Data integration in biological research: an overview (Q26785948)

5

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Rafael C. Jimenez

object named as

Rafael C Jimenez

3

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author name string

Vasileios Lapatas

1

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Michalis Stefanidakis

Journal of biological research (Thessalonike, Greece)

2

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language of work or name

English

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publication date

December 2015

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published in

1 reference

describes a project that uses

PubMed

volume

22

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page(s)

9

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issue

1

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Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/s40709-015-0032-5

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cites work

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The iPlant Collaborative: Cyberinfrastructure for Plant Biology

7 April 2017

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

7 April 2017

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The National Center for Biomedical Ontology

7 April 2017

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Pathway Commons, a web resource for biological pathway data

7 April 2017

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

7 April 2017

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big data: The future of biocuration

7 April 2017

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

7 April 2017

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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

7 April 2017

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From bytes to bedside: data integration and computational biology for translational cancer research

7 April 2017

1 reference

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MINT: the Molecular INTeraction database

7 April 2017

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NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

7 April 2017

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STRING 7--recent developments in the integration and prediction of protein interactions

7 April 2017

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PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways

7 April 2017

1 reference

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UniProt: the Universal Protein knowledgebase

7 April 2017

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Cytoscape: a software environment for integrated models of biomolecular interaction networks

7 April 2017

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The human genome browser at UCSC

7 April 2017

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DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions

7 April 2017

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The Ensembl genome database project

7 April 2017

1 reference

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The distributed annotation system

7 April 2017

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

7 April 2017

1 reference

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Data standards for Omics data: the basis of data sharing and reuse

7 April 2017

1 reference

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

The BioPAX community standard for pathway data sharing

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Bio2RDF: Towards a mashup to build bioinformatics knowledge systems

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Toward interoperable bioscience data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Utopia documents: linking scholarly literature with research data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

The minimum information about a genome sequence (MIGS) specification

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

ARIA2: automated NOE assignment and data integration in NMR structure calculation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Combo: a whole genome comparative browser

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Graph-based analysis and visualization of experimental results with ONDEX

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

BioModels: Content, Features, Functionality, and Use

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

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

7 April 2017

1 reference

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

taxize: taxonomic search and retrieval in R

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Reactome pathway analysis to enrich biological discovery in proteomics data sets

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Meeting Report: BioSharing at ISMB 2010

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

The Ontology Lookup Service: bigger and better

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Towards a data sharing culture: recommendations for leadership from academic health centers

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Cytoscape 2.8: new features for data integration and network visualization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Galaxy: a platform for interactive large-scale genome analysis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

VISTA: computational tools for comparative genomics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

SMART 4.0: towards genomic data integration

7 April 2017

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7 April 2017

1 reference

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

BioMart--biological queries made easy

7 April 2017

1 reference

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Towards recommendations for metadata and data handling in plant phenotyping.

9 May 2017

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

28 September 2017

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Methods of integrating data to uncover genotype-phenotype interactions

28 September 2017

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Genenames.org: the HGNC resources in 2015

28 September 2017

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Lean Big Data integration in systems biology and systems pharmacology

28 September 2017

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International ethics harmonization and the global alliance for genomics and health

28 September 2017

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

28 September 2017

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Quantifying reproducibility in computational biology: the case of the tuberculosis drugome

28 September 2017

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Data harmonization and federated analysis of population-based studies: the BioSHaRE project

28 September 2017

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

28 September 2017

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NCBO Technology: Powering semantically aware applications

28 September 2017

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

28 September 2017

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BioJS: an open source JavaScript framework for biological data visualization

28 September 2017

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

28 September 2017

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Knowledge representation in metabolic pathway databases.

28 September 2017

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The International Nucleotide Sequence Database Collaboration.

28 September 2017

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An encyclopedia of mouse DNA elements (Mouse ENCODE).

28 September 2017

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

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

ELIXIR: a distributed infrastructure for European biological data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Minimum information about a bioactive entity (MIABE).

28 September 2017

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Visualization of omics data for systems biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Visualization of image data from cells to organisms

28 September 2017

1 reference

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A survey of visualization tools for biological network analysis

28 September 2017

1 reference

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DAVID gene ID conversion tool

28 September 2017

1 reference

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State of the nation in data integration for bioinformatics

28 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

28 September 2017

Biobanking for Europe

1 reference

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The minimum information required for reporting a molecular interaction experiment (MIMIx).

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Context-sensitive data integration and prediction of biological networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Data standards: a call to action

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

The Gaggle: an open-source software system for integrating bioinformatics software and data sources

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Beyond the data deluge: data integration and bio-ontologies

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

A data integration methodology for systems biology

28 September 2017

1 reference

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CoGenT++: an extensive and extensible data environment for computational genomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

PRIDE: the proteomics identifications database

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

YeastHub: a semantic web use case for integrating data in the life sciences domain

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Ontologies in biology: design, applications and future challenges

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Genome annotation: from sequence to biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

XML, bioinformatics and data integration

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Kleisli: a new tool for data integration in biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

A protocol for maintaining multidatabase referential integrity.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Database links are a foundation for interoperability

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

SRS--an indexing and retrieval tool for flat file data libraries.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

ExPASy: SIB bioinformatics resource portal

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

How not to be a bioinformatician

31 May 2018

1 reference

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PRIDE Converter: making proteomics data-sharing easy

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Linked Open Science-Communicating, Sharing and Evaluating Data, Methods and Results for Executable Papers

31 May 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

Answering queries using views: A survey

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

Editorial. EQUATOR - reporting guidelines for "Enhancing the QUality and Transparency Of health Research".

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

The proteomics standards initiative.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

Using the KEGG database resource.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

Open Science: tools, approaches, and implications

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

NIH-NSF Visualization Research Challenges report summary.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4557916

On the Importance of Standardisation in Life Sciences

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26336651

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The Research Data Alliance: globally co-ordinated action against barriers to data publishing and sharing

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5

inferred from DOI database lookup

7 January 2021

based on heuristic

The European Nucleotide Archive

1 reference

https://api.crossref.org/works/10.1186%2FS40709-015-0032-5