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Introduction

This notebook demonstrates basic usage of BioThings Explorer, an engine for autonomously querying a distributed knowledge graph. BioThings Explorer can answer two classes of queries -- "EXPLAIN" and "PREDICT". EXPLAIN queries are described in EXPLAIN_demo.ipynb. Here, we describe PREDICT queries and how to use BioThings Explorer to execute them. A more detailed overview of the BioThings Explorer systems is provided in these slides.

PREDICT queries are designed to predict plausible relationships between one entity and an entity class. For example, in this notebook, we explore the question:

         "What drugs might be used to treat hyperphenylalaninemia?"

To experiment with an executable version of this notebook, .

Step 0: Load BioThings Explorer modules

First, install the biothings_explorer and biothings_schema packages, as described in this README. This only needs to be done once (but including it here for compability with ).





In [1]:



    


%%capture
!pip install git+https://github.com/biothings/biothings_explorer#egg=biothings_explorer



    


















    






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WARNING: You are using pip version 19.1.1, however version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Next, import the relevant modules:

  • Hint: Find corresponding bio-entity representation used in BioThings Explorer based on user input (could be any database IDs, symbols, names)
  • FindConnection: Find intermediate bio-entities which connects user specified input and output




In [1]:



    


# import modules from biothings_explorer
from biothings_explorer.hint import Hint
from biothings_explorer.user_query_dispatcher import FindConnection

Step 1: Find representation of "hyperphenylalaninemia" in BTE

In this step, BioThings Explorer translates our query string "hyperphenylalaninemia" into BioThings objects, which contain mappings to many common identifiers. Generally, the top result returned by the Hint module will be the correct item, but you should confirm that using the identifiers shown.

Search terms can correspond to any child of BiologicalEntity from the Biolink Model, including DiseaseOrPhenotypicFeature (e.g., "lupus"), ChemicalSubstance (e.g., "acetaminophen"), Gene (e.g., "CDK2"), BiologicalProcess (e.g., "T cell differentiation"), and Pathway (e.g., "Citric acid cycle").





In [2]:



    


ht = Hint()
# find all potential representations of hyperphenylalaninemia
hyperphenylalaninemia_hint = ht.query("hyperphenylalaninemia")
# select the correct representation of hyperphenylalaninemia
hyperphenylalaninemia = hyperphenylalaninemia_hint['Disease'][0]
hyperphenylalaninemia



    


















    
Out[2]:








{'MONDO': 'MONDO:0016543',
 'UMLS': 'C0751435',
 'name': 'hyperphenylalaninemia',
 'ORPHANET': '238583',
 'primary': {'identifier': 'MONDO',
  'cls': 'Disease',
  'value': 'MONDO:0016543'},
 'display': 'MONDO(MONDO:0016543) ORPHANET(238583) UMLS(C0751435) name(hyperphenylalaninemia)',
 'type': 'Disease'}

Step 2: Find drugs that are associated with genes which invovled in hyperphenylalaninemia

In this section, we find all paths in the knowledge graph that connect hyperphenylalaninemia to any entity that is a chemical compound. To do that, we will use FindConnection. This class is a convenient wrapper around two advanced functions for query path planning and query path execution. More advanced features for both query path planning and query path execution are in development and will be documented in the coming months.

The parameters for FindConnection are described below:





In [4]:



    


help(FindConnection.__init__)



    


















    






Help on function __init__ in module biothings_explorer.user_query_dispatcher:

__init__(self, input_obj, output_obj, intermediate_nodes, registry=None)
    Find relationships in the Knowledge Graph between an Input Object and an Output Object.
    
    Args:
        input_obj (required): must be an object returned from Hint corresponding to a specific biomedical entity.
                            Examples:
                Hint().query("Fanconi anemia")['DiseaseOrPhenotypicFeature'][0]
                Hint().query("acetaminophen")['ChemicalSubstance'][0]
    
        output_obj (required): must EITHER be an object returned from Hint corresponding to a specific biomedical
                            entity, OR be a string or list of strings corresponding to Biolink Entity classes.
                            Examples:
                Hint().query("acetaminophen")['ChemicalSubstance'][0]
                'Gene'
                ['Gene','ChemicalSubstance']
    
        intermediate_nodes (required): the semantic type(s) of the intermediate node(s).  Examples:
                None                         : no intermediate node, find direct connections only
                []                           : no intermediate node, find direct connections only
                ['BiologicalEntity']         : one intermediate node of any semantic type
                ['Gene']                     : one intermediate node that must be a Gene
                [('Gene','Pathway')]         : one intermediate node that must be a Gene or a Pathway
                ['Gene','Pathway']           : two intermediate nodes, first must be a Gene, second must be a Pathway.
                ['Gene',('Pathway','Gene')]  : two intermediate nodes, first must be a Gene, second must be a Pathway or Gene.
                                                **NOTE**: queries with more than one intermediate node are currently not supported

Here, we formulate a FindConnection query with "hyperphenylalaninemia" as the input_ojb, "ChemicalSubstance" as the output_obj (which corresponds to a Biolink Entity type). We further specify with the intermediate_nodes parameter that we are looking for paths joining hyperphenylalaninemia and chemical compounds with one intermediate node that is a Gene. (The ability to search for longer reasoning paths that include additional intermediate nodes will be added shortly.)





In [3]:



    


fc = FindConnection(input_obj=hyperphenylalaninemia, output_obj='ChemicalSubstance', intermediate_nodes=['Gene'])

We next execute the connect method, which performs the query path planning and query path execution process. In short, BioThings Explorer is deconstructing the query into individual API calls, executing those API calls, then assembling the results.

A verbose log of this process is displayed below:





In [4]:



    


# set verbose=True will display all steps which BTE takes to find the connection
fc.connect(verbose=True)



    


















    






==========
========== QUERY PARAMETER SUMMARY ==========
==========

BTE will find paths that join 'hyperphenylalaninemia' and 'ChemicalSubstance'.                   Paths will have 1 intermediate node.

Intermediate node #1 will have these type constraints: Gene



========== QUERY #1 -- fetch all Gene entities linked to hyperphenylalaninemia ==========
==========

==== Step #1: Query path planning ====

Because hyperphenylalaninemia is of type 'Disease', BTE will query our meta-KG for APIs that can take 'Disease' as input and 'Gene' as output

BTE found 7 apis:

API 1. hetio(1 API call)
API 2. scigraph(1 API call)
API 3. semmed_disease(15 API calls)
API 4. pharos(1 API call)
API 5. scibite(1 API call)
API 6. biolink(1 API call)
API 7. mydisease(1 API call)


==== Step #2: Query path execution ====
NOTE: API requests are dispatched in parallel, so the list of APIs below is ordered by query time.

API 7.1: http://mydisease.info/v1/query?fields=disgenet.genes_related_to_disease.gene_id (POST -d q=C0751435,C0751436&scopes=mondo.xrefs.umls, disgenet.xrefs.umls)
API 3.1: https://biothings.ncats.io/semmed/query?fields=affects (POST -d q=C0751435,C0751436&scopes=umls)
API 3.14: https://biothings.ncats.io/semmed/query?fields=caused_by (POST -d q=C0751435,C0751436&scopes=umls)
API 3.13: https://biothings.ncats.io/semmed/query?fields=disrupts (POST -d q=C0751435,C0751436&scopes=umls)
API 3.9: https://biothings.ncats.io/semmed/query?fields=disrupted_by (POST -d q=C0751435,C0751436&scopes=umls)
API 3.15: https://biothings.ncats.io/semmed/query?fields=negatively_regulated_by (POST -d q=C0751435,C0751436&scopes=umls)
API 3.2: https://biothings.ncats.io/semmed/query?fields=coexists_with (POST -d q=C0751435,C0751436&scopes=umls)
API 3.8: https://biothings.ncats.io/semmed/query?fields=derives_from (POST -d q=C0751435,C0751436&scopes=umls)
API 3.6: https://biothings.ncats.io/semmed/query?fields=treated_by (POST -d q=C0751435,C0751436&scopes=umls)
API 3.10: https://biothings.ncats.io/semmed/query?fields=affected_by (POST -d q=C0751435,C0751436&scopes=umls)
API 3.11: https://biothings.ncats.io/semmed/query?fields=negatively_regulates (POST -d q=C0751435,C0751436&scopes=umls)
API 3.5: https://biothings.ncats.io/semmed/query?fields=physically_interacts_with (POST -d q=C0751435,C0751436&scopes=umls)
API 3.7: https://biothings.ncats.io/semmed/query?fields=positively_regulated_by (POST -d q=C0751435,C0751436&scopes=umls)
API 3.4: https://biothings.ncats.io/semmed/query?fields=positively_regulates (POST -d q=C0751435,C0751436&scopes=umls)
API 3.3: https://biothings.ncats.io/semmed/query?fields=prevented_by (POST -d q=C0751435,C0751436&scopes=umls)
API 3.12: https://biothings.ncats.io/semmed/query?fields=related_to (POST -d q=C0751435,C0751436&scopes=umls)
API 6.1: https://api.monarchinitiative.org/api/bioentity/disease/MONDO:0016543/genes?rows=200
API 5.1: https://automat.renci.org/cord19_scibite_v2/disease/gene/MONDO:0016543
API 2.1: https://automat.renci.org/cord19_scigraph_v2/disease/gene/MONDO:0016543
API 4.1: https://automat.renci.org/pharos/disease/gene/MONDO:0016543
API 1.1: https://automat.renci.org/hetio/disease/gene/MONDO:0016543


==== Step #3: Output normalization ====

API 3.1 semmed_disease: No hits
API 3.2 semmed_disease: No hits
API 3.3 semmed_disease: No hits
API 3.4 semmed_disease: No hits
API 3.5 semmed_disease: No hits
API 3.6 semmed_disease: 6 hits
API 3.7 semmed_disease: No hits
API 4.1 pharos: 1 hits
API 3.8 semmed_disease: No hits
API 2.1 scigraph: No hits
API 3.9 semmed_disease: 3 hits
API 7.1 mydisease: 10 hits
API 3.10 semmed_disease: No hits
API 5.1 scibite: 1 hits
API 1.1 hetio: No hits
API 3.11 semmed_disease: No hits
API 3.12 semmed_disease: 14 hits
API 3.13 semmed_disease: No hits
API 3.14 semmed_disease: 17 hits
API 6.1 biolink: 4 hits
API 3.15 semmed_disease: No hits

After id-to-object translation, BTE retrieved 33 unique objects.


========== QUERY #2.1 -- fetch all ChemicalSubstance entities linked to Gene entites ==========
==========

==== Step #1: Query path planning ====

Because None is of type 'Gene', BTE will query our meta-KG for APIs that can take 'Gene' as input and 'ChemicalSubstance' as output

BTE found 10 apis:

API 1. semmed_gene(10 API calls)
API 2. scigraph(16 API calls)
API 3. hmdb(16 API calls)
API 4. mychem(3 API calls)
API 5. dgidb(16 API calls)
API 6. pharos(16 API calls)
API 7. scibite(16 API calls)
API 8. opentarget(16 API calls)
API 9. chembio(16 API calls)
API 10. cord_gene(1 API call)


==== Step #2: Query path execution ====
NOTE: API requests are dispatched in parallel, so the list of APIs below is ordered by query time.

API 7.15: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000145730&datasource=chembl&size=100&fields=drug
API 7.8: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000171759&datasource=chembl&size=100&fields=drug
API 7.7: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000166228&datasource=chembl&size=100&fields=drug
API 7.5: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000137880&datasource=chembl&size=100&fields=drug
API 7.1: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000151552&datasource=chembl&size=100&fields=drug
API 7.13: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000148602&datasource=chembl&size=100&fields=drug
API 7.6: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000198074&datasource=chembl&size=100&fields=drug
API 7.11: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000141837&datasource=chembl&size=100&fields=drug
API 7.3: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000131979&datasource=chembl&size=100&fields=drug
API 7.12: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000150787&datasource=chembl&size=100&fields=drug
API 7.10: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000170606&datasource=chembl&size=100&fields=drug
API 7.16: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000135775&datasource=chembl&size=100&fields=drug
API 7.4: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000142192&datasource=chembl&size=100&fields=drug
API 5.13: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=AKR1B10
API 5.7: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=CACNA1A
API 5.14: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=PAH
API 5.8: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=PTS
API 5.9: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=PAM
API 5.11: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=HSPA4
API 5.2: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=GCHFR
API 5.3: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=GCH1
API 5.5: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=QDPR
API 5.6: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=LRIT1
API 5.16: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=COG2
API 5.1: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=PCBD1
API 5.12: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=APP
API 6.16: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:338
API 8.1: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:57016
API 2.7: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:3308
API 4.8: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:2644
API 4.7: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:3308
API 6.1: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:57016
API 6.13: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:2643
API 6.10: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:351
API 4.2: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:5860
API 6.6: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:5805
API 6.3: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:773
API 6.15: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:5066
API 2.5: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:5092
API 2.14: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:26103
API 2.2: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:5860
API 4.1: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:57016
API 2.11: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:3034
API 4.5: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:5092
API 5.15: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=SHCBP1
API 6.4: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:22796
API 2.8: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:2644
API 2.12: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:5053
API 5.4: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=HAL
API 3.2: https://mychem.info/v1/query?fields=drugbank.id&size=250 (POST -d q=PCBD1,GCHFR,GCH1,HAL,QDPR,LRIT1,CACNA1A,PTS,PAM,APOB,HSPA4,APP,AKR1B10,PAH,SHCBP1,COG2&scopes=drugbank.enzymes.gene_name)
API 3.1: https://mychem.info/v1/query?fields=drugbank.id&size=250 (POST -d q=PCBD1,GCHFR,GCH1,HAL,QDPR,LRIT1,CACNA1A,PTS,PAM,APOB,HSPA4,APP,AKR1B10,PAH,SHCBP1,COG2&scopes=drugbank.targets.gene_name)
API 6.9: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:79801
API 6.7: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:3308
API 5.10: http://dgidb.genome.wustl.edu/api/v2/interactions.json?genes=APOB
API 7.2: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000084674&datasource=chembl&size=100&fields=drug
API 2.9: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:79801
API 6.2: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:5860
API 6.5: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:5092
API 6.14: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:26103
API 6.8: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:2644
API 2.16: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:338
API 6.11: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:3034
API 7.9: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000171241&datasource=chembl&size=100&fields=drug
API 4.6: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:5805
API 6.12: https://automat.renci.org/cord19_scibite_v2/gene/chemical_substance/NCBIGene:5053
API 4.12: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:5053
API 2.4: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:22796
API 7.14: https://platform-api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000084110&datasource=chembl&size=100&fields=drug
API 3.3: https://mychem.info/v1/query?fields=chembl.molecule_chembl_id&size=250 (POST -d q=PCBD1,GCHFR,GCH1,HAL,QDPR,LRIT1,CACNA1A,PTS,PAM,APOB,HSPA4,APP,AKR1B10,PAH,SHCBP1,COG2&scopes=drugcentral.bioactivity.uniprot.gene_symbol)
API 2.1: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:57016
API 2.13: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:2643
API 4.9: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:79801
API 8.2: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:5860
API 4.3: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:773
API 9.6: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:5805
API 8.7: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:3308
API 4.13: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:2643
API 4.4: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:22796
API 2.15: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:5066
API 2.3: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:773
API 4.14: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:26103
API 4.11: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:3034
API 2.10: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:351
API 4.15: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:5066
API 8.3: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:773
API 8.9: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:79801
API 4.16: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:338
API 8.8: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:2644
API 8.4: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:22796
API 8.15: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:5066
API 8.5: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:5092
API 8.6: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:5805
API 8.10: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:351
API 2.6: https://automat.renci.org/cord19_scigraph_v2/gene/chemical_substance/NCBIGene:5805
API 8.11: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:3034
API 8.14: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:26103
API 8.13: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:2643
API 4.10: https://automat.renci.org/pharos/gene/chemical_substance/NCBIGene:351
API 9.4: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:22796
API 8.12: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:5053
API 8.16: https://automat.renci.org/chembio/gene/chemical_substance/NCBIGene:338
API 9.1: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:57016
API 10.1: https://biothings.ncats.io/cord_gene/query?fields=associated_with (POST -d q=4193,6546,5237,9689,1388,603,4194,382,4806,29547,8646,8596,9752,23404,620,8582&scopes=hgnc)
API 9.7: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:3308
API 9.8: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:2644
API 9.9: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:79801
API 9.3: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:773
API 9.5: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:5092
API 9.2: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:5860
API 9.12: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:5053
API 9.10: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:351
API 9.11: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:3034
API 9.14: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:26103
API 9.15: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:5066
API 9.13: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:2643
API 9.16: https://automat.renci.org/hmdb/gene/chemical_substance/NCBIGene:338
API 1.1: https://biothings.ncats.io/semmedgene/query?fields=negatively_regulates (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.6: https://biothings.ncats.io/semmedgene/query?fields=positively_regulated_by (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.4: https://biothings.ncats.io/semmedgene/query?fields=affected_by (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.9: https://biothings.ncats.io/semmedgene/query?fields=disrupted_by (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.8: https://biothings.ncats.io/semmedgene/query?fields=disrupts (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.7: https://biothings.ncats.io/semmedgene/query?fields=negatively_regulated_by (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.10: https://biothings.ncats.io/semmedgene/query?fields=positively_regulates (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.5: https://biothings.ncats.io/semmedgene/query?fields=related_to (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.3: https://biothings.ncats.io/semmedgene/query?fields=affects (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)
API 1.2: https://biothings.ncats.io/semmedgene/query?fields=physically_interacts_with (POST -d q=C0017361,C0018293,C1412323,C0072774,C1364818,C1415465,C1335144,C1539766,C0314604,C1416822,C0031456,C0012312,C1710338,C1428072,C0074350,C0002085,C0014442,C1418251,C1418296,C1456413,C0041491,C0284927,C1419129,C1705543,C1415012,C1419182,C1412471,C1415760,C1415013,C0020239,C0030016,C1456357,C0017337&scopes=umls)


==== Step #3: Output normalization ====

API 7.1 opentarget: No hits
API 7.2 opentarget: 7 hits
API 7.3 opentarget: No hits
API 7.4 opentarget: 59 hits
API 7.5 opentarget: No hits
API 7.6 opentarget: No hits
API 7.7 opentarget: No hits
API 7.8 opentarget: 42 hits
API 7.9 opentarget: No hits
API 7.10 opentarget: No hits
API 7.11 opentarget: 19 hits
API 7.12 opentarget: No hits
API 7.13 opentarget: No hits
API 7.14 opentarget: No hits
API 7.15 opentarget: No hits
API 7.16 opentarget: No hits
API 6.1 scibite: 1 hits
API 6.2 scibite: No hits
API 6.3 scibite: No hits
API 6.4 scibite: No hits
API 6.5 scibite: No hits
API 6.6 scibite: No hits
API 6.7 scibite: 1 hits
API 6.8 scibite: 1 hits
API 6.9 scibite: No hits
API 6.10 scibite: 9 hits
API 6.11 scibite: No hits
API 6.12 scibite: 1 hits
API 6.13 scibite: 1 hits
API 6.14 scibite: No hits
API 6.15 scibite: No hits
API 6.16 scibite: 3 hits
API 1.1 semmed_gene: 2007 hits
API 1.2 semmed_gene: 15441 hits
API 1.3 semmed_gene: 1 hits
API 1.4 semmed_gene: 9 hits
API 2.1 scigraph: No hits
API 2.2 scigraph: No hits
API 2.3 scigraph: No hits
API 2.4 scigraph: No hits
API 2.5 scigraph: No hits
API 2.6 scigraph: 442 hits
API 2.7 scigraph: No hits
API 2.8 scigraph: No hits
API 2.9 scigraph: No hits
API 2.10 scigraph: 56 hits
API 2.11 scigraph: 1 hits
API 2.12 scigraph: 52 hits
API 2.13 scigraph: No hits
API 2.14 scigraph: No hits
API 2.15 scigraph: 19 hits
API 2.16 scigraph: 16 hits
API 1.5 semmed_gene: No hits
API 5.1 dgidb: 1 hits
API 5.2 dgidb: No hits
API 5.3 dgidb: 1 hits
API 5.4 dgidb: 1 hits
API 5.5 dgidb: 1 hits
API 5.6 dgidb: No hits
API 5.7 dgidb: 11 hits
API 5.8 dgidb: No hits
API 5.9 dgidb: 1 hits
API 5.10 dgidb: 17 hits
API 5.11 dgidb: 35 hits
API 5.12 dgidb: 22 hits
API 5.13 dgidb: 3 hits
API 5.14 dgidb: 8 hits
API 5.15 dgidb: No hits
API 5.16 dgidb: No hits
API 1.6 semmed_gene: 4883 hits
API 3.1 mychem: 51 hits
API 10.1 cord_gene: 723 hits
API 1.7 semmed_gene: 6577 hits
API 4.1 pharos: 44 hits
API 4.2 pharos: 3 hits
API 4.3 pharos: 1 hits
API 4.4 pharos: No hits
API 4.5 pharos: No hits
API 4.6 pharos: No hits
API 4.7 pharos: No hits
API 4.8 pharos: No hits
API 4.9 pharos: No hits
API 4.10 pharos: 358 hits
API 4.11 pharos: No hits
API 4.12 pharos: 2 hits
API 4.13 pharos: No hits
API 4.14 pharos: No hits
API 4.15 pharos: 5 hits
API 4.16 pharos: 49 hits
API 1.8 semmed_gene: 2 hits
API 8.1 chembio: 5 hits
API 8.2 chembio: 1 hits
API 8.3 chembio: 1 hits
API 8.4 chembio: No hits
API 8.5 chembio: 2 hits
API 8.6 chembio: 2 hits
API 8.7 chembio: 6 hits
API 8.8 chembio: 4 hits
API 8.9 chembio: 1 hits
API 8.10 chembio: 29 hits
API 8.11 chembio: 3 hits
API 8.12 chembio: 1 hits
API 8.13 chembio: 4 hits
API 8.14 chembio: No hits
API 8.15 chembio: 7 hits
API 8.16 chembio: 6 hits
API 3.2 mychem: 4 hits
API 1.9 semmed_gene: No hits
API 9.1 hmdb: 18 hits
API 9.2 hmdb: 11 hits
API 9.3 hmdb: 4 hits
API 9.4 hmdb: No hits
API 9.5 hmdb: 5 hits
API 9.6 hmdb: 6 hits
API 9.7 hmdb: No hits
API 9.8 hmdb: 2 hits
API 9.9 hmdb: No hits
API 9.10 hmdb: 5 hits
API 9.11 hmdb: 3 hits
API 9.12 hmdb: 11 hits
API 9.13 hmdb: 8 hits
API 9.14 hmdb: No hits
API 9.15 hmdb: 5 hits
API 9.16 hmdb: 4 hits
API 3.3 mychem: 15 hits
API 1.10 semmed_gene: 2314 hits

After id-to-object translation, BTE retrieved 9449 unique objects.

==========
========== Final assembly of results ==========
==========


In the #1 query, BTE found 33 unique Gene nodes
In the #2 query, BTE found 9449 unique ChemicalSubstance nodes

Step 3: Display and Filter results

This section demonstrates post-query filtering done in Python. Later, more advanced filtering functions will be added to the query path execution module for interleaved filtering, thereby enabling longer query paths. More details to come...

First, all matching paths can be exported to a data frame. Let's examine a sample of those results.





In [5]:



    


df = fc.display_table_view()

# because UMLS is not currently well-integrated in our ID-to-object translation system, removing UMLS-only outputs here
patternDel = "^UMLS:C\d+"
filter = df.output_id.str.contains(patternDel)
df = df[~filter]

patternDel2 = "^InChI="
filter2 = df.output_name.str.contains(patternDel2)
df = df[~filter2]

patternDel3 = "^umls:C\d+"
filter3 = df.node1_id.str.contains(patternDel3)
df = df[~filter3]

print(df.shape)
df.sample(10)



    


















    






(4541, 16)










    
Out[5]:











  
    

      
      input
      input_type
      pred1
      pred1_source
      pred1_api
      pred1_pubmed
      node1_type
      node1_name
      node1_id
      pred2
      pred2_source
      pred2_api
      pred2_pubmed
      output_type
      output_name
      output_id
    

  
  
    

      16504
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      10727395
      Gene
      C0014442
      UMLS:C0014442
      negatively_regulated_by
      SEMMED
      SEMMED Gene API
      11839529,19443747
      ChemicalSubstance
      U 0126
      name:U 0126
    

    

      8209
      HYPERPHENYLALANINAEMIA
      Disease
      related_to
      SEMMED
      SEMMED Disease API
      9675155
      Gene
      C0017337
      UMLS:C0017337
      positively_regulated_by
      SEMMED
      SEMMED Gene API
      21984199,26086415
      ChemicalSubstance
      ISOFLURANE
      name:ISOFLURANE
    

    

      31798
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      9222755,9667588
      Gene
      C0017337
      UMLS:C0017337
      positively_regulated_by
      SEMMED
      SEMMED Gene API
      17684401,18412988,17693008
      ChemicalSubstance
      MICRONUTRIENT
      name:MICRONUTRIENT
    

    

      1929
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      10874306
      Gene
      PTS
      NCBIGene:5805
      related_to
      Translator Text Mining Provider
      CORD Gene API
      None
      ChemicalSubstance
      .BETA.-D-GLUCOPYRANOSE
      name:.BETA.-D-GLUCOPYRANOSE
    

    

      10532
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      699146
      Gene
      C0030016
      UMLS:C0030016
      positively_regulated_by
      SEMMED
      SEMMED Gene API
      11731036
      ChemicalSubstance
      GENISTEIN
      name:GENISTEIN
    

    

      35512
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      10727395
      Gene
      C0014442
      UMLS:C0014442
      positively_regulates
      SEMMED
      SEMMED Gene API
      4291334,7358701,11980911
      ChemicalSubstance
      DEOXYCHOLATE
      name:DEOXYCHOLATE
    

    

      40287
      HYPERPHENYLALANINAEMIA
      Disease
      treated_by
      SEMMED
      SEMMED Disease API
      8841415
      Gene
      PTS
      NCBIGene:5805
      related_to
      scigraph
      Automat CORD19 Scigraph API
      None
      ChemicalSubstance
      CHLORAMBUCIL
      name:CHLORAMBUCIL
    

    

      40027
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      15133828
      Gene
      AKR1B10
      NCBIGene:57016
      negatively_regulates
      SEMMED
      SEMMED Gene API
      28322780
      ChemicalSubstance
      TIAPROFENIC ACID
      name:TIAPROFENIC ACID
    

    

      22054
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      28794131
      Gene
      HSPA4
      NCBIGene:3308
      positively_regulated_by
      SEMMED
      SEMMED Gene API
      26307981
      ChemicalSubstance
      MALONALDEHYDE
      name:MALONALDEHYDE
    

    

      45089
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      1301201,8892014,10495930,10495930
      Gene
      PAH
      NCBIGene:5053
      related_to
      Translator Text Mining Provider
      CORD Gene API
      None
      ChemicalSubstance
      CHEBI:46756
      CHEBI:CHEBI:46756

While most results are based on edges from semmed, edges from DGIdb, biolink, disgenet, and mychem.info were also retrieved from their respective APIs.

Next, let's examine which chemical compounds were most frequently mentioned.





In [6]:



    


df.output_name.value_counts().head(20)



    


















    
Out[6]:








PHARMACEUTICAL PREPARATIONS    122
HYDROGEN PEROXIDE              119
.BETA.-D-GLUCOPYRANOSE         116
NADH                           105
NITRIC OXIDE                   101
BINDING SITE                    97
3-METHYLADENINE DNA             94
CHOLESTEROL                     94
OXYGEN SPECIES, REACTIVE        92
ALCOHOL                         91
Name: output_name, dtype: int64

Hyperphenylalaninemia is a condition characterized by elevated levels of phenylalanine in the blood. This phenotype is strongly associated with phenylketonuria (PKU), an inherited, genetic disorder that affects the ability to metabolize phenylalanine. Sapropterin is a naturally-occurring cofactor associated with several enzymatic processes, including the metabolism of phenylalanine to tyrosine. It has been FDA-approved as a treatment for PKU patients. Tyrosine is also a precursor to several neurotransmitters, including norepinephrine and dopamine.

While several of the listed compounds would be considered positive controls, others on the list could be viewed as testable hypotheses and discovery opportunities to be evaluated by domain experts. For example, let's examine which genes link hyperphenylalaninemia to nitric oxide.





In [7]:



    


df[df.output_name=="NITRIC OXIDE"]



    


















    
Out[7]:











  
    

      
      input
      input_type
      pred1
      pred1_source
      pred1_api
      pred1_pubmed
      node1_type
      node1_name
      node1_id
      pred2
      pred2_source
      pred2_api
      pred2_pubmed
      output_type
      output_name
      output_id
    

  
  
    

      2318
      HYPERPHENYLALANINAEMIA
      Disease
      treated_by
      SEMMED
      SEMMED Disease API
      25261586,25261586
      Gene
      C1710338
      UMLS:C1710338
      negatively_regulates
      SEMMED
      SEMMED Gene API
      23769841
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      2319
      HYPERPHENYLALANINAEMIA
      Disease
      treated_by
      SEMMED
      SEMMED Disease API
      25261586,25261586
      Gene
      C1710338
      UMLS:C1710338
      negatively_regulates
      SEMMED
      SEMMED Gene API
      15265010
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      2320
      HYPERPHENYLALANINAEMIA
      Disease
      treated_by
      SEMMED
      SEMMED Disease API
      25261586,25261586
      Gene
      C1710338
      UMLS:C1710338
      physically_interacts_with
      SEMMED
      SEMMED Gene API
      25049660,23072349
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      2321
      HYPERPHENYLALANINAEMIA
      Disease
      treated_by
      SEMMED
      SEMMED Disease API
      25261586,25261586
      Gene
      C1710338
      UMLS:C1710338
      physically_interacts_with
      SEMMED
      SEMMED Gene API
      23806552,16831427
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      2322
      HYPERPHENYLALANINAEMIA
      Disease
      treated_by
      SEMMED
      SEMMED Disease API
      25261586,25261586
      Gene
      C1710338
      UMLS:C1710338
      positively_regulated_by
      SEMMED
      SEMMED Gene API
      10952392
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
    

    

      2422
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      28794131
      Gene
      HSPA4
      NCBIGene:3308
      positively_regulated_by
      SEMMED
      SEMMED Gene API
      7544743,9085348,9085348,9276725,10805410,10805...
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      2423
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      28794131
      Gene
      HSPA4
      NCBIGene:3308
      positively_regulates
      SEMMED
      SEMMED Gene API
      11374865
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      2424
      HYPERPHENYLALANINAEMIA
      Disease
      caused_by
      SEMMED
      SEMMED Disease API
      7766952
      Gene
      CACNA1A
      NCBIGene:773
      negatively_regulates
      SEMMED
      SEMMED Gene API
      23949212
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      2425
      HYPERPHENYLALANINAEMIA
      Disease
      related_to
      scibite
      Automat CORD19 Scibite API
      None
      Gene
      GCHFR
      NCBIGene:2644
      physically_interacts_with
      SEMMED
      SEMMED Gene API
      18372436,18372436,18372436
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      2426
      HYPERPHENYLALANINAEMIA
      Disease
      related_to
      scibite
      Automat CORD19 Scibite API
      None
      Gene
      GCHFR
      NCBIGene:2644
      physically_interacts_with
      SEMMED
      SEMMED Gene API
      21693765
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39812
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      caused_by
      SEMMED API
      semmeddisease
      28794131
      Gene
      HSPA4
      entrez:3308
      positively_regulated_by
      SEMMED API
      semmedgene
      7544743,9085348,9085348,9276725,10805410,10805...
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39813
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      caused_by
      SEMMED API
      semmeddisease
      28794131
      Gene
      HSPA4
      entrez:3308
      positively_regulates
      SEMMED API
      semmedgene
      11374865
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39814
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      caused_by
      SEMMED API
      semmeddisease
      28794131
      Gene
      HSPA4
      entrez:3308
      produces
      SEMMED API
      semmedgene
      10849439,16521562,24395610
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39815
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      caused_by
      SEMMED API
      semmeddisease
      7766952
      Gene
      CACNA1A
      entrez:773
      negatively_regulates
      SEMMED API
      semmedgene
      23949212
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39816
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      disrupted_by
      SEMMED API
      semmeddisease
      10051643
      Gene
      PAM
      entrez:5066
      associated_with
      CORD API
      cordgene
      None
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39817
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      27612877
      Gene
      COG2
      entrez:22796
      physically_interacts_with
      SEMMED API
      semmedgene
      16060915
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39818
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      27612877
      Gene
      COG2
      entrez:22796
      positively_regulated_by
      SEMMED API
      semmedgene
      25224628
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39819
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      27612877
      Gene
      COG2
      entrez:22796
      positively_regulates
      SEMMED API
      semmedgene
      27919363
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39820
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      27612877
      Gene
      COG2
      entrez:22796
      produces
      SEMMED API
      semmedgene
      26847282
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39821
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      27612877
      Gene
      APOB
      entrez:338
      coexists_with
      SEMMED API
      semmedgene
      9593815
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39822
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      25260610
      Gene
      APP
      entrez:351
      coexists_with
      SEMMED API
      semmedgene
      20021361,22810094
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39823
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      25260610
      Gene
      APP
      entrez:351
      coexists_with
      SEMMED API
      semmedgene
      20936504
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39824
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      25260610
      Gene
      APP
      entrez:351
      has_part
      SEMMED API
      semmedgene
      15371443
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39825
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      25260610
      Gene
      APP
      entrez:351
      negatively_regulates
      SEMMED API
      semmedgene
      20936504,21073661,22426388,26819495
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39826
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      25260610
      Gene
      APP
      entrez:351
      physically_interacts_with
      SEMMED API
      semmedgene
      19779140,22384120,26665235
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39827
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      25260610
      Gene
      APP
      entrez:351
      positively_regulates
      SEMMED API
      semmedgene
      23915297,23915297
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39828
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      25260610
      Gene
      APP
      entrez:351
      positively_regulates
      SEMMED API
      semmedgene
      9915130,9915130,9576964,10648444,17365664,1917...
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

    

      39829
      hyperphenylalaninemia
      DiseaseOrPhenotypicFeature
      related_to
      SEMMED API
      semmeddisease
      25260610
      Gene
      APP
      entrez:351
      produces
      SEMMED API
      semmedgene
      11027218,9915130,11241130,12944390,21718498
      ChemicalSubstance
      NITRIC OXIDE
      chembl:CHEMBL1200689
    

  



101 rows × 16 columns

BTE identifies a number of genes, including HSPA4 and GCH1, as being the key nodes that join hyperphenylalaninemia with nitric oxide.

Conclusions and caveats

This notebook demonstrated the use of BioThings Explorer in PREDICDT mode to identify chemical compounds related to hyperphenylalaninemia. BioThings Explorer autonomously queried a distributed knowledge graph of biomedical APIs to find the most common compounds, and several of the top hits had a clear biochemical and clinical relevance to hyperphenylalaninemia.

There are still many areas for improvement (and some areas in which BioThings Explorer is still buggy). And of course, BioThings Explorer is dependent on the accessibility of the APIs that comprise the distributed knowledge graph. Nevertheless, we encourage users to try other variants of the PREDICT queries demonstrated in this notebook.

Content source: biothings/biothings_explorer

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