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:
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 identifierwhen: when the identifier stopped being usednextofkin: 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.
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. |
Run tests using tox with the following commands in the shell:
$ pip install tox
$ toxThe tests are also run using GitHub Actions following all commits to the main branch and pull requests to the main branch.