Difference between revisions of "First-pass schedule, instructions, automation"

From WormBaseWiki
Jump to navigationJump to search
m (New page: =Papers for Firstpass are found on the [http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi WBPaperEditor] page:= ==Pick a paper and access the curation form== * Go to http:/...)
 
m
Line 10: Line 10:
 
 
 
''Alternatively''  
 
''Alternatively''  
−
* Access the curation.cgi from the WBPaperID page itselF
+
* Access the curation.cgi from the WBPaperID page itself
−
* Select the WBPaperID from left column to take you to the paper page
+
* Select the WBPaperID from left column to take you to the paper page-- '''ONLY SELECT PAPERS FROM WBPaper300000 AND ABOVE'''
 
* Select first-pass curate
 
* Select first-pass curate
 
''Note: the paper pdf can be accessed from the paper page along with supplemental materials.''
 
''Note: the paper pdf can be accessed from the paper page along with supplemental materials.''
  
 
Either action takes you to the curation.cgi (SEE BELOW)
 
Either action takes you to the curation.cgi (SEE BELOW)
−
 
  
 
==The firstpass page [http://tazendra.caltech.edu/~postgres/cgi-bin/curation.cgi curation.cgi]==
 
==The firstpass page [http://tazendra.caltech.edu/~postgres/cgi-bin/curation.cgi curation.cgi]==
Line 35: Line 34:
  
  
−
==What for and to whom a flag is sent==
+
==For what and to whom a flag is sent==
 
{| {{table}}
 
{| {{table}}
 
| align="center" style="background:#f0f0f0;"|'''Data type'''
 
| align="center" style="background:#f0f0f0;"|'''Data type'''
Line 101: Line 100:
 
|  
 
|  
 
|-
 
|-
−
| Site of Action : ||e.g. tissue/cell specific expression rescues mutant phenotype; RNAi in rrf-1 background determines that the gene acts in the germ line||E-mail raymond@its.caltech.edu
+
| Site of Action : ||e.g. anatomy(tissue/cell)-specific expression rescues mutant phenotype; RNAi in rrf-1 background determines that the gene acts in the germ line||E-mail raymond@its.caltech.edu
 
|-
 
|-
 
|  
 
|  
Line 113: Line 112:
 
|  
 
|  
 
|-
 
|-
−
| Allele Info :||||
+
| Extract Allele : ||Automated||'''Where is this information stored? How does this work?'''
−
|-
 
−
| Extract Allele : ||Automated||
 
 
|-
 
|-
 
|  
 
|  
Line 130: Line 127:
 
|-
 
|-
 
|  
 
|  
−
|-
 
−
| Interactions :||||
 
 
|-
 
|-
 
| Gene Interactions : ||e.g. daf-16(mu86) suppresses daf-2(e1370), daf-16(RNAi) suppresses daf-2(RNAi)||E-mail emsch@its.caltech.edu
 
| Gene Interactions : ||e.g. daf-16(mu86) suppresses daf-2(e1370), daf-16(RNAi) suppresses daf-2(RNAi)||E-mail emsch@its.caltech.edu
Line 140: Line 135:
 
|-
 
|-
 
|  
 
|  
−
|-
 
−
| Sequence :||||
 
 
|-
 
|-
 
| Sanger Gene Structure Correction : ||||E-mail worm-bug@sanger.ac.uk
 
| Sanger Gene Structure Correction : ||||E-mail worm-bug@sanger.ac.uk
Line 159: Line 152:
 
|  
 
|  
 
|-
 
|-
−
| Cell :||||
+
| '''RETIRE''' ''Cell Name :'' ||''New cell name is mentioned''||''E-mail raymond@its.caltech.edu''
−
|-
 
−
| Cell Name : ||New cell name is mentioned||E-mail raymond@its.caltech.edu
 
 
|-
 
|-
 
|  
 
|  
 
|-
 
|-
−
| Cell Function : ||New function of a cell is mentioned||E-mail raymond@its.caltech.edu
+
| Cell/Anatomy Function : ||New function of any anatomical part (e.g. cell) is mentioned (this often overlaps with mosaic analysis, site of action, or ablation data, so make sure to flag in instances where function was reported by other means) ||E-mail raymond@its.caltech.edu
 
|-
 
|-
 
|  
 
|  
 
|-
 
|-
−
| Ablation Data : ||cells were ablated using a laser or by other means (e.g. by expressing a cell-toxic protein)||E-mail raymond@its.caltech.edu
+
| Ablation Data : ||cell or anatomical unit was ablated using a laser or by other means (e.g. by expressing a cell-toxic protein)||E-mail raymond@its.caltech.edu
 
|-
 
|-
 
|  
 
|  
−
|-
 
−
| SNP :||||
 
 
|-
 
|-
 
| Extract New SNP : ||Reagent: new SNP not already in WB||E-mail dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
 
| Extract New SNP : ||Reagent: new SNP not already in WB||E-mail dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
Line 182: Line 171:
 
|-
 
|-
 
|  
 
|  
−
|-
 
−
| Supplemental :||||
 
 
|-
 
|-
 
| Supplemental Material : ||Is there supplemental material that needs to be downloaded? ||E-mail qwang@its.caltech.edu
 
| Supplemental Material : ||Is there supplemental material that needs to be downloaded? ||E-mail qwang@its.caltech.edu
 
|-
 
|-
 
|  
 
|  
−
|-
 
−
| Chemicals :||||
 
 
|-
 
|-
 
| Chemicals : ||Reagent (can this be automated using Chebi?)||
 
| Chemicals : ||Reagent (can this be automated using Chebi?)||
 
|-
 
|-
 
|  
 
|  
−
|-
 
−
| Human Diseases :||||
 
 
|-
 
|-
 
| Human Diseases : ||Are genes discussed that are related to genes involved in human disease? ||E-mail ranjana@its.caltech.edu
 
| Human Diseases : ||Are genes discussed that are related to genes involved in human disease? ||E-mail ranjana@its.caltech.edu
 
|-
 
|-
 
|  
 
|  
−
|-
 
−
| Comments :||||
 
 
|-
 
|-
 
| Comment : ||||
 
| Comment : ||||
 
|}
 
|}
 +
 +
 +
==Issues to resolve==
 +
* There are many papers on the firstpass list that are already firstpassed. Most of these papers are duplicates and have two WBPaperID assignments. Is there a way to resolve this?
 +
 +
* There are papers on the firstpass list that have been curated for data types by individual curators who have bypassed the firstpass pipeline.  Is there a way to mark the paper in the firstpass list as curated for a specific data type but not others? We do have a record of data type curation for each paper, is there some way of combining the first pass curation with the curation status form?
 +
 +
* How does the false positive work?
 +
 +
  
  
 
[[User:Kyook|kjy]] 19:43, 9 February 2009 (EST)
 
[[User:Kyook|kjy]] 19:43, 9 February 2009 (EST)

Revision as of 04:17, 10 February 2009

Papers for Firstpass are found on the WBPaperEditor page:

Pick a paper and access the curation form


Alternatively

  • Access the curation.cgi from the WBPaperID page itself
  • Select the WBPaperID from left column to take you to the paper page-- ONLY SELECT PAPERS FROM WBPaper300000 AND ABOVE
  • Select first-pass curate

Note: the paper pdf can be accessed from the paper page along with supplemental materials.

Either action takes you to the curation.cgi (SEE BELOW)

The firstpass page curation.cgi

  • At the top of the page are links to:
    • The tazendra site map (other forms)
    • Documentation for the set up, paths from, and changes to the curation.cgi form
    • Guidelines for the form which include some summary information about the fields and features, written by Raymond in 2001 and needs some updating.
  • For each data type you can check the box or enter text:
    • Check the box = a '"yes" is entered in to the field
    • Enter text = the text is recorded
  • E-mail is set for default send if there is a "yes" (from a check) or text in the data type flag box.
  • When done, you can see the preview of the submission, by selecting "Preview!"
  • If acceptable, Select "New Entry!"
  • First pass flags will be sent.


For what and to whom a flag is sent

Data type Description/Examples Curator Flagged
Gene Symbol (main/other/sequence) : New symbol for known locus or new locus defined. E-mail genenames@wormbase.org, vanauken@its.caltech.edu
Mapping Data : 3-factor mapping; Mapping with Df E-mail genenames@wormbase.org
Gene Function : Discussion of new function of a gene E-mail emsch@its.caltech.edu
Gene Regulation on Expression Level : Gene expression in a genetic background; Misexpression results E-mail xdwang@its.caltech.edu
Expression Data : Gene expression details through transgene, antibody, protein? E-mail wchen@its.caltech.edu, vanauken@its.caltech.edu
Marker : Reporters used as marker for something E-mail wchen@its.caltech.edu, vanauken@its.caltech.edu
Microarray : Any microarray data E-mail wchen@its.caltech.edu
RNAi : Phenotypes/results are discussed for less than 100 RNAi experiments E-mail garys@its.caltech.edu
Large-Scale RNAi : Phenotypes/results are discussed for more than 100 RNAi experiments E-mail raymond@its.caltech.edu
Transgene : Reagent: Integrated (and Extrachromosomal?) E-mail wchen@its.caltech.edu
Overexpression : Over expression of something results in a phenotype E-mail emsch@its.caltech.edu, garys@its.caltech.edu (add Variation phenotype people)
Structure Information : NMR structure, functional domain info for a protein (e.g. removal of the first 50aa causes mislocalization of the protein
Functional Complementation : ?
in vitro Protein Analysis : e.g. kinase assay
Mosaic Analysis : e.g. extra-chromosomal transgene loss in a particular cell lineage abolishes mutant rescue E-mail raymond@its.caltech.edu
Site of Action : e.g. anatomy(tissue/cell)-specific expression rescues mutant phenotype; RNAi in rrf-1 background determines that the gene acts in the germ line E-mail raymond@its.caltech.edu
Extract Antibody : Reagent E-mail wchen@its.caltech.edu
Covalent Modification : phosphorylation site is studies via mutagenesis and in vitro assay
Extract Allele : Automated Where is this information stored? How does this work?
Mutant Phenotype : Phenotype is reported for a variation. E-mail emsch@its.caltech.edu, garys@its.caltech.edu, kyook@its.caltech.edu, jolenef@its.caltech.edu
Non-N2_phenotype : Phenotypes of strains/non-C. elegans E-mail kyook@its.caltech.edu
Sequence Change : Mutation was sequenced E-mail genenames@wormbase.org
Gene Interactions : e.g. daf-16(mu86) suppresses daf-2(e1370), daf-16(RNAi) suppresses daf-2(RNAi) E-mail emsch@its.caltech.edu
Gene Product Interaction : protein-protein, RNA-protein, DNA-protein interactions, etc. E-mail emsch@its.caltech.edu
Sanger Gene Structure Correction : E-mail worm-bug@sanger.ac.uk
St. Louis Gene Structure Correction : E-mail wormticket@watson.wustl.edu
Sequence Features : DNA/RNA elements required for gene expression: promoters, introns, UTR\'s etc. E-mail emsch@its.caltech.edu, worm-bug@sanger.ac.uk, stlouis@wormbase.org
Mass Spec : key words: LCMS, COSY, NMR, mass spec, HRMS E-mail gw3@sanger.ac.uk, worm-bug@sanger.ac.uk
RETIRE Cell Name : New cell name is mentioned E-mail raymond@its.caltech.edu
Cell/Anatomy Function : New function of any anatomical part (e.g. cell) is mentioned (this often overlaps with mosaic analysis, site of action, or ablation data, so make sure to flag in instances where function was reported by other means) E-mail raymond@its.caltech.edu
Ablation Data : cell or anatomical unit was ablated using a laser or by other means (e.g. by expressing a cell-toxic protein) E-mail raymond@its.caltech.edu
Extract New SNP : Reagent: new SNP not already in WB E-mail dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
Extract SNP Verified by St. Louis : E-mail dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
Supplemental Material : Is there supplemental material that needs to be downloaded? E-mail qwang@its.caltech.edu
Chemicals : Reagent (can this be automated using Chebi?)
Human Diseases : Are genes discussed that are related to genes involved in human disease? E-mail ranjana@its.caltech.edu
Comment :


Issues to resolve

  • There are many papers on the firstpass list that are already firstpassed. Most of these papers are duplicates and have two WBPaperID assignments. Is there a way to resolve this?
  • There are papers on the firstpass list that have been curated for data types by individual curators who have bypassed the firstpass pipeline. Is there a way to mark the paper in the firstpass list as curated for a specific data type but not others? We do have a record of data type curation for each paper, is there some way of combining the first pass curation with the curation status form?
  • How does the false positive work?



kjy 19:43, 9 February 2009 (EST)

Retrieved from "https://wiki.wormbase.org/index.php?title=First-pass_schedule,_instructions,_automation&oldid=1605"