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.

Adding new gene paper connections

add info

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.	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 level change in genetic background, ie, gfp expression (or any other reporter) increases or decrease; expression level change under certain chemical/physical conditions, ie, drugs, heat shock, etc.; expression location change in genetic background, missexpression, ie, nucleus, cytoplasma, etc.; no change in gene expression in genetic background if mentioned in paper		E-mail xdwang@its.caltech.edu
Expression Data :	Include all experiments revealing the temporal and spatial (e.g. tissue and subcellular) distribution of genes in wild type background. For example: Reporter gene analysis, antibody staining, In situ hybridization, RT_PCR, Western Northern. Exclude all markers (such as antibodies or reporter genes used to label certain tissues or subcellular structure.) This flag also alerts curators so they can cross-checking CCC semi-automation for missed papers.		E-mail wchen@its.caltech.edu, vanauken@its.caltech.edu
Marker :	Reporters or antibodies used to mark certain tissue, subcellular structure or life stage.		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 transgene only. Textpresso will extract all the Is or In transgene names, please look for transgenes without official names, for example, authors said they used microbombardment but did not provide official names. Or if they provided a strain name and you know the strain contains a transgene. Ex transgenes will only be curated when they are used by other experiments, such as phenotype assay or Expr_pattern. So there is no need to flag them.		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 :	New or used antibodies created by labs; skip antibodies bought from companies		E-mail wchen@its.caltech.edu
Covalent Modification :	phosphorylation site is studies via mutagenesis and in vitro assay
Extract Allele :	Automated		How does this work? Where is this information stored? Who does it go to
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.	Table S4. PDZ domain specificity prediction	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 :	Function of any anatomical part (e.g. cell) is mentioned that has not been flagged already for mosaic analysis, site of action, or ablation data		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 :
Human Diseases :	Genes discussed are homolog/ortholog of a human disease gene		E-mail ranjana@its.caltech.edu
Comment :	e.g. no curatable		stays in Postgres

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)