ProteomeXchange provides globally coordinated proteomics data submission and dissemination.
The European Bioinformatics Institute's data resources 2014.
Activities at the Universal Protein Resource (UniProt).
Representing kidney development using the gene ontology.
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.
Integration of cardiac proteome biology and medicine by a specialized knowledgebase.
The Characterization, Design, and Function of the Mitochondrial Proteome: From Organs to Organisms.
Gene Ontology annotations and resources.
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
Maximising proteomics data for the scientific community
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.
Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
InterPro in 2011: new developments in the family and domain prediction database.
Toward community standards in the quest for orthologs.
The HUPO initiative on Model Organism Proteomes, iMOP.
The UniProt-GO Annotation database in 2011.
The Gene Ontology: enhancements for 2011.
Reorganizing the protein space at the Universal Protein Resource (UniProt).
InterPro in 2011: new developments in the family and domain prediction database.
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.
"4D Biology for health and disease" workshop report.
A posteriori quality control for the curation and reuse of public proteomics data.
Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria.
Ongoing and future developments at the Universal Protein Resource.
The impact of focused Gene Ontology curation of specific mammalian systems.
A guide to UniProt for protein scientists.
A large-scale protein-function database.
Recommendations for biomarker identification and qualification in clinical proteomics.
Comparative proteomics profiling reveals role of smooth muscle progenitors in extracellular matrix production.
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Mining Unique-m Substrings from Genomes
The Universal Protein Resource (UniProt) in 2010.
The Gene Ontology in 2010: extensions and refinements.
The Renal Gene Ontology Annotation Initiative.
On the importance of comprehensible classification models for protein function prediction.
QuickGO: a web-based tool for Gene Ontology searching.
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Approaching clinical proteomics: current state and future fields of application in cellular proteomics.
Prepublication data sharing.
Know your limits: assumptions, constraints and interpretation in systems biology.
Missing in action: enzyme functional annotations in biological databases.
Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.
ASTD: The Alternative Splicing and Transcript Diversity database.
The Universal Protein Resource (UniProt) 2009.
The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Systematic comparison of the human saliva and plasma proteomes.
Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands.
InterPro: the integrative protein signature database.
QuickGO: a user tutorial for the web-based Gene Ontology browser.
Finding one's way in proteomics: a protein species nomenclature.
Approaching clinical proteomics: current state and future fields of application in fluid proteomics.
Algorithms and databases.
Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain.
Building a biological space based on protein sequence similarities and biological ontologies.
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
The Gene Ontology - Providing a Functional Role in Proteomic Studies.
Altered proteome biology of cardiac mitochondria under stress conditions.
UniProtJAPI: a remote API for accessing UniProt data.
Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO?
Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria.
Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea.
The InterPro database and tools for protein domain analysis.
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
In silico characterization of proteins: UniProt, InterPro and Integr8.
Wiley-VCH and HUPO: A Global Effort to Advance Proteomic Science.
The Rice Annotation Project Database (RAP-DB): 2008 update.
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.
Analyzing large-scale proteomics projects with latent semantic indexing.
The speciation of the proteome.
MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Superieur, Lyon, France.
Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
The minimum information required for reporting a molecular interaction experiment (MIMIx).
The minimum information about a proteomics experiment (MIAPE).
High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Clinical proteomics: A need to define the field and to begin to set adequate standards.
Annotating the human proteome: beyond establishing a parts list.
New developments in the InterPro database.
IntAct--open source resource for molecular interaction data.
EMBL Nucleotide Sequence Database in 2006.
The EMBL Nucleotide Sequence and Genome Reviews Databases.
Proteomic data exchange and storage: the need for common standards and public repositories.
InterPro and InterProScan: tools for protein sequence classification and comparison.
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
Linking publication, gene and protein data.
The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results.
HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.
Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.
Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.
Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.
A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies.
Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.
Bioinformatics database infrastructure for biotechnology research.
UniSave: the UniProtKB sequence/annotation version database.
The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.
The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.
The Universal Protein Resource (UniProt): an expanding universe of protein information.
PRIDE: a public repository of protein and peptide identifications for the proteomics community.
EMBL Nucleotide Sequence Database: developments in 2005.
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
GOAnnotator: linking protein GO annotations to evidence text.
Genome Reviews: standardizing content and representation of information about complete genomes.
Evidence standards in experimental and inferential INSDC Third Party Annotation data.
Databases and resources for in silico proteome analysis.
[InterPro as a new tool for whole genome analysis. A comparative analysis of Mycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a case study]
Human Proteome Organisation Proteomics Standards Initiative. Pre-Congress Initiative.
Do you do text?
The transcriptional landscape of the mammalian genome.
The predictive power of the CluSTr database.
Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).
5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.
PRIDE: the proteomics identifications database.
Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.
InterProScan: protein domains identifier.
Dasty and UniProt DAS: a perfect pair for protein feature visualization.
Second proteomics standards initiative spring workshop.
Plant protein annotation in the UniProt Knowledgebase.
Annotating the human proteome.
Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.
The Universal Protein Resource (UniProt).
The importance of uniformity in reporting protein-function data.
The EMBL Nucleotide Sequence Database.
InterPro, progress and status in 2005.
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
E-MSD: an integrated data resource for bioinformatics.
Who tangos with GOA?-Use of Gene Ontology Annotation (GOA) for biological interpretation of '-omics' data and for validation of automatic annotation tools.
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
The Integr8 project--a resource for genomic and proteomic data.
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.
A common open representation of mass spectrometry data and its application to proteomics research.
Towards data management of the HUPO Human Brain Proteome Project pilot phase.
Filtering erroneous protein annotation.
Current status of proteomic standards development.
Advances in the development of common interchange standards for proteomic data.
The International Protein Index: an integrated database for proteomics experiments.
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Synergy between medical informatics and bioinformatics: facilitating genomic medicine for future health care.
Protein sequence databases.
Common interchange standards for proteomics data: Public availability of tools and schema.
UniProt: the Universal Protein knowledgebase.
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.
The Gene Ontology (GO) database and informatics resource.
The EMBL Nucleotide Sequence Database.
IntEnz, the integrated relational enzyme database.
IntAct: an open source molecular interaction database.
The Gene Ontology Annotation (GOA) Database--an integrated resource of GO annotations to the UniProt Knowledgebase.
Protein sequence database methods.
Proteomics and data standardisation
Further advances in the development of a data interchange standard for proteomics data.
The proteomics standards initiative.
Managing core resources for genomics and proteomics.
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
Increase of functional diversity by alternative splicing.
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.
The InterPro Database, 2003 brings increased coverage and new features.
The European Bioinformatics Institute's data resources.
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters.
The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
The Gene Ontology Annotation (GOA) Project--Application of GO in SWISS-PROT, TrEMBL and InterPro.
Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.
Integr8: enhanced inter-operability of European molecular biology databases.
Bioinformatics Resources for In Silico Proteome Analysis.
InterPro: an integrated documentation resource for protein families, domains and functional sites.
High-quality protein knowledge resource: SWISS-PROT and TrEMBL.
Applications of InterPro in protein annotation and genome analysis.
The EBI SRS server-new features.
The EBI SRS server--recent developments.
Interactive InterPro-based comparisons of proteins in whole genomes.
Tools and resources for identifying protein families, domains and motifs.
TEMBLOR - Perspectives of EBI Database Services.
Consistent integration of non-reliable heterogeneous information resources applied to the annotation of transmembrane proteins.
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT.
InterProScan--an integration platform for the signature-recognition methods in InterPro.
Evaluation of methods for the prediction of membrane spanning regions.
Clustering and analysis of protein families.
Application of InterPro for the functional classification of the proteins of fish origin in SWISS-PROT and TrEMBL.
The human proteomics initiative (HPI).
Functional information in SWISS-PROT: the basis for large-scale characterisation of protein sequences.
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.
InterPro--an integrated documentation resource for protein families, domains and functional sites.
A collection of well characterised integral membrane proteins.
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
A comparison of signal sequence prediction methods using a test set of signal peptides.
The role SWISS-PROT and TrEMBL play in the genome research environment.
Comparative genomics of the eukaryotes.
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.
Mus musculus in the SWISS-PROT database: its relevance to developmental research.
Protein sequence databases.
Representation of functional information in the SWISS-PROT data bank.
Report of the Second International Nomenclature Workshop. Cambridge, United Kingdom, May 1-2, 1999.
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database.
Swissknife - 'lazy parsing' of SWISS-PROT entries.
Removing redundancy in SWISS-PROT and TrEMBL.
EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation.
A novel method for automatic functional annotation of proteins.
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998.
The SWISS-PROT protein sequence database: its relevance to human molecular medical research.
The SWISS-PROT protein sequence data bank and its supplement TrEMBL.
Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.
The SWISS-PROT protein sequence data bank and its new supplement TREMBL.
Effect of the new oral antidiabetic agent (-)-BM 13.0913.Na on insulin resistance in lean and obese Zucker rats.
Development of glucose intolerance in obese (fa/fa) Zucker rats.
In vitro poly-(ADP-ribosyl)ation of chromatin proteins in the rat tapeworm, Hymenolepis diminuta.
Identification of ADPR-transferase activity in the rat tapeworm, Hymenolepis diminuta.
The EBI Metagenomics Archive, Integration and Analysis resource
Public Data Resources as the Foundation for a Worldwide Metagenomics Data Infrastructure
Proteomic Data Standardization, Deposition and Exchange
Protein Sequence Databases
MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects
Design, Implementation and Updating of Knowledge Bases
Computational Methods and Bioinformatic Tools
Biological Databases: Infrastructure, Content and Integration
Bioinformatics: Using the Molecular Biology Data