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bridgedbwebservice

BridgeDb Webservice

https://github.com/bridgedb/bridgedbwebservice

Science Score: 54.0%

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
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

BridgeDb Webservice

Basic Info
  • Host: GitHub
  • Owner: bridgedb
  • License: apache-2.0
  • Language: Java
  • Default Branch: main
  • Homepage:
  • Size: 854 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 3
  • Open Issues: 18
  • Releases: 9
Created over 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

DOI build codecov NWO

BridgeDb Webservice 2.x

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.

Running the webservice

Use the latest jar file available here: link

Downloading BridgeDb ID mapping databases

BridgeDb ID mapping databases are found on this website.

These derby databases are used to perform identifier mapping for a particular species.

The location of the downloaded files is needed for the below described gdb.config file.

Modifying the gdb.config file

The gdb.config ("gene database configuration") file in the repository should be customized to point to each local derby file you have downloaded.

For example, if you are only interested in mapping identifiers for Homo sapiens, your gdb.config file would look like:

bash Homo sapiens C:/.../Path_To_Derby_Database/Hs_Derby_Ensembl_XXX.bridge

where "Homo sapiens" and the path to the derby database are separated by a tab.

Starting the webservice

When starting the webservice, the gdb.config file will be parsed to determine which gene databases you have configured.

Navigating to the folder where you saved the jar file and run the following line:

bash java -jar target/BridgeDbWebservice-*-jar-with-dependencies.jar

The jar file takes three optional parameters, the port, a boolean if CORS should be enabled, and the server URL. For example, the following the are valid instructions to start a server:

bash java -jar target/BridgeDbWebservice-*-jar-with-dependencies.jar 8888 java -jar target/BridgeDbWebservice-*-jar-with-dependencies.jar 8888 false https://example.org/

Testing an endpoint

Point your browser to: http://localhost:8080/Human/attributeSet

Please see Swagger Documentation for your reference to see which endpoints are available for you to use.

Making a release

Update the version numbers in these three files:

  • pom.xml
  • CITATION.cff
  • src/main/resources/webservice.props

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: 2.1.7
date-released: 2024-01-03
url: "https://github.com/bridgedb/BridgeDbWebservice"
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

Total
  • Issues event: 2
  • Issue comment event: 1
  • Pull request review event: 1
  • Pull request event: 1
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 2
  • Issue comment event: 1
  • Pull request review event: 1
  • Pull request event: 1
  • Fork event: 1
  • Create event: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • egonw (4)
  • ariutta (3)
  • DeniseSl22 (1)
  • jmillanacosta (1)
Pull Request Authors
  • egonw (2)
  • jmillanacosta (2)
Top Labels
Issue Labels
bug (4) enhancement (3) question (2)
Pull Request Labels
bug (1)

Dependencies

.github/workflows/build.yml actions
  • actions/checkout v2 composite
  • actions/setup-java v1 composite
pom.xml maven
  • com.google.code.gson:gson 2.1 provided
  • com.googlecode.json-simple:json-simple 1.1
  • org.bridgedb.webservice:org.bridgedb.webservice.bridgerest 3.0.17
  • org.bridgedb:org.bridgedb 3.0.17
  • org.bridgedb:org.bridgedb.bio 3.0.17
  • org.bridgedb:org.bridgedb.rdb 3.0.17
  • org.json:json 20220924
  • org.restlet.jee:org.restlet.ext.json 2.3.7
  • org.restlet.jse:org.restlet 2.3.7
  • org.restlet.jse:org.restlet.ext.jackson 2.3.7
  • junit:junit 4.11 test