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)

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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. 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)