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Add documentation about PURLs #1080

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Apr 3, 2024
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Add documentation about PURLs #1080

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db9edc4
Add PURLs
cthoyt Apr 3, 2024
8979bb4
Update README.md
cthoyt Apr 3, 2024
266a92b
Update prefixcc.py
cthoyt Apr 3, 2024
fee07eb
Get rid of nulls in export
cthoyt Apr 3, 2024
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6 changes: 6 additions & 0 deletions exports/README.md
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Expand Up @@ -20,3 +20,9 @@ basis using GitHub Actions as a continuous integration server.
| [`rdf`](rdf) | Build of an RDF triple-store representing the registry, metaregistry, and collections |
| [`sssom`](sssom) | An export of prefix mappings in the Simple Standard for Sharing Ontology Mappings (SSSOM) format |
| [`contexts`](contexts) | Fit-for-purpose exports of JSON-LD contexts constructed from the Bioregistry |

## PURLs

The Bioregistry uses https://w3id.org to create persistent uniform resource locators (PURLs) for various
resources. These are configured on GitHub in the .htaccess file
in https://github.com/perma-id/w3id.org/tree/master/biopragmatics.
34 changes: 24 additions & 10 deletions exports/contexts/README.md
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Expand Up @@ -14,16 +14,30 @@ resources like `dcterms`, `rdf`, and `owl`.
### Generated via code

The rest are generated by specific code written in
the `bioregistry.export.prefix_maps` module.

| File | Description |
|-------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| [`bioregistry.context.jsonld`](bioregistry.context.jsonld) and [`bioregistry.context.ttl`](bioregistry.context.ttl) | Contains Bioregistry-normalized prefixes (lowercase, punctuation normalized) and the best URI prefixes for each based on the Bioregistry's ruleset. |
| [`bioregistry.epm.json`](bioregistry.epm.json) | An extended prefix map for the Bioregistry for use with the [`curies`](https://github.com/cthoyt/curies) package. That contains a prefix map and additional, unique prefix and URI prefix synonyms for each record |
| [`bioregistry.rpm.json`](bioregistry.rpm.json) | A reverse prefix map for the Bioregistry in which keys are URI prefixes (unique) and values are canonical Bioregistry prefixes (may be duplicates) for use in IRI compression only. |
| [`obo.context.jsonld`](obo.context.jsonld) and [`obo.context.ttl`](obo.context.ttl) | Contains prefixes and URI prefixes prioritized for the OBO Foundry and ontology contexts. |
| [`obo_synonyms.context.jsonld`](obo_synonyms.context.jsonld) and [`obo_synonyms.context.ttl`](obo_synonyms.context.ttl) | Contains prefixes, prefix's synonyms, and URI prefixes prioritized for the OBO Foundry and ontology contexts. |
| [`spar.context.jsonld`](spar.context.jsonld) and [`spar.context.ttl`](spar.context.ttl) | Contains prefixes from the [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies). |
the `bioregistry.export.prefix_maps` module. There are three flavors of exports for each context:

| Extension | PURL | Description |
|--------------------|---------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `*.epm.json` | `https://w3id.org/biopragmatics/*.epm.json` | An extended prefix map for use with the [`curies`](https://github.com/biopragmatics/curies) package. That contains a prefix map and additional, unique prefix and URI prefix synonyms for each record. |
| `*.context.jsonld` | `https://w3id.org/biopragmatics/*.context.jsonld` | Contains a JSON-LD-flavored simple prefix map in a `@context` |
| `*.context.ttl` | `https://w3id.org/biopragmatics/*.context.ttl` | Encodes a simple prefix map with the SHACL vocabulary |

File List:

| File | PURL | Description |
|--------------------------------------------------------------|------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| [`bioregistry.epm.json`](bioregistry.epm.json) | https://w3id.org/biopragmatics/bioregistry.epm.json | An extended prefix map for the Bioregistry for use with the [`curies`](https://github.com/biopragmatics/curies) package. That contains a prefix map and additional, unique prefix and URI prefix synonyms for each record. |
| [`bioregistry.context.jsonld`](bioregistry.context.jsonld) | https://w3id.org/biopragmatics/bioregistry.context.jsonld | Contains Bioregistry-normalized prefixes (lowercase, punctuation normalized) and the best URI prefixes for each based on the Bioregistry's ruleset. |
| [`bioregistry.context.ttl`](bioregistry.context.ttl) | https://w3id.org/biopragmatics/bioregistry.context.ttl | |
| [`obo.epm.json`](obo.epm.json) | https://w3id.org/biopragmatics/obo.epm.json | |
| [`obo.context.jsonld`](obo.context.jsonld) | https://w3id.org/biopragmatics/obo.context.jsonld | Contains prefixes and URI prefixes prioritized for the OBO Foundry and ontology contexts. |
| [`obo.context.ttl`](obo.context.ttl) | https://w3id.org/biopragmatics/obo.context.ttl | |
| [`obo_synonyms.context.ttl`](obo_synonyms.context.ttl) | https://w3id.org/biopragmatics/obo_synonyms.context.jsonld | Contains prefixes, prefix's synonyms, and URI prefixes prioritized for the OBO Foundry and ontology contexts. |
| [`obo_synonyms.context.jsonld`](obo_synonyms.context.jsonld) | https://w3id.org/biopragmatics/obo_synonyms.context.ttl | |
| [`spar.context.jsonld`](spar.context.jsonld) | https://w3id.org/biopragmatics/spar.context.jsonld | Contains prefixes from the [Semantic Publishing and Referencing (SPAR) Ontologies](http://www.sparontologies.net/ontologies). |
| [`spar.context.ttl`](spar.context.ttl) | https://w3id.org/biopragmatics/spar.context.ttl | |
| [`semweb.context.jsonld`](semweb.context.jsonld) | https://w3id.org/biopragmatics/semweb.context.jsonld | Contains prefixes for the semantic web, mostly W3C prefixes. |
| [`semweb.context.ttl`](semweb.context.ttl) | https://w3id.org/biopragmatics/semweb.context.ttl | |

## Prescriptive Contexts

Expand Down
8 changes: 7 additions & 1 deletion exports/registry/README.md
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Expand Up @@ -20,11 +20,15 @@ registry.
This file *should* contain all relevant fields. If you find something missing,
please make an issue.

This file can be accessed with the PURL: https://w3id.org/biopragmatics/bioregistry/registry.json

### [`registry.yml`](registry.yml)

This is exactly the same as the consensus `registry.json` but dumped as a YAML
file.

This file can be accessed with the PURL: https://w3id.org/biopragmatics/bioregistry/registry.yml

### [`registry.tsv`](registry.tsv)

This is a derived view over the registry in a tab-separated values document. It
Expand All @@ -34,7 +38,9 @@ most important.
If there's something additional you'd like included in this export, please open
an issue.

This file can be accessed with the PURL: https://w3id.org/biopragmatics/bioregistry/registry.tsv

### [`publications.tsv`](publications.tsv)

This is a derived view of all of the publications referenced by various records
This is a derived view of all the publications referenced by various records
in the Bioregistry.
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