The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro
Genome ResearchPublished 12 March 2003Open access
Evelyn Camon, Michele Magrane, Daniel Barrell, David Binns, Wolfgang Fleischmann, Paul Kersey
Citations347
SJR quartileQ1
SJR score3.91
SNIP1.37
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
GO vocabulary has been applied to the nonredundant proteome sets for all other completely sequenced organisms as well as to proteins from a wide range of organisms where the proteome is not yet complete.
Abstract
Gene Ontology Annotation (GOA) is a project run by the European Bioinformatics Institute (EBI) that aims to provide assignments of terms from the Gene Ontology (GO) resource to gene products in a number of its databases (http://www.ebi.ac.uk/GOA). In the first stage of this project, GO assignments have been applied to a data set representing the complete human proteome by a combination of electronic mappings and manual curation. This vocabulary has also been applied to the nonredundant proteome sets for all other completely sequenced organisms as well as to proteins from a wide range of organisms where the proteome is not yet complete.
Keywords
Biochemistry, Genetics and Molecular Biology
Nucleic Acids ResearchThe Pfam Protein Families Database
14,211 Citations2002Alex Bateman
In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up and new search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
Nucleic Acids ResearchThe SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999
3,238 Citations1999Amos Bairoch, Rolf Apweiler
Current developments of the database include: cross-references to additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT.
Nucleic Acids ResearchThe SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
3,133 Citations2000Amos Bairoch
The Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT, is described.
Nucleic Acids ResearchThe Ensembl genome database project
1,694 Citations2002Tim Hubbard
The Ensembl database project provides a bioinformatics framework to organise biology around the sequences of large genomes and is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources.
Nucleic Acids ResearchThe ENZYME database in 2000
1,140 Citations2000Amos Bairoch
The ENZYME database is a repository of information related to the nomenclature of enzymes that became an indispensable resource for the development of metabolic databases in recent years.
Nucleic Acids ResearchThe InterPro database, an integrated documentation resource for protein families, domains and functional sites
1,091 Citations2001Rolf Apweiler
InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects.
Nucleic Acids ResearchThe PROSITE database, its status in 2002
999 Citations2002Laurent Falquet
The PROSITE database consists of biologically significant patterns and profiles designed in such a way that with appropriate computational tools it can rapidly and reliably help to determine to which known family of proteins (if any) a new sequence belongs, or which known domain(s) it contains.
Genome ResearchCreating the Gene Ontology Resource: Design and Implementation
963 Citations2001The Gene Ontology Consortium
The Gene Ontology project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism, which includes building three extensive ontologies to describe molecular function, biological process, and cellular component.
Briefings in BioinformaticsPROSITE: A documented database using patterns and profiles as motif descriptors
931 Citations2002Christian J A Sigrist
The close relationship of PROSite with the SWISS-PROT protein database allows the evaluation of the sensitivity and specificity of the PROSITE motifs and their periodic reviewing.
Nucleic Acids ResearchRefSeq and LocusLink: NCBI gene-centered resources
914 Citations2001Kim D. Pruitt
Together, RefSeq and LocusLink provide a non-redundant view of genes and other loci to support research on genes and gene families, variation, gene expression and genome annotation.
The Mouseion at the JAXlibrary (Jackson Laboratory)Creating the gene ontology resource: design and implementation.
829 Citations2001Judith A. Blake, John Corradi +4 more
PubMed CentralThe Pfam Protein Families Database
770 Citations2002Bateman, Alex, Birney, Ewan +8 more
Nucleic Acids ResearchRecent improvements to the SMART domain-based sequence annotation resource
676 Citations2002Ivica Letunić
The SMART database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats and new advanced queries provide direct access to the SMART relational database using SQL.
Nucleic Acids ResearchTIGRFAMs: a protein family resource for the functional identification of proteins
485 Citations2001Daniel H. Haft
The term 'equivalog' is introduced to describe members of a set of homologous proteins that are conserved with respect to function since their last common ancestor to support the automated functional identification of proteins by sequence homology.
The Journal of ImmunologyCloning and expression of murine IL-12
469 Citations1992David S. Schoenhaut, A O Chua +7 more
The results indicate that the observed inability of human IL-12 to act on murine cells is largely determined by the p35 subunit.
Nucleic Acids ResearchSaccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
374 Citations2002Selina S. Dwight
SGD is annotating genes to the Gene Ontology, a structured representation of biological knowledge that can be shared across species, to provide its users with annotations that will allow relationships to be made between gene products, both within Saccharomyces cerevisiae and across species.
Nucleic Acids ResearchProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons
366 Citations2000F. Corpet
ProDom contains all protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases and results from a similar domain analysis as applied to completed genomes.
Nucleic Acids ResearchThe Protein Data Bank: unifying the archive
306 Citations2002John Westbrook
Progress has been made in validating all data in the PDB archive and in releasing a uniform archive for the community, and a collection of mmCIF data files for the P DB archive is produced.
Nucleic Acids ResearchThe Molecular Biology Database Collection: 2003 update
199 Citations2003A. D. Baxevanis
The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community that provide newvalue to the underlying data by virtue of curation, new data connections or other innovative approaches.
Nucleic Acids ResearchThe HSSP database of protein structure-sequence alignments and family profiles
198 Citations1998Carol L. Dodge
HSSP is a derived database merging structure (3D) and sequence (1-D) information that not only provides aligned sequence families, but also implies secondary and tertiary structures covering 33% of all sequences in SWISS-PROT.
Nucleic Acids ResearchThe Mouse Genome Database (MGD): the model organism database for the laboratory mouse
141 Citations2002Judith A. Blake
Recent integration of large datasets of mouse full-length cDNAs and radiation-hybrid mapped ESTs, the continued development and use of extensive structured vocabularies and the expansion of the representation of phenotypes highlight this year's developments.
BioinformaticsThe EBI SRS server—recent developments
131 Citations2002Evgeny M. Zdobnov, Rodrigo López +2 more
The InterPro database-Integrated Resource of Protein Domains and Functional Sites became a turning point in low level XML-SRS integration and the SRSQuickSearch JavaScript interfaces to SRS are introduced.
Nucleic Acids ResearchThe EMBL Nucleotide Sequence Database: major new developments
124 Citations2003Guenter Stoesser
The EMBL Nucleotide Sequence Database incorporates, organizes and distributes nucleotide sequences from all available public sources and links the main nucleotide and protein databases plus many other specialized molecular biology databases.
Nucleic Acids ResearchCluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins
121 Citations2001Evgenia V. Kriventseva
The CluSTr database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins, based on analysis of all pairwise comparisons between protein sequences, yielding a hierarchical organisation of clusters.
Nucleic Acids ResearchPRINTS and PRINTS-S shed light on protein ancestry
119 Citations2002Teresa K. Attwood
The PRINTS database houses a collection of protein fingerprints that may be used to make family and tentative functional assignments for uncharacterised sequences, and the use of its relational cousin,PRINTS-S, to model relationships between families, including those beyond the reach of conventional sequence analysis approaches is reported.
Nucleic Acids ResearchProteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes
114 Citations2001Rolf Apweiler
The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archaea and eukaryotes, giving a new perspective on families, domains and sites.
Genome ResearchPredicting Gene Ontology Functions from ProDom and CDD Protein Domains
95 Citations2002Jonathan Schug, Sharon Diskin +3 more
A heuristic algorithm for associating Gene Ontology defined molecular functions to protein domains as listed in the ProDom and CDD databases is described, indicating the utility of the approach and comparison with other methods in terms of coverage and agreement.
BioinformaticsA novel method for automatic functional annotation of proteins.
90 Citations1999Wolfgang Fleischmann, S Möller +2 more
A method of automatic annotation that produces highly reliable functional prediction using the language and the syntax of SWISS-PROT is developed and successfully used for the automatic annotation of a testset of unknown proteins.
Nucleic Acids ResearchThe FlyBase database of the Drosophila genome projects and community literature
86 Citations2002The FlyBase Consortium
FlyBase provides an integrated view of the fundamental genomic and genetic data on the major genetic model Drosophila melanogaster and related species through maps, gene ontologies, structured phenotypic and gene expression data, and anatomy.
Briefings in BioinformaticsFunctional information in SWISS-PROT: The basis for large-scale characterisation of protein sequences
63 Citations2001Rolf Apweiler
The SWISS-PROT protein sequence database plays an essential role here owing to its high level of functional information.
CytokineThe evolution of haematopoietic cytokine /receptor complexes
24 Citations1995Denis C. Shields, Dawn L. Harmon +2 more
A systematic analysis of primary sequence homology indicates that receptors for gp130-associated cytokines group into signal transducing and non-signal transduced receptors, which is consistent with the evolution of the interleukins 6, 11 and 12.
Comparative and Functional GenomicsTEMBLOR – Perspectives of EBI database services
5 Citations2002Henning Hermjakob, Rolf Apweiler
It is clear that distribution and storage of data in flat-files will have to be replaced in the future by more appropriate systems, and higher interoperability of databases is essential to cope with data of such magnitude and complexity.