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tiwid

This is where identifiers die

https://github.com/bridgedb/tiwid

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 (9.5%) to scientific vocabulary

Keywords

bridgedb hacktoberfest
Last synced: 6 months ago · JSON representation ·

Repository

This is where identifiers die

Basic Info
  • Host: GitHub
  • Owner: bridgedb
  • License: cc0-1.0
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 2.07 MB
Statistics
  • Stars: 4
  • Watchers: 9
  • Forks: 4
  • Open Issues: 6
  • Releases: 4
Topics
bridgedb hacktoberfest
Created about 5 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

Tests DOI

This is where identifiers die

This project collects identifiers that are, for some reason, no longer pointing to active records in the corresponding database. As such, these identifiers should no longer be used. By collecting them in a machine-readable way, we can make it easier to automate the detection of dead identifiers in data curation workflows.

The following is a short summary of the contents of this resource:

Data

The data in the data folder is structured like as follows. Filenames follow the namespace of the resources as defined by the Bioregistry and used in compact URIs. The content of the file is a comma-separated values file with one or more columns:

  • #did: the dead identifier
  • when: when the identifier stopped being used
  • nextofkin: the identifier that replaces the identifier (for some reason)
  • contributor: (optional) the ORCID identifier of the curator for the death/replacement

This model is incomplete and volatile, but applies to Release 1.

Outputs

Automatically generated artifacts can be found in the artifacts folder.

| Format | File | Description | |--------|----------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | TSV | collated.tsv | A collated version of all TSV in the data/ folder | | SSSOM | tiwid.sssom.tsv | An output in the Simple Standard for Sharing Ontological Mappings (SSSOM) format | | RDF | tiwid.ttl | An output in RDF, serialized with Turtle. This file can be readily converted to an OWL ontology with ROBOT with robot convert -i tiwid.ttl -o tiwid.owl. |

Tests

Run tests using tox with the following commands in the shell:

shell $ pip install tox $ tox

The tests are also run using GitHub Actions following all commits to the main branch and pull requests to the main branch.

Owner

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

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this data, please cite it as below."
title: BridgeDb Tiwid
url: "https://github.com/bridgedb/tiwid"
doi: 10.5281/zenodo.4479409
version: 4
date-released: 2025-07-31
authors:
  - family-names: Willighagen
    given-names: Egon
    orcid: 0000-0001-7542-0286
  - family-names: Slenter
    given-names: Denise
    orcid: 0000-0001-8449-1318
  - family-names: Hoyt
    given-names: Charles Tapley
  - family-names: Abbassi-Daloii
    given-names: Tooba
  - family-names: Conroy
    given-names: Matthew
  - family-names: Martinat
    given-names: Dominik
  - family-names: Javier
    given-names: Millán Acosta
    orcid: 0000-0002-4166-7093

GitHub Events

Total
  • Create event: 7
  • Release event: 1
  • Issues event: 1
  • Delete event: 2
  • Issue comment event: 7
  • Push event: 25
  • Pull request review comment event: 1
  • Pull request review event: 3
  • Pull request event: 9
Last Year
  • Create event: 7
  • Release event: 1
  • Issues event: 1
  • Delete event: 2
  • Issue comment event: 7
  • Push event: 25
  • Pull request review comment event: 1
  • Pull request review event: 3
  • Pull request event: 9

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 24 minutes
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 24 minutes
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • egonw (5)
  • cthoyt (1)
  • DominikMartinat (1)
Top Labels
Issue Labels
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Dependencies

.github/workflows/collate.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • ad-m/github-push-action master composite
.github/workflows/qa.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite