Genetics Markup by Textpresso and First Pass

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Instructions for Genetics

A note to authors

Congratulations on your paper being accepted by GENETICS for publication!

Now that your paper has been accepted, you have an opportunity to see your data incorporated into WormBase on a much faster time scale than data published in other journals. GENETICS has agreed to help you get your data into our database faster, by requesting that you fill out the following form before your paper hits the press, rather than us waiting for your paper to appear in Pubmed, which can take weeks to months. In addition, by giving us just a bit more detailed information than we would ask of authors of papers from other journals, we can help your paper become a more comprehensive resource portal to worm biology.

To fill out the form, either indicate by a check of the box if a specific data type exists in the body of your paper or list specific details that you use as part of your experiments. In the latter case, when we ask for specific details, these will be objects that you have created or used during the course of your research, such as alleles, RNAi probes, antibodies, integrated transgenes, etc., which do not exist in WormBase already. Please enter the objects into the space provided. If you would rather upload a file, please contact kyook@caltech.edu.

Thank you for your cooperation. We expect you to benefit greatly from participating in our data extraction and markup partnership with GENETICS, Textpresso and WormBase.


Best Wishes,

WormBase
http://wwww.wormbase.org
wormbase-help@wormbase.org

Please click the box next to the type of data found in the body of your publication.

If this is not a primary research article, please click here. You may ignore the fields below. Thank you. Click the "?" to find out more about the data type.



Genetics First Pass 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.

Actions Data type Section Data type PGdb name Instructions for author Curator Flagged
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.
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.
GENE IDENTIFICATION AND MAPPING:
Enter genes studied in this paper genestudied Please list any gene that is a focus of analysis in your paper.
Needs to be fed to textpresso. Genes studied in this paper ->Enter genes cloned in the paper (flagged-done) 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.
Needs to be fed to textpresso. Enter new strains NEW FIELD Please list any strain in your paper that doesn't exist in WormBase already.
Genetic mapping data (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 NEW FIELD 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 (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 (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 (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.
Need more specific data here. Small-scale RNAi (less than 100 experiments reported) (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) (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 (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 (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 (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. (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 (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 (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 (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 (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 (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 (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(flagged-done) microarray Please indicate if your paper reports any microarray data. wchen@its.caltech.edu
PROTEIN FUNCTION AND STRUCTURE:
Needs to be fed to textpresso. Enter new protein NEW FIELD Please list any protein that doesn't exist in WormBase already.
Protein analysis in vitro(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 (flagged) covalent Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysis
Structural information(flagged) structinfo Please indicate if your paper reports NMR or X-ray crystallographic information.
Mass spectrometry (flagged-done) 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
REAGENTS:
Enter C. elegans antibodies (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 (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 (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 (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 (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 NEW FIELD (was on the ancient curator first pass form) Please list any C. elegans cell or anatomy part reported in your paper that doesn't exist in WormBase already.
Ablation data (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 (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 (flagged-done) supplemental Please attach supplemental material. qwang@its.caltech.edu
NONE of the aforementioned data types are in this research article (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 NEW FIELD 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