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|
URI Prefix Discovery
====================
.. automodule:: curies.discovery
Discovering URI Prefixes from an Ontology
-----------------------------------------
A common place where discovering URI prefixes is important is when working with new ontologies.
In the following example, we look at the `Academic Event Ontology (AEON) <https://bioregistry.io/aeon>`_. This
is an ontology developed under OBO Foundry principles describing academic events. Accordingly, it includes many
URI references to terms in OBO Foundry ontologies.
In this tutorial, we use :func:`curies.discover` (and then :func:`curies.discover_from_rdf` as a nice convenience
function) to load the ontology in the RDF/XML format and discover putative URI prefixes.
.. code-block:: python
import curies
from curies.discovery import get_uris_from_rdf
ONTOLOGY_URL = "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl"
uris = get_uris_from_rdf(ONTOLOGY_URL, format="xml")
discovered_converter = curies.discover(uris)
# note, these two steps can be combine with curies.discover_from_rdf,
# and we'll do that in the following examples
We discovered the fifty URI prefixes in the following table. Many of them appear to be OBO Foundry URI prefixes or
semantic web prefixes, so in the next step, we'll use prior knowledge to reduce the false discovery rate.
============== ==============================================================================
curie_prefix uri_prefix
============== ==============================================================================
ns1 ``http://ontologydesignpatterns.org/wiki/Community:Parts_and_``
ns2 ``http://protege.stanford.edu/plugins/owl/protege#``
ns3 ``http://purl.obolibrary.org/obo/AEON_``
ns4 ``http://purl.obolibrary.org/obo/APOLLO_SV_``
ns5 ``http://purl.obolibrary.org/obo/BFO_``
ns6 ``http://purl.obolibrary.org/obo/CRO_``
ns7 ``http://purl.obolibrary.org/obo/ENVO_``
ns8 ``http://purl.obolibrary.org/obo/IAO_``
ns9 ``http://purl.obolibrary.org/obo/ICO_``
ns10 ``http://purl.obolibrary.org/obo/NCBITaxon_``
ns11 ``http://purl.obolibrary.org/obo/OBIB_``
ns12 ``http://purl.obolibrary.org/obo/OBI_``
ns13 ``http://purl.obolibrary.org/obo/OMO_``
ns14 ``http://purl.obolibrary.org/obo/OOSTT_``
ns15 ``http://purl.obolibrary.org/obo/RO_``
ns16 ``http://purl.obolibrary.org/obo/TXPO_``
ns17 ``http://purl.obolibrary.org/obo/bfo/axiom/``
ns18 ``http://purl.obolibrary.org/obo/valid_for_``
ns19 ``http://purl.obolibrary.org/obo/valid_for_go_``
ns20 ``http://purl.obolibrary.org/obo/valid_for_go_annotation_``
ns21 ``http://purl.obolibrary.org/obo/wikiCFP_``
ns22 ``http://purl.org/dc/elements/1.1/``
ns23 ``http://purl.org/dc/terms/``
ns24 ``http://usefulinc.com/ns/doap#``
ns25 ``http://wiki.geneontology.org/index.php/Involved_``
ns26 ``http://www.geneontology.org/formats/oboInOwl#``
ns27 ``http://www.geneontology.org/formats/oboInOwl#created_``
ns28 ``http://www.w3.org/1999/02/22-rdf-syntax-ns#``
ns29 ``http://www.w3.org/2000/01/rdf-schema#``
ns30 ``http://www.w3.org/2001/XMLSchema#``
ns31 ``http://www.w3.org/2002/07/owl#``
ns32 ``http://www.w3.org/2003/11/swrl#``
ns33 ``http://www.w3.org/2004/02/skos/core#``
ns34 ``http://www.w3.org/ns/prov#``
ns35 ``http://xmlns.com/foaf/0.1/``
ns36 ``https://en.wikipedia.org/wiki/Allen%27s_interval_``
ns37 ``https://groups.google.com/d/msg/bfo-owl-devel/s9Uug5QmAws/ZDRnpiIi_``
ns38 ``https://ror.org/``
ns39 ``https://w3id.org/scholarlydata/ontology/conference-ontology.owl#``
ns40 ``https://w3id.org/seo#``
ns41 ``https://www.confident-conference.org/index.php/Academic_Field:Information_``
ns42 ``https://www.confident-conference.org/index.php/Event:VIVO_``
ns43 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_``
ns44 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_orga_``
ns45 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_talk1_``
ns46 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_talk2_``
ns47 ``https://www.confident-conference.org/index.php/Event_Series:VIVO_``
ns48 ``https://www.wikidata.org/wiki/``
ns49 ``https://www.wikidata.org/wiki/Wikidata:Property_proposal/colocated_``
ns50 ``urn:swrl#``
============== ==============================================================================
In the following block, we chain together (extended) prefix maps from the OBO Foundry as well as
a "semantic web" prefix map to try and reduce the number of false positives by passing them
through the ``converter`` keyword argument.
.. code-block:: python
import curies
ONTOLOGY_URL = "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl"
SEMWEB_URL = "https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/semweb.context.jsonld"
base_converter = curies.chain([
curies.load_jsonld_context(SEMWEB_URL),
curies.get_obo_converter(),
])
discovered_converter = curies.discover_from_rdf(
ONTOLOGY_URL, format="xml", converter=base_converter
)
We reduced the number of putative URI prefixes in half in the following table. However, we can still identify
some putative URI prefixes that likely would have appeared in a more comprehensive (extended) prefix map such
as the Bioregistry such as:
- ``https://ror.org/`` for the `Research Organization Registry (ROR) <https://bioregistry.io/ror>`_
- ``https://w3id.org/seo#`` for the `Scientific Event Ontology (SEO) <https://bioregistry.io/seo>`_
- ``http://usefulinc.com/ns/doap#`` for the `Description of a Project (DOAP) vocabulary <https://bioregistry.io/doap>`_
Despite this, we're on our way! It's also obvious that several of the remaining putative URI prefixes come from
non-standard usage of the OBO PURL system (e.g., ``http://purl.obolibrary.org/obo/valid_for_go_annotation_``)
and some are proper false positives due to using ``_`` as a delimiter
(e.g., ``https://www.confident-conference.org/index.php/Event:VIVO_2021_talk2_``).
============== ==============================================================================
curie_prefix uri_prefix
============== ==============================================================================
ns1 ``http://ontologydesignpatterns.org/wiki/Community:Parts_and_``
ns2 ``http://protege.stanford.edu/plugins/owl/protege#``
ns3 ``http://purl.obolibrary.org/obo/AEON_``
ns4 ``http://purl.obolibrary.org/obo/bfo/axiom/``
ns5 ``http://purl.obolibrary.org/obo/valid_for_``
ns6 ``http://purl.obolibrary.org/obo/valid_for_go_``
ns7 ``http://purl.obolibrary.org/obo/valid_for_go_annotation_``
ns8 ``http://purl.obolibrary.org/obo/wikiCFP_``
ns9 ``http://usefulinc.com/ns/doap#``
ns10 ``http://wiki.geneontology.org/index.php/Involved_``
ns11 ``https://en.wikipedia.org/wiki/Allen%27s_interval_``
ns12 ``https://groups.google.com/d/msg/bfo-owl-devel/s9Uug5QmAws/ZDRnpiIi_``
ns13 ``https://ror.org/``
ns14 ``https://w3id.org/scholarlydata/ontology/conference-ontology.owl#``
ns15 ``https://w3id.org/seo#``
ns16 ``https://www.confident-conference.org/index.php/Academic_Field:Information_``
ns17 ``https://www.confident-conference.org/index.php/Event:VIVO_``
ns18 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_``
ns19 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_orga_``
ns20 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_talk1_``
ns21 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_talk2_``
ns22 ``https://www.confident-conference.org/index.php/Event_Series:VIVO_``
ns23 ``https://www.wikidata.org/wiki/``
ns24 ``https://www.wikidata.org/wiki/Wikidata:Property_proposal/colocated_``
ns25 ``urn:swrl#``
============== ==============================================================================
As a final step in our iterative journey of URI prefix discovery, we're going to use a cutoff for a minimum
of two appearances of a URI prefix to reduce the most spurious false positives.
.. code-block:: python
import curies
ONTOLOGY_URL = "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl"
SEMWEB_URL = "https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/semweb.context.jsonld"
base_converter = curies.chain([
curies.load_jsonld_context(SEMWEB_URL),
curies.get_obo_converter(),
])
discovered_converter = curies.discover_from_rdf(
ONTOLOGY_URL, format="xml", converter=base_converter, cutoff=2
)
We have reduced the list to a manageable set of 9 putative URI prefixes in the following table.
============== =========================================================================
curie_prefix uri_prefix
============== =========================================================================
ns1 ``http://purl.obolibrary.org/obo/AEON_``
ns2 ``http://purl.obolibrary.org/obo/bfo/axiom/``
ns3 ``http://purl.obolibrary.org/obo/valid_for_go_``
ns4 ``https://w3id.org/scholarlydata/ontology/conference-ontology.owl#``
ns5 ``https://w3id.org/seo#``
ns6 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_``
ns7 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_talk1_``
ns8 ``https://www.confident-conference.org/index.php/Event:VIVO_2021_talk2_``
ns9 ``urn:swrl#``
============== =========================================================================
Here are the calls to be made:
- ``ns1`` represents the AEON vocabulary itself and should be given the ``aeon`` prefix.
- ``ns2`` and ``ns3``` are all false positives
- ``ns6``, ``ns7``, and ``ns8`` are a tricky case - they have a meaningful overlap that can't be easily
automatically detected (yet). In this case, it makes the most sense to add the shortest one manually
to the base converter with some unique name (don't use ``ns6`` as it will cause conflicts later), like in:
.. code-block:: python
base_converter = curies.chain([
curies.load_jsonld_context(SEMWEB_URL),
curies.get_obo_converter(),
curies.load_prefix_map({"confident_event_vivo_2021": "https://www.confident-conference.org/index.php/Event:VIVO_2021_"}),
])
In reality, these are all part of the `ConfIDent Event <https://bioregistry.io/confident.event>`_ vocabulary,
which has the URI prefix ``https://www.confident-conference.org/index.php/Event:``.
- ``ns4`` represents the `Conference Ontology <https://bioregistry.io/conference>`_ and
should be given the ``conference`` prefix.
- ``ns5`` represents the `Scientific Event Ontology (SEO) <https://bioregistry.io/seo>`_ and
should be given the ``seo`` prefix.
- ``ns9`` represents the `Semantic Web Rule Language <https://bioregistry.io/registry/swrl>`_,
though using URNs is an interesting choice in serialization.
After we've made these calls, it's a good idea to write an (extended) prefix map. In this case, since we aren't working
with CURIE prefix synonyms nor URI prefix synonyms, it's okay to write a simple prefix map or a JSON-LD context without
losing information.
.. note::
Postscript: throughout this guide, we used the following Python code to create the RST tables:
.. code-block:: python
def print_converter(converter) -> None:
from tabulate import tabulate
rows = sorted(
[
(record.prefix, f"``{record.uri_prefix}``")
for record in discovered_converter.records
],
key=lambda t: int(t[0].removeprefix("ns")),
)
print(tabulate(rows, headers=["curie_prefix", "uri_prefix"], tablefmt="rst"))
Just Make It Work, or, A Guide to Being a Questionable Semantic Citizen
-----------------------------------------------------------------------
The goal of the :mod:`curies` package is to provide the tools towards making semantically well-defined data,
which has a meaningful (extended) prefix map associated with it. Maybe you're in an organization that doesn't really
care about the utility of nice prefix maps, and just wants to get the job done where you need to turn URIs into _some_
CURIEs.
Here's a recipe for doing this, based on the last example with AEON:
.. code-block:: python
import curies
ONTOLOGY_URL = "https://raw.githubusercontent.com/tibonto/aeon/main/aeon.owl"
# Use the Bioregistry as a base prefix since it's the most comprehensive one
base_converter = curies.get_bioregistry_converter()
# Only discover what the Bioregistry doesn't already have
discovered_converter = curies.discover_from_rdf(
ONTOLOGY_URL, format="xml", converter=base_converter
)
# Chain together the base converter with the discoveries
augmented_converter = curies.chain([base_converter, discovered_converter])
With the augmented converter, you can now convert all URIs in the ontology into CURIEs. They will have a smattering
of unintelligible prefixes with no meaning, but at least the job is done!
|
