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Open Source Science

https://github.com/bridgedb/wikidata2bridgedb

Creation of BridgeDb mapping databases from Wikidata

https://github.com/bridgedb/wikidata2bridgedb

Science Score: 67.0%

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
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.8%) to scientific vocabulary

Keywords

bridgedb covid-19 wikidata
Last synced: 6 months ago · JSON representation ·

Repository

Creation of BridgeDb mapping databases from Wikidata

Basic Info
  • Host: GitHub
  • Owner: bridgedb
  • License: apache-2.0
  • Language: Java
  • Default Branch: master
  • Homepage:
  • Size: 139 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 2
  • Open Issues: 4
  • Releases: 0
Topics
bridgedb covid-19 wikidata
Created almost 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation Authors

README.md

Wikidata2Bridgedb

Creation of human and SARS-related corona virus gene/protein mapping database.

How to get the data in the BridgeDb files?

The data comes from Wikidata, and can be retrieved by running the SPARQL queries in the queries folder with the Wikidata Query Service.

shell curl -H "Accept: text/tab-separated-values" --data-urlencode query@queries/publications.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o publications.tsv

How to create a Derby file

shell mvn clean install assembly:single java -cp target/Wikidata2BridgeDb-0.0.2-SNAPSHOT-jar-with-dependencies.jar org.bridgedb.wikidata.Publications

How to cite?

If you use material from this repository, please cite either or both of these:

  • Kutmon, Martina, & Willighagen, Egon. (2020). BridgeDb: Human and SARS-related corona virus gene/protein mapping database derived from Wikidata (Version 2020-05-20) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.3835696
  • Waagmeester A, Willighagen EL, Su AI, Kutmon M, Labra Gayo JE, Fernández-Álvarez D, et al. (2020). A protocol for adding knowledge to Wikidata, a case report. bioRxiv. http://biorxiv.org/lookup/doi/10.1101/2020.04.05.026336

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 the below paper."
title: Wikidata2Bridgedb
url: "https://github.com/bridgedb/Wikidata2Bridgedb"
preferred-citation:
  type: article
  title: "A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses"
  authors:
    - family-names: Waagmeester
      given-names: Andra
    - family-names: Willighagen
      given-names: Egon L.
    - family-names: Su
      given-names: Andrew I.
    - family-names: Kutmon
      given-names: Martina
    - family-names: Gayo
      given-names: Jose Emilio Labra
    - family-names: Fernández-Álvarez
      given-names: Daniel
    - family-names: Groom
      given-names: Quentin
    - family-names: Schaap
      given-names: Peter J.
    - family-names: Verhagen
      given-names: Lisa M.
    - family-names: Koehorst
      given-names: Jasper J.
  doi: 10.1186/S12915-020-00940-Y
  year: 2021
  month: 1
  day: 22
  journal: BMC Biology
  volume: 19
  issue: 12
  url: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00940-y

GitHub Events

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Last synced: 6 months ago

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  • Average time to close issues: 9 months
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  • Total issue authors: 2
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  • Average comments per issue: 1.14
  • Average comments per pull request: 0.0
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Top Authors
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  • egonw (6)
  • jpmvrijn (1)
Pull Request Authors
  • egonw (6)
  • dependabot[bot] (2)
  • jpmvrijn (1)
Top Labels
Issue Labels
enhancement (2) question (1)
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dependencies (2)

Dependencies

pom.xml maven
  • org.bridgedb:org.bridgedb 3.0.18
  • org.bridgedb:org.bridgedb.bio 3.0.18
  • org.bridgedb:org.bridgedb.rdb 3.0.18
  • org.bridgedb:org.bridgedb.rdb.construct 3.0.18
  • org.bridgedb:org.bridgedb.tools.qc 3.0.18
  • org.eclipse.rdf4j:rdf4j-repository-sparql 3.1.2
  • org.slf4j:slf4j-api 2.0.6
  • org.slf4j:slf4j-simple 2.0.6