First-pass schedule, instructions, automation

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Papers for Firstpass are found on the WBPaperEditor page:

Pick a paper and access the curation form


Alternatively

  • Access the curation.cgi from the WBPaperID page itself
  • Select the WBPaperID from left column to take you to the paper page-- ONLY SELECT PAPERS FROM WBPaper0030000 AND LATER
  • Select first-pass curate

Note: the paper pdf can be accessed from the paper page along with supplemental materials.

Either action takes you to the curation.cgi (SEE BELOW)

The firstpass page curation.cgi

  • At the top of the page are links to:
    • The tazendra site map (other forms)
    • Documentation for the set up, paths from, and changes to the curation.cgi form
    • Guidelines for the form which include some summary information about the fields and features, written by Raymond in 2001 and needs some updating.
  • For each data type you can check the box or enter text:
    • Check the box = a '"yes" is entered in to the field
    • Enter text = the text is recorded
  • E-mail is set for default send if there is a "yes" (from a check) or text in the data type flag box.
  • When done, you can see the preview of the submission, by selecting "Preview!"
  • If acceptable, Select "New Entry!"
  • First pass flags will be sent.

Adding new gene paper connections

add info

For what and to whom a flag is sent

Data type Description Examples Curator Flagged
Gene Symbol (main/other/sequence) : New symbol for known locus or new locus defined. Alerts curators to newly cloned genes so that they can update a previously existing concise description, if needed. "UNC-80 = F25C8.3";"These dsRNAs target two adjacent,antiparallel open reading frames: C41D11.7, termed eri-7, and C41D11.1, termed eri-6 (Fig. 1a)";

"We refer to the long F59F5.2/.8 transcript as glo-3 and the F59F5.2 transcript as glo-3 short (Figure 5A)."; "tbc-1=F20D1.2 table S3"; "nre-1 (uncloned)"; "we have designated K02B9.1 as meg-1 and K02B9.2 as meg-2 (meg, maternal-effect germ-cell defective)." ||E-mail genenames@wormbase.org, vanauken@its.caltech.edu

Mapping Data : 3-factor interval mapping; mapping with Df, breakpoints in suppl: In three-factor mapping with unc-11(e47) dpy-5(e61) the...defect mapped between the two genes (9/16 Dpy non-Unc and 4/14 Unc non-Dpy were chemotaxis defective);glo- 3(kx90), glo-3(kx94), and glo-3(zu446) were complemented by nDf19, indicating that glo-3(+) is not deleted by nDf19, similar to nearby genes vab-3 and daf-12;fig.1 Its right breakpoint was not mapped precisely but idDf3 completely removes sequences of fem-1, drp-1, T12E12.3, and T12E12.2 (A. Spence, personal communication).;mapping data in suppl methods: We mapped sa321 by its daf-7 suppression phenotype to the unc-62 dpy-11 interval (unc-62 (4/10) sa321 (6/10) dpy-11), which excludes scd-2. Therefore, sa321 is not allelic with scd-2. E-mail genenames@wormbase.org
Gene Function : Discussion of new function of a gene A Novel Role for the SMG-1 Kinase in Lifespan and Oxidative Stress Resistance in Caenorhabditis elegans;Here we describe the isolation of mutations in two adjacent, divergently transcribed open reading frames (eri-6 and eri-7) that fail to complement...The ERI-6/7 protein is a superfamily I helicase that both negatively regulates the exogenous RNAi pathway and functions in an endogenous RNAi pathway. E-mail emsch@its.caltech.edu
Gene Regulation on Expression Level : Gene expression level change in genetic background, ie, gfp expression (or any other reporter) increases or decrease; expression level change under certain chemical/physical conditions, ie, drugs, heat shock, etc.; expression location change in genetic background, missexpression, ie, nucleus, cytoplasma, etc.; no change in gene expression in genetic background if mentioned in paper Figure 5. Loss of hcf-1 Promotes the DAF-16 Transcriptional Regulation of Several Target Genes;To investigate whether SMG-1 controls DAF-16 sub-cellular localization...DAF-16::GFP was localized in both the cytoplasm and the nucleus in all tissues of worms after smg-1 inactivation...(Figure 3)... Conversely,under the same experimental conditions, daf-2 RNAi induced DAF-16::GFP nuclear accumulation (Figure 3)...SMG-1 does not regulate DAF-16 activity through its sequestration into the cytoplasm; 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)...A caveat to this result is that transgenes are generally expressed at higher levels when RNAi is defective. Quantitative RT–PCR revealed that eri-6/7 mRNA levels are not increased in animals lacking RDE-1 (data not shown). One explanation for these data is that the dsRNA element of eri-6/7 acts tissue-specifically as a sensor, and the changes in expression are too subtle to detect by quantitative RT–PCR on whole worms. E-mail xdwang@its.caltech.edu
Expression Data : Temporal and spatial (e.g. tissue, subcellular, etc) distribution of genes in a wild-type background. Include: Reporter gene analysis, antibody staining, In situ hybridization, RT_PCR, Western, Northern. Exclude: all markers (antibodies or reporter genes) used to label certain tissues or subcellular structure. This flag also alerts curators for cross-checking CCC semi-automation for missed papers. Figure 2. HCF-1 Is a Ubiquitously Expressed Nuclear Protein;eri-7 promoter::gfp and eri-6 promoter::rfp transgenes are expressed in overlapping patterns, with co-expression in hypodermal cells and two pairs of sensory head neurons (ASK and ASI; Fig. 2c). The eri-7 promoter also expresses in the somatic gonad. E-mail wchen@its.caltech.edu, vanauken@its.caltech.edu
Marker : Reporters or antibodies used to mark certain tissue, subcellular structure or life stage. E-mail wchen@its.caltech.edu, vanauken@its.caltech.edu
Microarray : Any microarray data yes E-mail wchen@its.caltech.edu
RNAi : Phenotypes/results are discussed for less than 100 RNAi experiments yes;Supplementary Table 3: lsy-12 phenotypic data E-mail garys@its.caltech.edu
Large-Scale RNAi : Phenotypes/results are discussed for more than 100 RNAi experiments yes E-mail raymond@its.caltech.edu
Transgene : Reagent: Integrated transgene only. Textpresso will extract all the Is or In transgene names, please look for transgenes without official names, for example, authors said they used microbombardment but did not provide official names. Or if they provided a strain name and you know the strain contains a transgene. Ex transgenes will only be curated when they are used by other experiments, such as phenotype assay or Expr_pattern. So there is no need to flag them. Textpresso : WBPaper00032232 muIs71 muIs84 rwIs3 xrIs87 -- 20081012 ...;Textpresso : WBPaper00032178 mgIs30 -- 20080921 ...Textpresso : WBPaper00032178.sup.1 mgIs30 pkIs1582 -- 20080921 ...;table 1 E-mail wchen@its.caltech.edu
Overexpression : Over expression of something results in a phenotype High expression of the constitutively activated SCD-2(neu*) receptor caused 100% of animals to arrest in the first larval stage (L1), with no overt anatomical defects;Fig. 6. CRIP overexpression also affects epithelial shape E-mail emsch@its.caltech.edu, garys@its.caltech.edu (add Variation phenotype people)
Structure Information : NMR structure, functional domain info for a protein (e.g. removal of the first 50aa causes mislocalization of the protein
Functional Complementation : 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||

in vitro Protein Analysis : e.g. kinase assay
Mosaic Analysis : e.g. extra-chromosomal transgene loss in a particular cell lineage abolishes mutant rescue E-mail raymond@its.caltech.edu
Site of Action : e.g. anatomy(tissue/cell)-specific expression rescues mutant phenotype; RNAi in rrf-1 background determines that the gene acts in the germ line By contrast, a gcy-28.d cDNA rescued chemotaxis when expressed under a panneuronal promoter (Figure 5C), under the AWC-selective odr-3 promoter (Figure 5D), or under the AWCON-selective str-2 promoter (Figure 5E). The results with gcy-28.c suggest that gcy-28 may have roles in multiple neurons; nevertheless, the full rescue with gcy-28.d suggests that gcy-28 can function cell-autonomously in AWCON.;Whereas mutant smn-1(ok355) animals expressing muscle-directed smn-1

showed only weak phenotypic rescue in a subset of animals, pan-neuronal expression of smn-1 produced stronger rescue effects (Fig. 7A).||E-mail raymond@its.caltech.edu

Extract Antibody : New or used antibodies created by labs; skip antibodies bought from companies in methods E-mail wchen@its.caltech.edu
Covalent Modification : 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||

Extract Allele : Automated How does this work? Where is this information stored? Who does it go to
Mutant Phenotype : Phenotype is reported for a variation. ERI-6/7 is required for endogenous RNAi E-mail emsch@its.caltech.edu, garys@its.caltech.edu, kyook@its.caltech.edu, jolenef@its.caltech.edu
Non-N2_phenotype : Phenotypes of strains/non-C. elegans E-mail kyook@its.caltech.edu
Sequence Change : 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 E-mail genenames@wormbase.org
Gene Interactions : 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 E-mail emsch@its.caltech.edu
Gene Product Interaction : 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||E-mail emsch@its.caltech.edu

Sanger Gene Structure Correction : An RNAi based screen of genes in the interval identified RNAi clone JA:F59F5.2 as inducing an adult Glo phenotype very similar to glo-3 class II and class III alleles (Table 2). 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). E-mail worm-bug@sanger.ac.uk
St. Louis Gene Structure Correction : 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). E-mail wormticket@watson.wustl.edu
Sequence Features : DNA/RNA elements required for gene expression: promoters, introns, UTR's etc. E-mail emsch@its.caltech.edu, worm-bug@sanger.ac.uk, stlouis@wormbase.org
Mass Spec : key words: LCMS, COSY, NMR, mass spec, HRMS E-mail gw3@sanger.ac.uk, worm-bug@sanger.ac.uk
RETIRE? Cell Name : New cell name is mentioned E-mail raymond@its.caltech.edu
Cell/Anatomy Function : 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 E-mail raymond@its.caltech.edu
Ablation Data : 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 E-mail raymond@its.caltech.edu
Extract New SNP : Reagent: new SNP not already in WB E-mail dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
Extract SNP Verified by St. Louis : fig.2: two SNPs mentioned E-mail dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
Supplemental Material : Is there supplemental material that needs to be downloaded? yes E-mail qwang@its.caltech.edu
Chemicals : used in assays, what about mutagens? paraquat;butanone, benzaldehyde;aldicarb
Human Diseases : Genes discussed are homolog/ortholog of a human disease gene The INhibitor of Growth (ING) family of type II tumor suppressors are encoded by five genes in

mammals and three genes in C. elegans...Here we identify and characterize ing-3, the C. elegans gene with the highest sequence identity to the human ING3 gene.;Deletion of smn-1, the Caenorhabditis elegans orthologue of the spinal muscular atrophy gene, results in locomotor dysfunction and reduced lifespan||E-mail ranjana@its.caltech.edu

Comment : e.g. no curatable;review;the paper is used for functional annotations stays in Postgres

Issues to resolve

  • There are many papers on the firstpass list that are already firstpassed. Most of these papers are duplicates and have two WBPaperID assignments. Is there a way to resolve this?
  • There are papers on the firstpass list that have been curated for data types by individual curators who have bypassed the firstpass pipeline. Is there a way to mark the paper in the firstpass list as curated for a specific data type but not others? We do have a record of data type curation for each paper, is there some way of combining the first pass curation with the curation status form?
  • How does the false positive work?



kjy 19:43, 9 February 2009 (EST)

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