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Gene Ontology: tool for the unification of biology
The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
The genome sequence of Drosophila melanogaster.
The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
This work describes the OBO Foundry initiative and provides guidelines for those who might wish to become involved and describes an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality.
The generic genome browser: a building block for a model organism system database.
The Generic Genome Browser (GBrowse) is described, a Web-based application for displaying genomic annotations and other features and easy integration with other components of a model organism system Web site.
Reactome: a knowledgebase of biological pathways
The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle.
Reactome knowledgebase of human biological pathways and processes
Improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa, Drosophila and Gallus gallus.
AmiGO: online access to ontology and annotation data
- S. Carbon, A. Ireland, C. Mungall, S. Shu, B. Marshall, S. Lewis
- Computer ScienceBioinform.
- 25 November 2008
AmiGO is a web application that allows users to query, browse and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO)…
Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource
The Gene Ontology (GO) project provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences.
Reactome: a knowledge base of biologic pathways and processes
This work uses Reactome to infer equivalent reactions in multiple nonhuman species, and presents data on the reliability of these inferred reactions for the distantly related eukaryote Saccharomyces cerevisiae.
Systematic determination of patterns of gene expression during Drosophila embryogenesis
Analyzing gene-expression patterns by in situ hybridization to whole-mount embryos provides an extremely rich dataset that can be used to identify genes involved in developmental processes that have been missed by traditional genetic analysis.