WormBase Literature Curation Workflow

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