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− | =Papers for Firstpass are found on the [http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi WBPaperEditor] page:=
| + | [[Caltech documentation]]<br> |
| + | [[First-pass to Curation]]<br> |
| + | [[First-pass_flagging_pipelines]] |
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− | ==Pick a paper and access the curation form== | + | =First-Pass Rotation= |
− | * Go to http://tazendra.caltech.edu/~postgres/cgi-bin/wbpaper_editor.cgi
| + | {| border=2 {{table}} |
− | * Choose your name
| + | | align="center" style="background:#f0f0f0;"|'''First-Pass Curator''' |
− | * Scroll down the page and select "Display All!"
| + | | align="center" style="background:#f0f0f0;"|'''Round 1''' |
− | * On the returned list of papers select "Not Curated!"
| + | | align="center" style="background:#f0f0f0;"|'''Round 2''' |
− | * 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}} | |
− | | align="center" style="background:#f0f0f0;"|'''Data type''' | |
− | | align="center" style="background:#f0f0f0;"|'''Description/Examples''' | |
− | | 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|| | + | | 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 | + | | 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 | + | | 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 | + | | 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 :|||| | + | | 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 | + | |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= |
| + | [http://goldturtle.caltech.edu/wcat/ Textpresso's Automation Explanation and Schedule http://goldturtle.caltech.edu/wcat/] |
| + | |
| + | |
| + | ---- |
| + | |
| + | =First-pass forms= |
| + | *[http://www.wormbase.org/wiki/index.php/Texpresso/Author/Curator_interim_form New textpresso/author/curator table] |
| + | **[http://tazendra.caltech.edu/~postgres/cgi-bin/curator_first_pass.cgi Example of new curator first-pass curation.cgi] |
| + | *[http://www.wormbase.org/wiki/index.php/First-pass_data_types_explained Old curator first-pass table] |
| + | *[[Author first-pass form]] |
| + | *[[Genetics Author pass form]] |
| + | *[[Data types used on first-pass forms]] |
| + | |
| + | ---- |
| + | |
| + | =Instructions for curators= |
| + | [http://www.wormbase.org/wiki/index.php/Instructions_for_curators Overview for curators (for the new form)] |
| + | |
| + | |
| + | ---- |
| + | |
| + | =Postgres data for individual data types= |
| + | *[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) |
| + | |
| + | |
| + | [[Category:Curation]] |