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ky_wbprojects / Data_types_used_on_first-pass_forms

First Pass Curator form

updated 2011-02-09

Links to live first-pass forms (do not enter any data):
afp = author first pass form -click here
cfp = curator first pass form -click here
jfp = journal first pass (GENETICS) form -click here

NOTE: All datatypes collected through the afp are also collected through the cfp and can be viewed on the cfp form.

"flagged" = WBPapers that have been flagged for that particular data type but not curated yet or not assessed for curation status yet
"flagged-done" = WBPapers that have been flagged and curated. These papers can be used as a source for verified curation flag examples.
Values in the 'Description for author' column are hidden under the '?' on the form.

SPECIES:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
afp onlymaterials and methods*C. elegans*new fieldcelegansUncheck if you are NOT reporting data for C. elegans.?default checked on
afp onlymaterials and methods*C. elegans other than Bristol*new fieldcnonbristolCheck if data for C. elegans natural isolates other than N2 (Bristol) are reported.e.g. Hawaiian, CB4855, CB4852, CB4507, LSJ1, etc.?
afp onlymaterials and methods*Nematodes other than C. elegans*nonntwonematodeCheck if data is reported for any species other than C. elegans, e.g., C. briggsae, Pristionchus pacificus, Brugia malayi, etc.?
afp onlymaterials and methods*Non-nematode species*new fieldnonnematodeCheck if data is reported for any non-nematode species.?
GENE IDENTIFICATION AND MAPPING:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
afp onlyThroughout paper*Genes studied in this paper*n/agenestudiedList any gene for which you report experimental results; do not include genetic markers.genenames, kimberlyBig text box, auto-opened.
afp, jfpabstract, M&M, results*Newly cloned gene*Gene SymbolgenesymbolCheck if your paper reports a new symbol for a known locus or the name of a newly defined locus.genenames@wormbase.org, vanauken@its.caltech.eduflagged-done
SVM, textpresso, jfpM&M, results*Newly created allele*Extract alleleextvariationCheck if your paper reports the identification of any allele that doesn't exist in WormBase already.kyook@caltech.edu
afp onlyM&M, results, supp.Genetic mapping datamapping datamappingdataCheck if your paper contains 3-factor interval mapping data, i.e., genetic data only. Include Df or Dp data, but no SNP interval mapping.genenames@wormbase.orgflagged
jfp onlyM&M, supp.StrainnewstrainsPlease enter strains that do not exist in WormBase and will be sent to the CGC.genenames@wormbase.org
jfp onlyM&M, results, supp.RearrangementnewbalancersPlease list any balancer in your paper that doesn't exist in WormBase already.genenames@wormbase.org
GENE FUNCTION:
Mutant, RNAi, overexpression, or chemical-based phenotypes: PLEASE SPECIFY DATA TYPE.
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
SVM, afp, jfpresultsPhenotype analysisMutant PhenotypenewmutantCheck if your paper reports phenotype due to mutation or overexpression analysis.garys@its.caltech.edu, kyook@caltech.edujfp only collects new three letter phenotype names; flagged-done
SVM, afpresultsSmall-scale RNAi (less than 100 experiments reported)RNAirnaiCheck if your paper reports gene knockdown phenotypes for less than 100 individual RNAi experiments.garys@its.caltech.edu, cgrove@caltech.eduflagged-done
SVM, afpresultsLarge-scale RNAi (less than 100 experiments reported)Large-Scale RNAilsrnaiCheck if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments.raymond@its.caltech.eduflagged-done
SVM (through phenotype analysis) afpresultsOverexpression phenotypeOverexpressionoverexprCheck if your paper reports an abnormal phenotype based on the overexpression of a gene or gene construct. E.g., ""...constitutively activated SCD-2(neu*) receptor caused 100% of animals to arrest in the first larval stage (L1)..."garys@its.caltech.edu, kyook@its.caltech.eduflagged
afpmaterials and methods; resultsChemicalsChemicalschemicalsCheck if the effects of small molecules, chemicals, or drugs were studied on worms. E.g., paraquat, butanone, benzaldehyde, aldicarb, etc. Mutagens used for the generation of mutant in genetic screens do not need to be indicated.flagged
afpresultsMosaic analysismosaicMosaic analysisCheck if your paper reports cell specific gene function based on mosaic analysis, e.g. extra-chromosomal transgene loss in a particular cell lineage leads to loss of mutant rescue, etc.raymond@its.caltech.eduflagged-done
afpresultsTissue or cell site of actionSite of actionsiteactionCheck if your paper reports anatomy-specific function for a gene.raymond@its.caltech.eduflagged-done
afpresultsTime of actionnew fieldtimeactionCheck if your paper reports a temporal requirement for gene function, that is, if gene activity was assayed, for example, through temperature-shift experiments.raymond@its.caltech.edu
afpthroughoutMolecular function of a gene productgenefuncGene functionCheck if your paper discusses a new function for a known or newly defined gene.flagged-done
Textpresso, afpHomolog of a human disease-associated gene.Human DiseasehumdisCheck if genes discussed in your paper are a homolog/ortholog of a human disease-related gene or if your study models some aspect of a human disease.ranjana@its.caltech.eduflagged
INTERACTIONS:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
SVM, afpresults, supplementalGenetic interactionsGene interactionsgeneintCheck if your paper reports the analysis of more than one gene at a time, e.g., double, triple, etc. mutants, including experiments where RNAi was concurrent with other RNAi-treatments or mutations.flagged-done
afp onlymaterials and methods (tools); resultsFunctional complementationFunctional ComplementationfunccompCheck if your paper reports functional redundancy between separate genes, e.g. the rescue of gen-A by overexpression of gen-B or any other extragenic sequence.flagged
SVM, textpresso, afpGene product interactions flagged-doneGene product interactiongeneprodCheck if your paper reports data on protein-protein, RNA-protein, DNA-protein or Y2H interactions, etc.
REGULATION OF GENE EXPRESSION:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
SVM, afpresults, supplementalNew expression pattern for a geneexpression pattern dataotherexprCheck if your paper reports new temporal or spatial (e.g., tissue, subcellular, etc.) data on the pattern of expression of any gene in a wild-type background. You can include: reporter gene analysis, antibody staining, In situ hybridization, RT-PCR, Western or Northern blot data.wchen@its.caltech.edu, vanauken@its.caltech.eduflagged-done
SVM, afpresults, supplementalAlterations in gene expression by genetic or other treatmentGene regulation on expression levelgeneregCheck if your paper reports changes or lack of changes in gene expression levels or patterns due to genetic, chemical, temperature, or any other experimental treatment.xdwang@its.caltech.eduflagged-done
afpRegulatory sequence featuresSequence featuresseqfeatCheck if your paper reports any gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression, promoters, introns, UTRs, DNA binding sites, etc.xdwang@its.caltech.edu, worm-bug@sanger.ac.uk, stlouis@wormbase.orgflagged
afpresults, supp.Position frequency matrix (PFM) or Position weight matrix (PWM)new fieldmatricesCheck if your paper reports PFMs or PWMs, which are typically used to define regulatory sites in genomic DNA (e.g., bound by transcription factors) or mRNA (e.g., bound by translational factors or miRNA). PFMs define simple nucleotide frequencies, while PWMs are scaled logarithmically against a background frequency.xdwang@its.caltech.edu
GEO, afpresults, supp.MicroarrayMicroarraymicroarrayCheck if your paper reports any microarray data.wchen@its.caltech.eduflagged-done
PROTEIN FUNCTION AND STRUCTURE:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
HMM, textpresso, afpmaterials and methods; resultsProtein analysis in vitroin vitro Protein analysisinvitroCheck if your paper reports any in vitro protein analysis such as kinase assays, agonist pharmacological studies,in vitro reconstitution studies, etc.flagged
afpmaterials and methods; resultsAnalysis of protein domains: Domain analysisnew fielddomanal (populated with information previously in "structureinformation")Check if your paper reports on a function of a particular domain within a protein.
afpmaterials and methods; resultsCovalent modificationCovalent modificationcovalentCheck if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysisflagged
afpmaterials and methods; resultsStructural informationStructure informationstructinfoCheck if your paper reports NMR or X-ray crystallographic information.flagged; besides structure info (e.g. x-ray crystallography data) Andrei also includes structure-function data (e.g. mutation at Ser-321 compromises folding, binding, etc.)
afpM&M, results, supp.Mass spectrometryMass SpecmassspecCheck if your paper reports data from any mass spec analysis; keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix.gw3@sanger.ac.uk, worm-bug@sanger.ac.ukflagged-done; From Gary "...only interested in papers that report the peptide sequences that the mass-spec fragments match. These peptides are usually created by one of the programs: MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix. So, the Description field should be:

Keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix|

REAGENTS:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
SVM, TextpressoM&M, resultsC. elegans antibodiesExtract AntibodyantibodyCheck if your paper reports the use of new or known antibodies created by your lab or someone elses lab; do not check this box if antibodies were commercially bought.wchen@its.caltech.eduflagged-done
Textpresso, jfpM&M, supp.Integrated transgenesTransgenetransgeneCheck if integrated transgenes were used in this paper. If the transgene does not have a canonical name, please list it in the "Add Information text area"kyook@its.caltech.eduflagged-done
afpM&M, results, fig, supp.Transgenes used as tissue markersMarkermarkerCheck if reporters (integrated transgenes) were used to mark certain tissues, subcellular structures, or life stages, etc. as a reference point to assay gene function or location.wchen@its.caltech.edu, vanauken@its.caltech.eduWen no longer curates these
GENOME SEQUENCE DATA:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
SVM, afpresults, figures: the authors may or may not state explicitly that lets say there is a novel exon. if i see a gene studied in some detail (e.g. new gene was cloned or gene structure is drawn in fig.), than i check amino acid length for the protein with the data in WB, and i will eyeball the diagrams of gene structures to see if there are obvious diffs. these are quick checks but they catch an occasional gene structure change not listed in the text.Gene structure correctionSanger Gene Structure Correction and St. Louis Gene Structure Correctionstructcorr (this use to be two different fields)Check if your paper reports a gene structure that is different from the one in WormBase, e.g., different splice-site, SL1 instead of SL2, etc.worm-bug@sanger.ac.uk, wormticket@watson.wustl.eduflagged
SVM-textpresso, afpSequencing mutant allelesSequence changeseqchangeCheck if your paper reports new sequence data for any mutation.genenames@wormbase.orgflagged
afp?New SNPsExtract New SNPnewsnpCheck if your paper reports a SNP that does not already exist in WormBase.mt3@sanger.ac.ukflagged
CELL DATA:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
jfp onlythroughoutAnatomynewcellPlease list any C. elegans cell or anatomy part reported in your paper that doesn't exist in WormBase already.raymond@caltech.edu
afpAblation dataAblation dataablationdataCheck if your paper reports data from an assay involving any cell or anatomical unit being ablated by laser or by other means (e.g., by expressing a cell-toxic protein).raymond@its.caltech.eduflagged-done
afpCell functionCell functioncellfuncCheck if your paper reports a function for any anatomical part (e.g., cell, tissue, etc.), which has not been indicated elsewhere on this form.raymond@its.caltech.eduflagged-done
IN SILICO DATA:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
afpPhylogenetic datanew fieldphylogeneticCheck if your paper reports any phylogenetic analysis.
afpOther bioinformatics analysisnew fieldothersilicoCheck if your paper reports any bioinformatic data not indicated anywhere else on this form.
OTHER:
Automation statusPaper SectionData typeFormer form namePGdb nameDescription for authorCurator FlaggedNotes about field
afpSupplemental materialsSupplemental materialsupplementalCheck if your paper has supplemental material.qwang@its.caltech.eduflagged-done
afpNONE of the aforementioned data types are in this research article flaggedCommentnocuratableCheck if none of the above pertains to your paper. Feel free to list the data type most pertinent to your research paper in the "Add information" text area.
afpAny feedback? Please feel free to give us feedback for this form or for any other topic pertinent to how we can better extract data from your paper.new fieldcommentComments from all authors and curators are accessible through the "Comment" button at the bottom of the page.kyook@caltech.edu, vanauken@caltech.edu

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