Data integration in biological research: an overview

Developing a guideline to standardize the citation of bioresources in journal articles (CoBRA)

(2015) Elena Bravo et al.   BMC Medicine

Better reporting for better research: a checklist for reproducibility

(2015) Amye Kenall et al.   BMC NEUROSCIENCE

Towards recommendations for metadata and data handling in plant phenotyping

(2015) Paweł Krajewski et al.   JOURNAL OF EXPERIMENTAL BOTANY

Methods of integrating data to uncover genotype–phenotype interactions

(2015) Marylyn D. Ritchie et al.   NATURE REVIEWS GENETICS

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

Data integration in the era of omics: current and future challenges

(2014) David Gomez-Cabrero et al.   BMC Systems Biology

Editorial

(2014) Jerry J. Sweet   CLINICAL NEUROPSYCHOLOGIST

The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data

(2014) Ronald Margolis et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Big linked cancer data: Integrating linked TCGA and PubMed

(2014) Muhammad Saleem et al.   Journal of Web Semantics

Genenames.org: the HGNC resources in 2015

(2014) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Lean Big Data integration in systems biology and systems pharmacology

(2014) Avi Ma’ayan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

International ethics harmonization and the global alliance for genomics and health

(2014) Bartha M Knoppers   Genome Medicine

Controlled vocabularies and ontologies in proteomics: Overview, principles and practice

(2013) Gerhard Mayer et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

BioJS: an open source JavaScript framework for biological data visualization

(2013) J. Gomez et al.   BIOINFORMATICS

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

(2013) Daniel Garijo et al.   PLoS One

NCBO Technology: Powering semantically aware applications

(2013) Patricia L Whetzel et al.   Journal of Biomedical Semantics

Quantifying the use of bioresources for promoting their sharing in scientific research

(2013) Laurence Mabile et al.   GigaScience

Knowledge representation in metabolic pathway databases

(2012) M. D. Stobbe et al.   BRIEFINGS IN BIOINFORMATICS

Identification of aberrant pathways and network activities from high-throughput data

(2012) J. Wang et al.   BRIEFINGS IN BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Toward interoperable bioscience data

(2012) Susanna-Assunta Sansone et al.   NATURE GENETICS

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

(2012) Sandra Orchard et al.   NATURE METHODS

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

The International Nucleotide Sequence Database Collaboration

(2012) Y. Nakamura et al.   NUCLEIC ACIDS RESEARCH

ExPASy: SIB bioinformatics resource portal

(2012) P. Artimo et al.   NUCLEIC ACIDS RESEARCH

Biodiversity e‐Science: LifeWatch, the European infrastructure on biodiversity and ecosystem research

(2012) A. Basset et al.   PLANT BIOSYSTEMS

ELIXIR: a distributed infrastructure for European biological data

(2012) Lindsey C. Crosswell et al.   TRENDS IN BIOTECHNOLOGY

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

European initiative towards quality standards in education and training for discovery, development and use of medicines

(2011) Heinrich Klech et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

The National Center for Biomedical Ontology

(2011) Mark A Musen et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

NCBO Resource Index: Ontology-based search and mining of biomedical resources

(2011) Clement Jonquet et al.   Journal of Web Semantics

Minimum information about a bioactive entity (MIABE)

(2011) Sandra Orchard et al.   NATURE REVIEWS DRUG DISCOVERY

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

(2011) N. Juty et al.   NUCLEIC ACIDS RESEARCH

Reactome pathway analysis to enrich biological discovery in proteomics data sets

(2011) Robin Haw et al.   PROTEOMICS

Meeting Report: BioSharing at ISMB 2010

(2011) Dawn Field et al.   Standards in Genomic Sciences

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

(2011) Laurence D. Parnell et al.   PLoS Computational Biology

Utopia documents: linking scholarly literature with research data

(2010) T. K. Attwood et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

Visualization of image data from cells to organisms

(2010) Thomas Walter et al.   NATURE METHODS

Next-generation sequencing: adjusting to data overload

(2010) Monya Baker   NATURE METHODS

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

The Ontology Lookup Service: bigger and better

(2010) R. Cote et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Calling International Rescue: knowledge lost in literature and data landslide!

(2009) Teresa K. Attwood et al.   BIOCHEMICAL JOURNAL

Visualising biological data: a semantic approach to tool and database integration

(2009) Steve Pettifer et al.   BMC BIOINFORMATICS

BioMart – biological queries made easy

(2009) Damian Smedley et al.   BMC GENOMICS

PRIDE Converter: making proteomics data-sharing easy

(2009) Harald Barsnes et al.   NATURE BIOTECHNOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

State of the nation in data integration for bioinformatics

(2008) Carole Goble et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Bio2RDF: Towards a mashup to build bioinformatics knowledge systems

(2008) François Belleau et al.   JOURNAL OF BIOMEDICAL INFORMATICS

The future of biocuration

(2008) Doug Howe et al.   NATURE

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

(2008) Chris F Taylor et al.   NATURE BIOTECHNOLOGY

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Towards a Data Sharing Culture: Recommendations for Leadership from Academic Health Centers

(2008) Heather A Piwowar et al.   PLOS MEDICINE

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining