Difference between revisions of "Datatypes flagged"
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[http://www.wormbase.org/wiki/index.php/First-pass_schedule%2C_instructions%2C_automation First-pass schedule and instructions] | [http://www.wormbase.org/wiki/index.php/First-pass_schedule%2C_instructions%2C_automation First-pass schedule and instructions] | ||
− | + | [http://www.wormbase.org/wiki/index.php/Author_first-pass_form] | |
+ | [http://www.wormbase.org/wiki/index.php/Genetics_Author_pass_form] | ||
'''''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''''' (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> |
Revision as of 15:29, 2 July 2009
First-pass schedule and instructions [1] [2]
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 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: action=Curate&paper=00000001&passwd=1241223658.1418967 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: 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 discusses 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: jfp.
Feedback: This is used to record thoughts, notes, comments about the form etc. Postgres character name: comment . Postgres table: afp, cfp, jfp.