Difference between revisions of "WormBase Literature Curation Workflow"
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| align="center" style="background:#f0f0f0;"|'''Ontologies or Controlled Vocabularies Used''' | | align="center" style="background:#f0f0f0;"|'''Ontologies or Controlled Vocabularies Used''' | ||
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− | |Genes | + | |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)|| |
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− | |Genes | + | |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)|| |
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|Variations: Allele||Mutations identified in forward or reverse genetic screens ||Textpresso (cats or script?)||Textpresso (cats or script?)|| Variations, Genes, CDS's, Transcripts|| | |Variations: Allele||Mutations identified in forward or reverse genetic screens ||Textpresso (cats or script?)||Textpresso (cats or script?)|| Variations, Genes, CDS's, Transcripts|| |
Revision as of 21:20, 16 December 2011
WormBase Data Types Curated 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 |