Intro to Biomedical Ontologies: Owlready2#
Biomedical ontologies is generally a tough-to-approach field, starting with “what is an ontology?”.
I often reply to that with “it’s a hairball of knowledge.”
Imagine if someone/group decided to “lets represent something close to a neuronal-connection of knowledge”.
For me, I am not an ontologist (creating new ontologies). I consider myself one of the few people who can figure out how to leverage ontologies to achieve very specific biomedical and clinical tasks.
import owlready2
hpo = owlready2.get_ontology("data/hp.owl").load()
# mondo = owlready2.get_ontology("data/mondo.owl").load()
efo = owlready2.get_ontology("data/efo.owl").load()
mfo = owlready2.get_ontology("data/MFOMD.owl").load()
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[1], line 3
1 import owlready2
----> 3 hpo = owlready2.get_ontology("data/hp.owl").load()
4 # mondo = owlready2.get_ontology("data/mondo.owl").load()
5 efo = owlready2.get_ontology("data/efo.owl").load()
File ~/.cache/pypoetry/virtualenvs/data-expressions-XOHyUNvQ-py3.10/lib/python3.10/site-packages/owlready2/namespace.py:988, in Ontology.load(self, only_local, fileobj, reload, reload_if_newer, url, **args)
986 if reload or (self.graph.get_last_update_time() == 0.0):
987 if _LOG_LEVEL: print("* Owlready2 * ...loading ontology %s from %s..." % (self.name, f), file = sys.stderr)
--> 988 fileobj = open(f, "rb")
989 try: new_base_iri = self.graph.parse(fileobj, default_base = self._orig_base_iri, **args)
990 finally: fileobj.close()
FileNotFoundError: [Errno 2] No such file or directory: 'data/hp.owl'
import re
# Crude searcher
def obo_searcher(ontology,
search_term,
second_pass_regex=None):
mondo_results = ontology.search(label = f"*{search_term}*", _case_sensitive=False)
if second_pass_regex:
data = [{
"concept": x,
"label": x.label,
"iri": x.iri,
"synonyms": x.hasExactSynonym,
"name": x.name,
"subclasses": list(x.subclasses()),
"xrefs": x.hasDbXref
} for x in mondo_results if (str(x.name) != "") & any( re.compile(f"{second_pass_regex}", re.I).match(item) for item in x.label)]
else:
data = [{
"concept": x,
"label": x.label,
"iri": x.iri,
"synonyms": x.hasExactSynonym,
"name": x.name,
"subclasses": list(x.subclasses()),
"xrefs": x.hasDbXref
} for x in mondo_results if str(x.name) != ""]
return (data)
search_term = "moyamoya"
results = obo_searcher(mfo, search_term)
Results: List of dictionary of ontology concepts and metadata#
results
[{'concept': obo.HP_0011834,
'label': ['Moyamoya phenomenon'],
'iri': 'http://purl.obolibrary.org/obo/HP_0011834',
'synonyms': [],
'name': 'HP_0011834',
'subclasses': [],
'xrefs': ['UMLS:C4023169']},
{'concept': obo.MONDO_0010448,
'label': ['moyamoya angiopathy-short stature-facial dysmorphism-hypergonadotropic hypogonadism syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010448',
'synonyms': ['Moyamoya disease-short stature-facial dysmorphism-hypergonadotropic hypogonadism',
'moyamoya disease 4, X-linked recessive'],
'name': 'MONDO_0010448',
'subclasses': [],
'xrefs': ['OMIM:300845', 'Orphanet:280679', 'UMLS:C3151857']},
{'concept': obo.MONDO_0016820,
'label': ['Moyamoya disease'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0016820',
'synonyms': ['idiopathic Moyamoya disease',
'progressive intracranial arterial occlusion'],
'name': 'MONDO_0016820',
'subclasses': [obo.MONDO_0010448, obo.MONDO_0014331],
'xrefs': ['DOID:13099',
'ICD9:437.5',
'MESH:D009072',
'MedDRA:10028047',
'NCIT:C84895',
'OMIMPS:252350',
'Orphanet:2573',
'SCTID:89142007',
'UMLS:C0026654']},
{'concept': obo.MONDO_0014331,
'label': ['Moyamoya disease with early-onset achalasia'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0014331',
'synonyms': ['moyamoya 6 with achalasia'],
'name': 'MONDO_0014331',
'subclasses': [],
'xrefs': ['OMIM:615750',
'Orphanet:401945',
'SCTID:718551002',
'UMLS:C3810403']},
{'concept': efo.EFO_0004250,
'label': ['obsolete_Moyamoya disease'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0004250',
'synonyms': ['Moya-Moya disease',
'Moyamoya syndrome',
'cerebrovascular Moyamoya disease',
'progressive intracranial occlusive arteropathy (Moyamoya)'],
'name': 'EFO_0004250',
'subclasses': [],
'xrefs': ['MeSH:D009072']},
{'concept': ORDO.Orphanet_2573,
'label': ['obsolete_Moyamoya disease'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_2573',
'synonyms': [],
'name': 'Orphanet_2573',
'subclasses': [],
'xrefs': ['ICD10:I67.5',
'MeSH:C536991',
'MeSH:D009072',
'MedDRA:10028047',
'OMIM:252350',
'OMIM:607151',
'OMIM:608796',
'OMIM:614042',
'UMLS:C0026654',
'UMLS:C2931384']},
{'concept': ORDO.Orphanet_280679,
'label': ['Moyamoya disease - short stature - facial dysmorphism - hypergonadotropic hypogonadism'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_280679',
'synonyms': [],
'name': 'Orphanet_280679',
'subclasses': [],
'xrefs': ['OMIM:300845']},
{'concept': ORDO.Orphanet_401945,
'label': ['obsolete_Moyamoya disease with early-onset achalasia'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_401945',
'synonyms': [],
'name': 'Orphanet_401945',
'subclasses': [],
'xrefs': ['ICD10:I67.5', 'OMIM:615750']}]
Check one concept#
results
[{'concept': obo.HP_0011834,
'label': ['Moyamoya phenomenon'],
'iri': 'http://purl.obolibrary.org/obo/HP_0011834',
'synonyms': [],
'name': 'HP_0011834',
'subclasses': [],
'xrefs': ['UMLS:C4023169']},
{'concept': obo.MONDO_0010448,
'label': ['moyamoya angiopathy-short stature-facial dysmorphism-hypergonadotropic hypogonadism syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010448',
'synonyms': ['Moyamoya disease-short stature-facial dysmorphism-hypergonadotropic hypogonadism',
'moyamoya disease 4, X-linked recessive'],
'name': 'MONDO_0010448',
'subclasses': [],
'xrefs': ['OMIM:300845', 'Orphanet:280679', 'UMLS:C3151857']},
{'concept': obo.MONDO_0016820,
'label': ['Moyamoya disease'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0016820',
'synonyms': ['idiopathic Moyamoya disease',
'progressive intracranial arterial occlusion'],
'name': 'MONDO_0016820',
'subclasses': [obo.MONDO_0010448, obo.MONDO_0014331],
'xrefs': ['DOID:13099',
'ICD9:437.5',
'MESH:D009072',
'MedDRA:10028047',
'NCIT:C84895',
'OMIMPS:252350',
'Orphanet:2573',
'SCTID:89142007',
'UMLS:C0026654']},
{'concept': obo.MONDO_0014331,
'label': ['Moyamoya disease with early-onset achalasia'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0014331',
'synonyms': ['moyamoya 6 with achalasia'],
'name': 'MONDO_0014331',
'subclasses': [],
'xrefs': ['OMIM:615750',
'Orphanet:401945',
'SCTID:718551002',
'UMLS:C3810403']},
{'concept': efo.EFO_0004250,
'label': ['obsolete_Moyamoya disease'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0004250',
'synonyms': ['Moya-Moya disease',
'Moyamoya syndrome',
'cerebrovascular Moyamoya disease',
'progressive intracranial occlusive arteropathy (Moyamoya)'],
'name': 'EFO_0004250',
'subclasses': [],
'xrefs': ['MeSH:D009072']},
{'concept': ORDO.Orphanet_2573,
'label': ['obsolete_Moyamoya disease'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_2573',
'synonyms': [],
'name': 'Orphanet_2573',
'subclasses': [],
'xrefs': ['ICD10:I67.5',
'MeSH:C536991',
'MeSH:D009072',
'MedDRA:10028047',
'OMIM:252350',
'OMIM:607151',
'OMIM:608796',
'OMIM:614042',
'UMLS:C0026654',
'UMLS:C2931384']},
{'concept': ORDO.Orphanet_280679,
'label': ['Moyamoya disease - short stature - facial dysmorphism - hypergonadotropic hypogonadism'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_280679',
'synonyms': [],
'name': 'Orphanet_280679',
'subclasses': [],
'xrefs': ['OMIM:300845']},
{'concept': ORDO.Orphanet_401945,
'label': ['obsolete_Moyamoya disease with early-onset achalasia'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_401945',
'synonyms': [],
'name': 'Orphanet_401945',
'subclasses': [],
'xrefs': ['ICD10:I67.5', 'OMIM:615750']}]
results[0]['concept'].hasExactSynonym
[]
Get is_a concepts#
is_a = results[0]['concept'].is_a
# it returns a list, since "stomach cancer" can be multiple things
[x.label for x in is_a]
[['Abnormal cerebral artery morphology']]
Get all ancestors#
ancestors = results[0]['concept'].ancestors()
# it returns a list of all ancestors
[x.label for x in ancestors]
[['Moyamoya phenomenon'],
[locstr('continuant', 'en'),
locstr('continuant', 'en'),
locstr('continuant', 'en')],
[locstr('quality', 'en'),
'quality',
locstr('quality', 'en'),
locstr('quality', 'en')],
['Abnormality of brain morphology', 'Abnormality of brain morphology'],
['Abnormal systemic arterial morphology'],
['Phenotypic abnormality', 'Phenotypic abnormality'],
[locstr('entity', 'en'), locstr('entity', 'en')],
['Abnormal nervous system morphology'],
['All'],
[],
[locstr('Abnormal vascular morphology', 'en')],
['Abnormality of the vasculature', 'Abnormality of the vasculature'],
['Abnormal cerebral vascular morphology',
'Abnormal cerebral vascular morphology'],
['experimental factor'],
['Abnormal cerebral artery morphology'],
['Abnormality of the cardiovascular system',
'Abnormality of the cardiovascular system'],
[locstr('specifically dependent continuant', 'en'),
'material property',
locstr('specifically dependent continuant', 'en'),
locstr('specifically dependent continuant', 'en')],
['Morphological central nervous system abnormality',
'Morphological central nervous system abnormality'],
['Abnormal blood vessel morphology'],
['phenotype'],
['Abnormality of the nervous system', 'Abnormality of the nervous system'],
['Abnormality of cardiovascular system morphology',
'Abnormality of cardiovascular system morphology']]
Get all descendants#
descendants = results[0]['concept'].descendants()
# Descendants tends to return itself
[(x.label, x.name) for x in descendants]
[(['Moyamoya phenomenon'], 'HP_0011834')]
Get all Subclasses#
subclasses = results[0]['concept'].subclasses()
# Descendants tends to return itself
[(x.label, x.name) for x in subclasses]
[]
Things to Note:#
label: actually returns a list of the synonyms relatediri: unique ID for this conceptname: concept ID, Even though this is an HPO term, sometimes ontologies can reference external ontologies as part of the “semantic web” reference.xrefs: Generally,owlready2has poor documentation, but it’s a single person(?) effort (and I never personally contributed) for not the most approachable field, so give him some slack. But the oddly named.hasDbXrefreturns a list of external cross-walks, which is one of the more useful things to know.
TODO Visual Interface#
results[0]
{'concept': obo.HP_0011834,
'label': ['Moyamoya phenomenon'],
'iri': 'http://purl.obolibrary.org/obo/HP_0011834',
'synonyms': [],
'name': 'HP_0011834',
'subclasses': [],
'xrefs': ['UMLS:C4023169']}
It’s hard to work with python objects#
For my mission - I want to try to create various plots using Altair.
Plotting libraries don’t know what to do with python objects.
Generally needs to more primitive data types - convert everything to string in our case.
results
[{'concept': obo.HP_0011834,
'label': ['Moyamoya phenomenon'],
'iri': 'http://purl.obolibrary.org/obo/HP_0011834',
'synonyms': [],
'name': 'HP_0011834',
'subclasses': [],
'xrefs': ['UMLS:C4023169']},
{'concept': obo.MONDO_0010448,
'label': ['moyamoya angiopathy-short stature-facial dysmorphism-hypergonadotropic hypogonadism syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010448',
'synonyms': ['Moyamoya disease-short stature-facial dysmorphism-hypergonadotropic hypogonadism',
'moyamoya disease 4, X-linked recessive'],
'name': 'MONDO_0010448',
'subclasses': [],
'xrefs': ['OMIM:300845', 'Orphanet:280679', 'UMLS:C3151857']},
{'concept': obo.MONDO_0016820,
'label': ['Moyamoya disease'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0016820',
'synonyms': ['idiopathic Moyamoya disease',
'progressive intracranial arterial occlusion'],
'name': 'MONDO_0016820',
'subclasses': [obo.MONDO_0010448, obo.MONDO_0014331],
'xrefs': ['DOID:13099',
'ICD9:437.5',
'MESH:D009072',
'MedDRA:10028047',
'NCIT:C84895',
'OMIMPS:252350',
'Orphanet:2573',
'SCTID:89142007',
'UMLS:C0026654']},
{'concept': obo.MONDO_0014331,
'label': ['Moyamoya disease with early-onset achalasia'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0014331',
'synonyms': ['moyamoya 6 with achalasia'],
'name': 'MONDO_0014331',
'subclasses': [],
'xrefs': ['OMIM:615750',
'Orphanet:401945',
'SCTID:718551002',
'UMLS:C3810403']},
{'concept': efo.EFO_0004250,
'label': ['obsolete_Moyamoya disease'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0004250',
'synonyms': ['Moya-Moya disease',
'Moyamoya syndrome',
'cerebrovascular Moyamoya disease',
'progressive intracranial occlusive arteropathy (Moyamoya)'],
'name': 'EFO_0004250',
'subclasses': [],
'xrefs': ['MeSH:D009072']},
{'concept': ORDO.Orphanet_2573,
'label': ['obsolete_Moyamoya disease'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_2573',
'synonyms': [],
'name': 'Orphanet_2573',
'subclasses': [],
'xrefs': ['ICD10:I67.5',
'MeSH:C536991',
'MeSH:D009072',
'MedDRA:10028047',
'OMIM:252350',
'OMIM:607151',
'OMIM:608796',
'OMIM:614042',
'UMLS:C0026654',
'UMLS:C2931384']},
{'concept': ORDO.Orphanet_280679,
'label': ['Moyamoya disease - short stature - facial dysmorphism - hypergonadotropic hypogonadism'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_280679',
'synonyms': [],
'name': 'Orphanet_280679',
'subclasses': [],
'xrefs': ['OMIM:300845']},
{'concept': ORDO.Orphanet_401945,
'label': ['obsolete_Moyamoya disease with early-onset achalasia'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_401945',
'synonyms': [],
'name': 'Orphanet_401945',
'subclasses': [],
'xrefs': ['ICD10:I67.5', 'OMIM:615750']}]
def sanitize(v):
if isinstance(v, list):
return [str(x) for x in v]
elif isinstance(v, dict):
return sanitize(v)
else:
return str(v)
def sanitize_results(data):
for d in data:
for k, v in d.items():
d[k] = sanitize(v)
return data
import polars as pl
sanitized_results = sanitize_results(results)
pl.from_dicts(sanitized_results)
shape: (8, 7)
| concept | label | iri | synonyms | name | subclasses | xrefs |
|---|---|---|---|---|---|---|
| str | list[str] | str | list[str] | str | list[str] | list[str] |
| "obo.HP_0011834… | ["Moyamoya phenomenon"] | "http://purl.ob… | [] | "HP_0011834" | [] | ["UMLS:C4023169"] |
| "obo.MONDO_0010… | ["moyamoya angiopathy-short stature-facial dysmorphism-hypergonadotropic hypogonadism syndrome"] | "http://purl.ob… | ["Moyamoya disease-short stature-facial dysmorphism-hypergonadotropic hypogonadism", "moyamoya disease 4, X-linked recessive"] | "MONDO_0010448" | [] | ["OMIM:300845", "Orphanet:280679", "UMLS:C3151857"] |
| "obo.MONDO_0016… | ["Moyamoya disease"] | "http://purl.ob… | ["idiopathic Moyamoya disease", "progressive intracranial arterial occlusion"] | "MONDO_0016820" | ["obo.MONDO_0010448", "obo.MONDO_0014331"] | ["DOID:13099", "ICD9:437.5", … "UMLS:C0026654"] |
| "obo.MONDO_0014… | ["Moyamoya disease with early-onset achalasia"] | "http://purl.ob… | ["moyamoya 6 with achalasia"] | "MONDO_0014331" | [] | ["OMIM:615750", "Orphanet:401945", … "UMLS:C3810403"] |
| "efo.EFO_000425… | ["obsolete_Moyamoya disease"] | "http://www.ebi… | ["Moya-Moya disease", "Moyamoya syndrome", … "progressive intracranial occlusive arteropathy (Moyamoya)"] | "EFO_0004250" | [] | ["MeSH:D009072"] |
| "ORDO.Orphanet_… | ["obsolete_Moyamoya disease"] | "http://www.orp… | [] | "Orphanet_2573" | [] | ["ICD10:I67.5", "MeSH:C536991", … "UMLS:C2931384"] |
| "ORDO.Orphanet_… | ["Moyamoya disease - short stature - facial dysmorphism - hypergonadotropic hypogonadism"] | "http://www.orp… | [] | "Orphanet_28067… | [] | ["OMIM:300845"] |
| "ORDO.Orphanet_… | ["obsolete_Moyamoya disease with early-onset achalasia"] | "http://www.orp… | [] | "Orphanet_40194… | [] | ["ICD10:I67.5", "OMIM:615750"] |
from pprint import pprint
pprint(sanitized_results)
[{'concept': 'obo.HP_0011834',
'iri': 'http://purl.obolibrary.org/obo/HP_0011834',
'label': ['Moyamoya phenomenon'],
'name': 'HP_0011834',
'subclasses': [],
'synonyms': [],
'xrefs': ['UMLS:C4023169']},
{'concept': 'obo.MONDO_0010448',
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010448',
'label': ['moyamoya angiopathy-short stature-facial '
'dysmorphism-hypergonadotropic hypogonadism syndrome'],
'name': 'MONDO_0010448',
'subclasses': [],
'synonyms': ['Moyamoya disease-short stature-facial '
'dysmorphism-hypergonadotropic hypogonadism',
'moyamoya disease 4, X-linked recessive'],
'xrefs': ['OMIM:300845', 'Orphanet:280679', 'UMLS:C3151857']},
{'concept': 'obo.MONDO_0016820',
'iri': 'http://purl.obolibrary.org/obo/MONDO_0016820',
'label': ['Moyamoya disease'],
'name': 'MONDO_0016820',
'subclasses': ['obo.MONDO_0010448', 'obo.MONDO_0014331'],
'synonyms': ['idiopathic Moyamoya disease',
'progressive intracranial arterial occlusion'],
'xrefs': ['DOID:13099',
'ICD9:437.5',
'MESH:D009072',
'MedDRA:10028047',
'NCIT:C84895',
'OMIMPS:252350',
'Orphanet:2573',
'SCTID:89142007',
'UMLS:C0026654']},
{'concept': 'obo.MONDO_0014331',
'iri': 'http://purl.obolibrary.org/obo/MONDO_0014331',
'label': ['Moyamoya disease with early-onset achalasia'],
'name': 'MONDO_0014331',
'subclasses': [],
'synonyms': ['moyamoya 6 with achalasia'],
'xrefs': ['OMIM:615750',
'Orphanet:401945',
'SCTID:718551002',
'UMLS:C3810403']},
{'concept': 'efo.EFO_0004250',
'iri': 'http://www.ebi.ac.uk/efo/EFO_0004250',
'label': ['obsolete_Moyamoya disease'],
'name': 'EFO_0004250',
'subclasses': [],
'synonyms': ['Moya-Moya disease',
'Moyamoya syndrome',
'cerebrovascular Moyamoya disease',
'progressive intracranial occlusive arteropathy (Moyamoya)'],
'xrefs': ['MeSH:D009072']},
{'concept': 'ORDO.Orphanet_2573',
'iri': 'http://www.orpha.net/ORDO/Orphanet_2573',
'label': ['obsolete_Moyamoya disease'],
'name': 'Orphanet_2573',
'subclasses': [],
'synonyms': [],
'xrefs': ['ICD10:I67.5',
'MeSH:C536991',
'MeSH:D009072',
'MedDRA:10028047',
'OMIM:252350',
'OMIM:607151',
'OMIM:608796',
'OMIM:614042',
'UMLS:C0026654',
'UMLS:C2931384']},
{'concept': 'ORDO.Orphanet_280679',
'iri': 'http://www.orpha.net/ORDO/Orphanet_280679',
'label': ['Moyamoya disease - short stature - facial dysmorphism - '
'hypergonadotropic hypogonadism'],
'name': 'Orphanet_280679',
'subclasses': [],
'synonyms': [],
'xrefs': ['OMIM:300845']},
{'concept': 'ORDO.Orphanet_401945',
'iri': 'http://www.orpha.net/ORDO/Orphanet_401945',
'label': ['obsolete_Moyamoya disease with early-onset achalasia'],
'name': 'Orphanet_401945',
'subclasses': [],
'synonyms': [],
'xrefs': ['ICD10:I67.5', 'OMIM:615750']}]
Test Drive it out with bigger use case#
obo_searcher(mfo, "diabetes")
[{'concept': obo.HP_0000819,
'label': ['Diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0000819',
'synonyms': [],
'name': 'HP_0000819',
'subclasses': [obo.HP_0000831,
obo.HP_0001953,
obo.HP_0004904,
obo.HP_0005978,
obo.HP_0009800,
obo.HP_0100651],
'xrefs': ['MSH:D003920', 'SNOMEDCT_US:73211009', 'UMLS:C0011849']},
{'concept': obo.HP_0000831,
'label': ['Insulin-resistant diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0000831',
'synonyms': ['Insulin resistant diabetes',
'Insulin resistant diabetes mellitus',
'Insulin-resistant diabetes'],
'name': 'HP_0000831',
'subclasses': [obo.HP_0000857, obo.HP_0000877],
'xrefs': ['UMLS:C0854110']},
{'concept': obo.HP_0000857,
'label': ['Neonatal insulin-dependent diabetes mellitus',
'Neonatal insulin-dependent diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0000857',
'synonyms': [],
'name': 'HP_0000857',
'subclasses': [obo.HP_0008255],
'xrefs': ['UMLS:C3278636', 'UMLS:C3278636']},
{'concept': obo.HP_0000863,
'label': ['Central diabetes insipidus', 'Central diabetes insipidus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0000863',
'synonyms': ['Neurohypophyseal diabetes insipidus',
'Neurohypophyseal diabetes insipidus'],
'name': 'HP_0000863',
'subclasses': [],
'xrefs': ['MSH:D020790',
'SNOMEDCT_US:45369008',
'UMLS:C0687720',
'MSH:D020790',
'SNOMEDCT_US:45369008',
'UMLS:C0687720']},
{'concept': obo.HP_0000873,
'label': ['Diabetes insipidus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0000873',
'synonyms': [],
'name': 'HP_0000873',
'subclasses': [obo.HP_0000863, obo.HP_0009806],
'xrefs': ['MSH:D003919', 'SNOMEDCT_US:15771004', 'UMLS:C0011848']},
{'concept': obo.HP_0000877,
'label': ['Insulin-resistant diabetes mellitus at puberty'],
'iri': 'http://purl.obolibrary.org/obo/HP_0000877',
'synonyms': ['Insulin-resistant diabetes mellitus at puberty'],
'name': 'HP_0000877',
'subclasses': [],
'xrefs': ['UMLS:C1837792']},
{'concept': obo.HP_0004904,
'label': ['Maturity-onset diabetes of the young'],
'iri': 'http://purl.obolibrary.org/obo/HP_0004904',
'synonyms': ['Maturity onset diabetes of the young'],
'name': 'HP_0004904',
'subclasses': [],
'xrefs': ['MSH:C562772', 'SNOMEDCT_US:609561005', 'UMLS:C0342276']},
{'concept': obo.HP_0005978,
'label': ['Type II diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0005978',
'synonyms': ['Diabetes mellitus Type II',
'Diabetes mellitus, noninsulin-dependent',
'NIDDM',
'NIDDM diabetes mellitus',
'Non-insulin dependent diabetes',
'Noninsulin dependent diabetes mellitus',
'Noninsulin-dependent diabetes',
'Type 2 diabetes',
'Type II diabetes'],
'name': 'HP_0005978',
'subclasses': [obo.HP_0008205],
'xrefs': ['MSH:D003924', 'SNOMEDCT_US:44054006', 'UMLS:C0011860']},
{'concept': obo.HP_0008205,
'label': ['Insulin-dependent but ketosis-resistant diabetes'],
'iri': 'http://purl.obolibrary.org/obo/HP_0008205',
'synonyms': [],
'name': 'HP_0008205',
'subclasses': [],
'xrefs': ['UMLS:C1842404']},
{'concept': obo.HP_0008255,
'label': ['Transient neonatal diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0008255',
'synonyms': [],
'name': 'HP_0008255',
'subclasses': [],
'xrefs': ['SNOMEDCT_US:237603002', 'UMLS:C0342273']},
{'concept': obo.HP_0009800,
'label': ['Maternal diabetes', 'Maternal diabetes'],
'iri': 'http://purl.obolibrary.org/obo/HP_0009800',
'synonyms': ['Maternal diabetes',
'gestational diabetes',
'Maternal diabetes',
'gestational diabetes'],
'name': 'HP_0009800',
'subclasses': [],
'xrefs': ['MSH:D016640',
'SNOMEDCT_US:11687002',
'UMLS:C0085207',
'UMLS:C4020778',
'MSH:D016640',
'SNOMEDCT_US:11687002',
'UMLS:C0085207',
'UMLS:C4020778']},
{'concept': obo.HP_0009806,
'label': ['Nephrogenic diabetes insipidus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0009806',
'synonyms': [],
'name': 'HP_0009806',
'subclasses': [],
'xrefs': ['MSH:D018500', 'SNOMEDCT_US:111395007', 'UMLS:C0162283']},
{'concept': obo.HP_0100651,
'label': ['Type I diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/HP_0100651',
'synonyms': ['Diabetes mellitus Type I',
'Juvenile diabetes mellitus',
'Type 1 diabetes',
'Type I diabetes'],
'name': 'HP_0100651',
'subclasses': [],
'xrefs': ['MSH:D003922', 'SNOMEDCT_US:46635009', 'UMLS:C0011854']},
{'concept': efo.EFO_0000400,
'label': ['diabetes mellitus'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0000400',
'synonyms': ['DM',
'DM - Diabetes mellitus',
'Diabetes',
'Diabetes NOS',
'Diabetes mellitus (disorder)',
'Diabetes mellitus, NOS',
'diabetes',
'diabetes mellitus',
'diabetes mellitus (disease)'],
'name': 'EFO_0000400',
'subclasses': [obo.HP_0000857,
obo.MONDO_0005147,
efo.EFO_1000897,
obo.MONDO_0005148,
efo.EFO_1001511,
efo.EFO_0004593,
efo.EFO_0010164,
efo.EFO_0801077,
efo.EFO_1001121],
'xrefs': ['DOID:9351',
'HP:0000819',
'ICD10:E13',
'ICD10:E14',
'ICD10CM:E08-E13',
'ICD9:250',
'MESH:D003920',
'MONDO:0005015',
'MeSH:D003920',
'MedDRA:10012601',
'MedDRA:10012624',
'MedDRA:10012625',
'NCIT:C2985',
'NCIt:C2985',
'OMIM:612227',
'SCTID:73211009',
'SNOMEDCT:73211009',
'UMLS:C0011847',
'UMLS:C0011849']},
{'concept': obo.MONDO_0000065,
'label': ['microvascular complications of diabetes, susceptibility'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0000065',
'synonyms': ['microvascular complications of diabetes'],
'name': 'MONDO_0000065',
'subclasses': [],
'xrefs': ['OMIMPS:603933', 'UMLS:CN357508']},
{'concept': obo.MONDO_0004782,
'label': ['diabetes insipidus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0004782',
'synonyms': [],
'name': 'MONDO_0004782',
'subclasses': [obo.MONDO_0007450, obo.MONDO_0016383],
'xrefs': ['DOID:9409',
'ICD10CM:E23.2',
'ICD9:253.5',
'MESH:D003919',
'NCIT:C43263',
'SCTID:15771004',
'UMLS:C0011848']},
{'concept': obo.MONDO_0005147,
'label': ['type 1 diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0005147',
'synonyms': ['IDDM',
'diabetes mellitis type 1',
'diabetes mellitis type I',
'immune mediated diabetes',
'insulin dependent diabetes',
'insulin-dependent diabetes mellitus',
'juvenile diabetes',
'type 1 diabetes',
'type I diabetes',
'type I diabetes mellitus'],
'name': 'MONDO_0005147',
'subclasses': [efo.EFO_0009706, efo.EFO_0009756, efo.EFO_0009757],
'xrefs': ['DOID:9744',
'EFO:0001359',
'MESH:D003922',
'NCIT:C2986',
'OMIM:222100',
'Orphanet:243377',
'SCTID:46635009']},
{'concept': obo.MONDO_0005148,
'label': ['type 2 diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0005148',
'synonyms': ['NIDDM',
'T2DM - type 2 diabetes mellitus',
'adult onset diabetes',
'adult-onset diabetes',
'diabetes mellitis type 2',
'diabetes mellitis type II',
'diabetes mellitus, noninsulin-dependent',
'diabetes mellitus, noninsulin-dependent, association with',
'diabetes mellitus, noninsulin-dependent, late onset',
'diabetes mellitus, type 2',
'diabetes mellitus, type II',
'diabetes, type 2',
'insulin resistance, severe, digenic',
'non-insulin dependent diabetes',
'non-insulin dependent diabetes mellitus',
'non-insulin-dependent diabetes mellitus',
'noninsulin dependent diabetes',
'noninsulin-dependent diabetes mellitus',
'type 2 diabetes',
'type 2 diabetes mellitus',
'type 2 diabetes mellitus non-insulin dependent',
'type II diabetes',
'type II diabetes mellitus'],
'name': 'MONDO_0005148',
'subclasses': [efo.EFO_0007346, efo.EFO_1001503],
'xrefs': ['DOID:9352',
'EFO:0001360',
'MESH:D003924',
'NCIT:C26747',
'OMIM:125853',
'SCTID:44054006',
'UMLS:CN244395']},
{'concept': obo.MONDO_0007450,
'label': ['neurohypophyseal diabetes insipidus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0007450',
'synonyms': ['ADH deficiency',
'AVP deficiency',
'Arginine vasopressin deficiency',
'antidiuretic hormone deficiency',
'diabetes insipidus of pituitary gland',
'hereditary CDI',
'hereditary neurogenic diabetes insipidus',
'pituitary diabetes insipidus',
'pituitary gland diabetes insipidus',
'vasopressin defective diabetes insipidus',
'vasopressin deficiency'],
'name': 'MONDO_0007450',
'subclasses': [],
'xrefs': ['DOID:12388',
'NCIT:C84933',
'OMIM:125700',
'Orphanet:30925',
'SCTID:45369008']},
{'concept': obo.MONDO_0007451,
'label': ['diabetes insipidus, nephrogenic, autosomal'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0007451',
'synonyms': ['diabetes insipidus, nephrogenic, 2',
'diabetes insipidus, nephrogenic, autosomal'],
'name': 'MONDO_0007451',
'subclasses': [],
'xrefs': ['DOID:0081061', 'OMIM:125800', 'UMLS:C1563706']},
{'concept': obo.MONDO_0016383,
'label': ['nephrogenic diabetes insipidus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0016383',
'synonyms': [],
'name': 'MONDO_0016383',
'subclasses': [obo.MONDO_0007451],
'xrefs': ['DOID:12387',
'ICD10CM:N25.1',
'ICD9:588.1',
'MESH:D018500',
'MedDRA:10029147',
'NCIT:C84919',
'Orphanet:223',
'SCTID:111395007',
'UMLS:C0162283']},
{'concept': obo.MONDO_0007669,
'label': ['renal cysts and diabetes syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0007669',
'synonyms': ['CAKUT with diabetes',
'HNF1B-MODY',
'HNF1B-related renal cysts and diabetes syndrome',
'MODY5',
'RCAD',
'RCAD syndrome',
'atypical FJHN',
'atypical familial juvenile hyperuricemic nephropathy',
'congenital anomalies of the kidney and urinary tract with diabetes',
'familial hypoplastic glomerulocystic kidney',
'hepatocyte nuclear Factor 1-beta-associated monogenic diabetes',
'hypoplastic type glomerulocystic kidney disease',
'maturity onset diabetes of the Young, type 5',
'renal cysts and diabetes syndrome',
'renal cysts-maturity-onset diabetes of the young syndrome',
'renal dysfunction-early-onset diabetes syndrome'],
'name': 'MONDO_0007669',
'subclasses': [],
'xrefs': ['DECIPHER:47',
'DOID:0111101',
'MESH:C535520',
'NCIT:C123018',
'OMIM:137920',
'Orphanet:93111',
'SCTID:446641003',
'UMLS:C0431693',
'UMLS:CN206512']},
{'concept': obo.MONDO_0018911,
'label': ['maturity-onset diabetes of the young'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0018911',
'synonyms': ['MODY',
'Mason-type diabetes',
'maturity onset diabetes of the young',
'maturity-onset diabetes of the young',
'maturity-onset diabetes of the young (disease)'],
'name': 'MONDO_0018911',
'subclasses': [obo.MONDO_0007669, obo.MONDO_0011667, obo.MONDO_0011668],
'xrefs': ['DOID:0050524',
'HP:0004904',
'MESH:C562772',
'NCIT:C114769',
'OMIM:606391',
'Orphanet:552',
'SCTID:609561005',
'UMLS:C0342276']},
{'concept': obo.MONDO_0008023,
'label': ['muscular atrophy-ataxia-retinitis pigmentosa-diabetes mellitus syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0008023',
'synonyms': ['Furukawa-Takagi-Nakao syndrome'],
'name': 'MONDO_0008023',
'subclasses': [],
'xrefs': ['ICD9:728.2', 'OMIM:158500', 'Orphanet:2579', 'SCTID:237611007']},
{'concept': obo.MONDO_0008843,
'label': ['atherosclerosis-deafness-diabetes-epilepsy-nephropathy syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0008843',
'synonyms': ['Feigenbaum-Bergeron-Richardson syndrome'],
'name': 'MONDO_0008843',
'subclasses': [],
'xrefs': ['MESH:C565928',
'OMIM:209010',
'Orphanet:1192',
'SCTID:720519003']},
{'concept': obo.MONDO_0009099,
'label': ['nephrogenic diabetes insipidus-intracranial calcification syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0009099',
'synonyms': ['Schofer-Beetz-Bohl syndrome'],
'name': 'MONDO_0009099',
'subclasses': [],
'xrefs': ['OMIM:221995', 'Orphanet:3145', 'SCTID:716200002']},
{'concept': obo.MONDO_0009581,
'label': ['intellectual disability-dysmorphism-hypogonadism-diabetes mellitus syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0009581',
'synonyms': [],
'name': 'MONDO_0009581',
'subclasses': [],
'xrefs': ['MESH:C537447',
'OMIM:249599',
'Orphanet:3044',
'SCTID:722454003',
'UMLS:C1855303']},
{'concept': obo.MONDO_0010255,
'label': ['diabetes mellitus, insulin-dependent, X-linked, susceptibility to'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010255',
'synonyms': ['diabetes mellitus, insulin-dependent, X-linked',
'diabetes mellitus, insulin-dependent, X-linked, susceptibility to'],
'name': 'MONDO_0010255',
'subclasses': [obo.MONDO_0012919],
'xrefs': ['OMIM:300136', 'UMLS:C1848042']},
{'concept': obo.MONDO_0010773,
'label': ['myopathy and diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010773',
'synonyms': [],
'name': 'MONDO_0010773',
'subclasses': [],
'xrefs': ['MESH:C564026', 'OMIM:500002', 'Orphanet:2596', 'UMLS:C1839028']},
{'concept': efo.EFO_1001511,
'label': ['monogenic diabetes'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_1001511',
'synonyms': ['monogenic diabetes',
'monogenic diabetes mellitus',
'rare genetic diabetes mellitus'],
'name': 'EFO_1001511',
'subclasses': [obo.MONDO_0018911,
obo.MONDO_0010773,
obo.MONDO_0010785,
obo.MONDO_0016391,
ORDO.Orphanet_183625],
'xrefs': ['MONDO:0015967',
'MedDRA:10075980',
'NCIT:C129739',
'Orphanet:183625',
'PMID:27207547',
'PMID:27271189',
'PMID:27474216']},
{'concept': obo.MONDO_0010785,
'label': ['maternally-inherited diabetes and deafness'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010785',
'synonyms': ['MIDD', 'mitochondrial diabetes'],
'name': 'MONDO_0010785',
'subclasses': [],
'xrefs': ['ICD9:250.80',
'MESH:C536246',
'NCIT:C131859',
'OMIM:520000',
'Orphanet:225',
'SCTID:237619009',
'UMLS:C0342289',
'UMLS:C4330695']},
{'concept': obo.MONDO_0010798,
'label': ['proximal tubulopathy-diabetes mellitus-cerebellar ataxia syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010798',
'synonyms': [],
'name': 'MONDO_0010798',
'subclasses': [],
'xrefs': ['MESH:C564014', 'OMIM:560000', 'Orphanet:3390', 'UMLS:C3151959']},
{'concept': obo.MONDO_0010802,
'label': ['pancreatic hypoplasia-diabetes-congenital heart disease syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010802',
'synonyms': ['Yorifuji-Okuno syndrome',
'pancreatic hypoplasia-diabetes-congenital heart disease syndrome'],
'name': 'MONDO_0010802',
'subclasses': [],
'xrefs': ['DOID:0111733',
'MESH:C564011',
'OMIM:600001',
'Orphanet:2255',
'SCTID:722206009']},
{'concept': obo.MONDO_0010813,
'label': ['pancreatic beta cell agenesis with neonatal diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0010813',
'synonyms': ['diabetes mellitus, insulin-dependent, neonatal',
'pancreatic beta cell agenesis with neonatal diabetes mellitus'],
'name': 'MONDO_0010813',
'subclasses': [],
'xrefs': ['MESH:C538111', 'OMIM:600089', 'Orphanet:28455', 'UMLS:C1838655']},
{'concept': obo.MONDO_0011667,
'label': ['maturity-onset diabetes of the young type 4'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0011667',
'synonyms': ['MODY type 4',
'MODY, type IV',
'MODY4',
'PDX1 maturity-onset diabetes of the young (disease)',
'PDX1-associated monogenic diabetes',
'maturity onset diabetes of the Young, type 4',
'maturity-onset diabetes of the young (disease) caused by mutation in PDX1'],
'name': 'MONDO_0011667',
'subclasses': [],
'xrefs': ['DOID:0111103',
'MESH:C563451',
'NCIT:C129746',
'OMIM:606392',
'SCTID:609571007']},
{'concept': obo.MONDO_0011668,
'label': ['maturity-onset diabetes of the young type 6'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0011668',
'synonyms': ['MODY type 6',
'MODY6',
'NEUROD1 maturity-onset diabetes of the young (disease)',
'NEUROD1-associated monogenic diabetes',
'maturity onset diabetes of the Young, type 6',
'maturity-onset diabetes of the young (disease) caused by mutation in NEUROD1',
'maturity-onset diabetes of the young 6',
'neurogenic differentiation Factor 1-associated monogenic diabetes'],
'name': 'MONDO_0011668',
'subclasses': [],
'xrefs': ['DOID:0111104',
'MESH:C565231',
'NCIT:C129745',
'OMIM:606394',
'SCTID:609573005',
'UMLS:C1853371']},
{'concept': obo.MONDO_0012192,
'label': ['permanent neonatal diabetes mellitus-pancreatic and cerebellar agenesis syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0012192',
'synonyms': ['pancreatic and cerebellar agenesis'],
'name': 'MONDO_0012192',
'subclasses': [],
'xrefs': ['MESH:C563796', 'OMIM:609069', 'Orphanet:65288', 'UMLS:C1836780']},
{'concept': obo.MONDO_0016391,
'label': ['neonatal diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0016391',
'synonyms': ['NDM',
'congenital diabetes mellitus',
'diabetes mellitus syndrome in newborn infant'],
'name': 'MONDO_0016391',
'subclasses': [obo.MONDO_0012192,
obo.MONDO_0012436,
obo.MONDO_0100164,
obo.MONDO_0020525],
'xrefs': ['DOID:11717',
'ICD10CM:P70.2',
'ICD9:775.1',
'MedDRA:10028933',
'NCIT:C99248',
'Orphanet:224',
'SCTID:49817004',
'UMLS:C0158981']},
{'concept': obo.MONDO_0012436,
'label': ['neonatal diabetes mellitus with congenital hypothyroidism'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0012436',
'synonyms': ['NDH syndrome',
'neonatal diabetes mellitus with congenital hypothyroidism'],
'name': 'MONDO_0012436',
'subclasses': [],
'xrefs': ['DOID:0060638',
'MESH:C565705',
'OMIM:610199',
'Orphanet:79118',
'UMLS:C1857775']},
{'concept': obo.MONDO_0012919,
'label': ['type 1 diabetes mellitus 20'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0012919',
'synonyms': ['HNF1A type 1 diabetes mellitus',
'IDDM20',
'diabetes mellitus, insulin-dependent, type 20',
'insulin-dependent diabetes mellitus 20',
'type 1 diabetes mellitus caused by mutation in HNF1A'],
'name': 'MONDO_0012919',
'subclasses': [],
'xrefs': ['DOID:0110757', 'MESH:C567286', 'OMIM:612520', 'UMLS:C2675866']},
{'concept': obo.MONDO_0015493,
'label': ['lipoatrophy with diabetes, leukomelanodermic papules, liver steatosis, and hypertrophic cardiomyopathy'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0015493',
'synonyms': [],
'name': 'MONDO_0015493',
'subclasses': [],
'xrefs': ['Orphanet:156156']},
{'concept': obo.MONDO_0018320,
'label': ['primary microcephaly-mild intellectual disability-young-onset diabetes syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0018320',
'synonyms': [],
'name': 'MONDO_0018320',
'subclasses': [],
'xrefs': ['Orphanet:391408', 'UMLS:CN204971']},
{'concept': obo.MONDO_0031481,
'label': ['microcephaly, epilepsy, and diabetes syndrome 1'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0031481',
'synonyms': ['MEDS1',
'primary microcephaly-epilepsy-permanent neonatal diabetes syndrome'],
'name': 'MONDO_0031481',
'subclasses': [],
'xrefs': ['OMIM:614231', 'Orphanet:306558', 'UMLS:C3280240']},
{'concept': obo.MONDO_0100164,
'label': ['permanent neonatal diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0100164',
'synonyms': ['PDMI',
'PNDM',
'monogenic diabetes of infancy',
'permanent diabetes mellitus of infancy'],
'name': 'MONDO_0100164',
'subclasses': [obo.MONDO_0019207,
obo.MONDO_0030087,
obo.MONDO_0030088,
obo.MONDO_0030089],
'xrefs': ['DOID:0060639',
'MESH:C563425',
'NCIT:C114902',
'OMIMPS:606176',
'Orphanet:99885',
'SCTID:609565001',
'UMLS:C1833104']},
{'concept': obo.MONDO_0019846,
'label': ['acquired central diabetes insipidus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0019846',
'synonyms': ['acquired CDI',
'acquired central diabetes insipidus',
'acquired neurogenic diabetes insipidus'],
'name': 'MONDO_0019846',
'subclasses': [],
'xrefs': ['ICD10CM:E23.2', 'Orphanet:95626']},
{'concept': obo.MONDO_0020525,
'label': ['transient neonatal diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0020525',
'synonyms': ['TNDM',
'transient neonatal diabetes mellitus',
'transient neonatal diabetes mellitus (disease)'],
'name': 'MONDO_0020525',
'subclasses': [],
'xrefs': ['DOID:0060334', 'HP:0008255', 'NCIT:C114899', 'SCTID:237603002']},
{'concept': obo.MONDO_0030087,
'label': ['diabetes mellitus, permanent neonatal 2'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0030087',
'synonyms': ['DIABETES MELLITUS, PERMANENT NEONATAL 2',
'Developmental Delay, Epilepsy, and Neonatal Diabetes 1',
'PNDM2',
'diabetes mellitus, permanent neonatal 2',
'diabetes, permanent neonatal 2, with or without neurologic features'],
'name': 'MONDO_0030087',
'subclasses': [],
'xrefs': ['OMIM:618856']},
{'concept': obo.MONDO_0030088,
'label': ['diabetes mellitus, permanent neonatal 3'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0030088',
'synonyms': ['DIABETES MELLITUS, PERMANENT NEONATAL 3',
'Developmental Delay, Epilepsy, and Neonatal Diabetes 2',
'PNDM3',
'diabetes mellitus, permanent neonatal 3',
'diabetes mellitus, permanent neonatal 3, with or without neurologic features'],
'name': 'MONDO_0030088',
'subclasses': [],
'xrefs': ['OMIM:618857']},
{'concept': obo.MONDO_0030089,
'label': ['diabetes mellitus, permanent neonatal 4'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0030089',
'synonyms': ['DIABETES MELLITUS, PERMANENT NEONATAL 4',
'PNDM4',
'diabetes mellitus, permanent neonatal 4'],
'name': 'MONDO_0030089',
'subclasses': [],
'xrefs': ['OMIM:618858']},
{'concept': obo.MONDO_0100328,
'label': ['microcephaly, epilepsy, and diabetes syndrome'],
'iri': 'http://purl.obolibrary.org/obo/MONDO_0100328',
'synonyms': [],
'name': 'MONDO_0100328',
'subclasses': [obo.MONDO_0031481],
'xrefs': ['OMIMPS:614231']},
{'concept': obo.OBA_2001012,
'label': ['age of onset of type 1 diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/OBA_2001012',
'synonyms': ['age at onset of type 1 diabetes mellitus',
'age type 1 diabetes mellitus symptoms begin'],
'name': 'OBA_2001012',
'subclasses': [],
'xrefs': []},
{'concept': obo.OBA_2001013,
'label': ['age of onset of type 2 diabetes mellitus'],
'iri': 'http://purl.obolibrary.org/obo/OBA_2001013',
'synonyms': ['age at onset of type 2 diabetes mellitus',
'age type 2 diabetes mellitus symptoms begin'],
'name': 'OBA_2001013',
'subclasses': [],
'xrefs': []},
{'concept': efo.EFO_0001359,
'label': ['obsolete_type I diabetes mellitus'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0001359',
'synonyms': ['Autoimmune Diabete',
'Autoimmune Diabetes',
'Brittle Diabetes Mellitus',
'DIABETES MELLITUS TYPE 01',
'DMI UNSPF NT ST UNCNTRLD',
'DMI UNSPF UNCNTRLD',
'Diabete, Autoimmune',
'Diabetes Mellitus, Brittle',
'Diabetes Mellitus, Insulin Dependent',
'Diabetes Mellitus, Insulin-Dependent',
'Diabetes Mellitus, Juvenile Onset',
'Diabetes Mellitus, Juvenile-Onset',
'Diabetes Mellitus, Ketosis Prone',
'Diabetes Mellitus, Ketosis-Prone',
'Diabetes Mellitus, Sudden Onset',
'Diabetes Mellitus, Sudden-Onset',
'Diabetes Mellitus, Type 1',
'Diabetes Mellitus, Type I',
'Diabetes mellitus type 1',
'Diabetes mellitus type 1 (disorder)',
'Diabetes mellitus type I',
'Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], not stated as uncontrolled, with unspecified complication',
'Diabetes mellitus type I [insulin dependent type] [IDDM] [juvenile type], uncontrolled, with unspecified complication',
'Diabetes, Autoimmune',
'IDDM',
'IDDM - Insulin-dependent diabetes mellitus',
'Insulin Dependent Diabetes',
'Insulin dependent diabetes mellitus',
'Insulin-Dependent Diabetes Mellitus',
'Juvenile Diabetes',
'Juvenile onset diabetes mellitus',
'Juvenile-Onset Diabetes Mellitus',
'Ketosis-Prone Diabetes Mellitus',
'Mellitus, Sudden-Onset Diabetes',
'Sudden-Onset Diabetes Mellitus',
'T1D',
'T1DM',
'Type 1 Diabetes',
'Type 1 Diabetes Mellitus',
'Type I Diabetes'],
'name': 'EFO_0001359',
'subclasses': [],
'xrefs': ['DOID:9744',
'ICD10:E10',
'MeSH:D003922',
'MedDRA:10045228',
'NCIt:C2986',
'OMIM:125852',
'OMIM:222100',
'OMIM:600320',
'OMIM:601388',
'OMIM:601942',
'OMIM:610155',
'OMIM:611895',
'OMIM:612520',
'OMIM:612522',
'SNOMEDCT:11530004',
'SNOMEDCT:46635009']},
{'concept': efo.EFO_0001360,
'label': ['obsolete_type II diabetes mellitus'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0001360',
'synonyms': ['Adult-Onset Diabetes',
'Adult-Onset Diabetes Mellitus',
'DIABETES MELLITUS TYPE 02',
'Diabetes Mellitus, Adult Onset',
'Diabetes Mellitus, Adult-Onset',
'Diabetes Mellitus, Ketosis Resistant',
'Diabetes Mellitus, Ketosis-Resistant',
'Diabetes Mellitus, Maturity Onset',
'Diabetes Mellitus, Maturity-Onset',
'Diabetes Mellitus, Non Insulin Dependent',
'Diabetes Mellitus, Non-Insulin-Dependent',
'Diabetes Mellitus, Noninsulin Dependent',
'Diabetes Mellitus, Slow Onset',
'Diabetes Mellitus, Slow-Onset',
'Diabetes Mellitus, Stable',
'Diabetes Mellitus, Type 2',
'Diabetes Mellitus, Type II',
'Diabetes, Type 2',
'Ketosis-Resistant Diabetes Mellitus',
'MODY',
'Maturity Onset Diabetes Mellitus',
'Maturity-Onset Diabetes Mellitus',
'NIDDM',
'Non-Insulin Dependent Diabetes',
'Non-Insulin Dependent Diabetes Mellitus',
'Slow-Onset Diabetes Mellitus',
'Stable Diabetes Mellitus',
'T2D',
'T2DM',
'T2DM - Type 2 Diabetes mellitus',
'Type 2 Diabetes',
'Type 2 Diabetes Mellitus',
'Type 2 Diabetes Mellitus Non-Insulin Dependent',
'Type II Diabetes',
'diabetes mellitus type 2',
'non-insulin-dependent diabetes mellitus'],
'name': 'EFO_0001360',
'subclasses': [],
'xrefs': ['DOID:9352',
'ICD10:E11',
'MeSH:D003924',
'MedDRA:10045242',
'NCIt:C26747',
'OMIM:125853',
'OMIM:601283',
'OMIM:616087',
'SNOMEDCT:44054006']},
{'concept': efo.EFO_0004593,
'label': ['gestational diabetes'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0004593',
'synonyms': ['GDM',
'diabetes in pregnancy',
'gestational diabetes',
'gestational diabetes mellitus',
'maternal gestational diabetes mellitus'],
'name': 'EFO_0004593',
'subclasses': [],
'xrefs': ['DOID:11714',
'ICD10:O24',
'MESH:D016640',
'MONDO:0005406',
'MedDRA:10018209',
'NCIT:C34942',
'NCIt:C34942',
'SCTID:11687002',
'SNOMEDCT:11687002',
'UMLS:C0085207']},
{'concept': efo.EFO_0004596,
'label': ['diabetes mellitus type 2 associated cataract'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0004596',
'synonyms': ['diabetes mellitus type 2 associated cataract'],
'name': 'EFO_0004596',
'subclasses': [],
'xrefs': ['MONDO:0005408']},
{'concept': efo.EFO_0004996,
'label': ['type 1 diabetes nephropathy'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0004996',
'synonyms': [],
'name': 'EFO_0004996',
'subclasses': [],
'xrefs': []},
{'concept': efo.EFO_0004997,
'label': ['type 2 diabetes nephropathy'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0004997',
'synonyms': [],
'name': 'EFO_0004997',
'subclasses': [],
'xrefs': []},
{'concept': efo.EFO_0006842,
'label': ['diabetes mellitus biomarker'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0006842',
'synonyms': [],
'name': 'EFO_0006842',
'subclasses': [efo.EFO_0004467,
efo.EFO_0004468,
efo.EFO_0004819,
efo.EFO_0005766,
efo.EFO_0008463,
efo.EFO_0008464,
efo.EFO_0008465],
'xrefs': []},
{'concept': efo.EFO_0007346,
'label': ['lipoatrophic diabetes'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0007346',
'synonyms': ['Diabetes Mellitus, Lipoatrophic',
'diabete, lipoatrophic',
'lipoatrophic diabetes'],
'name': 'EFO_0007346',
'subclasses': [],
'xrefs': ['DOID:11712',
'MESH:D003923',
'MONDO:0005827',
'MeSH:D003923',
'MedDRA:10024603',
'NCIT:C34537',
'SCTID:127012008',
'SCTID:71325002']},
{'concept': efo.EFO_0009706,
'label': ['latent autoimmune diabetes in adults'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0009706',
'synonyms': ['LADA'],
'name': 'EFO_0009706',
'subclasses': [],
'xrefs': ['MedDRA:10066389',
'Wikipedia:Latent_autoimmune_diabetes_in_adults']},
{'concept': efo.EFO_0009756,
'label': ['autoimmune type 1 diabetes'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0009756',
'synonyms': ['type 1A'],
'name': 'EFO_0009756',
'subclasses': [],
'xrefs': []},
{'concept': efo.EFO_0009757,
'label': ['idiopathic type 1 diabetes'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0009757',
'synonyms': ['type 1B'],
'name': 'EFO_0009757',
'subclasses': [efo.EFO_0009758],
'xrefs': []},
{'concept': efo.EFO_0009758,
'label': ['fulminant type 1 diabetes'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0009758',
'synonyms': [],
'name': 'EFO_0009758',
'subclasses': [],
'xrefs': []},
{'concept': efo.EFO_0009924,
'label': ['Drugs used in diabetes use measurement'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0009924',
'synonyms': [],
'name': 'EFO_0009924',
'subclasses': [],
'xrefs': ['PMID:31015401']},
{'concept': efo.EFO_0010164,
'label': ['insulin-resistant diabetes mellitus'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0010164',
'synonyms': ['insulin resistant diabetes',
'insulin resistant diabetes mellitus',
'insulin-resistant diabetes'],
'name': 'EFO_0010164',
'subclasses': [],
'xrefs': ['UMLS:C0854110']},
{'concept': efo.EFO_0010977,
'label': [locstr('macrovascular complications of diabetes', 'en')],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0010977',
'synonyms': [],
'name': 'EFO_0010977',
'subclasses': [],
'xrefs': ['PMID:33430853']},
{'concept': efo.EFO_0020032,
'label': [locstr('autosomal recessive transient neonatal diabetes mellitus', 'en')],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0020032',
'synonyms': [],
'name': 'EFO_0020032',
'subclasses': [],
'xrefs': ['Medgen:CN239376']},
{'concept': efo.EFO_0020040,
'label': [locstr('transient neonatal diabetes, dominant/recessive', 'en')],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0020040',
'synonyms': [],
'name': 'EFO_0020040',
'subclasses': [efo.EFO_0020032],
'xrefs': ['Medgen:CN239353']},
{'concept': efo.EFO_0801077,
'label': [locstr('cystic fibrosis-related diabetes', 'en')],
'iri': 'http://www.ebi.ac.uk/efo/EFO_0801077',
'synonyms': ['CFRD'],
'name': 'EFO_0801077',
'subclasses': [],
'xrefs': ['PMID:36206743']},
{'concept': ORDO.Orphanet_183625,
'label': ['Rare genetic diabetes mellitus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_183625',
'synonyms': [],
'name': 'Orphanet_183625',
'subclasses': [efo.EFO_0020040,
ORDO.Orphanet_181368,
ORDO.Orphanet_2255,
ORDO.Orphanet_552,
ORDO.Orphanet_65288],
'xrefs': []},
{'concept': efo.EFO_1001121,
'label': ['prediabetes syndrome'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_1001121',
'synonyms': ['Prediabetes',
'Prediabetic State',
'borderline diabetes',
'prediabetes',
'prediabetes syndrome',
'prediabetic state'],
'name': 'EFO_1001121',
'subclasses': [],
'xrefs': ['DOID:11716',
'MESH:D011236',
'MONDO:0006920',
'MeSH:D011236',
'MedDRA:10065542',
'NCIT:C122685',
'NCIt:C122685',
'UMLS:C0362046']},
{'concept': efo.EFO_1001503,
'label': ['type II diabetes mellitus with acanthosis nigricans'],
'iri': 'http://www.ebi.ac.uk/efo/EFO_1001503',
'synonyms': ['Diabetes Mellitus, Insulin-Resistant, with Acanthosis Nigricans, Type A',
'IRAN, Type A',
'Insulin Receptor Defect with Insulin-Resistant Diabetes Mellitus and Acanthosis Nigricans',
'Insulin-resistant diabetes mellitus AND acanthosis nigricans',
'Type 2 diabetes mellitus with acanthosis nigricans',
'Type 2 diabetes mellitus with acanthosis nigricans (disorder)',
'insulin-resistant diabetes mellitus and acanthosis nigricans',
'type 2 diabetes mellitus with acanthosis nigricans'],
'name': 'EFO_1001503',
'subclasses': [],
'xrefs': ['MeSH:C562710', 'SNOMEDCT:9859006']},
{'concept': ORDO.Orphanet_1192,
'label': ['Atherosclerosis - deafness - diabetes - epilepsy - nephropathy'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_1192',
'synonyms': ['Feigenbaum-Bergeron-Richardson syndrome'],
'name': 'Orphanet_1192',
'subclasses': [],
'xrefs': ['OMIM:209010']},
{'concept': ORDO.Orphanet_156156,
'label': ['obsolete_lipoatrophy with diabetes, leukomelanodermic papules, liver steatosis, and hypertrophic cardiomyopathy'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_156156',
'synonyms': [],
'name': 'Orphanet_156156',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_223,
'label': ['obsolete_nephrogenic diabetes insipidus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_223',
'synonyms': [],
'name': 'Orphanet_223',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_224,
'label': ['obsolete_neonatal diabetes mellitus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_224',
'synonyms': [],
'name': 'Orphanet_224',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_225,
'label': ['obsolete_maternally-inherited diabetes and deafness'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_225',
'synonyms': [],
'name': 'Orphanet_225',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_2255,
'label': ['Pancreatic hypoplasia - diabetes - congenital heart disease'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_2255',
'synonyms': ['Yorifuji-Okuno syndrome'],
'name': 'Orphanet_2255',
'subclasses': [],
'xrefs': ['OMIM:600001', 'UMLS:C2931296']},
{'concept': ORDO.Orphanet_2579,
'label': ['Muscular atrophy - ataxia - retinitis pigmentosa - diabetes mellitus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_2579',
'synonyms': ['Furukawa-Takagi-Nakao syndrome'],
'name': 'Orphanet_2579',
'subclasses': [],
'xrefs': ['MeSH:C538193', 'OMIM:158500', 'UMLS:C0342281', 'UMLS:C2931765']},
{'concept': ORDO.Orphanet_2596,
'label': ['obsolete_myopathy and diabetes mellitus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_2596',
'synonyms': [],
'name': 'Orphanet_2596',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_28455,
'label': ['obsolete_pancreatic beta cell agenesis with neonatal diabetes mellitus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_28455',
'synonyms': [],
'name': 'Orphanet_28455',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_3044,
'label': ['Intellectual disability - dysmorphism - hypogonadism - diabetes mellitus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_3044',
'synonyms': [],
'name': 'Orphanet_3044',
'subclasses': [],
'xrefs': ['ICD10:Q87.8', 'OMIM:249599']},
{'concept': ORDO.Orphanet_306558,
'label': ['obsolete_Primary microcephaly-epilepsy-permanent neonatal diabetes syndrome'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_306558',
'synonyms': [],
'name': 'Orphanet_306558',
'subclasses': [],
'xrefs': ['OMIM:614231']},
{'concept': ORDO.Orphanet_30925,
'label': ['Hereditary central diabetes insipidus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_30925',
'synonyms': ['Hereditary CDI', 'Hereditary neurogenic diabetes insipidus'],
'name': 'Orphanet_30925',
'subclasses': [],
'xrefs': ['ICD10:E23.2', 'OMIM:125700', 'OMIM:304900']},
{'concept': ORDO.Orphanet_3145,
'label': ['Nephrogenic diabetes insipidus - intracranial calcification'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_3145',
'synonyms': ['Schofer-Beetz-Bohl syndrome'],
'name': 'Orphanet_3145',
'subclasses': [],
'xrefs': ['OMIM:221995']},
{'concept': ORDO.Orphanet_3390,
'label': ['Proximal tubulopathy - diabetes mellitus - cerebellar ataxia'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_3390',
'synonyms': [],
'name': 'Orphanet_3390',
'subclasses': [],
'xrefs': ['ICD10:Q87.8', 'OMIM:560000']},
{'concept': ORDO.Orphanet_391408,
'label': ['obsolete_primary microcephaly-mild intellectual disability-young-onset diabetes syndrome'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_391408',
'synonyms': [],
'name': 'Orphanet_391408',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_65288,
'label': ['Permanent neonatal diabetes mellitus - pancreatic and cerebellar agenesis'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_65288',
'synonyms': ['Pancreatic and cerebellar agenesis'],
'name': 'Orphanet_65288',
'subclasses': [],
'xrefs': ['OMIM:609069']},
{'concept': ORDO.Orphanet_79118,
'label': ['obsolete_Neonatal diabetes - congenital hypothyroidism - congenital glaucoma - hepatic fibrosis - polycystic kidneys'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_79118',
'synonyms': [],
'name': 'Orphanet_79118',
'subclasses': [],
'xrefs': ['OMIM:610199']},
{'concept': ORDO.Orphanet_93111,
'label': ['obsolete_renal cysts and diabetes syndrome'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_93111',
'synonyms': [],
'name': 'Orphanet_93111',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_94062,
'label': ['obsolete_Coronary artery disease - hyperlipidemia - hypertension - diabetes - osteoporosis'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_94062',
'synonyms': [],
'name': 'Orphanet_94062',
'subclasses': [],
'xrefs': []},
{'concept': ORDO.Orphanet_99885,
'label': ['obsolete_Permanent neonatal diabetes mellitus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_99885',
'synonyms': ['Monogenic diabetes of infancy', 'PNDM'],
'name': 'Orphanet_99885',
'subclasses': [],
'xrefs': ['ICD10:P70.2', 'OMIM:606176']},
{'concept': ORDO.Orphanet_99886,
'label': ['obsolete_transient neonatal diabetes mellitus'],
'iri': 'http://www.orpha.net/ORDO/Orphanet_99886',
'synonyms': [],
'name': 'Orphanet_99886',
'subclasses': [],
'xrefs': []}]
Lets try plotting#
import polars as pl
mfo_df = pl.from_dicts(sanitize_results(obo_searcher(mfo, "diabetes")))
mfo_df
shape: (94, 7)
| concept | label | iri | synonyms | name | subclasses | xrefs |
|---|---|---|---|---|---|---|
| str | list[str] | str | list[str] | str | list[str] | list[str] |
| "obo.HP_0000819… | ["Diabetes mellitus"] | "http://purl.ob… | [] | "HP_0000819" | ["obo.HP_0000831", "obo.HP_0001953", … "obo.HP_0100651"] | ["MSH:D003920", "SNOMEDCT_US:73211009", "UMLS:C0011849"] |
| "obo.HP_0000831… | ["Insulin-resistant diabetes mellitus"] | "http://purl.ob… | ["Insulin resistant diabetes", "Insulin resistant diabetes mellitus", "Insulin-resistant diabetes"] | "HP_0000831" | ["obo.HP_0000857", "obo.HP_0000877"] | ["UMLS:C0854110"] |
| "obo.HP_0000857… | ["Neonatal insulin-dependent diabetes mellitus", "Neonatal insulin-dependent diabetes mellitus"] | "http://purl.ob… | [] | "HP_0000857" | ["obo.HP_0008255"] | ["UMLS:C3278636", "UMLS:C3278636"] |
| "obo.HP_0000863… | ["Central diabetes insipidus", "Central diabetes insipidus"] | "http://purl.ob… | ["Neurohypophyseal diabetes insipidus", "Neurohypophyseal diabetes insipidus"] | "HP_0000863" | [] | ["MSH:D020790", "SNOMEDCT_US:45369008", … "UMLS:C0687720"] |
| "obo.HP_0000873… | ["Diabetes insipidus"] | "http://purl.ob… | [] | "HP_0000873" | ["obo.HP_0000863", "obo.HP_0009806"] | ["MSH:D003919", "SNOMEDCT_US:15771004", "UMLS:C0011848"] |
| "obo.HP_0000877… | ["Insulin-resistant diabetes mellitus at puberty"] | "http://purl.ob… | ["Insulin-resistant diabetes mellitus at puberty"] | "HP_0000877" | [] | ["UMLS:C1837792"] |
| "obo.HP_0004904… | ["Maturity-onset diabetes of the young"] | "http://purl.ob… | ["Maturity onset diabetes of the young"] | "HP_0004904" | [] | ["MSH:C562772", "SNOMEDCT_US:609561005", "UMLS:C0342276"] |
| "obo.HP_0005978… | ["Type II diabetes mellitus"] | "http://purl.ob… | ["Diabetes mellitus Type II", "Diabetes mellitus, noninsulin-dependent", … "Type II diabetes"] | "HP_0005978" | ["obo.HP_0008205"] | ["MSH:D003924", "SNOMEDCT_US:44054006", "UMLS:C0011860"] |
| "obo.HP_0008205… | ["Insulin-dependent but ketosis-resistant diabetes"] | "http://purl.ob… | [] | "HP_0008205" | [] | ["UMLS:C1842404"] |
| "obo.HP_0008255… | ["Transient neonatal diabetes mellitus"] | "http://purl.ob… | [] | "HP_0008255" | [] | ["SNOMEDCT_US:237603002", "UMLS:C0342273"] |
| "obo.HP_0009800… | ["Maternal diabetes", "Maternal diabetes"] | "http://purl.ob… | ["Maternal diabetes", "gestational diabetes", … "gestational diabetes"] | "HP_0009800" | [] | ["MSH:D016640", "SNOMEDCT_US:11687002", … "UMLS:C4020778"] |
| "obo.HP_0009806… | ["Nephrogenic diabetes insipidus"] | "http://purl.ob… | [] | "HP_0009806" | [] | ["MSH:D018500", "SNOMEDCT_US:111395007", "UMLS:C0162283"] |
| … | … | … | … | … | … | … |
| "ORDO.Orphanet_… | ["Intellectual disability - dysmorphism - hypogonadism - diabetes mellitus"] | "http://www.orp… | [] | "Orphanet_3044" | [] | ["ICD10:Q87.8", "OMIM:249599"] |
| "ORDO.Orphanet_… | ["obsolete_Primary microcephaly-epilepsy-permanent neonatal diabetes syndrome"] | "http://www.orp… | [] | "Orphanet_30655… | [] | ["OMIM:614231"] |
| "ORDO.Orphanet_… | ["Hereditary central diabetes insipidus"] | "http://www.orp… | ["Hereditary CDI", "Hereditary neurogenic diabetes insipidus"] | "Orphanet_30925… | [] | ["ICD10:E23.2", "OMIM:125700", "OMIM:304900"] |
| "ORDO.Orphanet_… | ["Nephrogenic diabetes insipidus - intracranial calcification"] | "http://www.orp… | ["Schofer-Beetz-Bohl syndrome"] | "Orphanet_3145" | [] | ["OMIM:221995"] |
| "ORDO.Orphanet_… | ["Proximal tubulopathy - diabetes mellitus - cerebellar ataxia"] | "http://www.orp… | [] | "Orphanet_3390" | [] | ["ICD10:Q87.8", "OMIM:560000"] |
| "ORDO.Orphanet_… | ["obsolete_primary microcephaly-mild intellectual disability-young-onset diabetes syndrome"] | "http://www.orp… | [] | "Orphanet_39140… | [] | [] |
| "ORDO.Orphanet_… | ["Permanent neonatal diabetes mellitus - pancreatic and cerebellar agenesis"] | "http://www.orp… | ["Pancreatic and cerebellar agenesis"] | "Orphanet_65288… | [] | ["OMIM:609069"] |
| "ORDO.Orphanet_… | ["obsolete_Neonatal diabetes - congenital hypothyroidism - congenital glaucoma - hepatic fibrosis - polycystic kidneys"] | "http://www.orp… | [] | "Orphanet_79118… | [] | ["OMIM:610199"] |
| "ORDO.Orphanet_… | ["obsolete_renal cysts and diabetes syndrome"] | "http://www.orp… | [] | "Orphanet_93111… | [] | [] |
| "ORDO.Orphanet_… | ["obsolete_Coronary artery disease - hyperlipidemia - hypertension - diabetes - osteoporosis"] | "http://www.orp… | [] | "Orphanet_94062… | [] | [] |
| "ORDO.Orphanet_… | ["obsolete_Permanent neonatal diabetes mellitus"] | "http://www.orp… | ["Monogenic diabetes of infancy", "PNDM"] | "Orphanet_99885… | [] | ["ICD10:P70.2", "OMIM:606176"] |
| "ORDO.Orphanet_… | ["obsolete_transient neonatal diabetes mellitus"] | "http://www.orp… | [] | "Orphanet_99886… | [] | [] |
Diabetes Example#
sanitized_results = sanitize_results(obo_searcher(hpo, "diabetes"))
df = pl.from_dicts(sanitized_results)
df.head()
shape: (5, 7)
| concept | label | iri | synonyms | name | subclasses | xrefs |
|---|---|---|---|---|---|---|
| str | list[str] | str | list[str] | str | list[str] | list[str] |
| "obo.HP_0000819… | ["Diabetes mellitus"] | "http://purl.ob… | [] | "HP_0000819" | ["obo.HP_0000831", "obo.HP_0001953", … "obo.HP_0100651"] | ["MSH:D003920", "SNOMEDCT_US:73211009", "UMLS:C0011849"] |
| "obo.HP_0000831… | ["Insulin-resistant diabetes mellitus"] | "http://purl.ob… | ["Insulin resistant diabetes", "Insulin resistant diabetes mellitus", "Insulin-resistant diabetes"] | "HP_0000831" | ["obo.HP_0000857", "obo.HP_0000877"] | ["UMLS:C0854110"] |
| "obo.HP_0000857… | ["Neonatal insulin-dependent diabetes mellitus", "Neonatal insulin-dependent diabetes mellitus"] | "http://purl.ob… | [] | "HP_0000857" | ["obo.HP_0008255"] | ["UMLS:C3278636", "UMLS:C3278636"] |
| "obo.HP_0000863… | ["Central diabetes insipidus", "Central diabetes insipidus"] | "http://purl.ob… | ["Neurohypophyseal diabetes insipidus", "Neurohypophyseal diabetes insipidus"] | "HP_0000863" | [] | ["MSH:D020790", "SNOMEDCT_US:45369008", … "UMLS:C0687720"] |
| "obo.HP_0000873… | ["Diabetes insipidus"] | "http://purl.ob… | [] | "HP_0000873" | ["obo.HP_0000863", "obo.HP_0009806"] | ["MSH:D003919", "SNOMEDCT_US:15771004", "UMLS:C0011848"] |
import polars as pl
import altair as alt
search_input = alt.param(
value="",
bind=alt.binding(
input="search",
placeholder="Diseases/symptoms",
name="Search",
),
)
selection = alt.selection_multi(fields=["name"])
base = (
alt.Chart(df.to_pandas())
.encode(
tooltip=["name:N", "label:N", "xrefs:N", "synonyms:N"],
color=alt.Color("name:N").legend(None),
)
.transform_flatten(["synonyms"])
.transform_flatten(["label"])
.add_params(search_input)
)
name_chart = base.mark_rect(height=18, cornerRadius=5, limit=100).encode(
x=alt.value(185),
y=alt.Y("label:N", sort=alt.EncodingSortField("name"))
.axis(labels=False, ticks=False, grid=False, domainWidth=0)
.title(None),
# opacity=alt.condition(
# alt.expr.test(alt.expr.regexp(search_input, 'i'), alt.datum.synonyms),
# alt.Opacity("name:Q").legend(None),
# alt.value(0.05)
# ),
)
name_text = (
name_chart.mark_text(align="left", dx=0, dy=0, limit=170)
.encode(
x=alt.value(1),
text=alt.Text("label:N").title(None),
color=alt.value("white"),
)
.add_params(search_input, selection)
)
xref_chart = (
base.mark_rect(height=18, cornerRadius=5)
.encode(
x=alt.value(150),
y=alt.Y("xrefs:N", sort=alt.EncodingSortField("name"))
.axis(labels=False, ticks=False, grid=False, domainWidth=0)
.title(None),
)
.transform_flatten(["xrefs"])
.transform_calculate(
ontology=alt.expr.split(alt.datum.xrefs, ":")[0],
concept_id=alt.expr.split(alt.datum.xrefs, ":")[1],
)
)
xref_text = (
xref_chart.mark_text(align="left", dx=0, dy=0)
.encode(
x=alt.value(1),
text=alt.Text("xrefs").title(None),
color=alt.value("white"),
)
.add_params(search_input, selection)
)
(
(name_chart + name_text).properties(title="Concept Name", width=100)
| (xref_chart + xref_text).properties(title="External References", width=100)
).configure_concat(spacing=0).transform_filter(selection).configure_view(
strokeOpacity=0, strokeWidth=0
).properties(
title=alt.Title("Ontology Explorer", subtitle=[""])
)
/home/codespace/.cache/pypoetry/virtualenvs/data-expressions-XOHyUNvQ-py3.10/lib/python3.10/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'selection_multi' is deprecated. Use 'selection_point'
warnings.warn(message, AltairDeprecationWarning, stacklevel=1)
Rare Disease Example#
import polars as pl
import altair as alt
sanitized_results = sanitize_results(obo_searcher(hpo, "steven"))
df = pl.from_dicts(sanitized_results)
df.head()
search_input = alt.param(
value="",
bind=alt.binding(
input="search",
placeholder="Diseases/symptoms",
name="Search",
),
)
selection = alt.selection_multi(fields=["name"])
base = (
alt.Chart(df.to_pandas())
.encode(
tooltip=["name:N", "label:N", "xrefs:N", "synonyms:N"],
color=alt.Color("name:N").legend(None),
)
.transform_flatten(["synonyms"])
.transform_flatten(["label"])
.add_params(search_input)
)
name_chart = base.mark_rect(height=18, cornerRadius=5, limit=100).encode(
x=alt.value(185),
y=alt.Y("label:N", sort=alt.EncodingSortField("name"))
.axis(labels=False, ticks=False, grid=False, domainWidth=0)
.title(None),
# opacity=alt.condition(
# alt.expr.test(alt.expr.regexp(search_input, 'i'), alt.datum.synonyms),
# alt.Opacity("name:Q").legend(None),
# alt.value(0.05)
# ),
)
name_text = (
name_chart.mark_text(align="left", dx=0, dy=0, limit=170)
.encode(
x=alt.value(1),
text=alt.Text("label:N").title(None),
color=alt.value("white"),
)
.add_params(search_input, selection)
)
xref_chart = (
base.mark_rect(height=18, cornerRadius=5)
.encode(
x=alt.value(150),
y=alt.Y("xrefs:N", sort=alt.EncodingSortField("name"))
.axis(labels=False, ticks=False, grid=False, domainWidth=0)
.title(None),
)
.transform_flatten(["xrefs"])
.transform_calculate(
ontology=alt.expr.split(alt.datum.xrefs, ":")[0],
concept_id=alt.expr.split(alt.datum.xrefs, ":")[1],
)
)
xref_text = (
xref_chart.mark_text(align="left", dx=0, dy=0)
.encode(
x=alt.value(1),
text=alt.Text("xrefs").title(None),
color=alt.value("white"),
)
.add_params(search_input, selection)
)
(
(name_chart + name_text).properties(title="Concept Name", width=100)
| (xref_chart + xref_text).properties(title="External References", width=100)
).configure_concat(spacing=0).transform_filter(selection).configure_view(
strokeOpacity=0, strokeWidth=0
).properties(
title=alt.Title("Ontology Explorer", subtitle=[""])
)
/home/codespace/.cache/pypoetry/virtualenvs/data-expressions-XOHyUNvQ-py3.10/lib/python3.10/site-packages/altair/utils/deprecation.py:65: AltairDeprecationWarning: 'selection_multi' is deprecated. Use 'selection_point'
warnings.warn(message, AltairDeprecationWarning, stacklevel=1)