Texpresso/Author/Curator interim form

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Instructions for curators

With the move to the new paper editor, the instructions on this page are now obsolete. --kjy 18:03, 29 July 2010 (UTC)

Feature Requests


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. Click the "?" to find out more about the data type.

Automation status Paper Section Data type Old fp curation form name PGdb name Description for author Curator Flagged Notes about field
SPECIES:
materials and methods C. elegans default checked. new field celegans Uncheck if you are NOT reporting data for C. elegans.
materials and methods C. elegans other than Bristol new field cnonbristol Check if data for C. elegans natural isolates other than N2 (Bristol) are reported.e.g. Hawaiian, CB4855, CB4852, CB4507, LSJ1, etc.
materials and methods Nematodes other than C. elegans nonntwo nematode Check if data is reported for any species other than C. elegans, e.g., C. briggsae, Pristionchus pacificus, Brugia malayi, etc.
materials and methods Non-nematode species new field nonnematode Check if data is reported for any non-nematode species.
GENE IDENTIFICATION AND MAPPING:
Genes studied in this paper genestudied List any gene for which you report experimental results; do not include genetic markers. Big text box, auto-opened.
in progress Newly cloned gene (flagged-done) Gene Symbol genesymbol Check 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.edu
in progress Newly created allele Extract allele extvariation Check if your paper reports the identification of any allele that doesn't exist in WormBase already.
Genetic mapping data (flagged) mapping data mappingdata Check 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
GENE FUNCTION:
Mutant, RNAi, overexpression, or chemical-based phenotypes: PLEASE SPECIFY DATA TYPE.
DONE Phenotype analysis (flagged-done) Mutant Phenotype newmutant Check if your paper reports phenotype due to mutation or overexpression analysis. remove-emsch@its.caletch.edu, garys@its.caltech.edu, jolenef@its.caltech.edu
DONE Small-scale RNAi (less than 100 experiments reported) (flagged-done) RNAi rnai Check if your paper reports gene knockdown phenotypes for less than 100 individual RNAi experiments. garys@its.caltech.edu
DONE will be part of small scale RNAi pipeline Large-scale RNAi (less than 100 experiments reported) (flagged-done) Large-Scale RNAi lsrnai Check if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments. raymond@its.caltech.edu
DONE through phenotype analysis Overexpression phenotype (flagged) Overexpression overexpr Check 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)..." remove-emsch@its.caletch.edu, garys@its.caltech.edu, jolenef@its.caltech.edu
in progress materials and methods; results Chemicals (flagged) Chemicals chemicals Check 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.
Mosaic analysis (flagged-done) Mosaic analysis mosaic Check 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 siteaction Check if your paper reports anatomy-specific function for a gene. raymond@its.caltech.edu
Time of action new field timeaction Check 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
Molecular function of a gene product(flagged-done) Gene function genefunc Check if your paper discusses a new function for a known or newly defined gene. remove emsch@its.caletch.edu
in progress Homolog of a human disease-associated gene.(flagged) Human Disease humdis Check 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.edu
INTERACTIONS:
Genetic interactions (flagged-done) Gene interactions geneint Check 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. remove emsch@its.caletch.edu
materials and methods (tools); results Functional complementation (flagged) Functional Complementation funccomp Check 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 geneprod Check if your paper reports data on protein-protein, RNA-protein, DNA-protein or Y2H interactions, etc. remove emsch@its.caletch.edu
REGULATION OF GENE EXPRESSION:
some SVM (not great) New expression pattern for a gene (flagged-done) expression pattern data otherexpr Check 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
some SVM (not great) Alterations in gene expression by genetic or other treatment (flagged-done) Gene regulation on expression level genereg Check 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 (flagged) Sequence features seqfeat Check 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 Check 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, remove- emsch@its.caletch.edu
Microarray(flagged-done) Microarray microarray Check if your paper reports any microarray data. wchen@its.caltech.edu
PROTEIN FUNCTION AND STRUCTURE:
Kimberly said to remove this materials and methods; results Protein analysis in vitro(flagged) in vitro Protein analysis invitro Check if your paper reports any in vitro protein analysis such as kinase assays, agonist pharmacological studies, in vitro reconstitution studies, etc.
materials and methods; results Domain analysis new field domanal (populated with information previously in "structureinformation") Check if your paper reports on a function of a particular domain within a protein.
materials and methods; results Covalent modification (flagged) Covalent modification covalent Check if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysis
materials and methods; results Structural information(flagged) Structure information structinfo Check if your paper reports NMR or X-ray crystallographic information. 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.)
Mass spectrometry (flagged-done) Mass Spec massspec Check 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@ebi.ac.uk, worm-bug@sanger.ac.uk 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:
DONE C. elegans antibodies (flagged-done) Extract Antibody antibody Check if your paper reports the use of new or known antibodies created by your lab or someone else's lab; do not check this box if antibodies were commercially bought. wchen@its.caltech.edu
DONE Integrated transgenes (flagged-done) Transgene transgene Check 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" wchen@its.caltech.edu
Transgenes used as tissue markers Marker marker Check 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 (flagged) Sanger Gene Structure Correction and St. Louis Gene Structure Correction structcorr (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.edu

the authors may or may not state explicitly that let's 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.

Sequencing mutant alleles (flagged) Sequence change seqchange Check if your paper reports new sequence data for any mutation. genenames@wormbase.org
New SNPs (flagged) Extract New SNP newsnp Check if your paper reports a SNP that does not already exist in WormBase. dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
CELL DATA:
Ablation data (flagged-done) Ablation data ablationdata Check 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 (flagged-done) Cell function cellfunc Check 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 Check if your paper reports any phylogenetic analysis.
Other bioinformatics analysis new field othersilico Check if your paper reports any bioinformatic data not indicated anywhere else on this form.
OTHER:
Supplemental materials (flagged-done) Supplemental material supplemental Check if your paper has supplemental material. qwang@its.caltech.edu
NONE of the aforementioned data types are in this research article (flagged) Comment nocuratable Check 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.
Any 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 field comment Comments from all authors and curators are accessible through the "Comment" button at the bottom of the page. kyook@caltech.edu, vanauken@caltech.edu

--kjy 17:56, 29 July 2010 (UTC)