WormBase Literature Curation Workflow

WormBase Curated Data Types and Curation Methods

Please note that this page may be periodically updated as data types curated and curation methods change and improve.

Abbreviations Used:

CGC - Caenorhabditis Genetics Center

GEO - Gene Expression Omnibus

GO - Gene Ontology

HMM - Hidden Markov Model

PFM - Position Frequency Matrix

PWM - Position Weight Matrix

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
Genes and 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
Transgenes	Genomic constructs used as reporters to mark tissues and subcellular structures	Textpresso (cats or script?)	Manual curation	Gene, Strain
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 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
Concise descriptions	Free text descriptions that summarize key biological information about a gene	SVM, Textpresso category searches, Manual curation: author, curator	Textpresso category searches, Manual curation: curator	Genes, OMIM Database Identifiers
Gene Expression
Antibodies -C. elegans	Non-commercial antibodies, generated against C. elegans antigens	SVM (?), Textpresso (cats or script?)	Manual curation	Gene, Laboratory
Gene expression pattern	Temporal and/or spatial expression patterns for genes, transcripts, proteins	SVM	Manual curation: Curator, Textpresso categories (?)	Genes, Transcripts, Proteins, Antibodies, Images	GO, Life stage (CV or Ontology?), WAO
Expression pattern images	Images of expression patterns from published papers, laboratories	Textpresso (cats or scripts?), SVM (?)	Manual curation: curator	Genes, Anatomy Terms, Subcellular Localization	GO, WAO, Life stage (?)
Gene Ontology (GO): Cellular Component	Curation of the subcellular localization of gene products	SVM and Textpresso category searches	Textpresso category searches	Genes, GO terms	Gene Ontology
Gene regulation	Annotation of changes in gene expression (levels, temportal or spatial pattern, localization) upon genetic or environmental perturbation	SVM	Manual curation: curator	Genes, Proteins, Antibodies, Expression Patterns, Molecules	??
Regulatory features	Curation of nucleic acid sequences that regulate gene expression	SVM	Manual curation: curator	Genes, Sequences, ??	SO (?)
Cis-regulatory sites	Verified or predicted cis-regulatory sites as defined by PFM or PWM	Manual curation: author, curator	Manual curation: curator	Sequences, ??	SO(?)
Microarray data	Microarray data are imported from GEO and Array Express, mapped to C. elegans genomic sequence	Manual curation: Author, Curator	Manual curation: curator	Genes, Sequences, PCR products, ?	?
Protein structure and function
Protein analysis in vitro	Curation of protein function in vitro, e.g. enzymatic and transporter activities, overlaps with GO MF curation	HMMs, Manual curation: author, curator	HMMs, Manual curation: curator	Genes, Proteins, Molecules (Column 16?)	GO
Mass spectrometry data	Mass spectrometry data used for curating gene models	SVM	Manual curation: curator	Genes, Proteins, Sequences	SO (?)
Gene models, sequence changes
Gene structure corrections	Curation of genome sequence changes, alternative splice sites, poly(A) sites, etc.	SVM	Manual curation: curator	Genes, Sequences	SO (?)
Allele sequence	Curation of sequences associated with allelic variations	SVM, Textpresso(cats or scripts?)	Manual curation: curator	Genes, Sequences, Variations, PCR products (?)
SNP sequence	Curation of new and existing single nucleotide polymorphisms	Manual curation: author	Manual curation: curator	Gene, Sequence, Strain
Cell function