Difference between revisions of "WormBase Literature Curation Workflow"
From WormBaseWiki
Jump to navigationJump to searchLine 1: | Line 1: | ||
− | =WormBase Data Types | + | =WormBase Curated Data Types and Curation Methods= |
{| {{table border ="1"}} | {| {{table border ="1"}} | ||
| align="center" style="background:#f0f0f0;"|'''Data Types Curated from the Literature''' | | align="center" style="background:#f0f0f0;"|'''Data Types Curated from the Literature''' |
Revision as of 21:52, 16 December 2011
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 |