import json
import re
from functools import lru_cache
from urllib.parse import urlencode
from os.path import abspath, dirname, join, pardir
import requests
from indra.util import read_unicode_csv
MESH_URL = 'https://id.nlm.nih.gov/mesh/'
HERE = dirname(abspath(__file__))
RESOURCES = join(HERE, pardir, 'resources')
MESH_FILE = join(RESOURCES, 'mesh_id_label_mappings.tsv')
MESH_REV_LOOKUPS = join(RESOURCES, 'mesh_name_id_maps.json')
mesh_id_to_name = {}
mesh_name_to_id = {}
for mesh_id, mesh_label in read_unicode_csv(MESH_FILE, delimiter='\t'):
mesh_id_to_name[mesh_id] = mesh_label
mesh_name_to_id[mesh_label] = mesh_id
with open(MESH_REV_LOOKUPS, 'r') as f:
mesh_name_to_id_name = json.load(f)
[docs]@lru_cache(maxsize=1000)
def get_mesh_name_from_web(mesh_id):
"""Get the MESH label for the given MESH ID using the NLM REST API.
Parameters
----------
mesh_id : str
MESH Identifier, e.g. 'D003094'.
Returns
-------
str
Label for the MESH ID, or None if the query failed or no label was
found.
"""
url = MESH_URL + mesh_id + '.json'
resp = requests.get(url)
if resp.status_code != 200:
return None
mesh_json = resp.json()
try:
label = mesh_json['@graph'][0]['label']['@value']
except (KeyError, IndexError) as e:
return None
return label
[docs]def get_mesh_name(mesh_id, offline=False):
"""Get the MESH label for the given MESH ID.
Uses the mappings table in `indra/resources`; if the MESH ID is not listed
there, falls back on the NLM REST API.
Parameters
----------
mesh_id : str
MESH Identifier, e.g. 'D003094'.
offline : bool
Whether to allow queries to the NLM REST API if the given MESH ID is not
contained in INDRA's internal MESH mappings file. Default is False
(allows REST API queries).
Returns
-------
str
Label for the MESH ID, or None if the query failed or no label was
found.
"""
indra_mesh_mapping = mesh_id_to_name.get(mesh_id)
if offline or indra_mesh_mapping is not None:
return indra_mesh_mapping
# Look up the MESH mapping from NLM if we don't have it locally
return get_mesh_name_from_web(mesh_id)
[docs]def get_mesh_id_name(mesh_term, offline=False):
"""Get the MESH ID and name for the given MESH term.
Uses the mappings table in `indra/resources`; if the MESH term is not
listed there, falls back on the NLM REST API.
Parameters
----------
mesh_term : str
MESH Descriptor or Concept name, e.g. 'Breast Cancer'.
offline : bool
Whether to allow queries to the NLM REST API if the given MESH term is
not contained in INDRA's internal MESH mappings file. Default is False
(allows REST API queries).
Returns
-------
tuple of strs
Returns a 2-tuple of the form `(id, name)` with the ID of the
descriptor corresponding to the MESH label, and the descriptor name
(which may not exactly match the name provided as an argument if it is
a Concept name). If the query failed, or no descriptor corresponding to
the name was found, returns a tuple of (None, None).
"""
indra_mesh_id = mesh_name_to_id.get(mesh_term)
if indra_mesh_id is not None:
return indra_mesh_id, mesh_term
indra_mesh_id, new_term = \
mesh_name_to_id_name.get(mesh_term, (None, None))
if indra_mesh_id is not None:
return indra_mesh_id, new_term
if offline:
return None, None
# Look up the MESH mapping from NLM if we don't have it locally
return get_mesh_id_name_from_web(mesh_term)
[docs]@lru_cache(maxsize=1000)
def get_mesh_id_name_from_web(mesh_term):
"""Get the MESH ID and name for the given MESH term using the NLM REST API.
Parameters
----------
mesh_term : str
MESH Descriptor or Concept name, e.g. 'Breast Cancer'.
Returns
-------
tuple of strs
Returns a 2-tuple of the form `(id, name)` with the ID of the
descriptor corresponding to the MESH label, and the descriptor name
(which may not exactly match the name provided as an argument if it is
a Concept name). If the query failed, or no descriptor corresponding to
the name was found, returns a tuple of (None, None).
"""
url = MESH_URL + 'sparql'
query = """
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#>
PREFIX mesh: <http://id.nlm.nih.gov/mesh/>
PREFIX mesh2019: <http://id.nlm.nih.gov/mesh/2019/>
PREFIX mesh2018: <http://id.nlm.nih.gov/mesh/2018/>
PREFIX mesh2017: <http://id.nlm.nih.gov/mesh/2017/>
SELECT ?d ?dName ?c ?cName
FROM <http://id.nlm.nih.gov/mesh>
WHERE {
?d a meshv:Descriptor .
?d meshv:concept ?c .
?d rdfs:label ?dName .
?c rdfs:label ?cName
FILTER (REGEX(?dName,'^%s$','i') || REGEX(?cName,'^%s$','i'))
}
ORDER BY ?d
""" % (mesh_term, mesh_term)
args = {'query': query, 'format': 'JSON', 'inference': 'true'}
# Interestingly, the following call using requests.get to package the
# query does not work:
# resp = requests.get(url, data=args)
# But if the query string is explicitly urlencoded using urllib, it works:
query_string = '%s?%s' % (url, urlencode(args))
resp = requests.get(query_string)
# Check status
if resp.status_code != 200:
return None, None
try:
# Try to parse the json response (this can raise exceptions if we
# got no response).
mesh_json = resp.json()
# Choose the first entry (should usually be only one)
id_uri = mesh_json['results']['bindings'][0]['d']['value']
name = mesh_json['results']['bindings'][0]['dName']['value']
except (KeyError, IndexError, json.decoder.JSONDecodeError) as e:
return None, None
# Strip the MESH prefix off the ID URI
m = re.match('http://id.nlm.nih.gov/mesh/([A-Za-z0-9]*)', id_uri)
assert m is not None
id = m.groups()[0]
return id, name