Difference between revisions of "WormBase Literature Curation Workflow"

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|Gene Ontology (GO): Molecular Function||Annotation of gene product to GO molecular function terms based upon in vitro assays, mutant phenotypes||SVM, HMM, Manual Curation: Author, Curator||Semi-automated: HMM, Textpresso category searches||Genes, Variations, RNAi Experiments||Gene Ontology
 
|Gene Ontology (GO): Molecular Function||Annotation of gene product to GO molecular function terms based upon in vitro assays, mutant phenotypes||SVM, HMM, Manual Curation: Author, Curator||Semi-automated: HMM, Textpresso category searches||Genes, Variations, RNAi Experiments||Gene Ontology
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|Genetic interactions||Annotation of phenotype and type of interaction (e.g. suppression, enhancement) as a result of two or more genetic perturbations||
 
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Revision as of 17:45, 19 December 2011

WormBase Curated Data Types and Curation Methods

Data Types Curated from the Literature Data Type Description Paper Flagging Methods (triage) Data 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
Time of action Is this part of phenotype curation?
Gene Ontology (GO): Biological Process Annotation of gene products to GO biological process terms based upon mutant phenotypes, in vitro assays SVM, Manual Curation - Author, Curator Manual Curation - Curator, Phenotype2GO Pipeline Genes, Variations, RNAi Experiments Gene Ontology, Phenotype Ontology
Gene Ontology (GO): Molecular Function Annotation of gene product to GO molecular function terms based upon in vitro assays, mutant phenotypes SVM, HMM, Manual Curation: Author, Curator Semi-automated: HMM, Textpresso category searches Genes, Variations, RNAi Experiments Gene Ontology
Genetic interactions Annotation of phenotype and type of interaction (e.g. suppression, enhancement) as a result of two or more genetic perturbations