Difference between revisions of "Genetics Markup by Textpresso and First Pass"

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[http://www.wormbase.org/wiki/index.php?title=Instructions_for_Genetics&action=edit Note to authors]
 
[http://www.wormbase.org/wiki/index.php?title=Instructions_for_Genetics&action=edit Note to authors]
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[[jfp postgres table details]]
 
----
 
----
  
=Genetics First Pass form postgres table details=
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==Data types used in the first-pass forms==
''"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.''
 
 
 
{|| border="1" cellpadding="2"
 
| align="center" style="background:#f0f0f0;"|'''Actions'''
 
| align="center" style="background:#f0f0f0;"|'''Data type Section'''
 
| align="center" style="background:#f0f0f0;"|'''Data type'''
 
| align="center" style="background:#f0f0f0;"|'''PGdb name'''
 
| align="center" style="background:#f0f0f0;"|'''Instructions for author'''
 
| align="center" style="background:#f0f0f0;"|'''Curator Flagged'''
 
| align="center" style="background:#f0f0f0;"|'''suggested changes'''
 
|-
 
|||SPECIES:
 
|-
 
|||||''C. elegans''  (default checked)||celegans||Please uncheck if you are not reporting data for ''C. elegans''.||
 
|-
 
|||||''C. elegans'' other than Bristol||cnonbristol ||Please indicate if data for ''C. elegans'' isolates other than N2 (Bristol) are presented in this paper.||||change instructions to 'Please indicate if data for ''C. elegans'' isolates other than Bristol are presented in this paper."
 
|-
 
|||||Nematodes other than ''C. elegans''||nematode||Please indicate if data is presented for any species other than ''C. elegans'', e.g., ''C. briggsae'', ''Pristionchus pacificus'', ''Brugia malayi'', etc. ||
 
|-
 
|||||Non-nematode species||nonnematode||Please indicate if data is presented for any non-nematode species.||
 
|-
 
  
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'''''C. elegans''''' (default checked): Postgres character name: '''celegans.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''''C. elegans'' other than Bristol: '''  Data is present for ''C. elegans'' isolates other than Bristol, such as Hawaiian, CB4855, etc. Postgres character name: '''  cnonbristol.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Nematodes other than ''C. elegans'': '''  Data is presented for Caenorhabditis sister species e.g., briggsae, remanei,  and/or related nematodes, parasitic nematodes.Postgres character name: '''  nematode.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Non-nematode species: '''  Data is presented for Human, Mouse, SGD, Dog, Plant, etc. genes/proteins, other.Postgres character name: '''  nonnematode.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter genes studied in this paper: '''  List of gene(s) studied in the paper.Postgres character name: '''  genestudied.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter genes cloned in the paper : '''  List of genes newly identified, named, cloned, reassigned etc.Postgres character name: '''  genesymbol.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter new alleles: '''  Alleles reported in the paper that don't exist in WBPostgres character name: '''  extvariation.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp],  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter new strains: '''  Strains reported in the paper that are or will be made publicly available in the CGC.Postgres character name: '''  newstrains.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Genetic mapping data : '''  Determination of the location of the gene using genetic recombination, e.g., 2-factor recombination, 3-factor interval linkage, Df breakpoints, etc.Postgres character name: '''  mappingdata.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter new balancers: '''  List of balancers reported in paper that don't exist in WB.Postgres character name: '''  newbalancers .'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Phenotype analysis : '''  Indicates the paper reports phenotypes of mutants or phenotypic analysis of strains.Postgres character name: '''  newmutant.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Overexpression phenotype : '''  Indicates the paper reported phenotypes due to the overexpression of transgenes.Postgres character name: '''  overexpr.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Chemicals : '''  Indicates if chemicals or drug treatments were used to analyze strain behavior,  physiology, gene function, etc. of mutant or 'normal' worms.Postgres character name: '''  chemicals.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Small-scale RNAi (less than 100 experiments reported) : '''  Indicates that if gene function was assayed by RNA interference.Postgres character name: '''  rnai.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Large-scale RNAi (more than 100 experiments reported) : '''  Indicates that gene function was assayed by large RNA interference screens.Postgres character name: '''  lsrnai.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Mosaic analysis : '''  Indicates that gene function was assayed in specific cells using lineage analysis.Postgres character name: '''  mosaic.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Tissue or cell site of action : '''  Indicates that gene function was assayed in specific cells or tissues, such as in the case where gene function was rescued by cell/tissue-specific expression of the gene.Postgres character name: '''  siteaction.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Time of action: '''  Indicates that timing of gene function in development was assayed.Postgres character name: '''  timeaction.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Molecular function of a gene product : '''  Indicates that a new/novel molecular function or aspect of mol function for a gene was identified.Postgres character name: '''  genefunc.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Homolog of a human disease-associated gene. : '''  Indicates that a gene studied in the paper is a homolog of a human gene, which is directly associated with a disease.Postgres character name: '''  humdis.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Genetic interactions : '''  Indicates the paper reports results from experiments where genes were assayed for effect on the function of another gene.  Often this is made apparent by the analysis of double, triple, etc. mutants, or with the use of experiments where RNAi was used concurrent with other RNAi-treatment or mutations.Postgres character name: '''  geneint.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Functional complementation : '''  Indicates the paper reports results from experiments functional redundancy between separate genes, e.g., the rescue of gen-A by overexpression of gen-B, or any other extragenic sequence.  Also indicated by the rescue of gene function by a gene from another species.Postgres character name: '''  funccomp.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Gene product interactions : '''  Indicates the paper reports data on protein-protein, RNA-protein, DNA-protein, or Y2H interactions, etc.Postgres character name: '''  geneprod.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''New expression pattern for a gene : '''  Indicates that the 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.Postgres character name: '''  otherexpr.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Alterations in gene expression by genetic or other treatment : '''  Indicates that the paper reports changes or a lack of changes in gene expression levels or patterns in response to genetic, chemical, temperature, or any other experimental treatment.Postgres character name: '''  genereg.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Regulatory sequence features : '''  Indicates that the paper reports any gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression, promoters, introns, UTR's, DNA binding sites, etc.Postgres character name: '''  seqfeat.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Position frequency matrix (PFM) or Position weight matrix (PWM): '''  Indicates that the 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.Postgres character name: '''  matrices.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Microarray: '''  Indicates that the paper reports microarray-derived data.Postgres character name: '''  microarray .'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter new protein: '''  Lists proteins not found in WormBase.Postgres character name: '''  newprotein.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Protein analysis in vitro: '''  Indicates that the paper reports any in vitro protein analysis such as kinase assays, agonist pharmacological studies, reconstitution studies, etc.Postgres character name: '''  invitro.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Domain analysis: '''  Indicates that the paper reports results of experimentation done on a particular domain within a protein to assay the function of that domain.Postgres character name: '''  domanal.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Covalent modification : '''  Indicates that the paper reports on post-translational modifications of a gene product, as assayed by mutagenesis or in vitro analysis.Postgres character name: '''  covalent.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Structural information: '''  Indicates that the paper reports protein structural analysis, through NMR, X-Ray crystallography, etc.Postgres character name: '''  structinfo.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Mass spectrometry : '''  Indicates that the paper reports protein mass analysis through any mass spectrometry analysis (MS/MS, LCMS, HRMS).  Some Mass spec analysis programs include MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix.Postgres character name: '''  massspec.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter C. elegans antibodies : '''  List of antibodies generated in a noncommercial laboratory, against a C. elegans gene product.Postgres character name: '''  antibody.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter integrated transgenes  : '''  List of integrated transgenes used in this paper that doesn't exist in WormBase already, especially if the transgene does not have a canonical name: '''  .Postgres character name: '''  transgene.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Transgenes used as tissue markers: '''  List of reporters (integrated transgenes)  used to mark certain tissues, subcellular structures, or life stages, etc. as a reference to assay site of action of gene function or location.Postgres character name: '''  marker.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Gene structure correction : '''  Indicates that the paper reports a gene structure that is different from the one in WormBase, e.g., different splice-site, SL1 instead of SL2, etc.Postgres character name: '''  structcorr (this use to be two different fields).'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Sequencing mutant alleles : '''  Indicates that the paper reports sequence data for any mutation.Postgres character name: '''  seqchange.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''New SNPs : '''  List of SNPs reported in the paper that don't exist in WormBase already.Postgres character name: '''  newsnp.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Enter new cell/anatomy term: '''  List of C. elegans cells or anatomy parts reported in the paper that doesn't exist in WormBase already. Currently unknown if cells or anatomy parts of other nematodes will be collected here.Postgres character name: '''  newcell'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Ablation data : '''  Indicates that the 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).Postgres character name: '''  ablationdata.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Cell function : '''  Indicates that the paper reports a function for any anatomical part (e.g., cell, tissue, etc.), which has not been indicated elsewhere on this form.Postgres character name: '''  cellfunc.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Phylogenetic data: '''  Indicates that the paper dicusses evolutionary relationships between or among genes or gene products.Postgres character name: '''  phylogenetic.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Other bioinformatics analysis: '''  Indicates that the paper reports other bioinformatic data not indicated anywhere else on this form.  In general, this may include alignments.Postgres character name: '''  othersilico.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''Supplemental materials : '''  In the Author First-Pass form, checking this box indicates that supplementary material is attached to the paper.  In the curator first-pass checking the box indicates that the Supplementary Materials are missing.Postgres character name: '''  supplemental.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
 +
'''NONE of the aforementioned data types are in this research article:'''This is used as a default category for any paper where the author checked "here" for review or non primary research paper.Postgres character name: '''nocuratable.''' Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
  
|||GENE IDENTIFICATION AND MAPPING:
+
'''Enter authors: '''  List of authors for updating the paper details and author paper connections.Postgres character name: '''  authors.'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
|-
 
  
|||||Enter genes studied in this paper||genestudied||Please list any gene that is a focus of analysis in your paper.
+
'''Feedback: '''  This is used to record thoughts, notes, comments about the form etc.Postgres character name: '''   comment .'''  Postgres table:  [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/first_pass.cgi?action=Curate&paper=00000003&passwd=1228446342.8668923 afp], [http://tazendra.caltech.edu/~Postgres/cgi-bin/curator_first_pass.cgi cfp], [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.1418967 jfp]. <br>
||
 
|-
 
|Needs to be fed to textpresso.||||Enter genes cloned in the paper ||genesymbol ||Please list any gene in your paper that doesn't exist in WormBase already.||genenames@wormbase.org, vanauken@its.caltech.edu
 
|-
 
|Needs to be fed to textpresso, need to add curator contacts||||Enter new alleles||extvariation||Please list any allele in your paper that doesn't exist in WormBase already.||eventually jolene or geneames currently
 
|-
 
|Needs to be fed to textpresso.||||'''Enter any strains that you will be depositing into the CGC'''||newstrains||'''Please omit those strains that you will not be making publically available.'''||perhaps genename
 
|-
 
|||||Genetic mapping data [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=mappingdata (flagged)]||mappingdata||Please indicate 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.org
 
|-
 
|Needs to be fed to textpresso.||||Enter new balancers||newbalancers||Please list any balancer in your paper that doesn't exist in WormBase already.|| genenames@wormbase.org
 
|-
 
|||GENE FUNCTION:
 
|-
 
|||Mutant, overexpression, or chemical-based phenotypes||>keep sub data fields unhidden<
 
|-
 
|||||Phenotype analysis [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=newmutant (flagged-done)]||newmutant ||Please indicate if your paper reports any nonRNAi-based phenotype for a mutant. ||emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu
 
|-
 
|||||Overexpression phenotype [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=overexpression (flagged)]||overexpr||Please indicate 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)..." ||emsch@its.caltech.edu, garys@its.caltech.edu
 
|-
 
|||||Chemicals [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=chemicals (flagged)]||chemicals ||Please indicate if the effects of small molecules, chemicals, or drugs were studied on worms. E.g., paraquat, butanone, benzaldehyde, aldicarb, etc. The use of mutagens for the generation of mutants in genetic screens do not need to be indicated.|||
 
|-
 
|||New subheader section ->RNAi experimental details||>keep sub data fields unhidden<||||->If your paper reports RNAi experiments and the details for the probes used are not listed in supplemental materials, please enter the sequences or source of sequences used for these experiments so we can map these experiments in relation to the genome. You can enter this information in the form of standard primer pair names (e.g., sjj_ZK617.1, cenix:155-g4, mv_CAA3346 or the library used), genomic coordinates of the primers (e.g. IV:11970667..12012891, ZK1067:13703..22295, MtDNA:4504..5613), or cDNA/EST/OST clone names (e.g. AF071375, yk275g9, OSTR215B4_1). Otherwise, please give us the sequences of the primers or the exact sequence of the entire RNAi probe.
 
|-
 
|||||Small-scale RNAi (less than 100 experiments reported) [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=rnai (flagged-done)]|| rnai||Please tell us the sequences or source of sequences used for RNAi experiments so we can map these experiments in relation to the genome.  ||garys@its.caltech.edu
 
|-
 
|||||Large-scale RNAi (more than 100 experiments reported) [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=lsrnai (flagged-done)]||lsrnai||Please indicate if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments.||raymond@its.caltech.edu
 
|-
 
|||||Mosaic analysis [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=mosaic (flagged-done)]||mosaic ||->Please indicate 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.edu
 
|-
 
|||||Tissue or cell site of action [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=site (flagged-done)]||siteaction ||Please indicate if your paper reports anatomy-specific function for a gene.||raymond@its.caltech.edu
 
|-
 
|||||Time of action||timeaction||Please indicate if your paper reports a temporal requirement for gene function.||raymond@its.caltech.edu
 
|-
 
|||||Molecular function of a gene product [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=genefunction (flagged-done)]||genefunc||Please indicate if your paper discusses a new function for a known or newly defined gene.||emsch@its.caltech.edu
 
|-
 
|||||Homolog of a human disease-associated gene. [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=humandiseases (flagged)]||humdis ||Please indicate if any gene reported in your paper is a homolog/ortholog of a human disease-related gene or if your study models some aspect of a human disease.||ranjana@its.caltech.edu
 
|-
 
|||INTERACTIONS:
 
|-
 
|||||Genetic interactions [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneinteractions (flagged-done)]||geneint||Please indicate 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 used concurrent with other RNAi-treatments or mutations.||emsch@its.caltech.edu
 
|-
 
|||||Functional complementation [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=functionalcomplementation (flagged)]||funccomp||Please indicate 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.''||
 
|-
 
|||||Gene product interactions [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=geneproduct (flagged-done)]||geneprod||Please indicate if your paper reports data on protein-protein, RNA-protein, DNA-protein, or Y2H interactions, etc.|| emsch@its.caltech.edu
 
|-
 
|||REGULATION OF GENE EXPRESSION:
 
|-
 
|||||New expression pattern for a gene [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=expression (flagged-done)]||otherexpr ||Please indicate 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.edu
 
|-
 
|||||Alterations in gene expression by genetic or other treatment [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=generegulation (flagged-done)]|| genereg ||Please indicate 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.edu
 
|-
 
|||||Regulatory sequence features [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencefeatures (flagged)]
 
||seqfeat ||Please indicate if your paper reports any gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression, promoters, introns, UTR's, DNA binding sites, etc.||xdwang@its.caltech.edu, worm-bug@sanger.ac.uk, stlouis@wormbase.org
 
|-
 
|||||Position frequency matrix (PFM) or Position weight matrix (PWM)||matrices||Please indicate 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, emsch@its.caltech.edu
 
|-
 
|||||Microarray[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=microarray (flagged-done)]||microarray ||Please indicate if your paper reports any microarray data.||wchen@its.caltech.edu
 
|-
 
|||PROTEIN FUNCTION AND STRUCTURE:
 
|-
 
|'''*SILENCE THIS DATA TYPE*''' ||||Enter new protein||newprotein||Please list any protein that doesn't exist in WormBase already.||
 
|-
 
|||||Protein analysis ''in vitro''[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=invitro (flagged)]||invitro ||Please indicate if your paper reports any ''in vitro'' protein analysis such as kinase assays, agonist pharmacological studies, reconstitution studies, etc.||
 
|-
 
|||||Domain analysis||domanal ||Please indicate if your paper reports on a function of a particular domain within a protein.||
 
|-
 
|||||Covalent modification [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=covalent (flagged)]||covalent|| Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or ''in vitro'' analysis||
 
|-
 
|||||Structural information[http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structureinformation (flagged)]||structinfo||Please indicate if your paper reports NMR or X-ray crystallographic information.||
 
|-
 
|||||Mass spectrometry [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=massspec (flagged-done)]||massspec||Please indicate if your paper reports data from any mass spec analysis e.g., LCMS, HRMS, etc. Keywords: mass spectrometry, peptide, (and any one of the following:) MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix||gw3@sanger.ac.uk, worm-bug@sanger.ac.uk 
 
|-
 
|||REAGENTS:||
 
|-
 
|||||Enter ''C. elegans'' antibodies [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=antibody (flagged-done)]|| antibody ||Please list any new or known antibody created by your lab or another researcher's lab, that is used in this paper; do not check this box if antibodies were commercially bought.''||wchen@its.caltech.edu
 
|-
 
|Needs to be fed to Textpresso.||||Enter integrated transgenes [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=transgene (flagged-done)] ||transgene||->'''Please list any integrated transgene used in this paper that doesn't exist in WormBase already, especially if the transgene does not have a canonical name.''' ||wchen@its.caltech.edu
 
|-
 
|||||Transgenes used as tissue markers||marker||Please indicate 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.edu
 
|-
 
|||GENOME SEQUENCE DATA:
 
|-
 
|||||Gene structure correction [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=structurecorrectionsanger (flagged)]|| structcorr (this use to be two different fields)||Please indicate 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.edu
 
|-
 
|||||Sequencing mutant alleles [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=sequencechange (flagged)]||seqchange ||Please indicate if your paper reports new sequence data for any mutation.||genenames@wormbase.org
 
|-
 
|Needs to be fed to textpresso.||||New SNPs [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=newsnp (flagged)]||newsnp||Please list any SNP reported in your paper that doesn't exist in WormBase already.||dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
 
|-
 
|||CELL DATA:
 
|-
 
|Needs to be fed to textpresso and Raymond||||Enter new cell/anatomy term||newcell||Please list any C. elegans cell or anatomy part reported in your paper that doesn't exist in WormBase already.||
 
|-
 
|||||Ablation data [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=ablationdata (flagged-done)]||ablationdata ||Please indicate 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.edu
 
|-
 
|||||Cell function [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=cellfunction (flagged-done)]||cellfunc||Please indicate 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.edu
 
|-
 
|||IN SILICO DATA:
 
|-
 
||||||Phylogenetic data||phylogenetic||Please indicate if your paper reports any phylogenetic analysis.||
 
|-
 
||||||Other bioinformatics analysis||othersilico||Please indicate if your paper reports any bioinformatic data not indicated anywhere else on this form.||
 
|-
 
|||OTHER:
 
|-
 
|||||Supplemental materials [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fc&field=supplemental (flagged-done)]||supplemental||Please attach supplemental material.||qwang@its.caltech.edu
 
|-
 
|||||NONE of the aforementioned data types are in this research article [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=fnc&field=comment (flagged)]||nocuratable||Please indicate 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.||
 
|-
 
|Needs to go to Cecilia and Textpresso||||Enter authors||authors||Please list the e-mail address of any author on your paper that needs to be added to the WormBase database. These authors will receive a separate request from us for more information.||
 
|-
 
|||||Feedback||comment||Please give us feedback on this form or on any topic pertinent to how we can better extract data from your paper. ||kyook@caltech.edu, vanauken@caltech.edu
 
|}
 

Revision as of 15:16, 2 July 2009

[back]


Instructions for Genetics

Sample GENETICS Firstpass form

Note to GENETICS

Note to authors

jfp postgres table details


Data types used in the first-pass forms

C. elegans (default checked): Postgres character name: celegans. Postgres table: afp, cfp, jfp.
C. elegans other than Bristol: Data is present for C. elegans isolates other than Bristol, such as Hawaiian, CB4855, etc. Postgres character name: cnonbristol. Postgres table: afp, cfp, jfp.
Nematodes other than C. elegans: Data is presented for Caenorhabditis sister species e.g., briggsae, remanei, and/or related nematodes, parasitic nematodes.Postgres character name: nematode. Postgres table: afp, cfp, jfp.
Non-nematode species: Data is presented for Human, Mouse, SGD, Dog, Plant, etc. genes/proteins, other.Postgres character name: nonnematode. Postgres table: afp, cfp, jfp.
Enter genes studied in this paper: List of gene(s) studied in the paper.Postgres character name: genestudied. Postgres table: jfp.
Enter genes cloned in the paper : List of genes newly identified, named, cloned, reassigned etc.Postgres character name: genesymbol. Postgres table: afp, cfp, jfp.
Enter new alleles: Alleles reported in the paper that don't exist in WBPostgres character name: extvariation. Postgres table: afp, cfp, jfp.
Enter new strains: Strains reported in the paper that are or will be made publicly available in the CGC.Postgres character name: newstrains. Postgres table: jfp.
Genetic mapping data : Determination of the location of the gene using genetic recombination, e.g., 2-factor recombination, 3-factor interval linkage, Df breakpoints, etc.Postgres character name: mappingdata. Postgres table: afp, cfp, jfp.
Enter new balancers: List of balancers reported in paper that don't exist in WB.Postgres character name: newbalancers . Postgres table: jfp.
Phenotype analysis : Indicates the paper reports phenotypes of mutants or phenotypic analysis of strains.Postgres character name: newmutant. Postgres table: afp, cfp, jfp.
Overexpression phenotype : Indicates the paper reported phenotypes due to the overexpression of transgenes.Postgres character name: overexpr. Postgres table: afp, cfp, jfp.
Chemicals : Indicates if chemicals or drug treatments were used to analyze strain behavior, physiology, gene function, etc. of mutant or 'normal' worms.Postgres character name: chemicals. Postgres table: afp, cfp, jfp.
Small-scale RNAi (less than 100 experiments reported) : Indicates that if gene function was assayed by RNA interference.Postgres character name: rnai. Postgres table: afp, cfp, jfp.
Large-scale RNAi (more than 100 experiments reported) : Indicates that gene function was assayed by large RNA interference screens.Postgres character name: lsrnai. Postgres table: afp, cfp, jfp.
Mosaic analysis : Indicates that gene function was assayed in specific cells using lineage analysis.Postgres character name: mosaic. Postgres table: afp, cfp, jfp.
Tissue or cell site of action : Indicates that gene function was assayed in specific cells or tissues, such as in the case where gene function was rescued by cell/tissue-specific expression of the gene.Postgres character name: siteaction. Postgres table: afp, cfp, jfp.
Time of action: Indicates that timing of gene function in development was assayed.Postgres character name: timeaction. Postgres table: afp, cfp, jfp.
Molecular function of a gene product : Indicates that a new/novel molecular function or aspect of mol function for a gene was identified.Postgres character name: genefunc. Postgres table: afp, cfp, jfp.
Homolog of a human disease-associated gene. : Indicates that a gene studied in the paper is a homolog of a human gene, which is directly associated with a disease.Postgres character name: humdis. Postgres table: afp, cfp, jfp.
Genetic interactions : Indicates the paper reports results from experiments where genes were assayed for effect on the function of another gene. Often this is made apparent by the analysis of double, triple, etc. mutants, or with the use of experiments where RNAi was used concurrent with other RNAi-treatment or mutations.Postgres character name: geneint. Postgres table: afp, cfp, jfp.
Functional complementation : Indicates the paper reports results from experiments functional redundancy between separate genes, e.g., the rescue of gen-A by overexpression of gen-B, or any other extragenic sequence. Also indicated by the rescue of gene function by a gene from another species.Postgres character name: funccomp. Postgres table: afp, cfp, jfp.
Gene product interactions : Indicates the paper reports data on protein-protein, RNA-protein, DNA-protein, or Y2H interactions, etc.Postgres character name: geneprod. Postgres table: afp, cfp, jfp.
New expression pattern for a gene : Indicates that the 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.Postgres character name: otherexpr. Postgres table: afp, cfp, jfp.
Alterations in gene expression by genetic or other treatment : Indicates that the paper reports changes or a lack of changes in gene expression levels or patterns in response to genetic, chemical, temperature, or any other experimental treatment.Postgres character name: genereg. Postgres table: afp, cfp, jfp.
Regulatory sequence features : Indicates that the paper reports any gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression, promoters, introns, UTR's, DNA binding sites, etc.Postgres character name: seqfeat. Postgres table: afp, cfp, jfp.
Position frequency matrix (PFM) or Position weight matrix (PWM): Indicates that the 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.Postgres character name: matrices. Postgres table: afp, cfp, jfp.
Microarray: Indicates that the paper reports microarray-derived data.Postgres character name: microarray . Postgres table: afp, cfp, jfp.
Enter new protein: Lists proteins not found in WormBase.Postgres character name: newprotein. Postgres table: jfp.
Protein analysis in vitro: Indicates that the paper reports any in vitro protein analysis such as kinase assays, agonist pharmacological studies, reconstitution studies, etc.Postgres character name: invitro. Postgres table: afp, cfp, jfp.
Domain analysis: Indicates that the paper reports results of experimentation done on a particular domain within a protein to assay the function of that domain.Postgres character name: domanal. Postgres table: afp, cfp, jfp.
Covalent modification : Indicates that the paper reports on post-translational modifications of a gene product, as assayed by mutagenesis or in vitro analysis.Postgres character name: covalent. Postgres table: afp, cfp, jfp.
Structural information: Indicates that the paper reports protein structural analysis, through NMR, X-Ray crystallography, etc.Postgres character name: structinfo. Postgres table: afp, cfp, jfp.
Mass spectrometry : Indicates that the paper reports protein mass analysis through any mass spectrometry analysis (MS/MS, LCMS, HRMS). Some Mass spec analysis programs include MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix.Postgres character name: massspec. Postgres table: afp, cfp, jfp.
Enter C. elegans antibodies : List of antibodies generated in a noncommercial laboratory, against a C. elegans gene product.Postgres character name: antibody. Postgres table: afp, cfp, jfp.
Enter integrated transgenes : List of integrated transgenes used in this paper that doesn't exist in WormBase already, especially if the transgene does not have a canonical name: .Postgres character name: transgene. Postgres table: jfp.
Transgenes used as tissue markers: List of reporters (integrated transgenes) used to mark certain tissues, subcellular structures, or life stages, etc. as a reference to assay site of action of gene function or location.Postgres character name: marker. Postgres table: afp, cfp, jfp.
Gene structure correction : Indicates that the paper reports a gene structure that is different from the one in WormBase, e.g., different splice-site, SL1 instead of SL2, etc.Postgres character name: structcorr (this use to be two different fields). Postgres table: afp, cfp, jfp.
Sequencing mutant alleles : Indicates that the paper reports sequence data for any mutation.Postgres character name: seqchange. Postgres table: afp, cfp, jfp.
New SNPs : List of SNPs reported in the paper that don't exist in WormBase already.Postgres character name: newsnp. Postgres table: afp, cfp, jfp.
Enter new cell/anatomy term: List of C. elegans cells or anatomy parts reported in the paper that doesn't exist in WormBase already. Currently unknown if cells or anatomy parts of other nematodes will be collected here.Postgres character name: newcell Postgres table: afp, cfp, jfp.
Ablation data : Indicates that the 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).Postgres character name: ablationdata. Postgres table: afp, cfp, jfp.
Cell function : Indicates that the paper reports a function for any anatomical part (e.g., cell, tissue, etc.), which has not been indicated elsewhere on this form.Postgres character name: cellfunc. Postgres table: afp, cfp, jfp.
Phylogenetic data: Indicates that the paper dicusses evolutionary relationships between or among genes or gene products.Postgres character name: phylogenetic. Postgres table: afp, cfp, jfp.
Other bioinformatics analysis: Indicates that the paper reports other bioinformatic data not indicated anywhere else on this form. In general, this may include alignments.Postgres character name: othersilico. Postgres table: afp, cfp, jfp.
Supplemental materials : In the Author First-Pass form, checking this box indicates that supplementary material is attached to the paper. In the curator first-pass checking the box indicates that the Supplementary Materials are missing.Postgres character name: supplemental. Postgres table: afp, cfp, jfp.
NONE of the aforementioned data types are in this research article:This is used as a default category for any paper where the author checked "here" for review or non primary research paper.Postgres character name: nocuratable. Postgres table: afp, cfp, jfp.

Enter authors: List of authors for updating the paper details and author paper connections.Postgres character name: authors. Postgres table: afp, cfp, jfp.

Feedback: This is used to record thoughts, notes, comments about the form etc.Postgres character name: comment . Postgres table: afp, cfp, jfp.