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.

Automation status	Data type Section	Data type	Current fp curation form name	PGdb name	Description for author	Curator Flagged
	GENE IDENTIFICATION AND MAPPING:
		C. elegans CHANGE NAME TO C. elegans other than Bristol	new field	celegans	Please indicate if data forC. elegans isolates other than Bristol are presented in this paper.
		Nematodes other than C. elegans	nonntwo	nematodes	Please indicate if data is presented for any species other than C. elegans(italicize), 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 were 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.
in progress		Newly cloned gene (flagged-done)	Gene Symbol	genesymbol	Please indicate 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	extractedvariation	Please indicate if your paper reports the identification of any allele that doesn't exist in WormBase already.
		Genetic mapping data (flagged)	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: The data fields in this section are changed and reordered.	The new order of data fields are: Phenotype Analysis section (keep suborder), Mosaic Analysis, Cell or tissue site of action, Time of action, Gene function, and Homolog of a human disease-associated gene.
	Phenotype Analysis CHANGE NAME TO Mutant, RNAi, overexpression, or chemical-based phenotypes :	PLEASE SPECIFY DATA TYPE. (make pop up text instructions bolder and more noticeable)
		Allele phenotype analysis (flagged-done)	Mutant Phenotype	newmutant	Please indicate if your paper reports any phenotype for a mutant.	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 phenotype (flagged)	Overexpression	overexpression	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)..." "\" marks are showing on the page	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.
	moved	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
	moved	Tissue or cell site of action (flagged-done)	Site of action	site	Please indicate if your paper reports anatomy (tissue or cell)-specific expression function for a gene.	raymond@its.caltech.edu
	moved	Developmental time of action CHANGE NAME TO Time of action	new field	timeofaction	Please indicate if your paper reports a temporal requirement for gene function.	raymond@its.caltech.edu
	reordered	Gene function CHANGE NAME TO Molecular function of a gene product (flagged-done)	Gene function	genefunction	Please indicate if your paper discusses a new function for a known or newly defined gene.	emsch@its.caltech.edu
in progress	reordered	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-related gene.	ranjana@its.caltech.edu
	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 where RNAi was concurrent with other RNAi-treatments or mutations.	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 data on protein-protein, RNA-protein, DNA-protein, or Y2H interactions, etc.	emsch@its.caltech.edu
	GENE EXPRESSION AND FUNCTION CHANGE NAME TO REGULATION OF GENE EXPRESSION:
		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
in progress		Alterations in gene expression by genetic background or other treatment CHANGE NAME TO Alterations in gene expression by genetic 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, 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	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 such 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
	Tools used for obtaining an expression pattern for a new gene CHANGE TO OWN SECTION NAMED REAGENTS:
in progress		C. elegans antibodies (flagged-done)	Extract Antibody	antibody	Please indicate 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	Please indicate 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
		Cell or tissue reporter CHANGE NAME TO Transgenes used as tissue markers	Marker	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)	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 SNP that 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 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	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. "\" marks are showing on the page
		Comment (flagged)	new field	comment	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.	this should go to someone