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''' | ||
|- | |- | ||
− | | | + | |'''Genetics''' |
|- | |- | ||
− | |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)|| | + | |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|| | |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|| | + | |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? | |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|| | ||
+ | |- | ||
+ | |'''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?) | |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 | + | |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) | ||
|- | |- | ||
− | |Functional complementation|| | + | |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''' | ||
+ | |- | ||
+ | | | ||
|} | |} |
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 | |||||