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