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

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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:/...)
 
 
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=Papers for Firstpass are found on the [http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi WBPaperEditor] page:=
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[[Caltech documentation]]<br>
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[[First-pass to Curation]]<br>
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[[First-pass_flagging_pipelines]]
  
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==Pick a paper and access the curation form==
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=First-Pass Rotation=
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* Go to http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi
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{| border=2 {{table}}
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* Choose your name
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| align="center" style="background:#f0f0f0;"|'''First-Pass Curator'''
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* Scroll down the page and select "Display All!"
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| align="center" style="background:#f0f0f0;"|'''Round 1'''
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* On the returned list of papers select "Not Curated!"
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| align="center" style="background:#f0f0f0;"|'''Round 2'''
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* Scroll/Page down to a paper and select "Curate!" 
 
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''Alternatively''
 
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* Access the curation.cgi from the WBPaperID page itselF
 
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* Select the WBPaperID from left column to take you to the paper page
 
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* Select first-pass curate
 
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''Note: the paper pdf can be accessed from the paper page along with supplemental materials.''
 
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Either action takes you to the curation.cgi (SEE BELOW)
 
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==The firstpass page [http://tazendra.caltech.edu/~postgres/cgi-bin/curation.cgi curation.cgi]==
 
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*At the top of the page are links to:
 
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**The tazendra site map (other forms)
 
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**Documentation for the set up, paths from, and changes to the curation.cgi form
 
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**Guidelines  for the form which include some summary information about the fields and features,  written by Raymond in 2001 and needs some updating.
 
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*For each data type you can check the box or enter text:
 
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**Check the box = a '"yes" is entered in to the field
 
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**Enter text = the text is recorded
 
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*E-mail is set for default send if there is a "yes" (from a check) or text in the data type flag box.
 
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*When done, you can see the preview of the submission, by selecting "Preview!"
 
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*If acceptable,  Select "New Entry!"
 
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*First pass flags will be sent.
 
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==What for and to whom a flag is sent==
 
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{| {{table}}
 
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| align="center" style="background:#f0f0f0;"|'''Data type'''
 
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| align="center" style="background:#f0f0f0;"|'''Description/Examples'''
 
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| align="center" style="background:#f0f0f0;"|'''Curator Flagged'''
 
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| Gene Symbol (main/other/sequence) : ||New symbol for known locus or new locus defined. ||E-mail genenames@wormbase.org, vanauken@its.caltech.edu
 
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| Mapping Data : ||3-factor mapping;  Mapping with Df||E-mail genenames@wormbase.org
 
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| Gene Function : ||Discussion of new function of a gene||E-mail emsch@its.caltech.edu
 
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| Gene Regulation on Expression Level : ||Gene expression in a genetic background; Misexpression results||E-mail xdwang@its.caltech.edu
 
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| Expression Data : ||Gene expression details through transgene, antibody, protein? ||E-mail wchen@its.caltech.edu, vanauken@its.caltech.edu
 
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| Marker : ||Reporters used as marker for something||E-mail wchen@its.caltech.edu, vanauken@its.caltech.edu
 
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| Microarray : ||Any microarray data||E-mail wchen@its.caltech.edu
 
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| RNAi : ||Phenotypes/results are discussed for less than 100 RNAi experiments||E-mail garys@its.caltech.edu
 
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| Large-Scale RNAi : ||Phenotypes/results are discussed for more than 100 RNAi experiments||E-mail raymond@its.caltech.edu
 
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| Transgene : ||Reagent: Integrated (and Extrachromosomal?)||E-mail wchen@its.caltech.edu
 
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| Overexpression : ||Over expression of something results in a phenotype ||E-mail emsch@its.caltech.edu, garys@its.caltech.edu (add Variation phenotype people)
 
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| Structure Information : ||NMR structure, functional domain info for a protein (e.g. removal of the first 50aa causes mislocalization of the protein||
 
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| Functional Complementation : ||?||
 
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| in vitro Protein Analysis : ||e.g. kinase assay||
 
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| Mosaic Analysis : ||e.g. extra-chromosomal transgene loss in a particular cell lineage abolishes mutant rescue||E-mail raymond@its.caltech.edu
 
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| 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
 
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| Extract Antibody : ||Reagent ||E-mail wchen@its.caltech.edu
 
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| Covalent Modification : ||phosphorylation site is studies via mutagenesis and in vitro assay||
 
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| Allele Info :||||
 
 
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| Extract Allele : ||Automated||
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| Karen  ||2/16-3/1|| 7/6-7/19
 
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| Xiaodong ||3/2-3/15 ||7/20-8/1
 
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| 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
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| Raymond ||3/16-3/29 ||8/3-8/16
 
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| Jolene ||3/30-4/12: New forms active||8/17-8/30
 
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| Non-N2_phenotype : ||Phenotypes of strains/non-C. elegans||E-mail kyook@its.caltech.edu
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| Gary ||4/13-4/26: Author forms sent out||8/31-9-13
 
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| Ranjana ||4/27-5/10: Author feedback coming in ||9/14-9/27
 
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| Sequence Change : ||Mutation was sequenced ||E-mail genenames@wormbase.org
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| Erich ||5/11-5/24||9/28-10/11
 
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| Wen ||5/25- 6/7||10/12-10/35
 
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| Interactions :||||
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| Kimberly ||6/8-6/21||10/26-11/8
 
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| Gene Interactions : ||e.g. daf-16(mu86) suppresses daf-2(e1370), daf-16(RNAi) suppresses daf-2(RNAi)||E-mail emsch@its.caltech.edu
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|WormBase re-evalutation||6/22-7/5: IWM||(?)
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| Gene Product Interaction : ||protein-protein, RNA-protein, DNA-protein interactions, etc.||E-mail emsch@its.caltech.edu
 
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| Sequence :||||
 
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| Sanger Gene Structure Correction : ||||E-mail worm-bug@sanger.ac.uk
 
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| St. Louis Gene Structure Correction : ||||E-mail wormticket@watson.wustl.edu
 
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| 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
 
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| Mass Spec : ||key words: LCMS, COSY, NMR, mass spec, HRMS||E-mail gw3@sanger.ac.uk, worm-bug@sanger.ac.uk
 
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| Cell :||||
 
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| Cell Name : ||New cell name is mentioned||E-mail raymond@its.caltech.edu
 
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| Cell Function : ||New function of a cell is mentioned||E-mail raymond@its.caltech.edu
 
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| 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
 
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| SNP :||||
 
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| Extract New SNP : ||Reagent: new SNP not already in WB||E-mail dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
 
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| Extract SNP Verified by St. Louis : ||||E-mail dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
 
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| Supplemental :||||
 
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| Supplemental Material : ||Is there supplemental material that needs to be downloaded? ||E-mail qwang@its.caltech.edu
 
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| Chemicals :||||
 
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| Chemicals : ||Reagent (can this be automated using Chebi?)||
 
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| Human Diseases :||||
 
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| Human Diseases : ||Are genes discussed that are related to genes involved in human disease? ||E-mail ranjana@its.caltech.edu
 
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| Comments :||||
 
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| Comment : ||||
 
 
|}
 
|}
  
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----
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=Automation=
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[http://goldturtle.caltech.edu/wcat/ Textpresso's Automation Explanation and Schedule  http://goldturtle.caltech.edu/wcat/]
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----
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=First-pass forms=
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*[http://www.wormbase.org/wiki/index.php/Texpresso/Author/Curator_interim_form New textpresso/author/curator table]
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**[http://tazendra.caltech.edu/~postgres/cgi-bin/curator_first_pass.cgi Example of new curator first-pass curation.cgi]
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*[http://www.wormbase.org/wiki/index.php/First-pass_data_types_explained  Old curator first-pass table]
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*[[Author first-pass form]]
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*[[Genetics Author pass form]]
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*[[Data types used on first-pass forms]]
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----
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=Instructions for curators=
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[http://www.wormbase.org/wiki/index.php/Instructions_for_curators Overview for curators (for the new form)]
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----
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=Postgres data for individual data types=
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*[http://www.wormbase.org/wiki/index.php/FP_curator_comments_for_St.Louis_and_Sanger_structure_correction_data_type St.Louis and Sanger structure correction data type curator comments]
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----
  
 
[[User:Kyook|kjy]] 19:43, 9 February 2009 (EST)
 
[[User:Kyook|kjy]] 19:43, 9 February 2009 (EST)
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[[Category:Curation]]

Latest revision as of 23:04, 13 August 2010

Caltech documentation
First-pass to Curation
First-pass_flagging_pipelines

First-Pass Rotation

First-Pass Curator Round 1 Round 2
Karen 2/16-3/1 7/6-7/19
Xiaodong 3/2-3/15 7/20-8/1
Raymond 3/16-3/29 8/3-8/16
Jolene 3/30-4/12: New forms active 8/17-8/30
Gary 4/13-4/26: Author forms sent out 8/31-9-13
Ranjana 4/27-5/10: Author feedback coming in 9/14-9/27
Erich 5/11-5/24 9/28-10/11
Wen 5/25- 6/7 10/12-10/35
Kimberly 6/8-6/21 10/26-11/8
WormBase re-evalutation 6/22-7/5: IWM (?)


Automation

Textpresso's Automation Explanation and Schedule http://goldturtle.caltech.edu/wcat/


First-pass forms

Instructions for curators

Overview for curators (for the new form)


Postgres data for individual data types


kjy 19:43, 9 February 2009 (EST)

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