In [1]:
from biothings_explorer.user_query_dispatcher import FindConnection
from biothings_explorer.hint import Hint
ht = Hint()
# find all potential representations of CML
cml_hint = ht.query("MONDO:0011996")
# select the correct representation of CML
cml = cml_hint['Disease'][0]
cml
# find all potential representations of imatinib
imatinib_hint = ht.query("imatinib")
# select the correct representation of imatinib
imatinib = imatinib_hint['ChemicalSubstance'][0]
imatinib
fc = FindConnection(input_obj=cml, output_obj=imatinib, intermediate_nodes='Gene')
fc.connect(verbose=True)
==========
========== QUERY PARAMETER SUMMARY ==========
==========
BTE will find paths that join 'chronic myelogenous leukemia' and 'imatinib'. Paths will have 1 intermediate node.
Intermediate node #1 will have these type constraints: Gene
==========
========== QUERY #1 -- fetch all Gene entities linked to 'chronic myelogenous leukemia' ==========
==========
==== Step #1: Query path planning ====
Because chronic myelogenous leukemia is of type 'Disease', BTE will query our meta-KG for APIs that can take 'Disease' as input and 'Gene' as output
BTE found 9 apis:
API 1. DISEASES(1 API call)
API 2. mydisease(1 API call)
API 3. cord_disease(1 API call)
API 4. pharos(1 API call)
API 5. scigraph(1 API call)
API 6. semmed_disease(15 API calls)
API 7. scibite(1 API call)
API 8. hetio(1 API call)
API 9. biolink(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 2.1: http://mydisease.info/v1/query?fields=disgenet.genes_related_to_disease.gene_id (POST -d q=C0023473,C1292772&scopes=mondo.xrefs.umls, disgenet.xrefs.umls)
API 6.8: https://biothings.ncats.io/semmed/query?fields=negatively_regulates (POST -d q=C0023473,C1292772&scopes=umls)
API 6.7: https://biothings.ncats.io/semmed/query?fields=positively_regulated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 6.5: https://biothings.ncats.io/semmed/query?fields=derives_from (POST -d q=C0023473,C1292772&scopes=umls)
API 6.1: https://biothings.ncats.io/semmed/query?fields=positively_regulates (POST -d q=C0023473,C1292772&scopes=umls)
API 6.3: https://biothings.ncats.io/semmed/query?fields=disrupts (POST -d q=C0023473,C1292772&scopes=umls)
API 6.2: https://biothings.ncats.io/semmed/query?fields=disrupted_by (POST -d q=C0023473,C1292772&scopes=umls)
API 6.13: https://biothings.ncats.io/semmed/query?fields=negatively_regulated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 1.1: https://pending.biothings.io/DISEASES/query?fields=DISEASES.associatedWith (POST -d q=DOID:8552&scopes=DISEASES.doid)
API 6.9: https://biothings.ncats.io/semmed/query?fields=prevented_by (POST -d q=C0023473,C1292772&scopes=umls)
API 3.1: https://api.monarchinitiative.org/api/bioentity/disease/MONDO:0011996/genes?rows=200
API 6.10: https://biothings.ncats.io/semmed/query?fields=caused_by (POST -d q=C0023473,C1292772&scopes=umls)
API 6.6: https://biothings.ncats.io/semmed/query?fields=physically_interacts_with (POST -d q=C0023473,C1292772&scopes=umls)
API 9.1: https://biothings.ncats.io/cord_disease/query?fields=associated_with (POST -d q=DOID:8552&scopes=doid)
API 6.14: https://biothings.ncats.io/semmed/query?fields=related_to (POST -d q=C0023473,C1292772&scopes=umls)
API 6.4: https://biothings.ncats.io/semmed/query?fields=affects (POST -d q=C0023473,C1292772&scopes=umls)
API 6.11: https://biothings.ncats.io/semmed/query?fields=treated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 6.15: https://biothings.ncats.io/semmed/query?fields=coexists_with (POST -d q=C0023473,C1292772&scopes=umls)
API 6.12: https://biothings.ncats.io/semmed/query?fields=affected_by (POST -d q=C0023473,C1292772&scopes=umls)
API 8.1: https://automat.renci.org/hetio/disease/gene/MONDO:0011996
API 5.1: https://automat.renci.org/cord19_scigraph_v2/disease/gene/MONDO:0011996
API 7.1: https://automat.renci.org/cord19_scibite_v2/disease/gene/MONDO:0011996
API 4.1: https://automat.renci.org/pharos/disease/gene/MONDO:0011996
==== Step #3: Output normalization ====
API 6.1 semmed_disease: No hits
API 6.2 semmed_disease: 26 hits
API 6.3 semmed_disease: No hits
API 9.1 cord_disease: 146 hits
API 6.4 semmed_disease: No hits
API 6.5 semmed_disease: No hits
API 3.1 biolink: 4 hits
API 6.6 semmed_disease: No hits
API 6.7 semmed_disease: No hits
API 2.1 mydisease: 52 hits
API 6.8 semmed_disease: No hits
API 5.1 scigraph: 3 hits
API 6.9 semmed_disease: 7 hits
API 1.1 DISEASES: 3 hits
API 6.10 semmed_disease: 90 hits
API 6.11 semmed_disease: 133 hits
API 6.12 semmed_disease: 65 hits
API 4.1 pharos: 7 hits
API 8.1 hetio: No hits
API 6.13 semmed_disease: No hits
API 6.14 semmed_disease: 550 hits
API 6.15 semmed_disease: No hits
API 7.1 scibite: 12 hits
After id-to-object translation, BTE retrieved 751 unique objects.
==========
========== QUERY #2 -- fetch all Gene entities linked to 'imatinib' ==========
==========
==== Step #1: Query path planning ====
Because imatinib is of type 'ChemicalSubstance', BTE will query our meta-KG for APIs that can take 'ChemicalSubstance' as input and 'Gene' as output
BTE found 10 apis:
API 1. chembio(1 API call)
API 2. dgidb(2 API calls)
API 3. hmdb(1 API call)
API 4. ctd(2 API calls)
API 5. pharos(1 API call)
API 6. scigraph(1 API call)
API 7. scibite(1 API call)
API 8. semmed_chemical(13 API calls)
API 9. cord_chemical(1 API call)
API 10. mychem(3 API calls)
==== Step #2: Query path execution ====
NOTE: API requests are dispatched in parallel, so the list of APIs below is ordered by query time.
API 9.8: https://biothings.ncats.io/semmedchemical/query?fields=affected_by (POST -d q=C0935989&scopes=umls)
API 9.10: https://biothings.ncats.io/semmedchemical/query?fields=negatively_regulated_by (POST -d q=C0935989&scopes=umls)
API 10.1: https://mychem.info/v1/query?fields=drugbank.enzymes (POST -d q=DB00619&scopes=drugbank.id)
API 9.12: https://biothings.ncats.io/semmedchemical/query?fields=negatively_regulates (POST -d q=C0935989&scopes=umls)
API 9.1: https://biothings.ncats.io/semmedchemical/query?fields=positively_regulated_by (POST -d q=C0935989&scopes=umls)
API 9.5: https://biothings.ncats.io/semmedchemical/query?fields=related_to (POST -d q=C0935989&scopes=umls)
API 4.2: http://ctdbase.org/tools/batchQuery.go?inputType=chem&report=genes_curated&format=json&inputTerms=D000068877
API 10.3: https://mychem.info/v1/query?fields=drugbank.targets (POST -d q=DB00619&scopes=drugbank.id)
API 9.7: https://biothings.ncats.io/semmedchemical/query?fields=disrupted_by (POST -d q=C0935989&scopes=umls)
API 8.1: https://biothings.ncats.io/cord_chemical/query?fields=associated_with (POST -d q=CHEBI:45783&scopes=chebi)
API 9.4: https://biothings.ncats.io/semmedchemical/query?fields=produced_by (POST -d q=C0935989&scopes=umls)
API 9.11: https://biothings.ncats.io/semmedchemical/query?fields=produces (POST -d q=C0935989&scopes=umls)
API 10.2: https://mychem.info/v1/query?fields=drugcentral.bioactivity (POST -d q=CHEMBL941,CHEMBL1642&scopes=chembl.molecule_chembl_id)
API 4.1: http://ctdbase.org/tools/batchQuery.go?inputType=chem&report=genes_curated&format=json&inputTerms=C097613
API 2.1: http://dgidb.genome.wustl.edu/api/v2/interactions.json?drugs=CHEMBL941
API 9.13: https://biothings.ncats.io/semmedchemical/query?fields=positively_regulates (POST -d q=C0935989&scopes=umls)
API 9.9: https://biothings.ncats.io/semmedchemical/query?fields=physically_interacts_with (POST -d q=C0935989&scopes=umls)
API 9.3: https://biothings.ncats.io/semmedchemical/query?fields=disrupts (POST -d q=C0935989&scopes=umls)
API 2.2: http://dgidb.genome.wustl.edu/api/v2/interactions.json?drugs=CHEMBL1642
API 9.2: https://biothings.ncats.io/semmedchemical/query?fields=coexists_with (POST -d q=C0935989&scopes=umls)
API 9.6: https://biothings.ncats.io/semmedchemical/query?fields=affects (POST -d q=C0935989&scopes=umls)
API 6.1: https://automat.renci.org/cord19_scigraph_v2/chemical_substance/gene/CHEBI:45783
API 5.1: https://automat.renci.org/pharos/chemical_substance/gene/CHEBI:45783
API 7.1: https://automat.renci.org/cord19_scibite_v2/chemical_substance/gene/CHEBI:45783
API 1.1: https://automat.renci.org/chembio/chemical_substance/gene/CHEBI:45783
API 3.1: https://automat.renci.org/hmdb/chemical_substance/gene/CHEBI:45783
==== Step #3: Output normalization ====
API 9.1 semmed_chemical: 39 hits
API 9.2 semmed_chemical: 138 hits
API 10.1 mychem: 9 hits
API 9.3 semmed_chemical: No hits
API 2.1 dgidb: 34 hits
API 2.2 dgidb: 5 hits
API 9.4 semmed_chemical: 12 hits
API 9.5 semmed_chemical: No hits
API 10.2 mychem: 80 hits
API 9.6 semmed_chemical: No hits
API 9.7 semmed_chemical: No hits
API 4.1 ctd: No hits
API 4.2 ctd: 199 hits
API 1.1 chembio: No hits
API 9.8 semmed_chemical: No hits
API 9.9 semmed_chemical: 300 hits
API 9.10 semmed_chemical: 38 hits
API 9.11 semmed_chemical: No hits
API 5.1 pharos: 6 hits
API 7.1 scibite: 8 hits
API 8.1 cord_chemical: 172 hits
API 10.3 mychem: 9 hits
API 9.12 semmed_chemical: 171 hits
API 3.1 hmdb: No hits
API 9.13 semmed_chemical: 98 hits
API 6.1 scigraph: 3 hits
After id-to-object translation, BTE retrieved 730 unique objects.
==========
========== Final assembly of results ==========
==========
BTE found 255 unique intermediate nodes connecting 'chronic myelogenous leukemia' and 'imatinib'
As you can see above, by default, BTE will query all APIs integrated.
In [2]:
from biothings_explorer.registry import Registry
reg = Registry()
reg.show_all_apis()
Out[2]:
['mygene',
'ctd',
'cord_gene',
'cord_protein',
'cord_chemical',
'cord_disease',
'cord_cell',
'cord_molecular_activity',
'cord_biological_process',
'cord_cellular_component',
'cord_anatomy',
'cord_genomic_entity',
'semmed_gene',
'semmed_chemical',
'semmed_disease',
'semmed_biological_process',
'semmed_anatomy',
'semmed_phenotype',
'scibite',
'biolink',
'opentarget',
'dgidb',
'mydisease',
'mychem',
'myvariant',
'DISEASES',
'scigraph',
'pharos',
'hmdb',
'hetio',
'chembio']
The Registry class stores all APIs used in BTE.
To remove one or more API from the registry, use the method below:
In [3]:
reg.remove_apis(['biolink', 'dgidb'])
biolink has been successfully removed!
dgidb has been successfully removed!
check the current api list
In [4]:
reg.show_all_apis()
Out[4]:
['mygene',
'ctd',
'cord_gene',
'cord_protein',
'cord_chemical',
'cord_disease',
'cord_cell',
'cord_molecular_activity',
'cord_biological_process',
'cord_cellular_component',
'cord_anatomy',
'cord_genomic_entity',
'semmed_gene',
'semmed_chemical',
'semmed_disease',
'semmed_biological_process',
'semmed_anatomy',
'semmed_phenotype',
'scibite',
'opentarget',
'mydisease',
'mychem',
'myvariant',
'DISEASES',
'scigraph',
'pharos',
'hmdb',
'hetio',
'chembio']
So now, the "biolink" and "dgidb" are removed from the registry
We then pass the registry as a parameter to the FindConnection Class.
In [5]:
fc = FindConnection(input_obj=cml, output_obj=imatinib, intermediate_nodes='Gene', registry=reg)
fc.connect(verbose=True)
==========
========== QUERY PARAMETER SUMMARY ==========
==========
BTE will find paths that join 'chronic myelogenous leukemia' and 'imatinib'. Paths will have 1 intermediate node.
Intermediate node #1 will have these type constraints: Gene
==========
========== QUERY #1 -- fetch all Gene entities linked to 'chronic myelogenous leukemia' ==========
==========
==== Step #1: Query path planning ====
Because chronic myelogenous leukemia is of type 'Disease', BTE will query our meta-KG for APIs that can take 'Disease' as input and 'Gene' as output
BTE found 8 apis:
API 1. DISEASES(1 API call)
API 2. mydisease(1 API call)
API 3. pharos(1 API call)
API 4. scigraph(1 API call)
API 5. semmed_disease(15 API calls)
API 6. scibite(1 API call)
API 7. hetio(1 API call)
API 8. cord_disease(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 2.1: http://mydisease.info/v1/query?fields=disgenet.genes_related_to_disease.gene_id (POST -d q=C0023473,C1292772&scopes=mondo.xrefs.umls, disgenet.xrefs.umls)
API 5.1: https://biothings.ncats.io/semmed/query?fields=positively_regulates (POST -d q=C0023473,C1292772&scopes=umls)
API 8.1: https://biothings.ncats.io/cord_disease/query?fields=associated_with (POST -d q=DOID:8552&scopes=doid)
API 5.9: https://biothings.ncats.io/semmed/query?fields=prevented_by (POST -d q=C0023473,C1292772&scopes=umls)
API 1.1: https://pending.biothings.io/DISEASES/query?fields=DISEASES.associatedWith (POST -d q=DOID:8552&scopes=DISEASES.doid)
API 5.13: https://biothings.ncats.io/semmed/query?fields=negatively_regulated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 5.3: https://biothings.ncats.io/semmed/query?fields=disrupts (POST -d q=C0023473,C1292772&scopes=umls)
API 5.5: https://biothings.ncats.io/semmed/query?fields=derives_from (POST -d q=C0023473,C1292772&scopes=umls)
API 5.2: https://biothings.ncats.io/semmed/query?fields=disrupted_by (POST -d q=C0023473,C1292772&scopes=umls)
API 5.6: https://biothings.ncats.io/semmed/query?fields=physically_interacts_with (POST -d q=C0023473,C1292772&scopes=umls)
API 5.7: https://biothings.ncats.io/semmed/query?fields=positively_regulated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 5.8: https://biothings.ncats.io/semmed/query?fields=negatively_regulates (POST -d q=C0023473,C1292772&scopes=umls)
API 5.4: https://biothings.ncats.io/semmed/query?fields=affects (POST -d q=C0023473,C1292772&scopes=umls)
API 5.12: https://biothings.ncats.io/semmed/query?fields=affected_by (POST -d q=C0023473,C1292772&scopes=umls)
API 5.10: https://biothings.ncats.io/semmed/query?fields=caused_by (POST -d q=C0023473,C1292772&scopes=umls)
API 5.11: https://biothings.ncats.io/semmed/query?fields=treated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 5.15: https://biothings.ncats.io/semmed/query?fields=coexists_with (POST -d q=C0023473,C1292772&scopes=umls)
API 5.14: https://biothings.ncats.io/semmed/query?fields=related_to (POST -d q=C0023473,C1292772&scopes=umls)
API 3.1: https://automat.renci.org/pharos/disease/gene/MONDO:0011996
API 4.1: https://automat.renci.org/cord19_scigraph_v2/disease/gene/MONDO:0011996
API 6.1: https://automat.renci.org/cord19_scibite_v2/disease/gene/MONDO:0011996
API 7.1: https://automat.renci.org/hetio/disease/gene/MONDO:0011996
==== Step #3: Output normalization ====
API 5.1 semmed_disease: No hits
API 5.2 semmed_disease: 26 hits
API 5.3 semmed_disease: No hits
API 8.1 cord_disease: 146 hits
API 5.4 semmed_disease: No hits
API 5.5 semmed_disease: No hits
API 5.6 semmed_disease: No hits
API 5.7 semmed_disease: No hits
API 2.1 mydisease: 52 hits
API 5.8 semmed_disease: No hits
API 4.1 scigraph: 3 hits
API 5.9 semmed_disease: 7 hits
API 1.1 DISEASES: 3 hits
API 5.10 semmed_disease: 90 hits
API 5.11 semmed_disease: 133 hits
API 5.12 semmed_disease: 65 hits
API 3.1 pharos: 7 hits
API 7.1 hetio: No hits
API 5.13 semmed_disease: No hits
API 5.14 semmed_disease: 550 hits
API 5.15 semmed_disease: No hits
API 6.1 scibite: 12 hits
After id-to-object translation, BTE retrieved 750 unique objects.
==========
========== QUERY #2 -- fetch all Gene entities linked to 'imatinib' ==========
==========
==== Step #1: Query path planning ====
Because imatinib is of type 'ChemicalSubstance', BTE will query our meta-KG for APIs that can take 'ChemicalSubstance' as input and 'Gene' as output
BTE found 9 apis:
API 1. chembio(1 API call)
API 2. hmdb(1 API call)
API 3. ctd(2 API calls)
API 4. pharos(1 API call)
API 5. scigraph(1 API call)
API 6. scibite(1 API call)
API 7. semmed_chemical(13 API calls)
API 8. cord_chemical(1 API call)
API 9. mychem(3 API calls)
==== Step #2: Query path execution ====
NOTE: API requests are dispatched in parallel, so the list of APIs below is ordered by query time.
API 3.1: http://ctdbase.org/tools/batchQuery.go?inputType=chem&report=genes_curated&format=json&inputTerms=C097613
API 3.2: http://ctdbase.org/tools/batchQuery.go?inputType=chem&report=genes_curated&format=json&inputTerms=D000068877
API 9.3: https://mychem.info/v1/query?fields=drugbank.targets (POST -d q=DB00619&scopes=drugbank.id)
API 8.5: https://biothings.ncats.io/semmedchemical/query?fields=related_to (POST -d q=C0935989&scopes=umls)
API 7.1: https://biothings.ncats.io/cord_chemical/query?fields=associated_with (POST -d q=CHEBI:45783&scopes=chebi)
API 8.1: https://biothings.ncats.io/semmedchemical/query?fields=positively_regulated_by (POST -d q=C0935989&scopes=umls)
API 8.4: https://biothings.ncats.io/semmedchemical/query?fields=produced_by (POST -d q=C0935989&scopes=umls)
API 8.7: https://biothings.ncats.io/semmedchemical/query?fields=disrupted_by (POST -d q=C0935989&scopes=umls)
API 8.11: https://biothings.ncats.io/semmedchemical/query?fields=produces (POST -d q=C0935989&scopes=umls)
API 8.8: https://biothings.ncats.io/semmedchemical/query?fields=affected_by (POST -d q=C0935989&scopes=umls)
API 8.10: https://biothings.ncats.io/semmedchemical/query?fields=negatively_regulated_by (POST -d q=C0935989&scopes=umls)
API 9.1: https://mychem.info/v1/query?fields=drugbank.enzymes (POST -d q=DB00619&scopes=drugbank.id)
API 9.2: https://mychem.info/v1/query?fields=drugcentral.bioactivity (POST -d q=CHEMBL941,CHEMBL1642&scopes=chembl.molecule_chembl_id)
API 8.12: https://biothings.ncats.io/semmedchemical/query?fields=negatively_regulates (POST -d q=C0935989&scopes=umls)
API 8.2: https://biothings.ncats.io/semmedchemical/query?fields=coexists_with (POST -d q=C0935989&scopes=umls)
API 8.9: https://biothings.ncats.io/semmedchemical/query?fields=physically_interacts_with (POST -d q=C0935989&scopes=umls)
API 8.6: https://biothings.ncats.io/semmedchemical/query?fields=affects (POST -d q=C0935989&scopes=umls)
API 8.13: https://biothings.ncats.io/semmedchemical/query?fields=positively_regulates (POST -d q=C0935989&scopes=umls)
API 8.3: https://biothings.ncats.io/semmedchemical/query?fields=disrupts (POST -d q=C0935989&scopes=umls)
API 2.1: https://automat.renci.org/hmdb/chemical_substance/gene/CHEBI:45783
API 1.1: https://automat.renci.org/chembio/chemical_substance/gene/CHEBI:45783
API 4.1: https://automat.renci.org/pharos/chemical_substance/gene/CHEBI:45783
API 6.1: https://automat.renci.org/cord19_scibite_v2/chemical_substance/gene/CHEBI:45783
API 5.1: https://automat.renci.org/cord19_scigraph_v2/chemical_substance/gene/CHEBI:45783
==== Step #3: Output normalization ====
API 8.1 semmed_chemical: 39 hits
API 8.2 semmed_chemical: 138 hits
API 9.1 mychem: 9 hits
API 8.3 semmed_chemical: No hits
API 8.4 semmed_chemical: 12 hits
API 8.5 semmed_chemical: No hits
API 9.2 mychem: 80 hits
API 8.6 semmed_chemical: No hits
API 8.7 semmed_chemical: No hits
API 3.1 ctd: No hits
API 3.2 ctd: 199 hits
API 1.1 chembio: No hits
API 8.8 semmed_chemical: No hits
API 8.9 semmed_chemical: 300 hits
API 8.10 semmed_chemical: 38 hits
API 8.11 semmed_chemical: No hits
API 4.1 pharos: 6 hits
API 6.1 scibite: 8 hits
API 7.1 cord_chemical: 172 hits
API 9.3 mychem: 9 hits
API 8.12 semmed_chemical: 171 hits
API 2.1 hmdb: No hits
API 8.13 semmed_chemical: 98 hits
API 5.1 scigraph: 3 hits
After id-to-object translation, BTE retrieved 722 unique objects.
==========
========== Final assembly of results ==========
==========
BTE found 255 unique intermediate nodes connecting 'chronic myelogenous leukemia' and 'imatinib'
If you look through the query log above, the API "biolink" and "dgidb" are no longer querid.
In [11]:
reg.refine_api_list(["semmed_chemical", "semmed_disease"])
In [12]:
reg.show_all_apis()
Out[12]:
['semmed_chemical', 'semmed_disease']
In [13]:
fc = FindConnection(input_obj=cml, output_obj=imatinib, intermediate_nodes='Gene', registry=reg)
fc.connect(verbose=True)
==========
========== QUERY PARAMETER SUMMARY ==========
==========
BTE will find paths that join 'chronic myelogenous leukemia' and 'imatinib'. Paths will have 1 intermediate node.
Intermediate node #1 will have these type constraints: Gene
==========
========== QUERY #1 -- fetch all Gene entities linked to 'chronic myelogenous leukemia' ==========
==========
==== Step #1: Query path planning ====
Because chronic myelogenous leukemia is of type 'Disease', BTE will query our meta-KG for APIs that can take 'Disease' as input and 'Gene' as output
BTE found 1 apis:
API 1. semmed_disease(15 API calls)
==== Step #2: Query path execution ====
NOTE: API requests are dispatched in parallel, so the list of APIs below is ordered by query time.
API 1.1: https://biothings.ncats.io/semmed/query?fields=positively_regulates (POST -d q=C0023473,C1292772&scopes=umls)
API 1.8: https://biothings.ncats.io/semmed/query?fields=negatively_regulates (POST -d q=C0023473,C1292772&scopes=umls)
API 1.3: https://biothings.ncats.io/semmed/query?fields=disrupts (POST -d q=C0023473,C1292772&scopes=umls)
API 1.5: https://biothings.ncats.io/semmed/query?fields=derives_from (POST -d q=C0023473,C1292772&scopes=umls)
API 1.7: https://biothings.ncats.io/semmed/query?fields=positively_regulated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 1.6: https://biothings.ncats.io/semmed/query?fields=physically_interacts_with (POST -d q=C0023473,C1292772&scopes=umls)
API 1.9: https://biothings.ncats.io/semmed/query?fields=prevented_by (POST -d q=C0023473,C1292772&scopes=umls)
API 1.13: https://biothings.ncats.io/semmed/query?fields=negatively_regulated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 1.2: https://biothings.ncats.io/semmed/query?fields=disrupted_by (POST -d q=C0023473,C1292772&scopes=umls)
API 1.11: https://biothings.ncats.io/semmed/query?fields=treated_by (POST -d q=C0023473,C1292772&scopes=umls)
API 1.15: https://biothings.ncats.io/semmed/query?fields=coexists_with (POST -d q=C0023473,C1292772&scopes=umls)
API 1.4: https://biothings.ncats.io/semmed/query?fields=affects (POST -d q=C0023473,C1292772&scopes=umls)
API 1.14: https://biothings.ncats.io/semmed/query?fields=related_to (POST -d q=C0023473,C1292772&scopes=umls)
API 1.10: https://biothings.ncats.io/semmed/query?fields=caused_by (POST -d q=C0023473,C1292772&scopes=umls)
API 1.12: https://biothings.ncats.io/semmed/query?fields=affected_by (POST -d q=C0023473,C1292772&scopes=umls)
==== Step #3: Output normalization ====
API 1.1 semmed_disease: No hits
API 1.2 semmed_disease: 26 hits
API 1.3 semmed_disease: No hits
API 1.4 semmed_disease: No hits
API 1.5 semmed_disease: No hits
API 1.6 semmed_disease: No hits
API 1.7 semmed_disease: No hits
API 1.8 semmed_disease: No hits
API 1.9 semmed_disease: 7 hits
API 1.10 semmed_disease: 90 hits
API 1.11 semmed_disease: 133 hits
API 1.12 semmed_disease: 65 hits
API 1.13 semmed_disease: No hits
API 1.14 semmed_disease: 550 hits
API 1.15 semmed_disease: No hits
After id-to-object translation, BTE retrieved 617 unique objects.
==========
========== QUERY #2 -- fetch all Gene entities linked to 'imatinib' ==========
==========
==== Step #1: Query path planning ====
Because imatinib is of type 'ChemicalSubstance', BTE will query our meta-KG for APIs that can take 'ChemicalSubstance' as input and 'Gene' as output
BTE found 1 apis:
API 1. semmed_chemical(13 API calls)
==== Step #2: Query path execution ====
NOTE: API requests are dispatched in parallel, so the list of APIs below is ordered by query time.
API 1.4: https://biothings.ncats.io/semmedchemical/query?fields=produced_by (POST -d q=C0935989&scopes=umls)
API 1.1: https://biothings.ncats.io/semmedchemical/query?fields=positively_regulated_by (POST -d q=C0935989&scopes=umls)
API 1.10: https://biothings.ncats.io/semmedchemical/query?fields=negatively_regulated_by (POST -d q=C0935989&scopes=umls)
API 1.7: https://biothings.ncats.io/semmedchemical/query?fields=disrupted_by (POST -d q=C0935989&scopes=umls)
API 1.5: https://biothings.ncats.io/semmedchemical/query?fields=related_to (POST -d q=C0935989&scopes=umls)
API 1.8: https://biothings.ncats.io/semmedchemical/query?fields=affected_by (POST -d q=C0935989&scopes=umls)
API 1.11: https://biothings.ncats.io/semmedchemical/query?fields=produces (POST -d q=C0935989&scopes=umls)
API 1.13: https://biothings.ncats.io/semmedchemical/query?fields=positively_regulates (POST -d q=C0935989&scopes=umls)
API 1.9: https://biothings.ncats.io/semmedchemical/query?fields=physically_interacts_with (POST -d q=C0935989&scopes=umls)
API 1.6: https://biothings.ncats.io/semmedchemical/query?fields=affects (POST -d q=C0935989&scopes=umls)
API 1.12: https://biothings.ncats.io/semmedchemical/query?fields=negatively_regulates (POST -d q=C0935989&scopes=umls)
API 1.2: https://biothings.ncats.io/semmedchemical/query?fields=coexists_with (POST -d q=C0935989&scopes=umls)
API 1.3: https://biothings.ncats.io/semmedchemical/query?fields=disrupts (POST -d q=C0935989&scopes=umls)
==== Step #3: Output normalization ====
API 1.1 semmed_chemical: 39 hits
API 1.2 semmed_chemical: 138 hits
API 1.3 semmed_chemical: No hits
API 1.4 semmed_chemical: 12 hits
API 1.5 semmed_chemical: No hits
API 1.6 semmed_chemical: No hits
API 1.7 semmed_chemical: No hits
API 1.8 semmed_chemical: No hits
API 1.9 semmed_chemical: 300 hits
API 1.10 semmed_chemical: 38 hits
API 1.11 semmed_chemical: No hits
API 1.12 semmed_chemical: 171 hits
API 1.13 semmed_chemical: 98 hits
After id-to-object translation, BTE retrieved 410 unique objects.
==========
========== Final assembly of results ==========
==========
BTE found 176 unique intermediate nodes connecting 'chronic myelogenous leukemia' and 'imatinib'
If you look through the query log above, BTE is only querying "semmed_chemical" and "semmed_disease" now.
Content source: biothings/biothings_explorer
Similar notebooks: