-
Protocol
Data Mining, Quality and Management in the Life Sciences
With the evermore emphasis put on open science and its invaluable benefits to the scientific community, it is no longer the case where a research project simply ends with a scientific publication. The benefits...
-
Article
Open AccessWhither systems medicine?
New technologies to generate, store and retrieve medical and research data are inducing a rapid change in clinical and translational research and health care. Systems medicine is the interdisciplinary approach...
-
Article
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
-
Protocol
A Guide to UniProt for Protein Scientists
One of the essential requirements of the proteomics community is a high quality annotated nonredundant protein sequence database with stable identifiers and an archival service to enable protein identification...
-
Chapter
Practical Applications of the Gene Ontology Resource
The Gene Ontology (GO) is a controlled vocabulary that represents knowledge about the functional attributes of gene products in a structured manner and can be used in both computational and human analyses. Thi...
-
Article
A large-scale protein-function database
-
Article
Open AccessFinding one's way in proteomics: a protein species nomenclature
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 only one sin...
-
Article
Missing in action: enzyme functional annotations in biological databases
Annotations of enzyme function provide critical starting points for generating and testing biological hypotheses, but the quality of functional annotations is hindered by uncertain assignments for uncharacteri...
-
Protocol
Algorithms and Databases
The capacity of proteomics methods and mass spectrometry instrumentation to generate data has grown substantially over the past years. This data volume growth has in turn led to an increased reliance on softwa...
-
Article
Open AccessMINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data
In the absence of consolidated pipelines to archive biological data electronically, information dispersed in the literature must be captured by manual annotation. Unfortunately, manual annotation is time consu...
-
Article
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
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 exploring the ...
-
Article
Open AccessThe speciation of the proteome
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. At the other side the protein e...
-
Article
In Silico Characterization of Proteins: UniProt, InterPro and Integr8
Nucleic acid sequences from genome sequencing projects are submitted as raw data, from which biologists attempt to elucidate the function of the predicted gene products. The protein sequences are stored in pub...
-
Chapter
Annotating the Human Proteome
The completion of the human genome has shifted the attention from deciphering the sequence to the identification and characterization of the functional components including genes. Improved gene prediction algo...
-
Article
Open AccessThe Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is ...
-
Article
Open AccessBroadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
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, making access to this very difficul...
-
Article
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
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 of an expe...
-
Article
The minimum information required for reporting a molecular interaction experiment (MIMIx)
A wealth of molecular interaction data is available in the literature, ranging from large-scale datasets to a single interaction confirmed by several different techniques. These data are all too often reported...
-
Article
The minimum information about a proteomics experiment (MIAPE)
Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and d...
-
Protocol
Proteomic Data Exchange and Storage
The ever increasing volumes of proteomic data now being produced by laboratories across the world have resulted in major issues in data storage and accessibility. The further demands of multilaboratory initiat...
