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Data Structures
===============
A *semantic space* is a collections of identifiers for concepts. For example,
the Chemical Entities of Biomedical Interest (ChEBI) has a semantic space
including identifiers for chemicals. Within ChEBI's semantic space,
`138488` corresponds to the chemical `alsterpaullone <https://www.ebi.ac.uk/chebi/searchId.do?chebiId=138488>`_.
.. warning::
`138488` is a *local unique identifier*. Other semantic spaces might use the same local
unique identifier to refer to a different concept in their respective domain.
Therefore, local unique identifiers should be qualified with some additional information saying what semantic space
it comes from. The two common formalisms for doing this are Uniform Resource Identifiers (URIs) and
Compact URIs (CURIEs):
.. image:: syntax_demo.svg
:alt: Demo of URI and CURIE for alsterpaullone.
In many applications, it's important to be able to convert between CURIEs and URIs.
Therefore, we need a data structure that connects the CURIE prefixes like ``CHEBI``
to the URI prefixes like ``http://purl.obolibrary.org/obo/CHEBI_``.
Prefix Maps
-----------
A prefix map is a dictionary data structure where keys represent CURIE prefixes
and their associated values represent URI prefixes. Ideally, these are constrained
to be bijective (i.e., no duplicate keys, no duplicate values), but this is not always
done in practice. Here's an example prefix map containing information about semantic
spaces from a small selection of OBO Foundry ontologies:
.. code-block:: json
{
"CHEBI": "http://purl.obolibrary.org/obo/CHEBI_",
"MONDO": "http://purl.obolibrary.org/obo/MONDO_",
"GO": "http://purl.obolibrary.org/obo/GO_"
}
Prefix maps have the benefit of being simple and straightforward.
They appear in many linked data applications, including:
- the ``@prefix`` declarations at the top of Turtle (RDF) documents and SPARQL queries
- `JSON-LD <https://www.w3.org/TR/json-ld11/#prefix-definitions>`_
- XML documents
- OWL ontologies
.. note::
Prefix maps can be loaded using :meth:`curies.Converter.from_prefix_map`.
*However*, prefix maps have the main limitation that they do not have first-class support for
synonyms of CURIE prefixes or URI prefixes. In practice, a variety of synonyms are used
for both. For example, the NCBI Taxonomy database appears with many different CURIE prefixes:
============== ====================================
CURIE Prefix Resource(s)
============== ====================================
``taxonomy`` Identifiers.org, Name-to-Thing
``taxon`` Gene Ontology Registry
``NCBITaxon`` OBO Foundry, Prefix Commons, OntoBee
``NCBITAXON`` BioPortal
``NCBI_TaxID`` Cellosaurus
``ncbitaxon`` OLS
``P685`` Wikidata
``fj07xj`` FAIRsharing
============== ====================================
Similarly, many different URIs can be constructed for the same ChEBI local unique identifier. Using
alsterpaullone as an example, this includes (many omitted):
==================================================== ===================
URI Prefix Provider
==================================================== ===================
``https://www.ebi.ac.uk/chebi/searchId.do?chebiId=`` ChEBI (first-party)
``https://identifiers.org/CHEBI:`` Identifiers.org
``https://identifiers.org/CHEBI/`` Identifiers.org
``http://identifiers.org/CHEBI:`` Identifiers.org
``http://identifiers.org/CHEBI/`` Identifiers.org
``http://purl.obolibrary.org/obo/CHEBI_`` OBO Foundry
``https://n2t.net/chebi:`` Name-to-thing
==================================================== ===================
In practice, we need to be able to support the fact that there are many CURIE prefixes
and URI prefixes for most semantic spaces as well as specify which CURIE prefix and
URI prefix is the "preferred" one in a given context. Prefix maps, unfortunately, have no way to
address this. Therefore, we're going to introduce a new data structure.
.. _epms:
Extended Prefix Maps
--------------------
Extended Prefix Maps (EPMs) address the issues with prefix maps by including explicit
fields for CURIE prefix synonyms and URI prefix synonyms while maintaining an explicit
field for the preferred CURIE prefix and URI prefix. An abbreviated example (just
containing an entry for ChEBI) looks like:
.. code-block:: json
[
{
"prefix": "CHEBI",
"uri_prefix": "http://purl.obolibrary.org/obo/CHEBI_",
"prefix_synonyms": ["chebi"],
"uri_prefix_synonyms": [
"https://identifiers.org/chebi:"
]
}
]
An EPM is simply a list of records (see :class:`curies.Record` and :class:`curies.Records`).
EPMs have the benefit that they are still
encoded in JSON and can easily be encoded in YAML, TOML, RDF, and other schemata. Further, prefix maps can be
automatically upgraded into EPMs (with some caveats) using :func:`curies.upgrade_prefix_map`.
.. note::
We are introducing this as a new standard in the :mod:`curies` package. They
can be loaded using :meth:`curies.Converter.from_extended_prefix_map`.
We provide a Pydantic model representing it. Later, we hope to have an external, stable definition
of this data schema.
A JSON schema for EPMs is available at https://w3id.org/biopragmatics/schema/epm.json.
It can be updated at https://github.com/biopragmatics/curies/tree/main/docs/make_schema.py.
|
