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Function

Function coveres annotations to gene and gene products using controlled vocabularies known as ontologies. The most common one is called The Gene Ontology (GO); GO is a combination of three controlled, hierarchical vocabularies designed to describe the molecular functions, biological processes and cellular components of gene products in a species-independent manner. GO annotations for rat genes in RatMine have been supplied by the Rat Genome Database. Included in RatMine are serveral other onologies such as Mammalian Phenotype (MP), Pathway (PW), and Disease (DO).
Current data

GO annotation in RatMine ...

The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism. The GO collaborators are developing three structured, controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner.

RatMine has GO annotations for R. norvigicus.

  • R. norvegicus - GO annotations for R. norvegicus gene products assigned by Rat Genome Database

Evidence Codes ...

Every GO annotation indicates the type of evidence that supports it; these evidence codes correspond to broad categories of experimental or other support. The codes are listed below. For more information, go to Guide to GO Evidence Codes.

EXP = Inferred from Experiment

IDA = Inferred from Direct Assay

IPI = Inferred from Physical Interaction

IMP = Inferred from Mutant Phenotype

IGI = Inferred from Genetic Interaction

IEP = Inferred from Expression Pattern

ISS = Inferred from Sequence or Structural Similarity

ISO = Inferred from Sequence Orthology

ISA = Inferred from Sequence Alignment

ISM = Inferred from Sequence Model

IGC = Inferred from Genomic Context

RCA = inferred from Reviewed Computational Analysis

TAS = Traceable Author Statement

NAS = Non-traceable Author Statement

IC = Inferred by Curator

ND = No biological Data available

IEA = Inferred from Electronic Annotation

NR = Not Recorded


Qualifiers ...

The Qualifier column is used for flags that modify the interpretation of an annotation. Allowable values are 'contributes_to', 'colocalizes_with' and 'NOT'. 'colocalizes_with' is used only with cellular component terms. 'contributes_to' is used only with molecular function terms. 'NOT' is used with terms from any of the three ontologies.

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Related template queries

Chromosome and Disease [and child terms] --> Genes

Disease Term Identifier [and children of this term] -> Genes

Disease Term [and children of this term] -> Genes

Gene -> GO Biological Process

Gene --> GO Terms

Gene --> Homologue Disease Annotations

Gene --> Homologue Mammalian Phenotype

Gene --> Homologue RGD Pathway Annotation

Gene --> Mammalian Phenotype Ontology

Gene --> RGD Pathway Ontology

GO term name [and children of this term] --> Genes

GO Term and Chromosome --> Genes

GO term name --> GO term identifier

GO term name --> Genes in one specific organism

Disease Term and Chromosome --> Genes

Gene --> Disease Ontology

Pathway Term -> Genes

QTL --> Genes in QTL region

Pathway Ontology ID -> Genes

Pathway Term and Chromosome --> Genes

Pathway Term [and children of this pathway] -> Genes

Protein --> UniProt Features

Mammalian Phenotype and Chromosome --> Genes

Mammalian Phenoype term name [and children of this term] --> Genes

Query starting points

These links will take you to the Query Builder pages which allow you to make new queries and create template queries of your own