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Automate generation of RO-Wikidata mappings in SSSOM #444

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Automate generation of RO-Wikidata mappings in SSSOM #444

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43a9c68
Copy original script (needs a bit of work)
cthoyt Mar 19, 2021
345f44b
Reorganize automated generation code
cthoyt Mar 19, 2021
3346adf
Update generate_wikidata_mapping.py
cthoyt Mar 19, 2021
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38 changes: 20 additions & 18 deletions src/mappings/ro-to-wikidata.sssom.tsv
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Expand Up @@ -6,21 +6,23 @@
#mapping_provider: http://obofoundry.org/ontology/ro
#subject_source: http://purl.obolibrary.org/obo/ro.owl
subject_id subject_label predicate_id object_id object_label match_type comments
RO:0001025 owl:equivalentProperty wd:P276 location Curated derived from wikidata via SPARQL
RO:0002211 owl:equivalentProperty wd:P128 regulates (molecular biology) Curated derived from wikidata via SPARQL
BFO:0000051 owl:equivalentProperty wd:P527 has part Curated derived from wikidata via SPARQL
BFO:0000050 owl:equivalentProperty wd:P361 part of Curated derived from wikidata via SPARQL
RO:0002204 owl:equivalentProperty wd:P702 encoded by Curated derived from wikidata via SPARQL
RO:0002205 owl:equivalentProperty wd:P688 encodes Curated derived from wikidata via SPARQL
RO:0002411 owl:equivalentProperty wd:P828 has cause Curated derived from wikidata via SPARQL
RO:0002162 owl:equivalentProperty wd:P703 found in taxon Curated derived from wikidata via SPARQL
RO:0002404 owl:equivalentProperty wd:P1542 has effect Curated derived from wikidata via SPARQL
RO:0002405 owl:equivalentProperty wd:P1536 immediate cause of Curated derived from wikidata via SPARQL
RO:0003001 owl:equivalentProperty wd:P2849 produced by Curated derived from wikidata via SPARQL
RO:0002302 owl:equivalentProperty wd:P2176 drug used for treatment Curated derived from wikidata via SPARQL
RO:0002008 owl:equivalentProperty wd:P1382 partially coincident with Curated derived from wikidata via SPARQL
RO:0002005 owl:equivalentProperty wd:P3189 innervated by Curated derived from wikidata via SPARQL
RO:0002202 owl:equivalentProperty wd:P3094 develops from Curated derived from wikidata via SPARQL
RO:0000087 owl:equivalentProperty wd:P2868 subject has role Curated derived from wikidata via SPARQL
RO:0002379 owl:equivalentProperty wd:P3403 coextensive with Curated derived from wikidata via SPARQL
RO:0002134 owl:equivalentProperty wd:P3190 innervates Curated derived from wikidata via SPARQL
BFO:0000050 part of owl:equivalentProperty wd:P361 part of Curated derived from wikidata via SPARQL
BFO:0000051 has part owl:equivalentProperty wd:P527 has part Curated derived from wikidata via SPARQL
RO:0000087 has role owl:equivalentProperty wd:P2868 subject has role Curated derived from wikidata via SPARQL
RO:0001025 located in owl:equivalentProperty wd:P276 location Curated derived from wikidata via SPARQL
RO:0002005 innervated_by owl:equivalentProperty wd:P3189 innervated by Curated derived from wikidata via SPARQL
RO:0002008 coincident with owl:equivalentProperty wd:P1382 partially coincident with Curated derived from wikidata via SPARQL
RO:0002134 innervates owl:equivalentProperty wd:P3190 innervates Curated derived from wikidata via SPARQL
RO:0002162 in taxon owl:equivalentProperty wd:P703 found in taxon Curated derived from wikidata via SPARQL
RO:0002202 develops from owl:equivalentProperty wd:P3094 develops from Curated derived from wikidata via SPARQL
RO:0002204 gene product of owl:equivalentProperty wd:P702 encoded by Curated derived from wikidata via SPARQL
RO:0002205 has gene product owl:equivalentProperty wd:P688 encodes Curated derived from wikidata via SPARQL
RO:0002211 regulates owl:equivalentProperty wd:P128 regulates (molecular biology) Curated derived from wikidata via SPARQL
RO:0002302 is treated by substance owl:equivalentProperty wd:P2176 drug used for treatment Curated derived from wikidata via SPARQL
RO:0002379 spatially coextensive with owl:equivalentProperty wd:P3403 coextensive with Curated derived from wikidata via SPARQL
RO:0002404 causally downstream of owl:equivalentProperty wd:P1542 has effect Curated derived from wikidata via SPARQL
RO:0002405 immediately causally downstream of owl:equivalentProperty wd:P1536 immediate cause of Curated derived from wikidata via SPARQL
RO:0002411 causally upstream of owl:equivalentProperty wd:P828 has cause Curated derived from wikidata via SPARQL
RO:0003001 produced by owl:equivalentProperty wd:P2849 produced by Curated derived from wikidata via SPARQL
RO:0012001 has small molecule activator owl:equivalentProperty wd:P3771 activator of Curated derived from wikidata via SPARQL
RO:0012002 has small molecule inhibitor owl:equivalentProperty wd:P3776 inhibitor of Curated derived from wikidata via SPARQL
98 changes: 98 additions & 0 deletions src/tools/generate_wikidata_mapping.py
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# -*- coding: utf-8 -*-

"""Generates summaries of the relation ontology.

This script requires the installation of the :mod:`requests` library.
"""

import json
import os
import textwrap

import requests

HERE = os.path.abspath(os.path.dirname(__file__))
SSSOM_PATH = os.path.abspath(os.path.join(HERE, os.pardir, 'mappings', 'ro-to-wikidata.sssom.tsv'))
OBO_PATH = os.path.abspath(os.path.join(HERE, os.pardir, os.pardir, 'ro.json'))


def get_id_name_mapping():
"""Get a mapping from RO_XXXXXXX identifiers to their labels."""
with open(OBO_PATH) as file:
obo_json = json.load(file)
return {
node['id'][len('http://purl.obolibrary.org/obo/'):]: node['lbl']
for node in obo_json['graphs'][0]['nodes']
if 'lbl' in node
}


# URL for the Wikidata SPARQL service
WIKIDATA_SPARQL_ENDPOINT = 'https://query.wikidata.org/bigdata/namespace/wdq/sparql'

MAPPING_SPARQL = '''
SELECT ?prop ?propLabel ?ro_id
WHERE {
?prop wdt:P3590 ?ro_id .
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}
'''


def get_query(query: str):
"""Get the results of a SPARQL query to the Wikidata SPARQL endpoint as JSON."""
res = requests.get(
WIKIDATA_SPARQL_ENDPOINT,
params={'query': query, 'format': 'json'},
)
res.raise_for_status()
res_json = res.json()
return res_json['results']['bindings']


def main():
ro_id_name = get_id_name_mapping()

predicate = 'owl:equivalentProperty'
match_type = 'Curated'
comments = 'derived from wikidata via SPARQL'

headers = [
'subject_id', 'subject_label', 'predicate_id', 'object_id', 'object_label', 'match_type', 'comments',
]
with open(SSSOM_PATH, 'w') as file:
print(textwrap.dedent('''\
#curie_map:
# wd: http://www.wikidata.org/entity/
# RO: http://purl.obolibrary.org/obo/RO_
# BFO: http://purl.obolibrary.org/obo/BFO_
#license: https://creativecommons.org/publicdomain/zero/1.0/
#mapping_provider: http://obofoundry.org/ontology/ro
#subject_source: http://purl.obolibrary.org/obo/ro.owl
''').rstrip(), file=file)
print(*headers, sep='\t', file=file)

rows = [
(
row['ro_id']['value'],
row['prop']['value'][len('http://www.wikidata.org/entity/'):],
row['propLabel']['value']
)
for row in get_query(MAPPING_SPARQL)
]
for ro_id, wd_id, wd_label in sorted(rows):
print(
ro_id.replace('_', ':'),
ro_id_name[ro_id],
predicate,
f'wd:{wd_id}',
wd_label,
match_type,
comments,
sep='\t',
file=file,
)


if __name__ == '__main__':
main()