Texpresso/Author/Curator interim form
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New First Pass Curator 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.
Left overs:Automation status | Data type Section | Data type | Old curation form name | PGdb name | Description for author | Curator Flagged |
GENE IDENTIFICATION AND MAPPING: | ||||||
C. elegans | new field | celegans | Please indicate if C. elegans isolates other than Bristol are discussed in this paper | |||
Nematodes other than C. elegans | new field | nematodes | Please indicate if data is presented for any species other than C. elegans, e.g., C. briggsae, Pristionchus pacificus, Brugia malayi, etc. | |||
Genes studied in this paper | new field | rgngene | Please use text box below to list any genes that are a focus of analysis in this research article. | This information actually is the same info that a curator would enter through the WBpaper editor page, so it should get tied to that pipeline somehow. Also the text box for this data field should be auto-opened. | ||
Newly cloned gene (flagged-done) | Gene Symbol | genesymbol | Please indicate if your paper presents a new symbol for a known locus or the name of a newly defined locus. | genenames@wormbase.org, vanauken@its.caltech.edu | ||
in progress | Newly created allele | Extract allele | extractedvariation | Please indicate if your paper reports the identification of any new alleles. | ||
Genetic mapping data (flagged) | mapping data | mappingdata | Please indicated if your paper contains 3-factor interval mapping data, i.e., genetic data only, including with Df or Dp data but no SNP interval mapping. | genenames@wormbase.org | ||
GENE FUNCTION: | ||||||
Gene function (flagged-done) | Gene function | genefunction | Please indicate if your paper discusses a new function for a known gene or a newly defined gene. | emsch@its.caltech.edu | ||
in progress | Homolog of a human disease-associated gene (flagged) | Human Disease | humandiseases | Please indicate if genes discussed in your paper are a homolog/ortholog of a human disease gene. | ranjana@its.caltech.edu | |
Phenotype Analysis based on: | ||||||
Allele analysis (flagged-done) | Mutant Phenotype | newmutant | Please indicate if any phenotype is reported for a mutant variation. | emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu | ||
in progress | Small-scale RNAi (less than 100 experiments reported) (flagged-done) | RNAi | rnai | Please indicate if your paper reports gene knockdown phenotypes for less than 100 individual RNAi experiments. | garys@its.caltech.edu | |
Large-scale RNAi (less than 100 experiments reported) (flagged-done) | Large-Scale RNAi | lsrnai | Please indicate if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments. | raymond@its.caltech.edu | ||
Overexpression (flagged) | Overexpression | overexpression | Please indicated 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 | ||
in progress | Chemicals (flagged) | Chemicals | chemicals | Please indicate 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. | ||
INTERACTIONS: | ||||||
Genetic interactions (flagged-done) | Gene interactions | geneinteractions | Please indicate if your paper reports the analysis of more than one gene at a time, e.g. double, triple, etc. mutants, including experiments that included RNAi concurrent with other RNAi-treated worms or mutants | emsch@its.caltech.edu | ||
Functional complementation (flagged) | Functional Complementation | functionalcomplementation | 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 (flagged-done) | Gene product interaction | geneproduct | Please indicate if your paper reports protein-protein, RNA-protein, DNA-protein interactions, including Y2H, etc. | emsch@its.caltech.edu | ||
GENE EXPRESSION AND FUNCTION: | ||||||
New expression pattern for a gene (flagged-done) | expression pattern data | otherexpression | 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 | ||
Tools used for obtaining an expression pattern for a new gene: | ||||||
in progress | C. elegans antibodies (flagged-done) | Extract Antibody | antibodies | Please indicate if your paper reports the use of new or used antibodies created by your lab or someone else's lab; do not check this box if antibodies used were commercially bought. | wchen@its.caltech.edu | |
DONE | Integrated transgenes (flagged-done) | Transgene | transgene | Please indicate if integrated transgenes are used in this paper. If the transgene does not have a canonical name, please list it in the "Add Information text area" | wchen@its.caltech.edu | |
Cell or tissue reporters | Marker | marker | Please indicate if reporters (integrated transgenes or antibodies) 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 | ||
Regulation of gene expression patterns: | ||||||
in progress | Alterations in gene expression by genetic background or other treatment (flagged-done) | Gene regulation on expression level | generegulation | Please indicate if your paper reports changes or lack of changes in gene expression levels or patterns due to genetic background, exposure to chemicals or temperature or any other experimental treatment. | xdwang@its.caltech.edu | |
Regulatory sequence features (flagged) | Sequence features | sequencefeatures | 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) | new field | matrices | Please indicate if your paper reports PFMs or PWMs that 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 | ||
Mosaic analysis (flagged-done) | Mosaic analysis | 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 (flagged-done) | Site of action | site | Please indicate if your paper reports anatomy(tissue/cell)-specific expression function for a gene. | raymond@its.caltech.edu | ||
Developmental time of action | new field | timeofaction | Please indicate if your paper reports a temporal requirement for gene function. | raymond@its.caltech.edu | ||
Microarray(flagged-done) | Microarray | microarray | Please indicate if your paper reports any microarray data. | wchen@its.caltech.edu | ||
PROTEIN FUNCTION AND STRUCTURE: | ||||||
Protein analysis in vitro(flagged) | in vitro Protein analysis | invitro | Please indicate if your paper reports any in vitro protein analysis including such things as kinase assays, agonist pharmacological studies, in vitro reconstitution studies, etc. | |||
Domain analysis | new field | domainanalysis note, should be populated with information previously in "structureinformation" | Please indicate if your paper reports on a function of a particular domain within a protein. | |||
Covalent modification (flagged) | Covalent modification | covalent | Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysis | |||
Structural information(flagged) | Structure information | structureinformation | Please indicate if your paper reports NMR or X-ray crystallographic information. | |||
Mass spectrometry (flagged-done) | Mass Spec | massspec | Please indicate if your paper reports data from any mass spec analysis e.g., LCMS, COSY, HRMS, etc. | gw3@sanger.ac.uk, worm-bug@sanger.ac.uk | ||
GENOME SEQUENCE DATA: | ||||||
Gene structure correction (flagged) | Sanger Gene Structure Correction and St. Louis Gene Structure Correction | structurecorrectionsanger (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 | ||
Sequencing mutant alleles (flagged) | Sequence change | sequencechange | Please indicate if your paper reports new sequence data for any mutation. | genenames@wormbase.org | ||
New SNPs (flagged) | Extract New SNP | newsnp | Please indicate if your paper reports a new SNP, i.e. it does not already exist in WormBase. | dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu | ||
retired? | ? | Extract SNP verified by St. Louis (flagged) | Extract SNP verified by St.Louis | "fig.2: two SNPs mentioned"; any SNP mentioned; "For nekl-1, cDNA clones indicated that the predicted gene annotation was incorrect." | dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu | |
CELL DATA: | ||||||
Ablation data (flagged-done) | Ablation data | ablationdata | Please indicate if your paper reports any 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 (flagged-done) | Cell function | cellfunction | 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 | new field | phylogenetic | Please indicate if your paper reports any phylogenetic analysis. | |||
Other bioinformatics analysis | new field | othersilico | Please indicate if your paper reports any bioinformatic data not indicated anywhere else on this form. | |||
OTHER: | ||||||
Supplemental materials (flagged-done) | Supplemental material | supplemental | Please indicate if your paper has supplemental material. | qwang@its.caltech.edu | ||
NONE of the aforementioned data types are in this research article | Comment | 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. | |||
Comment (flagged) | new field | comment | Please feel free to give us feedback on this form or on any other topic pertinent to how we can better extract data from your paper. | this should go to someone | ||
? | Non-N2_phenotype | ?nematodes? | used to be for gathering information on phenotypes of non-C. elegans nematodes |