interactiondb
A BridgeDb Derby database to map interactions from different databases to each other. This database can be used to annotate interactions in PathVisio and Wikipathways.
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (2.6%) to scientific vocabulary
Repository
A BridgeDb Derby database to map interactions from different databases to each other. This database can be used to annotate interactions in PathVisio and Wikipathways.
Basic Info
Statistics
- Stars: 2
- Watchers: 5
- Forks: 2
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
Interaction Bridge Database
This is a java application to create a BridgeDb derby database to map identifiers of interactions from different databases to each other. It has been created using the interaction mapping from Rhea (http://www.ebi.ac.uk/rhea/). The identifier from Rhea is mapped to identifiers from Enzyme Code, EcoCyc, MetaCyc, Macie, Reactome, Kegg Reaction, Unipathway, and Uniprot. This database can be used to annotate interactions in PathVisio(http://www.pathvisio.org/), which are displayed in Wikipathways (http://wikipathways.org/index.php/WikiPathways) as linkouts to the corresponding databases fetched through the webservice from BridgeDB.
Find the build information in our Wiki
Owner
- Name: BridgeDb
- Login: bridgedb
- Kind: organization
- Location: Netherlands
- Website: https://www.bridgedb.org/
- Repositories: 37
- Profile: https://github.com/bridgedb
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: BridgeDb
message: 'If you use this software, please cite it as below.'
type: software
authors:
- given-names: 'Martijn P.'
family-names: Van Iersel
- given-names: Alexander R.
family-names: Pico
- given-names: Thomas
family-names: Kelder
- given-names: Jianjiong
family-names: Gao
- given-names: Ho
family-names: Isaac
- given-names: Kristina
family-names: Hanspers
- given-names: Bruce R.
family-names: Conklin
- given-names: Chris T.
family-names: Evelo
identifiers:
- type: url
value: 'https://github.com/bridgedb/BridgeDb'
description: Source code repository for BridgeDb
- type: doi
value: 10.1186/1471-2105-11-5
description: >-
Article: The BridgeDb framework: standardized
access to gene, protein and metabolite
identifier mapping services
repository-code: 'https://github.com/bridgedb/BridgeDb'
url: 'https://bridgedb.github.io/'
preferred-citation:
type: article
authors:
- given-names: 'Martijn P.'
family-names: Van Iersel
- given-names: Alexander R.
family-names: Pico
- given-names: Thomas
family-names: Kelder
- given-names: Jianjiong
family-names: Gao
- given-names: Ho
family-names: Isaac
- given-names: Kristina
family-names: Hanspers
- given-names: Bruce R.
family-names: Conklin
- given-names: Chris T.
family-names: Evelo
doi: "10.1186/1471-2105-11-5"
journal: "BMC Bioinformatics"
title: "The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services"
issue: 5
volume: 11
year: 2010
keywords:
- identifier mapping
- Genes
- Proteins
- Metabolites
- Biological data
license: Apache-2.0
version: 3.0.13
date-released: '2022-01-14'