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https://github.com/bridgedb/bridgedb-webservice

BridgeDb Webservice

https://github.com/bridgedb/bridgedb-webservice

Science Score: 18.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

BridgeDb Webservice

Basic Info
  • Host: GitHub
  • Owner: bridgedb
  • License: apache-2.0
  • Language: Java
  • Default Branch: main
  • Size: 3.38 MB
Statistics
  • Stars: 1
  • Watchers: 5
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Archived
Created over 4 years ago · Last pushed over 3 years ago
Metadata Files
Readme License Citation

README.md

build docker stars docker pulls

BridgeDb Webservice

The BridgeDb Webservice provides a REST service to access identifier mapping data. It uses the BridgeDb Java library and RESTlet technologies to make the webservice available. There is a BridgeDb Docker available for easy use.

Compiling the webservice

A jar with all dependencies is created with the following command:

shell mvn clean package

Downloading BridgeDb ID mapping databases

BridgeDb ID mapping databases are found on this website. The location of the downloaded files is needed for the below described gdb.config file.

Installing the Derby libraries

Because when embedding Derby in the BridgeDb Server jar makes them impossible to find, you still need them locally. Copy the Derby jars (derbyclient.jar) to this folder.

Starting the webservice

The service can be run with (only HTTP is supported):

shell sh startServer.sh

Run the server at a different port with:

shell sh startServer.sh -p 8082

This will look for a local gdb.config file that has a tab-separated values content, linking species to BridgeDb Derby files, for example:

Human /path/to/databases/Hs_Derby_Ensembl_105.bridge

Testing the webservice

Test the service by asking for the properties of a species for which you downloaded ID mapping databases, e.g. http://localhost:8183/Human/properties

Owner

  • Name: BridgeDb
  • Login: bridgedb
  • Kind: organization
  • Location: Netherlands

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: BridgeDb Webservice
version: 3.0.14
date-released: 2022-05-28
url: "https://github.com/bridgedb/BridgeDb"
preferred-citation:
  - type: article
    authors:
      - family-names: Van Iersel
        given-names: Martijn P.
      - family-names: Pico
        given-names: Alexander R.
      - family-names: Kelder
        given-names: Thomas
      - family-names: Gao
        given-names: Jianjiong
      - family-names: Isaac
        given-names: Ho
      - family-names: Hanspers
        given-names: Kristina
      - family-names: Conklin
        given-names: Bruce R.
      - family-names: Evelo
        given-names: Chris T.
    title: "The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services"
    year: 2010
    journal: BMC Bioinformatics
    volume: 11
    issue: 5
    doi: 10.1186/1471-2105-11-5
    url: https://doi.org/10.1186/1471-2105-11-5

GitHub Events

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Last Year

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 2
  • Total pull requests: 2
  • Average time to close issues: 11 months
  • Average time to close pull requests: 15 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 2.5
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • egonw (2)
Pull Request Authors
  • hbasaric (2)
Top Labels
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enhancement (2)
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Dependencies

org.bridgedb.server/pom.xml maven
  • commons-cli:commons-cli ${commons-cli.version}
  • org.apache.derby:derby ${derby.version}
  • org.apache.derby:derbyclient ${derby.version}
  • org.apache.derby:derbytools ${derby.version}
  • org.bridgedb.webservice:org.bridgedb.webservice.bridgerest ${bridgedb.version}
  • org.bridgedb:org.bridgedb ${bridgedb.version}
  • org.bridgedb:org.bridgedb.bio ${bridgedb.version}
  • org.bridgedb:org.bridgedb.rdb ${bridgedb.version}
  • org.restlet.jee:org.restlet.ext.servlet 2.0.15
  • org.junit.jupiter:junit-jupiter-api ${junit5.jupiter.version} test
  • org.junit.jupiter:junit-jupiter-engine ${junit5.jupiter.version} test
  • org.junit.platform:junit-platform-surefire-provider ${junit-platform-surefire-provider} test
  • org.junit.vintage:junit-vintage-engine ${junit5.jupiter.version} test
.github/workflows/build.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v1 composite