Jfp postgres table details

Work Flow

Acceptance to first-pass

Genetics First Pass form postgres table details

"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.

Textpresso Markup object	Data type Section	Data type	PGdb name	Instructions for author	Curator Flagged on author first-pass form	Actions for jfp (journal first-pass form)
	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.	Currently done through textpresso scan of abstract
Gene		Enter genes cloned in the paper	genesymbol	Please list any gene in your paper that doesn't exist in WormBase already.	genenames@wormbase.org, vanauken@its.caltech.edu	Send to genenames@wormbase.org
Variation		Enter new alleles	extvariation	Please list any allele in your paper that doesn't exist in WormBase already.	genenames@wormbase.org	Send to kyook@wormbase.org
Strain		Enter new strains	newstrains	Please enter strains that do not exist in WormBase already.	N/A	Send to genenames@wormbase.org
		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
Rearrangement		Enter new balancers	newbalancers	Please list any balancer in your paper that doesn't exist in WormBase already.	N/A	Send to genenames@wormbase.org
	GENE FUNCTION:
	Mutant, overexpression, or chemical-based phenotypes	>keep sub data fields unhidden<
		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	Send to kyook@wormbase.org, garys@caltech.edu (only three-letter short names are requested)
		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
		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.
	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.
		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
		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
		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	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	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.	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	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	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	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	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	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	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	microarray	Please indicate if your paper reports any microarray data.	wchen@its.caltech.edu
	PROTEIN FUNCTION AND STRUCTURE:
*SILENCE THIS DATA TYPE*		Enter new protein	newprotein	Please list any protein that doesn't exist in WormBase already.		We don't have a 'protein curator per se, so links go to Gene pages, we do not need to capture Protein names
		Protein analysis in vitro	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	covalent	Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysis
		Structural information	structinfo	Please indicate if your paper reports NMR or X-ray crystallographic information.
		Mass spectrometry	massspec	Please indicate if your paper reports data from any mass spec analysis e.g., LCMS, HRMS, etc. 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
	REAGENTS:
Antibody		Enter C. elegans antibodies	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
Transgene		Enter integrated transgenes	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	Send kyook@wormbase.org
		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	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	seqchange	Please indicate if your paper reports new sequence data for any mutation.	genenames@wormbase.org
Variation? I don't know how authors will present this data, it could be in the form of actual sequence rather than simple name.		New SNPs	newsnp	Please list any SNP reported in your paper that doesn't exist in WormBase already.	mt3@sanger.ac.uk
	CELL DATA:
Anatomy		Enter new cell/anatomy term	newcell	Please list any C. elegans cell or anatomy part reported in your paper that doesn't exist in WormBase already.	Was retired from cfp.	Send to raymond@its.caltech.edu
		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
		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.
Author		Enter authors	authors	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.	New
		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