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biothings / biothings_explorer_jsonld

Apache License 2.0
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mydisease.info/v1/disease/ data lacks gene and variant associations #10

Open lhannest opened 5 years ago

lhannest commented 5 years ago

http://mydisease.info/v1/disease/MONDO:0018911 appears to relate MONDO:0018911 to genes and variants, but the biothings explorer client doesn't illuminate this.

>>> import biothings_explorer_test as bt
>>> locator = bt.APILocator()
>>> [a for a in s if a['endpoint'].startswith('http://mydisease.info/v1/disease/')]
[
{'endpoint': 'http://mydisease.info/v1/disease/{mondoid}', 'predicate': 'EquivalentAssociation', 'subject': {'prefix': 'mondo', 'semantic_type': 'disease'}, 'object': {'prefix': 'omim.disease', 'semantic_type': 'disease'}},
{'endpoint': 'http://mydisease.info/v1/disease/{mondoid}', 'predicate': 'EquivalentAssociation', 'subject': {'prefix': 'mondo', 'semantic_type': 'disease'}, 'object': {'prefix': 'umls.disease', 'semantic_type': 'disease'}},
{'endpoint': 'http://mydisease.info/v1/disease/{mondoid}', 'predicate': 'EquivalentAssociation', 'subject': {'prefix': 'mondo', 'semantic_type': 'disease'}, 'object': {'prefix': 'doid', 'semantic_type': 'disease'}},
{'endpoint': 'http://mydisease.info/v1/disease/{mondoid}', 'predicate': 'HasDescriptionAssociation', 'subject': {'prefix': 'mondo', 'semantic_type': 'disease'}, 'object': {'prefix': 'diseaseDescription', 'semantic_type': 'disease'}},
{'endpoint': 'http://mydisease.info/v1/disease/{mondoid}', 'predicate': 'EquivalentAssociation', 'subject': {'prefix': 'mondo', 'semantic_type': 'disease'}, 'object': {'prefix': 'diseasename', 'semantic_type': 'disease'}}
]
kevinxin90 commented 5 years ago

Hi Lance, these are organized under the query endpoint in MyDisease.info. If you would like to use BioThings Explorer to query for variants related to a specific disease, you could do the following:

In [1]: from biothings_explorer_test import fetch_output
In [2]: fetch_output(input_prefix='mondo', output_prefix='dbsnp', input_value='0018911')

If you would like to use BioThings Explorer to query for genes related to a specific disease, you could do the following:

In [1]: from biothings_explorer_test import fetch_output
In [2]: fetch_output(input_prefix='mondo', output_prefix='ncbigene', input_value='0018911')
kevinxin90 commented 5 years ago

@lhannest Also, FYI, The python client for biothings explorer is still under development. There might be changes to some of the functions in the near future. Will keep you updated.