK
- Wen will leave files in the same directories, so curators will need to overwrite or replace if you want a new file
- Ghost objects? Allele-phenotype didn't have correct life stages; fixed
Anatomy terms
- Juancarlos changed obsolete anatomy terms to red text in the Term Info section of the OA
- We will update the anatomy terms somewhat periodically
- Some terms get deprecated; if a term gets deleted, a replacement needs to be found
- Merges can be dealt with more automatically
- Raymond will periodically check for "floating" anatomy terms
- Update went smoothly
- Not many 'obsolete' terms being used
- Many subsumed terms
- Paper-anatomy term associations in Citace Minus; Raymond will take care of them
- Kimberly uses legacy data for anatomy term associations to papers
- Cell/Cell-Group issues
Interaction OA
- Interaction OA and dumper script essentially finished
- Curators should check the OA on the sandbox once more before we make it live
- Interaction summary vs. Remark
- Interaction summary is for biological info/summary
- Remark is more for technical details
- We will ask Juancarlos if Remark data from old Interaction objects can be transferred to Interaction_summary field/table
- Make Interaction type unique (single ontology field)
- Move the "Phenotype" field to the first TAB
- Error checks
- 5 Fatal errors (Interaction does not get dumped) if the following are not satisfied
- 1) There are at least two interactors
- 2) There is a reference
- 3) The Interactor types are compatible
- 4) There is an Interaction ID
- 5) There is an Interaction type
- 1 Non-fatal error (Interaction gets dumped but error is reported in error file on dump)
- Interaction type and directionality of interactors
- 5 Fatal errors (Interaction does not get dumped) if the following are not satisfied
- Additional error check for Karen - duplicate interactions on multiple rows
- "Check Data" button, what is it doing now? Can it do all the same checks as the dumper?