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 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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|'''Genetics'''
 
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|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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|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: Author, Curator||Genes, CGC names, Sequence names, Other names (synonyms)||
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|-
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|Genes cloned||Molecular characterization of a locus||SVM (variation sequence change), Manual curation: Author||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||
 
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|-
|Strains||Laboratory and natural isolates of nematode strains||Manual curation||Manual curation||Gene, Variation||
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|Strains||Laboratory and natural isolates of nematode strains||Manual curation: Author, Curator||Manual curation: Curator||Gene, Variation||
 
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|-
 
|Genetic mapping||2- and 3-factor mapping data, chromosomal deficiency breakpoints||?? which SVM ??||Manual curation||Gene, Variation|| Are any deficiences annotated with phenotypes?
 
|Genetic mapping||2- and 3-factor mapping data, chromosomal deficiency breakpoints||?? which SVM ??||Manual curation||Gene, Variation|| Are any deficiences annotated with phenotypes?
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|-
 
|-
 
|Transgenes||Genomic constructs used as reporters to mark tissues and subcellular structures||Textpresso (cats or script?)||Manual curation||Gene, Strain||
 
|Transgenes||Genomic constructs used as reporters to mark tissues and subcellular structures||Textpresso (cats or script?)||Manual curation||Gene, Strain||
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|-
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|'''Gene Function'''
 
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|-
 
|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?)
 
|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?)
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|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): 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
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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 manual curation: HMM, Textpresso category searches, curator||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||SVM ?||Textpresso categories, Manual curation: Curator||Genes, Variations, RNAi experiments||Worm Phenotype Ontology, Genetic Interaction Ontology (in progress)
 
|Genetic interactions||Annotation of phenotype and type of interaction (e.g. suppression, enhancement) as a result of two or more genetic perturbations||SVM ?||Textpresso categories, Manual curation: Curator||Genes, Variations, RNAi experiments||Worm Phenotype Ontology, Genetic Interaction Ontology (in progress)
 
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|-
|Functional complementation||
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|Functional complementation||Phenotypic rescue of mutant Gene A as a result of Gene B expression||Manual curation: Author, Curator||Manual Curation: Author||Gene, Transgene (?), Variation, WPO (?)
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|-
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|Gene product interactions (physical interactions||Gene product interactions with other gene products (protein, nucleic acids), some overlap with GO MF curation||SVM, Manual curation: Author||Semi-automated manual curation: Textpresso category searches, curator||Genes, Proteins, Sequences||Gene Ontology, BioGRID Experimental Systems Vocabulary
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|-
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|''C. elegans'' human disease gene homologs||Identification of ''C. elegans'' genes homologous to human genes associated with disease, gene model tag and incorporated into free text descriptions||Textpresso: category searches||Manual curation: curator||Gene, Protein, Disease||MeSH (?), Disease Ontology (?)
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|'''Gene Expression'''
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|
 
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Revision as of 18:22, 19 December 2011

WormBase Curated Data Types and Curation Methods

Abbreviations Used:

CGC - Caenorhabditis Genetics Center

GO - Gene Ontology

HMM - Hidden Markov Model

SO - Sequence Ontology

SVM - Support Vector Machine

WAO - Worm Anatomy Ontology

WPO - Worm Phenotype Ontology

Data Types Curated from the Literature Data Type Description Paper Flagging Methods (triage) Data Extraction Methods Entities Involved Ontologies or Controlled Vocabularies Used
Genetics
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: Author, Curator Genes, CGC names, Sequence names, Other names (synonyms)
Genes cloned Molecular characterization of a locus SVM (variation sequence change), Manual curation: Author 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: Author, Curator Manual curation: Curator 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
Gene Function
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 manual curation: HMM, Textpresso category searches, curator 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 SVM ? Textpresso categories, Manual curation: Curator Genes, Variations, RNAi experiments Worm Phenotype Ontology, Genetic Interaction Ontology (in progress)
Functional complementation Phenotypic rescue of mutant Gene A as a result of Gene B expression Manual curation: Author, Curator Manual Curation: Author Gene, Transgene (?), Variation, WPO (?)
Gene product interactions (physical interactions Gene product interactions with other gene products (protein, nucleic acids), some overlap with GO MF curation SVM, Manual curation: Author Semi-automated manual curation: Textpresso category searches, curator Genes, Proteins, Sequences Gene Ontology, BioGRID Experimental Systems Vocabulary
C. elegans human disease gene homologs Identification of C. elegans genes homologous to human genes associated with disease, gene model tag and incorporated into free text descriptions Textpresso: category searches Manual curation: curator Gene, Protein, Disease MeSH (?), Disease Ontology (?)
Gene Expression