-
Examples
+
Examples
-
+
+
-{% endblock %}
+
+
+
+ - Schizophrenia
+ -
+ A mental disorder characterized by continuous or relapsing episodes of psychosis.
+
+
+ - Microcephaly
+ -
+ A medical condition involving a smaller-than-normal head.
+
+
+ - Rett syndrome
+ -
+ A genetic disorder that typically becomes apparent after 6–18 months of age and almost exclusively in females.
+
+
+ - Zika fever
+ -
+ An infectious disease caused by the Zika virus.
+
+
+ - Fatty liver disease
+ -
+ A condition where excess fat builds up in the liver.
+
+
+
-
+
+
+
+
+
+
If you know the identifier, then Scholia can make a lookup based on the identifier:
+
+
+ - omim/137580
+ - Look up OMIM ID 137580. This will redirect to Tourette syndrome.
+
+
+
+
+
+{% endblock %}
diff --git a/scholia/app/views.py b/scholia/app/views.py
index 6dc099424..703542822 100644
--- a/scholia/app/views.py
+++ b/scholia/app/views.py
@@ -16,7 +16,7 @@
from ..arxiv import get_metadata as get_arxiv_metadata
from ..query import (arxiv_to_qs, cas_to_qs, atomic_symbol_to_qs, doi_to_qs,
doi_prefix_to_qs, github_to_qs, biorxiv_to_qs,
- chemrxiv_to_qs,
+ chemrxiv_to_qs, omim_to_qs,
identifier_to_qs, inchikey_to_qs, issn_to_qs, orcid_to_qs,
viaf_to_qs, q_to_class, q_to_dois, random_author,
twitter_to_qs, cordis_to_qs, mesh_to_qs, pubmed_to_qs,
@@ -1084,6 +1084,23 @@ def redirect_mesh(meshid):
return render_template('404.html', error=could_not_find("MeSH ID"))
+@main.route('/omim/
')
+def redirect_omim(omimID):
+ """Detect and redirect for OMIM identifiers.
+
+ Parameters
+ ----------
+ omim : str
+ OMIM identifier.
+
+ """
+ qs = omim_to_qs(omimID)
+ if len(qs) > 0:
+ q = qs[0]
+ return redirect(url_for('app.show_author', q=q), code=302)
+ return render_template('404.html', error=could_not_find("OMIM ID"))
+
+
@main.route('/orcid/')
def redirect_orcid(orcid):
"""Detect and redirect for ORCID.
diff --git a/scholia/query.py b/scholia/query.py
index 20c2e6979..b9c62d2fa 100644
--- a/scholia/query.py
+++ b/scholia/query.py
@@ -18,6 +18,7 @@
scholia.query mesh-to-q
scholia.query ncbi-gene-to-q
scholia.query ncbi-taxon-to-q
+ scholia.query omim-to-q
scholia.query orcid-to-q
scholia.query pubchem-to-q
scholia.query pubmed-to-q
@@ -772,6 +773,37 @@ def issn_to_qs(issn):
for item in data['results']['bindings']]
+def omim_to_qs(omimID):
+ """Convert OMIM identifier to Wikidata ID.
+
+ Parameters
+ ----------
+ omim : str
+ OMIM identifier
+
+ Returns
+ -------
+ qs : list of str
+ List of strings with Wikidata IDs.
+
+ Examples
+ --------
+ >>> omim_to_qs('181500') == ['Q41112']
+ True
+
+ """
+ query = 'select ?disease where {{ ?disease wdt:P492 "{omimID}" }}'.format(
+ omimID=escape_string(omimID))
+
+ url = 'https://query.wikidata.org/sparql'
+ params = {'query': query, 'format': 'json'}
+ response = requests.get(url, params=params, headers=HEADERS)
+ data = response.json()
+
+ return [item['disease']['value'][31:]
+ for item in data['results']['bindings']]
+
+
def orcid_to_qs(orcid):
"""Convert orcid to Wikidata ID.
@@ -1757,6 +1789,11 @@ def main():
if len(qs) > 0:
print(qs[0])
+ elif arguments['omim-to-q']:
+ qs = omim_to_qs(arguments[''])
+ if len(qs) > 0:
+ print(qs[0])
+
elif arguments['orcid-to-q']:
qs = orcid_to_qs(arguments[''])
if len(qs) > 0: