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	Old curation form name; PGdb name	Description for author	Curator Flagged
	GENE IDENTIFICATION AND MAPPING:
		C. elegans	new field = celegans	Please indicate if C. elegans isolates other than Bristol are discussed in this paper
		Nematodes other than C. elegans	new field = nematodes	Please indicate if data is presented for any species other than C. elegans, e.g., C. briggsae, Pristionchus pacificus, Brugia malayi, etc.
		Newly cloned gene (flagged-done)	Gene Symbol ; genesymbol	Please indicate if your paper presents 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 new alleles.
		Genetic mapping data (flagged)	mapping data ; mappingdata	Please indicated if your paper contains 3-factor interval mapping data, i.e., genetic data only, including with Df or Dp data but no SNP interval mapping.	genenames@wormbase.org
	GENE FUNCTION:
		Gene function (flagged-done)	Gene function ; genefunction	Please indicate if your paper discusses a new function for a known gene or a newly defined gene.	emsch@its.caltech.edu
in progress		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 gene.	ranjana@its.caltech.edu
	Phenotype Analysis based on:
		Allele analysis (flagged-done)	Mutant Phenotype; newmutant	Please indicate if any phenotype is reported for a mutant variation.	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 (flagged)	Overexpression ; overexpression	Please indicated 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
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.
	INTERACTIONS:
	GENE EXPRESSION AND FUNCTION:
		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
	Tools used for obtaining an expression pattern for a new gene:
in progress		C. elegans antibodies (flagged-done)	Extract Antibody ; antibodies	Please indicate if your paper reports the use of new or used antibodies created by your lab or someone else's lab; do not check this box if antibodies used were commercially bought.	wchen@its.caltech.edu
DONE		Integrated transgenes (flagged-done)	Transgene ; transgene	Please indicate if integrated transgenes are 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/Tissue reporters	Marker ; marker	Please indicate if reporters (integrated transgenes or antibodies) 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
	Regulation of gene expression patterns:
in progress		Gene expression altered by genetic background 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 such as 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 Postition weight matrix (PWM)	new field = matrices	Please indicate if your paper reports PFMs or PWMs that 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
		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
		Tissue or cell site of action (flagged-done)	Site of action ; site	Please indicate if your paper reports anatomy(tissue/cell)-specific expression function for a gene.	raymond@its.caltech.edu
		Developmental time of action	new field = timeofaction	Please indicate if your paper reports a temporal requirement for gene function.	raymond@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 including such things as kinase assays, agonist pharmacological studies, in vitro reconstitution studies, etc.
		Domain Analysis	new field = domainanalysis	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 Structural information (flagged):	NMR structure, functional domain info for a protein	"removal of the first 50aa causes mislocalization of the protein"; "fig.1, fig.8"; "yes, in paper and supplemental materials"; "FIGURE 5. The let-7 sequence is required for formation of the M1 and M2 complexes."; "functional domains of gld-2, fig 3"; "Fig. 3. Comparison of RDE-4 binding properties to variants lacking, or with mutations in, dsRBM1."
	Functional Complementation Functional Complementation (flagged):	Functional redundancy, rescue by overexpression of extragenic sequence	"exc-2 is rescued by exc-9 overexpression"; "...meg-2 functions redundantly with meg-1. Each transgene can rescue the sterility of meg-1(vr10) or meg-1(vr11)... The partial rescue of meg-1 mutants by GFPTMEG-2 suggests that extra copies of MEG-2 can compensate for the absence of MEG-1, implying that the overall level of MEG-1 and MEG-2 is important for proper germline development."; "In transformation experiments, we identified a cosmid, C26G6, which could rescue the egl-32 phenotype. Subclones of this cosmid containing the predicted open reading frame (ORF) T08G11.2 can also rescue egl-32 (Figures 3a & b). Several lines of evidence, however, suggest that egl-32 does not encode T08G11.2, but rather that they are interacting loci"
	Covalent Modification Covalent modification (flagged):	phosphorylation site is studies via mutagenesis and in vitro assay	"Analysis of cDNA sequences derived from the eri-7 pre-mRNA stabilized in rnp-5 RNAi-treated animals revealed adenosine to guanosine transitions at four positions located within the direct repeat (Fig. 2d). These transitions are indicative of adenosine to inosine editing of the eri-7 59-UTR by an adenosine deaminase (ADAR)24"
	Non-N2_phenotype :	Phenotypes of strains/non-C. elegans
	Sequence Change Sequencing mutant alleles (flagged):	Mutation was sequenced	"the hcf- 1(pk924) mutant has a large deletion that should result in a frame shift leading to an early stop codon, and likely represents a null mutant (Figure S1) [35]."; "table 2: unnamed mutations"; "FIGURE 5. Predicted structure of the glo-3 gene and encoded protein. (A) The structure of the glo-3 gene and the location and phenotypic class of mutations are shown"; "lin-15 mutation p.834"	genenames@wormbase.org
	Gene Interaction and Epistasis Genetic interactions (flagged-done):	analysis of more than one gene at a time, e.g. double, triple, etc. mutants, RNAi concurrent with other RNAi-treated worms or mutants	"e.g. daf-16(mu86) suppresses daf-2(e1370), daf-16(RNAi) suppresses daf-2(RNAi)"; "hcf-1, daf-16;daf-18, smg-1"; "eri-6, eri-7"; "gene interactions large-scale, table"; "Epistasis analysis in figure 2 and table 2"	emsch@its.caltech.edu
	Gene Product Interaction Gene product interactions (flagged-done):	protein-protein, RNA-protein, DNA-protein interactions, Y2H, etc.,	"Table S4. PDZ domain specificity prediction"; "Figure 5. Loss of hcf-1 Promotes the DAF-16 transcriptional Regulation of Several Target Genes...Figure 6. HCF-1 Forms a Protein Complex with DAF-16 in C. elegans..."; "Interestingly, the eri-6/7 transsplicing reporter is more highly and broadly expressed when RNAi is attenuated by inactivation of the Argonaute gene rde-1 (Supplementary Fig. 12), suggesting that the eri-6/7 is a target of RNAi..."; "Fig. 1. Identification of genes that regulate clec-85::gfp expression"	emsch@its.caltech.edu
	Sanger Gene Structure Correction Gene structure correction - need to make sure Sanger is responsible for the clone (flagged):	Gene Structure Correction (Gene Structure is different from the one in Wormbase: e.g. different splice-site, SL1 instead of SL2, etc.)	"...JA:F59F5.2 targets two predicted genes, F59F5.2 and F59F5.8. Two previously isolated cDNAs, yk1328a05 and yk571h2, suggested that F59F5.2 and F59F5.8 are a single gene that is alternatively spliced to produce two transcripts. We independently isolated F59F5.2/.8 cDNAs from both adult and embryonic stages, supporting the conclusion that F59F5.2 and F59F5.8 are a single gene (see MATERIALS AND METHODS). We refer to the long F59F5.2/.8 transcript as glo-3 and the F59F5.2 transcript as glo-3 short (Figure 5A)."	worm-bug@sanger.ac.uk
	St. Louis Gene Structure Correction Gene structure correction - need to make sure StLouis is responsible for the clone (flagged):	Gene Structure Correction (Gene Structure is different from the one in Wormbase: e.g. different splice-site, SL1 instead of SL2, etc.)	"C41D11.1 and C41D11.7 fig.1"; "We confirmed two of three forms by isolation of cDNAs (gcy-28.a and gcy-28.c, corresponding to T01A4.1a and T01A4.1c, respectively) and identified a fourth splice form, T01A4.1d (gcy-28.d), which fuses the upstream predicted gene T01A4.2 to T01A4.1 (Figure 4A)."; "page 3: By contrast, 235 of the indels occurred in regions with no perfectly aligning Solexa read, suggesting a possible error in the C. elegans reference genome,"	wormticket@watson.wustl.edu
	Mass Spec Mass spectrometry (flagged-done):	key words: LCMS, COSY, mass spec, HRMS		gw3@sanger.ac.uk, worm-bug@sanger.ac.uk
	Cell/Anatomy Function Cell function (flagged-done):	Function of any anatomical part (e.g. cell) is mentioned that has not been flagged already for mosaic analysis, site of action, or ablation data	"Figure 3 and Supp table 2 have information on predicted navigation circuit."	raymond@its.caltech.edu
	Ablation Data Ablation data (flagged-done):	cell or anatomical unit was ablated using a laser or by other means (e.g. by expressing a cell-toxic protein)	"Killing AWCON in wild-type animals abolished the net migration toward butanone (Figure 3A; Wes and Bargmann, 2001"	raymond@its.caltech.edu
	Extract New SNP New SNPs (flagged):	Reagent: new SNP not already in WB	"page 3: By contrast, 235 of the indels occurred in regions with no perfectly aligning Solexa read, suggesting a possible error in the C. elegans reference genome,"	dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
retired?	Extract SNP Verified by St. Louis (flagged):	Authors report reference genome is incorrect	"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
	Supplemental Material Supplemental materials (flagged-done):	Flag if supplemental material was not already downloaded.	yes	qwang@its.caltech.edu
	Comment (flagged):	e.g. no curatable;review;the paper is used for functional annotations		stays in Postgres