First-pass schedule, instructions, automation

Papers for Firstpass are found on the WBPaperEditor page:

Pick a paper and access the curation form

• Go to http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi
• Choose your name
• Scroll down the page and select "Display All!"
• On the returned list of papers select "Not Curated!"
• Scroll/Page down to a paper and select "Curate!"

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 WBPaper0030000 AND LATER
• 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. Alerts curators to newly cloned genes so that they can update a previously existing concise description, if needed. For example, UNC-80 = F25C8.3	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 :	Subcellular localization. Also alerts curators so they can cross-checking CCC |semi-automation for |missed papers.	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)