First-pass schedule, instructions, automation

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Revision as of 00:43, 10 February 2009 by Kyook (talk | contribs) (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:/...)
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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
  • 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.


What for 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. 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
Allele Info :
Extract Allele : Automated
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
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 Product Interaction : protein-protein, RNA-protein, DNA-protein interactions, etc. E-mail emsch@its.caltech.edu
Sequence :
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
Cell :
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
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
SNP :
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 :
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?)
Human Diseases :
Human Diseases : Are genes discussed that are related to genes involved in human disease? E-mail ranjana@its.caltech.edu
Comments :
Comment :


kjy 19:43, 9 February 2009 (EST)

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