Finding one's way in proteomics: a protein species nomenclature (2009)
Schlüter, Hartmut, Apweiler, Rolf, Holzhütter, Hermann-Georg, Jungblut, Peter R
Abstract Our knowledge of proteins has greatly improved in recent years, driven by new technologies in the fields of molecular biology and proteome research. It has become clear that from a single...
The Gene Ontology Annotation (GOA) Database (2009)
Rachael Huntley, Emily Dimmer, Daniel Barrell, David Binns, Rolf Apweiler
The Gene Ontology (GO) is a well-established, structured vocabulary that has been successfully used for 10 years in the annotation of proteins. GO terms, created in consultation with the biology...
Cardiovascular Gene Ontology Annotation Initiative (2009)
Varsha K. Khodiyar, Daniel G. Barrell, Peter Scambler, Mike Hubank, Rolf Apweiler, Philippa J. Talmud, ...
Gene Ontology (GO) provides a controlled vocabulary, which is used by several groups around the world to provide functional annotation to proteins across a wide range of species...
The GOA database in 2009--an integrated Gene Ontology Annotation resource (2009)
Barrell, Daniel, Dimmer, Emily, Huntley, Rachael P., Binns, David, ODonovan, Claire, Apweiler, Rolf
The Gene Ontology Annotation (GOA) project at the EBI (http://www.ebi.ac.uk/goa) provides high-quality electronic and manual associations (annotations) of Gene Ontology (GO) terms to UniProt...
InterPro: the integrative protein signature database (2009)
Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse...
Apweiler, Rolf, Aslanidis, Charalampos, Deufel, Thomas, Gerstner, Andreas, Hansen, Jens, Hochstrasser, Dennis, ...
The field of clinical proteomics offers opportunities to identify new disease biomarkers in body fluids, cells and tissues. These biomarkers can be used in clinical applications for diagnosis,...
Getting a grip on proteomics data - Proteomics Data Collection (ProDaC) (2009)
Eisenacher, Martin, Martens, Lennart, Kohl, Michael, Barsnes, Harald, Helsens, Kenny, Häkkinen, Jari, ...
In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the...
Ye, Kai, Schulz, Marcel H., Long, Quan, Apweiler, Rolf, Ning, Zemin
Motivation: There is a strong demand in the genomic community to develop effective algorithms to reliably identify genomic variants. Indel detection using next-gen data is difficult and...
QuickGO: a web-based tool for Gene Ontology searching (2009)
Binns, David, Dimmer, Emily, Huntley, Rachael, Barrell, Daniel, O'Donovan, Claire, Apweiler, Rolf
Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups...
Sandra Orchard, Weimin Zhu, All K. Julian, Henning Hermjakob, Rolf Apweiler
The Protein Standards Initiative (PSI) group of the Human Proteome Organisation (HUPO) has been tasked with the establishment of common standards for data exchange in the field of proteomics [1]. The...
Lennart Martens, Ra Orchard, Rolf Apweiler, Henning Hermjakob
The MCP guidelines on the publication of the underlying data supporting proteomics papers (1) spearheaded a movement toward more structured sharing of (high quality) data. The original MCP guidelines...
Evelyn Camon, Emily Dimmer, Daniel Barrell, Nicola Mulder, Rolf Apweiler, Fiona M. Mccarthy, ...
electronic and manual annotations to the UniProt Knowledgebase using the standardized vocabulary of the Gene Ontology (GO). As a supplementary archive of GO annotation, GOA promotes a high level of...
The Functional Genomics Experiment model (FuGE): (2008)
Andrew R Jones, Michael Miller, Ruedi Aebersold, Rolf Apweiler, Catherine A Ball, Alvis Brazma, ...
an extensible framework for standards in functional genomics
Chatr-aryamontri, Andrew, Kerrien, Samuel, Khadake, Jyoti, Orchard, Sandra, Ceol, Arnaud, Licata, Luana, ...
Abstract Background In the absence of consolidated pipelines to archive biological data electronically, information dispersed in the literature must be captured by manual annotation. Unfortunately,...
1 Overview of the HUPO Plasma Proteome Project: Results from (2008)
Gilbert S. Omenn, David J. States, Marcin Adamski, Thomas W. Blackwell, Rajasree Menon, Henning Hermjakob, ...
the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database*
Taylor, Chris, Field, Dawn, Sansone, Susanna-Assunta, Apweiler, Rolf, Ashburner, Michael, Ball, Cathy, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those...
Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Asburner, Michael, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated...
The speciation of the proteome (2008)
Jungblut, Peter R, Holzhütter, Hermann G, Apweiler, Rolf, Schlüter, Hartmut
Abstract Introduction In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms....
Paul J. Kersey, Jorge Duarte, Allyson Williams, Youla Karavidopoulou, Ewan Birney, Rolf Apweiler
Despite the complete determination of the genome sequence of several higher eukaryotes, their proteomes remain relatively poorly defined. Information about proteins identified by different...
Prodom Smart, Tigrfams The Consortium, Interpro An Integrated, The Interpro, Consortium Nicola, J. Mulder, ...
is a group of scientists responsible for the production and maintenance of InterPro
Bioinformatics Plant Protein Annotation in the UniProt Knowledgebase 1 (2008)
Michel Schneider, Amos Bairoch, Cathy H. Wu, Rolf Apweiler
Archive, the UniProt Knowledgebase (UniProtKB), and the UniProt Reference Clusters. The UniProtKB consists of two sections: UniProtKB/Swiss-Prot (fully manually curated entries) and UniProtKB/TrEMBL...
BMC Biology BioMed Central (2008)
Samuel Kerrien, Ra Orchard, Luisa Montecchi-palazzi, Bruno Ar, Antony F Quinn, Nisha Vinod, ...
Software Broadening the horizon – level 2.5 of the HUPO-PSI format for
An application of latent topic document analysis to large-scale proteomics databases (2008)
Sebastian Klie, Lennart Martens, Juan Antonio Vizcaino, Richard Cote, Phil Jones, Rolf Apweiler, ...
Abstract. Since the advent of public data repositories for proteomics data, readily accessible results from high-throughput experiments have been accumulating steadily. Several large-scale projects...
The speciation of the proteome (2008)
Jungblut, Peter R., Holzhütter, Hermann G., Apweiler, Rolf, Schlüter, Hartmut
Abstract Introduction In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms....
Cochrane, Guy, Akhtar, Ruth, Aldebert, Philippe, Althorpe, Nicola, Baldwin, Alastair, Bates, Kirsty, ...
The Ensembl Trace Archive (http://trace.ensembl.org/) and the EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), known together as the European Nucleotide Archive, continue to see growth...
UniProtJAPI: a remote API for accessing UniProt data (2008)
Patient, Samuel, Wieser, Daniela, Kleen, Michael, Kretschmann, Ernst, Jesus Martin, Maria, Apweiler, Rolf
Summary: Programmatic access to the UniProt Knowledgebase (UniProtKB) is essential for many bioinformatics applications dealing with protein data. We have created a Java library named UniProtJAPI,...
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries (2008)
Côté, Richard G., Jones, Philip, Martens, Lennart, Apweiler, Rolf, Hermjakob, Henning
The Ontology Lookup Service (OLS) (http://www.ebi.ac.uk/ols) provides interactive and programmatic interfaces to query, browse and navigate an ever increasing number of biomedical ontologies and...
Integrated Relational Enzyme Database (IntEnz) (2007)
Astrid Fleischmann, Kirill Degtayarenko, Michael Darsow, Wolfgang Fleischmann, Rolf Apweiler
IntEnz [1] is the name for the Integrated relational enzyme database. IntEnz is supported by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) [2]...
Michael Schroeder, Rolf Apweiler
heterogeneous information resources applied to the annotation of transmembrane proteins
of proteins in whole genomes (2007)
Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Er Kanapin, Youla Karavidopoulou, Paul Kersey, ...
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...
Steffen Moller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler
Many databases in molecular biology face the problem that the ever increasing rate of data production can not be handled any more with traditional methods, especially human curation. Therefore a...
EDITtoTrEMBL: A Distributed Approach to High-Quality (2007)
Automated Protein Sequence, Steffen Moller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler
Many databases in molecular biology face the problem that the ever increasing rate of data production can not be handled any more with traditional methods, especially human curation. Therefore a...
Daniela Wieser, Ernst Kretschmann, Astrid Rakow, André Hackmann, Rolf Apweiler
Manual annotation of database entries by specifically trained staff yields highly reliable information on biomolecular data. However, automated annotation approaches of protein data are becoming...
Côté, Richard G, Jones, Philip, Martens, Lennart, Kerrien, Samuel, Reisinger, Florian, Lin, Quan, ...
Abstract Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins...
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions (2007)
Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, ...
Abstract Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats,...
Jones, Andrew R, Miller, Michael, Aebersold, Ruedi, Apweiler, Rolf, Ball, Catherine A, Brazma, Alvis, ...
The Functional Genomics Experiment data model (FuGE) has been developed to facilitate convergence of data standards for high-throughput, comprehensive analyses in biology. FuGE models the components...
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
New developments in the interpro database (2007)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE,
EMBL Nucleotide Sequence Database in 2006 (2007)
Kulikova, Tamara, Akhtar, Ruth, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baldwin, Alastair, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and...
New developments in the InterPro database (2007)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs,...
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
GOAnnotator: linking protein GO annotations to evidence text (2006)
Couto, Francisco M, Silva, Mário J, Lee, Vivian, Dimmer, Emily, Camon, Evelyn, Apweiler, Rolf, ...
Abstract Background Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead...
Orchard, Sandra, Apweiler, Rolf, Barkovich, Robert, Field, Dawn, Garavelli, John S., Horn, David, ...
The theme of the third annual Spring workshop of the HUPO-PSI was proteomics and beyond and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups...
Apweiler, Rolf, Arnold, Georg, Becker, Albert, Blüggel, Martin, Carrette, Odile, ...
The Human Proteome Organisation (HUPO) initiated several projects focusing on the proteome analysis of distinct human organs. The Brain Proteome Project (BPP) is the initiative dedicated to the...
Côté, Richard G, Jones, Philip, Apweiler, Rolf, Hermjakob, Henning
Abstract Background With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to...
Sandra Orchard, Paul Kersey, Henning Hermjakob, Rolf Apweiler
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields...
Sandra Orchard, Paul Kersey, Weimin Zhu, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Rapid progress has...
node of the International Nucleotide Sequence Database Collaboration (2006)
Tamara Kulikova, Ruth Akhtar, Nicola Althorpe, Mikael Andersson, Francesco Nardone, Maria Pilar, ...
UniSave: the UniProtKB Sequence/Annotation Version database. Bioinformatics (2006)
Rasko Leinonen, Francesco Nardone, Weimin Zhu, Rolf Apweiler
Associate Editor: Dmitrij Frishman (2006)
Rasko Leinonen, Francesco Nardone, Weimin Zhu, Rolf Apweiler
Summary: The UniProtKB Sequence/Annotation Version database (UniSave) is a comprehensive archive of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. All changed Swiss-Prot and TrEMBL entries...
Bmc Bioinformatics, Richard G Côté, Philip Jones, Rolf Apweiler, Henning Hermjakob, Henning Hermjakob
Software The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
UniSave: the UniProtKB Sequence/Annotation Version database (2006)
Leinonen, Rasko, Nardone, Francesco, Zhu, Weimin, Apweiler, Rolf
Summary: The UniProtKB Sequence/Annotation Version database (UniSave) is a comprehensive archive of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. All changed Swiss-Prot and TrEMBL entries...
EMBL Nucleotide Sequence Database in 2006 (2006)
Kulikova, Tamara, Akhtar, Ruth, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baldwin, Alastair, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and...
EMBL Nucleotide Sequence Database: developments in 2005 (2006)
Cochrane, Guy, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baker, Wendy, Baldwin, Alastair, ...
The EMBL Nucleotide Sequence Database (www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation,...
The Universal Protein Resource (UniProt): an expanding universe of protein information (2006)
Wu, Cathy H., Apweiler, Rolf, Bairoch, Amos, Natale, Darren A., Barker, Winona C., Boeckmann, Brigitte, ...
The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein...
Jones, Philip, Côté, Richard G., Martens, Lennart, Quinn, Antony F., Taylor, Chris F., Derache, William, ...
PRIDE, the ‘PRoteomics IDEntifications database’ (http://www.ebi.ac.uk/pride) is a database of protein and peptide identifications that have been described in the scientific literature. These...
EMBL Nucleotide Sequence Database in 2006 (2006)
Kulikova, Tamara, Akhtar, Ruth, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baldwin, Alastair, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl) at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and...
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA (2005)
Camon, Evelyn B, Barrell, Daniel G, Dimmer, Emily C, Lee, Vivian, Magrane, Michele, Maslen, John, ...
Abstract Background The Gene Ontology Annotation (GOA) database http://www.ebi.ac.uk/GOA aims to provide high-quality supplementary GO annotation to proteins in the UniProt Knowledgebase. Like many...
BIOINFORMATICS APPLICATIONS NOTE Databases and ontologies (2005)
Philip Jones, Nisha Vinod, Thomas Down, Andre Hackmann, Andreas Kahari, Ernst Kretschmann, ...
Vol. 21 no. 14 2005, pages 3198–3199 doi:10.1093/bioinformatics/bti506
Annotating the human proteome (2005)
Ra Orchard, Henning Hermjakob, Rolf Apweiler
The completion of the human genome has shifted the attention from deciphering the sequence to the identification and characterization of the encoded components. The identification and functional...
Integr8 and genome reviews: integrated views of complete genomes and proteomes (2005)
Paul Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, ...
Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes. For over 190 species, Integr8 provides access to general information, recent publications, and a...
The embl nucleotide sequence database (2005)
Carola Kanz, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, ...
BIOINFORMATICS ORIGINAL PAPER Sequence analysis The predictive power of the CluSTr database (2005)
Robert Petryszak, Ernst Kretschmann, Daniela Wieser, Rolf Apweiler
Summary: The CluSTr database employs a fully automatic singlelinkage hierarchical clustering method based on a similarity matrix. In order to compute the matrix, first all-against-all pair-wise...
S. Orchard, L. Montecchi-palazzi, H. Hermjakob, R. Apweiler, Sandra Orchard, Luisa Montecchi-palazzi, ...
Controlled vocabularies provide a roadmap through complex biological data. Proteomic data is increasing in volume and is currently poorly served by public repositories due to the large number of...
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA (2005)
Bmc Bioinformatics, Evelyn B Camon, Daniel G Barrell, Emily C Dimmer, Vivian Lee, Michele Magrane, ...
from A critical assessment of text mining methods in molecular biology
Francisco M. Couto, Mário J. Silva, Vivian Lee, Evelyn Camon, Rolf Apweiler, Harald Kirsch, ...
Technical reports are available at
InterPro, progress and status in 2005 (2005)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
The EMBL Nucleotide Sequence Database (www.ebi. (2005)
Guy Cochrane, Nicola Althorpe, Mikael Andersson, Matias Castro, Karyn Duggan, Ruth Eberhardt, ...
The Universal Protein Resource (UniProt) (2005)
Bairoch, Amos, Apweiler, Rolf, Wu, Cathy H., Barker, Winona C., Boeckmann, Brigitte, Ferro, Serenella, ...
The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the...
InterPro, progress and status in 2005 (2005)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
The EMBL Nucleotide Sequence Database (2005)
Kanz, Carola, Aldebert, Philippe, Althorpe, Nicola, Baker, Wendy, Baldwin, Alastair, Bates, Kirsty, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences...
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes (2005)
Kersey, Paul, Bower, Lawrence, Morris, Lorna, Horne, Alan, Petryszak, Robert, Kanz, Carola, ...
Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes. For over 190 species, Integr8 provides access to general information, recent publications, and a...
Dasty and UniProt DAS: a perfect pair for protein feature visualization (2005)
Jones, Philip, Vinod, Nisha, Down, Thomas, Hackmann, Andre, Kahari, Andreas, Kretschmann, Ernst, ...
Summary: In this study, we present two freely available and complementary Distributed Annotation System (DAS) resources: a DAS reference server that provides up-to-date sequence and annotation from...
Blaschke, Christian, Yeh, Alexander, Camon, Evelyn, Colosimo, Marc, Apweiler, Rolf, Hirschman, Lynette, ...
The predictive power of the CluSTr database (2005)
Petryszak, Robert, Kretschmann, Ernst, Wieser, Daniela, Apweiler, Rolf
Summary: The CluSTr database employs a fully automatic single-linkage hierarchical clustering method based on a similarity matrix. In order to compute the matrix, first all-against-all pair-wise...
Dasty and UniProt DAS: a perfect pair for protein feature visualization (2005)
Jones, Philip, Vinod, Nisha, Down, Thomas, Hackmann, Andre, Kahari, Andreas, Kretschmann, Ernst, ...
Summary: Here we present two freely available and complementary DAS resources: a DAS reference server that provides up-to-date sequence and annotation from UniProt, with additional feature links and...
The predictive power of the CluSTr database (2005)
Petryszak, Robert, Kretschmann, Ernst, Wieser, Daniela, Apweiler, Rolf
Summary: The CluSTr database employs a fully automatic single-linkage hierarchical clustering method, based on a similarity matrix. In order to compute the matrix, firstly all-against-all pair-wise...
Blaschke, Christian, Yeh, Alexander, Camon, Evelyn, Colosimo, Marc, Apweiler, Rolf, Hirschman, Lynette, ...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Integrating Genomic and Proteomic Data: The Integr8 Project (2004)
Pruess, Manuela, Kersey, Paul, Apweiler, Rolf
Integr8 (http://www.ebi.ac.uk/integr8/) has been developed to provide an integration layer for the exploitation of genomic and proteomic data. High-quality databases from major bioinformatics centres...
The EMBL Nucleotide Sequence Database (2004)
Tamara Kulikova, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Guy Cochrane, ...
Rasko Leinonen, Federico Garcia Diez, David Binns, Wolfgang Fleischmann, Rodrigo Lopez, Rolf Apweiler
Summary: UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant publicly accessible resources....
UniProt: the Universal Protein Knowledgebase (2004)
Rolf Apweiler, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, ...
To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities...
Protein Sequence Databases (2004)
Rolf Apweiler, Amos Bairoch, Cathy H Wu
PIR-PSD Protein Information Resource Protein Sequence Database RefSeq Reference Sequence TrEMBL Translation from EMBL UniParc UniProt Archive Introduction With the availability of over 165 completed...
doi:10.1093/nar/gki070 The Universal Protein Resource (UniProt) (2004)
Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, ...
The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the...
Leinonen, Rasko, Diez, Federico Garcia, Binns, David, Fleischmann, Wolfgang, Lopez, Rodrigo, Apweiler, Rolf
Summary: UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant publicly accessible resources....
Leinonen, Rasko, Diez, Federico Garcia, Binns, David, Fleischmann, Wolfgang, Lopez, Rodrigo, Apweiler, Rolf
Summary: UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant, publicly accessible resources....
UniProt: the Universal Protein knowledgebase (2004)
Apweiler, Rolf, Bairoch, Amos, Wu, Cathy H., Barker, Winona C., Boeckmann, Brigitte, Ferro, Serenella, ...
To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss‐Prot, TrEMBL and PIR protein database...
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology (2004)
Camon, Evelyn, Magrane, Michele, Barrell, Daniel, Lee, Vivian, Dimmer, Emily, Maslen, John, ...
The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high‐quality electronic and manual annotations to the UniProt Knowledgebase (Swiss‐Prot, TrEMBL and...
The EMBL Nucleotide Sequence Database (2004)
Kulikova, Tamara, Aldebert, Philippe, Althorpe, Nicola, Baker, Wendy, Bates, Kirsty, Browne, Paul, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), maintained at the European Bioinformatics Institute (EBI), incorporates, organizes and distributes nucleotide sequences from public...
IntEnz, the integrated relational enzyme database (2004)
Fleischmann, Astrid, Darsow, Michael, Degtyarenko, Kirill, Fleischmann, Wolfgang, Boyce, Sinéad, Axelsen, Kristian B., ...
IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature...
IntAct: an open source molecular interaction database (2004)
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
Leinonen, Rasko, Diez, Federico Garcia, Binns, David, Fleischmann, Wolfgang, Lopez, Rodrigo, Apweiler, Rolf
Summary: UniProt Archive (UniParc) is the most comprehensive, non-redundant protein sequence database available. Its protein sequences are retrieved from predominant publicly accessible resources....
Increase of functional diversity by alternative splicing (2003)
Kriventseva,Evgenia V., Koch,Ina, Apweiler,Rolf, Vingron,Martin, Bork,Peer, Gelfand,Mikhail S., ...
A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Increase of functional diversity by alternative splicing (2003)
Kriventseva, Evgenia V., Koch, Ina, Apweiler, Rolf, Vingron, Martin, Bork, Peer, Gelfand, Mikhail S., ...
A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by...
The swiss-prot protein knowledgebase and its supplement trembl in 2003 (2003)
Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-claude Blatter, Anne Estreicher, Elisabeth Gasteiger, ...
The SWISS-PROT protein knowledgebase
The InterPro Database, 2003 brings increased coverage and new features (2003)
Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
Ra Orchard, Weimin Zhu, Luisa Montecchi-palazzi, Henning Hermjakob, Rolf Apweiler, Henning Hermjakob Embl
The inaugural meeting of the PSI in October 2002 brought together representatives from the database producer, user and software producer communities
Sandra Orchard, Paul Kersey, Henning Hermjakob, Rolf Apweiler
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields...
Sandra Orchard, Paul Kersey, Weimin Zhu, Luisa Montecchi-Palazzi, Henning Hermjakob, Rolf Apweiler
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Rapid progress has...
Bioinformatics Resources for In Silico Proteome Analysis (2003)
In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise...
Camon, Evelyn, Magrane, Michele, Barrell, Daniel, Binns, David, Fleischmann, Wolfgang, Kersey, Paul, ...
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...
The InterPro Database, 2003 brings increased coverage and new features (2003)
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 (2003)
Boeckmann, Brigitte, Bairoch, Amos, Apweiler, Rolf, Blatter, Marie-Claude, Estreicher, Anne, Gasteiger, Elisabeth, ...
The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein...
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes (2003)
Pruess, Manuela, Fleischmann, Wolfgang, Kanapin, Alexander, Karavidopoulou, Youla, Kersey, Paul, Kriventseva, Evgenia, ...
The Proteome Analysis database (http://www.ebi.ac.uk/proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the...
The European Bioinformatics Institute's data resources (2003)
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
Camon, Evelyn, Magrane, Michele, Barrell, Daniel, Binns, David, Fleischmann, Wolfgang, Kersey, Paul, ...
DOI: 10.1093/nar/gkg066 The European Bioinformatics Institute’s data resources (2002)
Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola Mulder, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
The EBI SRS server-recent developments (2002)
Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold
Abstract. The current data explosion is intractable without advanced data management systems. The numerous data sets become really useful when they are interconnected under a uniform interface-...
The EBI SRS server - recent developments (2002)
Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold
Motivation: The current data explosion is intractable without advanced data management systems. The numerous data sets become really useful when they are interconnected under a uniform...
The EBI SRS server - new features (2002)
Evgeny M. Zdobnov, Rodrigo Lopez, Rolf Apweiler
Summary: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI...
Mulder, Nicola J., Apweiler, Rolf, Attwood, Terri K., Bairoch, Amos, Bateman, Alex, ...
The exponential increase in the submission of nucleotide sequences to the nucleotide sequence database by genome sequencing centres has resulted in a need for rapid, automatic methods for...
High-quality protein knowledge resource: SWISS-PROT and TrEMBL (2002)
O'Donovan, Claire, Martin, Maria Jesus, Gattiker, Alexandre, Gasteiger, Elisabeth, Bairoch, Amos, Apweiler, Rolf
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational...
Applications of InterPro in protein annotation and genome analysis (2002)
Biswas, Margaret, O'Rourke, John F., Camon, Evelyn, Fraser, Gill, Kanapin, Alexander, Karavidopoulou, Youla, ...
The applications of InterPro span a range of biologically important areas that includes automatic annotation of protein sequences and genome analysis. In automatic annotation of protein sequences...
The EBI SRS server--new features (2002)
Zdobnov, Evgeny M., Lopez, Rodrigo, Apweiler, Rolf, Etzold, Thure
Motivation: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The...
The EBI SRS server--recent developments (2002)
Zdobnov, Evgeni M., Lopez, Rodrigo, Apweiler, Rolf, Etzold, Thure
Motivation: The current data explosion is intractable without advanced data management systems. The numerous data sets become really useful when they are interconnected under a uniform...
Tools and resources for identifying protein families, domains and motifs (2001)
Mulder, Nicola J, Apweiler, Rolf
Abstract With the large influx of raw sequence data from genome sequencing projects, there is a need for reliable automatic methods for protein sequence analysis and classification. The most useful...
Application of InterPro for the functional classification of the proteins of fish origin in (2001)
Margaret Biswas, Alex Kanapin, Rolf Apweiler
InterPro
Using the molecular biology data (2001)
Evgeni M. Zdobnov, Rodrigo Lopez, Rolf Apweiler, Thure Etzold
The goal of this article is to introduce the most important of the different molecular biology databases available to researchers. Recent advances in technology have resulted in an information...
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins (2001)
Evgenia V. Kriventseva, Wolfgang Fleischmann, Evgeni M. Zdobnov, Rolf Apweiler
The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on...
Evaluation of methods for the prediction of membrane spanning regions (2001)
Möller, Steffen, Croning, Michael D. R., Apweiler, Rolf
Motivation: A variety of tools are available to predict the topology of transmembrane proteins. To date no independent evaluation of the performance of these tools has been published. A better...
Kretschmann, Ernst, Fleischmann, Wolfgang, Apweiler, Rolf
Motivation: The gap between the amount of newly submitted protein data and reliable functional annotation in public databases is growing. Traditional manual annotation by literature curation and...
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins (2001)
Kriventseva, Evgenia V., Fleischmann, Wolfgang, Zdobnov, Evgeni M., Apweiler, Rolf
The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on...
Apweiler, Rolf, Biswas, Margaret, Fleischmann, Wolfgang, Kanapin, Alexander, Karavidopoulou, Youla, Kersey, Paul, ...
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...
With the rapid growth of sequence databases, there is an increasing need for reliable functional characterisation and annotation of newly predicted proteins. To cope with such large data volumes,...
InterProScan - an integration platform for the signature-recognition methods in InterPro (2001)
Zdobnov, Evgeni M., Apweiler, Rolf
Summary: InterProScan is a tool that scans given protein sequences against the protein signatures of the InterPro member databases, currently – PROSITE, PRINTS, Pfam, ProDom and SMART. The number...
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al. (2001)
A comparison of signal sequence prediction methods using a test set of signal peptides (2000)
Menne, Kerstin M.L., Hermjakob, Henning, Apweiler, Rolf
Summary: We describe the creation of a test set containing secretory and non-secretory proteins. Five existing prediction programs for signal sequences and their cleavage sites are compared on the...
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 (2000)
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational...
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL (2000)
Kersey, Paul, Hermjakob, Henning, Apweiler, Rolf
Summary: The program varsplic.pl uses information present in the SWISS-PROT and TrEMBL databases to create new records for alternatively spliced isoforms. These new records can be used in similarity...
The SWISS-PROT protein sequence data bank and its supplement TrEMBL (1999)
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, structure of its domains,...
The SWISS-PROT protein sequence data bank and its supplement TrEMBL (1999)
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational...
The SWISS-PROT protein sequence data bank and its supplement TrEMBL (1999)
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational...
The SWISS-PROT protein sequence data bank and its supplement TrEMBL (1999)
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational...
EDITtoTrEMBL: A Distributed Approach to High-Quality Automated Protein Sequence Annotation (1999)
Steffen Möller, Ulf Leser, Wolfgang Fleischmann, Rolf Apweiler
Summary: Many databases in molecular biology face the problem that the ever increasing rate of data production can not be handled any more with traditional methods, especially human curation....
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998 (1998)
SWISS-PROT (http://www.expasy.ch/ ) is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains...
Heidelberg, Univ., Diss., 1994.
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins
Kriventseva, Evgenia V., Fleischmann, Wolfgang, Zdobnov, Evgeni M., Apweiler, Rolf
The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on...
Apweiler, Rolf, Biswas, Margaret, Fleischmann, Wolfgang, Kanapin, Alexander, Karavidopoulou, Youla, Kersey, Paul, ...
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...
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational...
Tools and resources for identifying protein families, domains and motifs
Mulder, Nicola J, Apweiler, Rolf
With the large influx of raw sequence data from genome sequencing projects, there is a need for reliable automatic methods for protein sequence analysis and classification. The most useful tools use...
The InterPro Database, 2003 brings increased coverage and new features
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
The European Bioinformatics Institute's data resources
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
Boeckmann, Brigitte, Bairoch, Amos, Apweiler, Rolf, Blatter, Marie-Claude, Estreicher, Anne, Gasteiger, Elisabeth, ...
The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein...
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes
Pruess, Manuela, Fleischmann, Wolfgang, Kanapin, Alexander, Karavidopoulou, Youla, Kersey, Paul, Kriventseva, Evgenia, ...
The Proteome Analysis database (http://www.ebi.ac.uk/proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the...
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
Camon, Evelyn, Magrane, Michele, Barrell, Daniel, Lee, Vivian, Dimmer, Emily, Maslen, John, ...
The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD)...
IntAct: an open source molecular interaction database
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
IntEnz, the integrated relational enzyme database
Fleischmann, Astrid, Darsow, Michael, Degtyarenko, Kirill, Fleischmann, Wolfgang, Boyce, Sinéad, Axelsen, Kristian B., ...
IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature...
The EMBL Nucleotide Sequence Database
Kulikova, Tamara, Aldebert, Philippe, Althorpe, Nicola, Baker, Wendy, Bates, Kirsty, Browne, Paul, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), maintained at the European Bioinformatics Institute (EBI), incorporates, organizes and distributes nucleotide sequences from public...
UniProt: the Universal Protein knowledgebase
Apweiler, Rolf, Bairoch, Amos, Wu, Cathy H., Barker, Winona C., Boeckmann, Brigitte, Ferro, Serenella, ...
To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro
Camon, Evelyn, Magrane, Michele, Barrell, Daniel, Binns, David, Fleischmann, Wolfgang, Kersey, Paul, ...
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...
Bioinformatics Resources for In Silico Proteome Analysis
Pruess, Manuela, Apweiler, Rolf
In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise...
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
Kersey, Paul, Bower, Lawrence, Morris, Lorna, Horne, Alan, Petryszak, Robert, Kanz, Carola, ...
Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes. For over 190 species, Integr8 provides access to general information, recent publications, and a...
The Universal Protein Resource (UniProt)
Bairoch, Amos, Apweiler, Rolf, Wu, Cathy H., Barker, Winona C., Boeckmann, Brigitte, Ferro, Serenella, ...
The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the...
The EMBL Nucleotide Sequence Database
Kanz, Carola, Aldebert, Philippe, Althorpe, Nicola, Baker, Wendy, Baldwin, Alastair, Bates, Kirsty, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
EMBL Nucleotide Sequence Database: developments in 2005
Cochrane, Guy, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baker, Wendy, Baldwin, Alastair, ...
The EMBL Nucleotide Sequence Database () at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to...
PRIDE: a public repository of protein and peptide identifications for the proteomics community
Jones, Philip, Côté, Richard G., Martens, Lennart, Quinn, Antony F., Taylor, Chris F., Derache, William, ...
PRIDE, the ‘PRoteomics IDEntifications database’ () is a database of protein and peptide identifications that have been described in the scientific literature. These identifications will...
The Universal Protein Resource (UniProt): an expanding universe of protein information
Wu, Cathy H., Apweiler, Rolf, Bairoch, Amos, Natale, Darren A., Barker, Winona C., Boeckmann, Brigitte, ...
The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein...
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
Côté, Richard G, Jones, Philip, Apweiler, Rolf, Hermjakob, Henning
Plant Protein Annotation in the UniProt Knowledgebase1
Schneider, Michel, Bairoch, Amos, Wu, Cathy H., Apweiler, Rolf
The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium....
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins
Kriventseva, Evgenia V., Fleischmann, Wolfgang, Zdobnov, Evgeni M., Apweiler, Rolf
The CluSTr (Clusters of SWISS-PROT and TrEMBL proteins) database offers an automatic classification of SWISS-PROT and TrEMBL proteins into groups of related proteins. The clustering is based on...
Apweiler, Rolf, Biswas, Margaret, Fleischmann, Wolfgang, Kanapin, Alexander, Karavidopoulou, Youla, Kersey, Paul, ...
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...
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational...
Tools and resources for identifying protein families, domains and motifs
Mulder, Nicola J, Apweiler, Rolf
With the large influx of raw sequence data from genome sequencing projects, there is a need for reliable automatic methods for protein sequence analysis and classification. The most useful tools use...
The InterPro Database, 2003 brings increased coverage and new features
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Barrell, Daniel, Bateman, Alex, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one...
The European Bioinformatics Institute's data resources
Brooksbank, Catherine, Camon, Evelyn, Harris, Midori A., Magrane, Michele, Martin, Maria Jesus, Mulder, Nicola, ...
As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics...
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
Boeckmann, Brigitte, Bairoch, Amos, Apweiler, Rolf, Blatter, Marie-Claude, Estreicher, Anne, Gasteiger, Elisabeth, ...
The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein...
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes
Pruess, Manuela, Fleischmann, Wolfgang, Kanapin, Alexander, Karavidopoulou, Youla, Kersey, Paul, Kriventseva, Evgenia, ...
The Proteome Analysis database (http://www.ebi.ac.uk/proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the...
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
Camon, Evelyn, Magrane, Michele, Barrell, Daniel, Lee, Vivian, Dimmer, Emily, Maslen, John, ...
The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD)...
IntAct: an open source molecular interaction database
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
IntEnz, the integrated relational enzyme database
Fleischmann, Astrid, Darsow, Michael, Degtyarenko, Kirill, Fleischmann, Wolfgang, Boyce, Sinéad, Axelsen, Kristian B., ...
IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature...
The EMBL Nucleotide Sequence Database
Kulikova, Tamara, Aldebert, Philippe, Althorpe, Nicola, Baker, Wendy, Bates, Kirsty, Browne, Paul, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), maintained at the European Bioinformatics Institute (EBI), incorporates, organizes and distributes nucleotide sequences from public...
UniProt: the Universal Protein knowledgebase
Apweiler, Rolf, Bairoch, Amos, Wu, Cathy H., Barker, Winona C., Boeckmann, Brigitte, Ferro, Serenella, ...
To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
The Gene Ontology Annotation (GOA) Project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro
Camon, Evelyn, Magrane, Michele, Barrell, Daniel, Binns, David, Fleischmann, Wolfgang, Kersey, Paul, ...
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...
Bioinformatics Resources for In Silico Proteome Analysis
Pruess, Manuela, Apweiler, Rolf
In the growing field of proteomics, tools for the in silico analysis of proteins and even of whole proteomes are of crucial importance to make best use of the accumulating amount of data. To utilise...
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
Kersey, Paul, Bower, Lawrence, Morris, Lorna, Horne, Alan, Petryszak, Robert, Kanz, Carola, ...
Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes. For over 190 species, Integr8 provides access to general information, recent publications, and a...
The Universal Protein Resource (UniProt)
Bairoch, Amos, Apweiler, Rolf, Wu, Cathy H., Barker, Winona C., Boeckmann, Brigitte, Ferro, Serenella, ...
The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the...
The EMBL Nucleotide Sequence Database
Kanz, Carola, Aldebert, Philippe, Althorpe, Nicola, Baker, Wendy, Baldwin, Alastair, Bates, Kirsty, ...
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences...
InterPro, progress and status in 2005
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam,...
Plant Protein Annotation in the UniProt Knowledgebase1
Schneider, Michel, Bairoch, Amos, Wu, Cathy H., Apweiler, Rolf
The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium....
EMBL Nucleotide Sequence Database: developments in 2005
Cochrane, Guy, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baker, Wendy, Baldwin, Alastair, ...
The EMBL Nucleotide Sequence Database () at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to...
PRIDE: a public repository of protein and peptide identifications for the proteomics community
Jones, Philip, Côté, Richard G., Martens, Lennart, Quinn, Antony F., Taylor, Chris F., Derache, William, ...
PRIDE, the ‘PRoteomics IDEntifications database’ () is a database of protein and peptide identifications that have been described in the scientific literature. These identifications will...
The Universal Protein Resource (UniProt): an expanding universe of protein information
Wu, Cathy H., Apweiler, Rolf, Bairoch, Amos, Natale, Darren A., Barker, Winona C., Boeckmann, Brigitte, ...
The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein...
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
Côté, Richard G, Jones, Philip, Apweiler, Rolf, Hermjakob, Henning
GOAnnotator: linking protein GO annotations to evidence text
Couto, Francisco M, Silva, Mário J, Lee, Vivian, Dimmer, Emily, Camon, Evelyn, Apweiler, Rolf, ...
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
Camon, Evelyn B, Barrell, Daniel G, Dimmer, Emily C, Lee, Vivian, Magrane, Michele, Maslen, John, ...
EMBL Nucleotide Sequence Database in 2006
Kulikova, Tamara, Akhtar, Ruth, Aldebert, Philippe, Althorpe, Nicola, Andersson, Mikael, Baldwin, Alastair, ...
The EMBL Nucleotide Sequence Database () at the EMBL European Bioinformatics Institute, UK, offers a large and freely accessible collection of nucleotide sequences and accompanying annotation. The...
New developments in the InterPro database
Mulder, Nicola J., Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs,...
Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., ...
We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates...
Côté, Richard G, Jones, Philip, Martens, Lennart, Kerrien, Samuel, Reisinger, Florian, Lin, Quan, ...
Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
Kerrien, Samuel, Orchard, Sandra, Montecchi-Palazzi, Luisa, Aranda, Bruno, Quinn, Antony F, Vinod, Nisha, ...
Cochrane, Guy, Akhtar, Ruth, Aldebert, Philippe, Althorpe, Nicola, Baldwin, Alastair, Bates, Kirsty, ...
The Ensembl Trace Archive (http://trace.ensembl.org/) and the EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/), known together as the European Nucleotide Archive, continue to see growth...
Orchard, Sandra, Kersey, Paul, Hermjakob, Henning, Apweiler, Rolf
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields...
The Gene Ontology Annotation (GOA) Project—Application of GO in SWISS-PROT, TrEMBL and InterPro
Camon, Evelyn, Barrell, Daniel, Brooksbank, Catherine, Magrane, Michele, Apweiler, Rolf
Orchard, Sandra, Kersey, Paul, Zhu, Weimin, Montecchi-Palazzi, Luisa, Hermjakob, Henning, Apweiler, Rolf
The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Rapid progress has...
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
Côté, Richard G., Jones, Philip, Martens, Lennart, Apweiler, Rolf, Hermjakob, Henning
The Ontology Lookup Service (OLS) (http://www.ebi.ac.uk/ols) provides interactive and programmatic interfaces to query, browse and navigate an ever increasing number of biomedical ontologies and...
The speciation of the proteome
Jungblut, Peter R, Holzhütter, Hermann G, Apweiler, Rolf, Schlüter, Hartmut
Chatr-aryamontri, Andrew, Kerrien, Samuel, Khadake, Jyoti, Orchard, Sandra, Ceol, Arnaud, Licata, Luana, ...
InterPro: the integrative protein signature database
Hunter, Sarah, Apweiler, Rolf, Attwood, Teresa K., Bairoch, Amos, Bateman, Alex, Binns, David, ...
The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse...
The GOA database in 2009—an integrated Gene Ontology Annotation resource
Barrell, Daniel, Dimmer, Emily, Huntley, Rachael P., Binns, David, O’Donovan, Claire, Apweiler, Rolf
The Gene Ontology Annotation (GOA) project at the EBI (http://www.ebi.ac.uk/goa) provides high-quality electronic and manual associations (annotations) of Gene Ontology (GO) terms to UniProt...
Finding one's way in proteomics: a protein species nomenclature
Schlüter, Hartmut, Apweiler, Rolf, Holzhütter, Hermann-Georg, Jungblut, Peter R
Our knowledge of proteins has greatly improved in recent years, driven by new technologies in the fields of molecular biology and proteome research. It has become clear that from a single gene not...
QuickGO: a web-based tool for Gene Ontology searching
Binns, David, Dimmer, Emily, Huntley, Rachael, Barrell, Daniel, O'Donovan, Claire, Apweiler, Rolf
Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups...