Project page for author first pass form

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Instructions

[Sample Author Firstpass form]

Instructions for authors

Congratulations on the publication of your paper!
"title" journal, date
Please click the box next to the type of data your publication includes.
If this is not a primary research article (e.g., this is a review, book chapter, etc.), please click here.

If your paper contains experiments on C. elegans and related nematodes, please continue with the form below.
Click the "?" to find out more about the data type.

Author First-pass form postgres table details

Species	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:
nematode		Genes studied in this paper	genestudied	Please use text box below to list any genes that were a focus of analysis in this research article.
nematode		Newly cloned gene	genesymbol	Please indicate if your paper reports a new symbol for a known locus or the name of a newly defined locus, if it doesn't exist in WormBase already.	genenames@wormbase.org, vanauken@its.caltech.edu
elegans		Genetic mapping data	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
	GENE FUNCTION:
		Mutant, overexpression, or chemical-based phenotypes
nematode?		Phenotype analysis	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
elegans		Overexpression phenotype	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
nematode		Chemicals	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.
elegans		Small-scale RNAi (less than 100 experiments reported)	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
elegans		Large-scale RNAi (more than 100 experiments reported)	lsrnai	Please indicate if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments.	raymond@its.caltech.edu
elegans		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
elegans		Tissue or cell site of action	siteaction	Please indicate if your paper reports anatomy-specific function for a gene.	raymond@its.caltech.edu
elegans		Time of action	timeaction	Please indicate if your paper reports a temporal requirement for gene function.	raymond@its.caltech.edu
elegans		Molecular function of a gene product	genefunc	Please indicate if your paper discusses a new function for a known or newly defined gene.	emsch@its.caltech.edu
elegans		Homolog of a human disease-associated gene.	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:
elegans		Genetic interactions	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
any gene expressed in elegans or elegans gene in anything else?		Functional complementation	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.
elegans		Gene product interactions	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:
elegans		New expression pattern for a C. elegans gene	otherexpr	Please indicate if your paper reports new temporal or spatial (e.g., tissue, subcellular, etc.) data on the pattern of expression of any C. elegans 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
elegans		Alterations in C. elegans gene expression by genetic or other treatment	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
elegans		Regulatory sequence features	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
elegans		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
elegans		Microarray	microarray	Please indicate if your paper reports any microarray data.	wchen@its.caltech.edu
	PROTEIN FUNCTION AND STRUCTURE:
elegans		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.
elegans		Domain analysis	domanal	Please indicate if your paper reports on a function of a particular domain within a protein.
elegans		Covalent modification (flagged)	covalent	Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysis
elegans		Structural information(flagged)	structinfo	Please indicate if your paper reports NMR or X-ray crystallographic information.
elegans		Mass spectrometry (flagged-done)	massspec	Please indicate if your paper reports data from any mass spec analysis e.g., LCMS, COSY, HRMS, etc.	gw3@ebi.ac.uk, worm-bug@sanger.ac.uk
	REAGENTS:
elegans		C. elegans antibodies	antibody	Please list any new or known C. elegans 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
elegans		Integrated transgenes expressed in C.elegans	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
elegans		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:
nematode?		Gene structure correction	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
nematode?	Sequencing mutant alleles	seqchange	Please indicate if your paper reports new sequence data for any mutation.	genenames@wormbase.org
nematode?		New SNPs	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:
elegans		Ablation data	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
elegans		Cell function	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:
elegans		Phylogenetic data	phylogenetic	Please indicate if your paper reports any phylogenetic analysis.
elegans		Other bioinformatics analysis	othersilico	Please indicate if your paper reports any bioinformatic data not indicated anywhere else on this form.
	OTHER:
nematode		Supplemental materials	supplemental	Please attach supplemental material.	qwang@its.caltech.edu
nematode		NONE of the aforementioned data types are in this research article	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.
all		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