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Bio4j specifications

Information


Unique identifier OMICS_32295
Name Bio4j
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for Bio4j

Bio4j citations

 (7)
library_books

Representing and querying disease networks using graph databases

2016
BioData Min
PMCID: 4960687
PMID: 27462371
DOI: 10.1186/s13040-016-0102-8

[…] sing a graph data model and has been applied to plant systems biology, a domain where the data is typically fragmented across a large number of data sources and often poorly annotated. More recently, Bio4j [] uses a graph database (Neo4j) to integrate data from several major repositories such as Uniprot KB [], Gene Ontology (GO) [], RefSeq [], NCBI Taxonomy [], and Expasy Enzyme DB [].The need to […]

library_books

Changes in selective pressures associated with human population expansion may explain metabolic and immune related pathways enriched for signatures of positive selection

2016
BMC Genomics
PMCID: 4955149
PMID: 27444955
DOI: 10.1186/s12864-016-2783-2

[…] We also used the Search Tool for the Retrieval of Interacting Genes (STRING) database [] to find genes that interact with the candidate genes identified using Bio4j. The Protein-Protein Interaction (PPI) networks can reveal additional genes associated with metabolic syndrome, which could then be evaluated for signatures of positive selection. More details f […]

library_books

Big Data: the challenge for small research groups in the era of cancer genomics

2015
Br J Cancer
PMCID: 4815885
PMID: 26492224
DOI: 10.1038/bjc.2015.341

[…] uiring extensive maintenance and computing power (). Different types of NoSQL databases, including document-based (e.g., MonoDB), column-family based (e.g., Cassandra or HBase) and graph-based (e.g., Bio4J) databases, have been implemented to integrate NGS with metadata. Despite their heightened requirements, NoSQLs have shown to fare better in performance tests for scalability and extensibility, […]

library_books

Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP Seq)

2015
Sci Rep
PMCID: 4345404
PMID: 25727450
DOI: 10.1038/srep08635

[…] enerated in BLASTXML format. This was followed by assignment of the unaligned query reads into their respective Operational Taxonomic Units (OTU) based on their BLAST hits/results using an integrated Bio4j and Metagenomics7 (MG7) system, an open source system for massive analysis of sequences from metagenomics samples. MG7 carries out taxonomic classification of short reads by associating reads an […]

library_books

Informatic system for a global tissue–fluid biorepository with a graph theory–oriented graphical user interface

2014
J Extracell Vesicles
PMCID: 4172698
PMID: 25317275
DOI: 10.3402/jev.v3.24247

[…] h database, Bio4j, a bioinformatics-oriented derivative of Neo4j, comes prepopulated with data from UniProt KB, Gene Ontology, UniRef, RefSeq, NCBI taxonomy, and Expasy Enzyme DB (). At installation, Bio4j version 0.8 thus has more than 190 million nodes and more than 1.2 trillion edges (relationships between nodes) (). A transition from Postgres to Bio4j would offer the inclusion of these ontolog […]

library_books

A Systems Biology Approach to the Characterization of Stress Response in Dermacentor reticulatus Tick Unfed Larvae

2014
PLoS One
PMCID: 3931811
PMID: 24586875
DOI: 10.1371/journal.pone.0089564

[…] used.The GO analysis for the 500 more represented unigenes was based on the GO annotations included in the Uniprot entry of the representative protein of each cluster. The GO analysis was done using Bio4j Go Tools developed by Era7 Bioinformatics and available at http://gotools.bio4j.com:8080/Bio4jTestServer/Bio4jGoToolsWeb.html. Bio4j Go Tools is a set of GO related Web Services using the open s […]

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Bio4j institution(s)
oh no sequences! research group, Era7 bioinformatics
Bio4j funding source(s)
Supported by the INNPACTO program grant IPT-2011-0735-010000.

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