WormBase Literature Curation Workflow

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WormBase Curated Data Types and Curation Methods

Data Types Curated from the Literature Data Type Description Paper Flagging Methods (triage) Extraction Methods Entities Involved Ontologies or Controlled Vocabularies Used
Genes studied Genes for which experimental results are reported are linked to the publication n/a - applies to all publications Perl script (abstract only), Manual curation Genes, CGC (Caenorhabditis Genetics Center) names, Sequence names, Other names (synonyms)
Genes cloned Molecular characterization of a locus SVM (variation sequence change), Manual curation Manual curation WormBase Gene IDs, CGC (Caenorhabditis Genetics Center) names, Sequence names, Other names (synonyms)
Variations: Allele Mutations identified in forward or reverse genetic screens Textpresso (cats or script?) Textpresso (cats or script?) Variations, Genes, CDS's, Transcripts
Strains Laboratory and natural isolates of nematode strains Manual curation Manual curation Gene, Variation
Genetic mapping 2- and 3-factor mapping data, chromosomal deficiency breakpoints ?? which SVM ?? Manual curation Gene, Variation Are any deficiences annotated with phenotypes?
Chromosomal rearrangements Nomenclature, genetic boundaries ?? which SVM ?? Manual curation Gene Worm Phenotype Ontology
Antibodies -C. elegans Non-commercial antibodies, generated against C. elegans antigens Textpresso (cats or script?) Manual curation Gene, Laboratory
Transgenes Genomic constructs used as reporters to mark tissues and subcellular structures Textpresso (cats or script?) Manual curation Gene, Strain
Phenotype analysis Annotation of phenotypes resulting from genomic perturbations or natural variation SVM Manual curation, Textpresso ?? Variations, Rearrangements, Transgenes, Natural Variants Worm Anatomy Ontology, Worm Phenotype Ontology, Life Stage Ontology, Chemical Ontology (or Controlled Vocabulary?)
Molecules (e.g. chemicals, drugs, small molecules) Curation of molecules used to study behavior, physiology, gene function, etc. Manual curation - author, curator Manual curation - curator Molecules, Variation, Strain, Transgene, RNAi, Rearrangement Worm Phenotype Ontology
RNAi experiments Annotation of sequences used for and phenotype resulting from RNA interference experiments SVM Manual curation - Curator (Textpresso cats?) Sequence, Gene Worm Phenotype Ontology