Datatypes flagged

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First-pass schedule and instructions

Data types

Papers with italicized data types are being flagged by SVM or are in the process of being developed for SVM recognition based on information posted on the Caltech documentation page.

Species

C. elegans (default checked): Postgres character name: celegans. Postgres table: afp, cfp, jfp

C. elegans other than Bristol: Data is present for C. elegans isolates other than Bristol, such as Hawaiian, CB4855, etc. Postgres character name: cnonbristol. Postgres table: afp, cfp, jfp

Nematodes other than C. elegans: Data is presented for Caenorhabditis sister species e.g., briggsae, remanei, and/or related nematodes, parasitic nematodes. Postgres character name: nematode. Postgres table: afp, cfp, jfp

Non-nematode species: Data is presented for Human, Mouse, SGD, Dog, Plant, etc. genes/proteins, other. Postgres character name: nonnematode. Postgres table: afp, cfp, jfp

Genetic Entities

Genes studied in this paper: Gene(s) studied in the paper. Postgres character name: genestudied. Postgres table: jfp

Genes cloned in the paper : Genes newly identified, named, cloned, reassigned etc. Postgres character name: genesymbol. Postgres table: afp, cfp, jfp. note:"Currently being combined with seqchange. Could possibly employ secondary screen with categories." see here for more info.

New alleles: Alleles reported in the paper that don't already exist in WormBase. Postgres character name: extvariation. Postgres table: afp, cfp, jfp

New strains: Worm strains reported in the paper that don't already exist in WormBase. Postgres character name: newstrains. Postgres table: jfp

Genetic mapping data : The location of the gene was determined using genetic recombination, e.g., 2-factor recombination, 3-factor interval linkage, Df breakpoints, etc. Postgres character name: mappingdata. Postgres table: afp, cfp, jfp

New balancers: Balancers reported in paper that don't exist in WB. Postgres character name: newbalancers . Postgres table: jfp

Gene Function

Phenotype analysis : Analysis of gene function through the characterisation of mutants. In addition this data type includes the characterisation of non-mutated worm strain variants. Characterisation through RNAi analysis is flagged by the "Small-scale RNAi, and Large-scale RNAi data types". Postgres character name: newmutant. Postgres table: afp, cfp, jfp

Overexpression phenotype : Phenotypes due to the overexpression of transgenes. Postgres character name: overexpr. Postgres table: afp, cfp, jfp

Chemicals : Chemicals or drug treatments were used to analyze strain behavior, physiology, gene function, etc. of mutant or 'normal' worms. Postgres character name: chemicals. Postgres table: afp, cfp, jfp

Small-scale RNAi (less than 100 experiments reported) : Gene function was assayed by RNA interference. Postgres character name: rnai. Postgres table: afp, cfp, jfp

Large-scale RNAi (more than 100 experiments reported) : Gene function was assayed by large RNA interference screens. Postgres character name: lsrnai. Postgres table: afp, cfp, jfp

Mosaic analysis : Gene function was assayed in specific cells using lineage analysis. Postgres character name: mosaic. Postgres table: afp, cfp, jfp

Tissue or cell site of action : Gene function was assayed in specific cells or tissues, such as in the case where gene function was rescued by cell/tissue-specific expression of the gene. Postgres character name: siteaction. Postgres table: afp, cfp, jfp

Time of action: Timing of a gene's function was assayed, for example with temperature-shift experiments. Postgres character name: timeaction. Postgres table: afp, cfp, jfp

Molecular function of a gene product : A new/novel molecular function or aspect of mol function for a gene was identified. Postgres character name: genefunc. Postgres table: afp, cfp, jfp

Genetic interactions : Genes were assayed for effect on the function of another gene. Often this is made apparent by the analysis of double, triple, etc. mutants, or with the use of experiments where RNAi was used concurrent with other RNAi-treatment or mutations. Postgres character name: geneint. Postgres table: afp, cfp, jfp

Functional complementation : Functional redundancy between separate genes is reported, e.g., the rescue of gen-A by overexpression of gen-B, or any other extragenic sequence. Also indicated by the rescue of gene function by a gene from another species. Postgres character name: funccomp. Postgres table: afp, cfp, jfp

Gene product interactions : Protein-protein, RNA-protein, DNA-protein, or Y2H interactions, etc. are reported. Postgres character name: geneprod. Postgres table: afp, cfp, jfp. note: this data type is being assessed for SVM recognition for GO (molecular function?)

Homolog of a human disease-associated gene. : Gene studied in the paper is a homolog of a human gene, which is directly associated with a disease. Postgres character name: humdis. Postgres table: afp, cfp, jfp

Regulation of gene expression

New expression pattern for a gene : New temporal or spatial (e.g., tissue, subcellular, etc.) data on the pattern of expression of any gene in a wild-type background, this data type includes reporter gene analysis, antibody staining, In situ hybridization, RT-PCR, Western or Northern blot data. Postgres character name: otherexpr. Postgres table: afp, cfp, jfp

Alterations in gene expression by genetic or other treatment : Changes or a lack of changes in gene expression levels or patterns in response to genetic, chemical, temperature, or any other experimental treatment. Postgres character name: genereg. Postgres table: afp, cfp, jfp

Regulatory sequence features : Gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression, promoters, introns, UTR's, DNA binding sites, etc. Postgres character name: seqfeat. Postgres table: afp, cfp, jfp

Position frequency matrix (PFM) or Position weight matrix (PWM): The 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. Postgres character name: matrices. Postgres table: afp, cfp, jfp

Microarray: Microarray-derived data. Postgres character name: microarray . Postgres table: afp, cfp, jfp

Protein function/structure

Protein analysis in vitro: Any in vitro protein analysis such as kinase assays, agonist pharmacological studies, reconstitution studies, etc. Postgres character name: invitro. Postgres table: afp, cfp, jfp

Domain analysis: Experimentation done on a particular domain within a protein to assay the function of that domain. Postgres character name: domanal. Postgres table: afp, cfp, jfp

Covalent modification : Post-translational modifications of a gene product, as assayed by mutagenesis or in vitro analysis. Postgres character name: covalent. Postgres table: afp, cfp, jfp

Structural information: Protein structural analysis, through NMR, X-Ray crystallography, etc. Postgres character name: structinfo. Postgres table: afp, cfp, jfp

Mass spectrometry : Protein mass analysis through any mass spectrometry analysis (MS/MS, LCMS, HRMS). Some Mass spec analysis programs include MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix. Postgres character name: massspec. Postgres table: afp, cfp, jfp

Cell expression

C. elegans antibodies : Antibodies generated in a noncommercial laboratory, against a C. elegans gene product. Postgres character name: antibody. Postgres table: jfp.

Integrated transgenes  : Integrated transgenes used in this paper that doesn't exist in WormBase already, especially if the transgene does not have a canonical name: . Postgres character name: transgene. Postgres table: jfp. note: this data type is recognized by pattern matching

Transgenes used as tissue markers: Reporters (integrated transgenes) used to mark certain tissues, subcellular structures, or life stages, etc. as a reference to assay site of action of gene function or location. Postgres character name: marker. Postgres table: afp, cfp, jfp

Genome structure/sequence changes

Gene structure correction : Gene structure that is different from the one in WormBase, e.g., different splice-site, SL1 instead of SL2, etc. Postgres character name: structcorr (this use to be two different fields). Postgres table: afp, cfp, jfp.
note: This data type has been divided into four categories, which are all under development for automated recognition and flagging by SVM:

  • a change in a gene's structure
  • the addition of an isoform
  • a change to one of the SL1/SL2 or polyA site features
  • a sequence correction in the N2 reference genome

Sequencing mutant alleles : Sequence data for any mutation. Postgres character name: seqchange. Postgres table: afp, cfp, jfp

New SNPs : SNPs that don't exist in WormBase already. Postgres character name: newsnp. Postgres table: afp, cfp, jfp. note: this data type can be removed from the pipeline; input of snp errors/new sequences come directly from the community.

Cell function

Enter new cell/anatomy term: C. elegans cells or anatomy parts reported in the paper that doesn't exist in WormBase already. Currently unknown if cells or anatomy parts of other nematodes will be collected here. Postgres character name: newcell Postgres table: jfp

Ablation data : Any cell or anatomical unit was ablated by laser or by other means (e.g., by expressing a cell-toxic protein). Postgres character name: ablationdata. Postgres table: afp, cfp, jfp

Cell function : Function for any anatomical part (e.g., cell, tissue, etc.), which has not been indicated elsewhere on this form. Postgres character name: cellfunc. Postgres table: afp, cfp, jfp

In silico

Phylogenetic data: Evolutionary relationships between or among genes or gene products. Postgres character name: phylogenetic. Postgres table: afp, cfp, jfp

Other bioinformatics analysis: Other bioinformatic data not indicated anywhere else on this form. In general, this may include alignments. Postgres character name: othersilico. Postgres table: afp, cfp, jfp

Supplemental materials

Supplemental materials : In the Author First-Pass form, checking this box indicates that supplementary material is attached to the paper. In the curator first-pass checking the box indicates that the Supplementary Materials are missing. Postgres character name: supplemental. Postgres table: afp, cfp, jfp

Misc

NONE of the aforementioned data types are in this research article : This is used as a default category for any paper where the author checked "here" for review or non primary research paper. Postgres character name: nocuratable. Postgres table: afp, cfp, jfp

Enter authors: Authors that need to have their information in WB updated and need author-paper connections made. Postgres character name: authors. Postgres table: jfp

Feedback: Thoughts, notes, comments about the form etc. Postgres character name: comment . Postgres table: afp, cfp, jfp