BridgeDb
Names
More detailed information about this field from each metasource.
BridgeDb
metasource: Fairsharing.org
version: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
bridgedb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
Names
More detailed information about this field from each metasource.
BridgeDb
metasource: Fairsharing.orgversion: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
bridgedb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
Names
More detailed information about this field from each metasource.
BridgeDb
metasource: Fairsharing.orgversion: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
bridgedb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interactions.
Description
More detailed information about this field from each metasource.
BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interactions.
metasource: Fairsharing.orgversion: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
BridgeDb is a framework to map identifiers between various databases. It includes a Java library that provides an API to work with identifier-identifier mapping databases and resources.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
Webpage:
https://bridgedb.github.ioWebpage
More detailed information about this field from each metasource.
https://bridgedb.github.io
metasource: Fairsharing.orgversion: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
http://www.bridgedb.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
Licence:
Name: Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain DedicationLicence name
More detailed information about this field from each metasource.
Creative Commons CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
metasource: Fairsharing.orgversion: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Apache-2.0
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/publicdomain/zero/1.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
PMID: 20047655
metasource: Fairsharing.org
version: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
http://dx.doi.org/10.1007/978-3-319-11964-9_7
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
Publications
More detailed information about this field from each metasource.
The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
PMID: 20047655
metasource: Fairsharing.org
version: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
http://dx.doi.org/10.1007/978-3-319-11964-9_7
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
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The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
PubMed citations: 67.
67 articles citing: The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
A Simple Standard for Sharing Ontological Mappings (SSSOM). PMID:35616100
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
Integrative OMICS Data-Driven Procedure Using a Derivatized Meta-Analysis Approach. PMID:35186042
Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity. PMID:35094093
Complex Portal 2022: new curation frontiers. PMID:34718729
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. PMID:34478489
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Interpreting the lipidome: bioinformatic approaches to embrace the complexity. PMID:34091802
Quo Vadis Caenorhabditis elegans Metabolomics-A Review of Current Methods and Applications to Explore Metabolism in the Nematode. PMID:33947148
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. PMID:33482803
WikiPathways: connecting communities. PMID:33211851
Endocrine-disrupting chemicals: implications for human health. PMID:32707118
Identification of genes and miRNA associated with idiopathic recurrent pregnancy loss: an exploratory data mining study. PMID:32487076
Biospytial: spatial graph-based computing for ecological Big Data. PMID:32391910
Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model. PMID:32231124
Improving lipid mapping in Genome Scale Metabolic Networks using ontologies. PMID:32215752
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Identification of Biological Pathways Contributing to Marbling in Skeletal Muscle to Improve Beef Cattle Breeding. PMID:32117419
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Distributed flux balance analysis simulations of serial biomass fermentation by two organisms. PMID:31945096
Identification of microRNAs in skeletal muscle associated with lung cancer cachexia. PMID:31828982
Ontology-based metabolomics data integration with quality control. PMID:31179719
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome. PMID:30847002
Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials. PMID:30622555
Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data. PMID:30535020
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. PMID:30246165
Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data. PMID:29291722
Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin D. PMID:29233860
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. PMID:29136241
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Reactome pathway analysis: a high-performance in-memory approach. PMID:28249561
Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes. PMID:28183786
New insights in Rett syndrome using pathway analysis for transcriptomics data. PMID:27517371
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
Reactome from a WikiPathways Perspective. PMID:27203685
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Taking Bioinformatics to Systems Medicine. PMID:26677177
Analysis of volatile organic compounds in exhaled breath to diagnose ventilator-associated pneumonia. PMID:26608483
Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. PMID:26467653
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. PMID:26298294
A reproducible approach to high-throughput biological data acquisition and integration. PMID:26157642
PathVisio 3: an extendable pathway analysis toolbox. PMID:25706687
SPARQL-enabled identifier conversion with Identifiers.org. PMID:25638809
White adipose tissue reference network: a knowledge resource for exploring health-relevant relations. PMID:25466819
BridgeDb app: unifying identifier mapping services for Cytoscape. PMID:25110584
NetPathMiner: R/Bioconductor package for network path mining through gene expression. PMID:25075120
CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis. PMID:24340000
NOA: a cytoscape plugin for network ontology analysis. PMID:23749961
The ChEMBL database as linked open data. PMID:23657106
Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum. PMID:23593322
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. PMID:23547033
Knowledge Driven Variable Selection (KDVS) - a new approach to enrichment analysis of gene signatures obtained from high-throughput data. PMID:23302187
Architecture for interoperable software in biology. PMID:23235920
A travel guide to Cytoscape plugins. PMID:23132118
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Overview of biological database mapping services for interoperation between different 'omics' datasets. PMID:22155608
Assembling global maps of cellular function through integrative analysis of physical and genetic networks. PMID:21886098
Exploring pathway interactions in insulin resistant mouse liver. PMID:21843341
Developing a kidney and urinary pathway knowledge base. PMID:21624162
Answering biological questions: querying a systems biology database for nutrigenomics. PMID:21437033
The Micronutrient Genomics Project: a community-driven knowledge base for micronutrient research. PMID:21189865
Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies. PMID:21052526
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PMID:20824171
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. PMID:20426876 - http://dx.doi.org/10.1007/978-3-319-11964-9_7
Tags:
Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metabolomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
proteomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:37.972276
Tags
More detailed information about this field from each metasource.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: BridgeDb; BridgeDb; DOI: https://doi.org/10.25504/FAIRsharing.5ry74y; Last edited: June 17, 2021, 9:12 a.m.; Last accessed: Jan 03 2022 7:06 p.m.
metabolomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
proteomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
rare diseases
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:24:37.972276
molecular interaction metabolomics proteomics genomics rare diseases
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