Guidelines for Users on Submitting/Reporting Data to WormBase

Rationale

In an attempt to facilitate the deposition of information into WormBase, we have created this section on the WormBase Wiki. We want to make researchers aware of the information required for the proper curation of different data sets so they can include this in their publications or provide this information to WormBase directly.

DATA TYPES

List of all data types

Data types extracted from each paper	Definition/examples
Species of focus in paper	i.e., C. elegans, C. elegans other than Bristol, nematodes other than C. elegans, or non-nematode species.
Genes studied or cloned	C. elegans or other Caenorhabditis studied or newly identified in the paper.
Alleles	new alleles that do not exist in WormBase already.
Genetic mapping data	gene location was determined using genetic tools, e.g., 2-factor, 3-factor interval linkage, Df breakpoints, etc.
Phenotype analysis	phenotypes of mutants or phenotypic analysis of \"wild-type\" nematode strains.
Overexpression phenotype	phenotypes caused by the overexpression of transgenes.
Chemicals	chemicals or drug used to analyze strain behavior, physiology, gene function, etc. of mutant or \'normal\' worms.
Small-scale and large-scale RNAi experiments	RNAi sequences used in gene function assays and their phenotypic outcome.
Mosaic analysis	results of lineage analysis experiments assaying gene function in specific cells.
Tissue or cell site of action	results of experiments where 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.
Time of action	results of experiments where the timing of a gene's function was assayed, for example with temperature-shift experiments.
Molecular function of a gene product	a new/novel molecular function or aspect of molecular function for a gene.
Homolog of a human disease-associated gene	whether or not a gene studied in the paper is a homolog of a human gene, which is directly associated with a disease.
Genetic interactions	genes were demonstrated to have an 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.
Functional complementation	functional redundancy was demonstrated between separate genes, e.g., the rescue of gen-A by overexpression of gen-B, or any other extragenic sequence, or by the rescue of gene function by a gene from another species.
Gene product interactions	physical interactions were demonstrated between protein-protein, RNA-protein, DNA-protein, or through Y2H experiments, etc.
Expression patterns	new temporal or spatial (e.g., tissue, subcellular, etc.) patterns of expression of any gene in a wild-type background, which includes reporter gene analysis, antibody staining, In situ hybridization, RT-PCR, Western or Northern blot data.
Gene regulation	alterations in gene expression levels or patterns were reported in response to genetic, chemical, temperature, or any other experimental treatment.
Regulatory sequence features	any gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression, promoters, introns, UTR's, DNA binding sites, etc.
Position frequency matrix (PFM) or Position weight matrix (PWM)	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.
Microarray data	self-explanatory
Protein analysis in vitro	any in vitro protein analysis such as kinase assays, agonist pharmacological studies, reconstitution studies.
Domain analysis	particular domains within a protein were targeted for genetic or molecular analysis.
Covalent modification	post-translational modifications of a gene product were assayed by mutagenesis or in vitro analysis.
Structural information	protein structure data from NMR, X-Ray crystallography, etc.
Mass spectrometry	small peptide mass data from mass spectrometry analysis (MS/MS, LCMS, HRMS) using analysis programs such as MASCOT, SEQUEST, X!Tandem, OMSSA, MassMatrix.
C. elegans antibodies	antibodies generated against C. elegans gene products in a noncommercial laboratory.
Integrated transgenes	integrated transgenes that don't exist in WormBase already.
Transgenes used as tissue markers	reporter constructs (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.
Gene structure correction	gene structures differ from the ones in WormBase, e.g., different splice-sites, 3'UTR, etc.
Sequence of mutant alleles	sequence data for any mutation.
New SNPs	SNPs were reported that don\'t exist in WormBase already.
Ablation data	cells or anatomical unit were ablated by laser or other means (e.g., by expressing a cell-toxic protein).
Cell function	novel functions for any anatomical part (e.g., cell, tissue, etc.).
Phylogenetic data	evolutionary relationships between or among genes or gene products.
Other bioinformatics analysis	other bioinformatic data not covered by other data types.

Specific data types

1. RNAi curation
   1. Reporting sequence for RNAi
2. Transgene curation
3. Antibody curation
4. Allele curation
   1. Reporting Genetic (Phenotype) information for an allele

WormBase Online Data Submission Forms

You can submit your data so curators can more quickly integrate it into WormBase by clicking the following link SUBMIT and following the instructions for each data type.