from kgforge.core import KnowledgeGraphForge
token="eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICI5T0R3Z1JSTFVsTTJHbFphVDZjVklnenJsb0lzUWJmbTBDck1icXNjNHQ4In0.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.E8HLmA9pCcNY0A-6HVbK-IAeyBA1ZAicZcSgW8JBhmZj2vyuz03MHTTenePqfXEXP2iQos67ssXZA2sAyfpCDrokt9amtkmrn10hRgetX4q-5-VTZfBhyW7XE2WjHsPjh-c9FiPbpP1HwwjnWQTsnaDeXOQPmUJ6K7FfbOYdqcRAXBP4gPyuqTzdPMRhZIPb-e45Yr7sLYa2Fh5Npq2_ILEspPUP1JFPrvecVMri-8fa8eu3vd4LYR4CRnjAZd50IgIhBDAjP80V5siV8kJrGMoY0b4J5KHXhVhovgZjwHPVdishXuQVAyyhqCQAFACB_WzL6mSp2LXkGW91H0A88A"
A configuration file is needed in order to create a KnowledgeGraphForge session. A configuration can be generated using the notebook 00-Initialization.ipynb.
forge = KnowledgeGraphForge("/Users/mfsy/dev/apps/forked/nexus-forge/examples/configurations/prod-forge-nexus-entity-resolver.yml",
token=token,
bucket="dke/myverycoolproj",
endpoint="https://staging.nexus.ocp.bbp.epfl.ch/v1",
debug=True)
https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fbluebrain.github.io%2Fnexus%2Fcontexts%2Fresource.json/source https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/neurosciencegraph/datamodels/_/https%3A%2F%2Fbluebrain.github.io%2Fnexus%2Fcontexts%2Fresource.json/source 200 https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fbbp.neuroshapes.org https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/neurosciencegraph/datamodels/_/https%3A%2F%2Fbbp.neuroshapes.org 200 https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fneuroshapes.org https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/neurosciencegraph/datamodels/_/https%3A%2F%2Fneuroshapes.org 200 https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fbluebrain.github.io%2Fnexus%2Fcontexts%2Fresource.json/source https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/neurosciencegraph/datamodels/_/https%3A%2F%2Fbluebrain.github.io%2Fnexus%2Fcontexts%2Fresource.json/source 200 https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fbluebrain.github.io%2Fnexus%2Fcontexts%2Fresource.json/source https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/bbp/agents/_/https%3A%2F%2Fbluebrain.github.io%2Fnexus%2Fcontexts%2Fresource.json/source 200
from kgforge.version import __version__
__version__
'0.5.3.dev4+g33bc591.d20210331'
from kgforge.core.commons.strategies import ResolvingStrategy
With the forge.resolvers()
method, the user can inspect the available scopes, resolvers, and targets.
A scope is linked to a data source (directory, store, or URL). Each scope will have at least one resolver, which is an implementation of the Forge Resolver. A resolver can have multiple targets, and it will delimitate the resolution within the resolver's scope.
forge.resolvers()
Available scopes: - agent : - resolver: AgentResolver - targets: agents - entity : - resolver: EntityLinkerElasticSearch - targets: terms - ontology : - resolver: OntologyResolver - targets: terms
res= forge.resolve("somato", scope="ontology", type="Class", strategy=ResolvingStrategy.ALL_MATCHES)
[('somato', [{'id': 'http://api.brain-map.org/api/v2/data/Structure/1006', 'type': 'Class', 'label': 'Primary somatosensory area, trunk, layer 1', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-tr1', 'prefLabel': 'Primary somatosensory area, trunk, layer 1', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1026', 'type': 'Class', 'label': 'Primary somatosensory area, upper limb, layer 6b', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ul6b', 'prefLabel': 'Primary somatosensory area, upper limb, layer 6b', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1030', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 1', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll1', 'prefLabel': 'Primary somatosensory area, lower limb, layer 1', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1035', 'type': 'Class', 'label': 'Supplemental somatosensory area, layer 4', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSs4', 'prefLabel': 'Supplemental somatosensory area, layer 4', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1038', 'type': 'Class', 'label': 'Primary somatosensory area, barrel field, layer 6a', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-bfd6a', 'prefLabel': 'Primary somatosensory area, barrel field, layer 6a', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1047', 'type': 'Class', 'label': 'Primary somatosensory area, barrel field, layer 4', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-bfd4', 'prefLabel': 'Primary somatosensory area, barrel field, layer 4', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1062', 'type': 'Class', 'label': 'Primary somatosensory area, barrel field, layer 6b', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-bfd6b', 'prefLabel': 'Primary somatosensory area, barrel field, layer 6b', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1128', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 5', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll5', 'prefLabel': 'Primary somatosensory area, lower limb, layer 5', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/113', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 2/3', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll2/3', 'prefLabel': 'Primary somatosensory area, lower limb, layer 2/3', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/12993', 'type': 'Class', 'label': 'Somatosensory areas, layer 1', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SS1', 'prefLabel': 'Somatosensory areas, layer 1', 'subClassOf': 'nsg:BrainRegion'}])] ddddd ('somato', [{'id': 'http://api.brain-map.org/api/v2/data/Structure/1006', 'type': 'Class', 'label': 'Primary somatosensory area, trunk, layer 1', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-tr1', 'prefLabel': 'Primary somatosensory area, trunk, layer 1', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1026', 'type': 'Class', 'label': 'Primary somatosensory area, upper limb, layer 6b', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ul6b', 'prefLabel': 'Primary somatosensory area, upper limb, layer 6b', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1030', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 1', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll1', 'prefLabel': 'Primary somatosensory area, lower limb, layer 1', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1035', 'type': 'Class', 'label': 'Supplemental somatosensory area, layer 4', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSs4', 'prefLabel': 'Supplemental somatosensory area, layer 4', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1038', 'type': 'Class', 'label': 'Primary somatosensory area, barrel field, layer 6a', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-bfd6a', 'prefLabel': 'Primary somatosensory area, barrel field, layer 6a', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1047', 'type': 'Class', 'label': 'Primary somatosensory area, barrel field, layer 4', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-bfd4', 'prefLabel': 'Primary somatosensory area, barrel field, layer 4', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1062', 'type': 'Class', 'label': 'Primary somatosensory area, barrel field, layer 6b', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-bfd6b', 'prefLabel': 'Primary somatosensory area, barrel field, layer 6b', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1128', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 5', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll5', 'prefLabel': 'Primary somatosensory area, lower limb, layer 5', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/113', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 2/3', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll2/3', 'prefLabel': 'Primary somatosensory area, lower limb, layer 2/3', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/12993', 'type': 'Class', 'label': 'Somatosensory areas, layer 1', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SS1', 'prefLabel': 'Somatosensory areas, layer 1', 'subClassOf': 'nsg:BrainRegion'}])
re = forge.resolve("EPFL", scope="agent", strategy=ResolvingStrategy.BEST_MATCH)
re
forge.as_dataframe(res)
id | type | label | definition | isDefinedBy | notation | prefLabel | subClassOf | |
---|---|---|---|---|---|---|---|---|
0 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, lower limb, layer 5 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-ll5 | Primary somatosensory area, lower limb, layer 5 | nsg:BrainRegion | |
1 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, lower limb, layer 2/3 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-ll2/3 | Primary somatosensory area, lower limb, layer 2/3 | nsg:BrainRegion | |
2 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, lower limb, layer 1 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-ll1 | Primary somatosensory area, lower limb, layer 1 | nsg:BrainRegion | |
3 | http://api.brain-map.org/api/v2/data/Structure... | Class | Supplemental somatosensory area, layer 4 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSs4 | Supplemental somatosensory area, layer 4 | nsg:BrainRegion | |
4 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, barrel field, laye... | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-bfd6a | Primary somatosensory area, barrel field, laye... | nsg:BrainRegion | |
5 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, barrel field, layer 4 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-bfd4 | Primary somatosensory area, barrel field, layer 4 | nsg:BrainRegion | |
6 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, barrel field, laye... | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-bfd6b | Primary somatosensory area, barrel field, laye... | nsg:BrainRegion | |
7 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, trunk, layer 1 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-tr1 | Primary somatosensory area, trunk, layer 1 | nsg:BrainRegion | |
8 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, upper limb, layer 6b | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-ul6b | Primary somatosensory area, upper limb, layer 6b | nsg:BrainRegion | |
9 | http://api.brain-map.org/api/v2/data/Structure... | Class | Somatosensory areas, layer 1 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SS1 | Somatosensory areas, layer 1 | nsg:BrainRegion |
To find resources using resolver, you can use regex expressions within the provided string.
Resolve a resource for female
in the terms.
result = forge.resolve(
["diabetes","covid-19"],
scope="entity",
target = "terms",
limit=10,
threshold=0.8,
strategy=ResolvingStrategy.EXACT_MATCH
)
[]
type(result)
NoneType
forge.as_dataframe(result["diabetes"])
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-14-356ff7b7f793> in <module> ----> 1 forge.as_dataframe(result["diabetes"]) TypeError: 'NoneType' object is not subscriptable
result = forge.resolve("0befef0a-134a-455f-8244-c09940fffee0",
scope="entity",
target = "terms",
limit=10,
threshold=1.0,
strategy=ResolvingStrategy.ALL_MATCHES
)
{ "size": 10, "_source": { "exclude": ["embedding"] }, "query": { "script_score": { "query": { "exists": { "field": "embedding" } }, "script": { "source": "doc['embedding'].size() == 0 ? 0 : (cosineSimilarity(params.queryVector, doc['embedding'])+1.0) / 2", "params": { "queryVector": [-0.06318674236536026, 0.017056960612535477, -0.05687783658504486, -0.04961063712835312, -0.055770013481378555, 0.07958485931158066, 0.11064236611127853, -0.10723460465669632, 0.12150656431913376, 0.06838510185480118, -0.16287577152252197, 0.0036786971613764763, -0.12537777423858643, 0.02500958926975727, 0.09008166939020157, 0.045686326920986176, 0.07828816771507263, -0.001064969110302627, 0.15681831538677216, 0.13517893850803375, -0.028591299429535866, -0.04068496450781822, 0.05460236594080925, 0.015284581109881401, 0.07718798518180847, 0.009188370779156685, -0.0941006988286972, 0.08962488174438477, -0.026030832901597023, 0.19158291816711426, 0.03038346767425537, 0.08494362235069275, -0.08508966863155365, 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-0.055352307856082916, -0.0033038537949323654, 0.08546634763479233, 0.0906103253364563, 0.0015061864396557212, -0.029740462079644203, -0.11008624732494354, 0.045565348118543625, 0.04666541516780853, 0.0706753060221672, 0.03676597401499748, -0.1258198618888855, 0.02330753207206726, 0.007685295306146145, 0.10492029041051865, -0.07350043952465057, 0.012367922812700272, -0.040422920137643814, 0.13253985345363617, -0.07163478434085846, 0.13930170238018036, 0.06291647255420685, 0.01020688097923994, 0.024039441719651222, 0.02229279838502407, 0.06631708145141602, 0.09703384339809418, 0.08566532284021378, 0.14827390015125275, -0.11922971904277802, 0.10077875852584839, 0.14910706877708435, 0.10825697332620621, 0.1725500524044037, 0.10821139067411423, -0.02815954200923443, -0.054691825062036514, 0.037509188055992126, 0.012780158780515194, 0.03460140898823738, 0.026123233139514923, 0.06865038722753525, -0.10310269892215729, -0.11820479482412338, 0.03926319256424904, 0.08443860709667206, 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'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2Fdf95cc4c-b99b-4e08-a8e8-b4a4fe722485/incoming', '_outgoing': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2Fdf95cc4c-b99b-4e08-a8e8-b4a4fe722485/outgoing'}, {'score': 0.69894576, '@id': 'https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/635b6cac-c948-45d1-b258-8d564738635f', '@type': 'http://schema.org/SoftwareAgent', 'name': 'random name 02b7437e-c1f7-401c-990f-cc09cab93125', 'version': '0.0.1', '_self': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F635b6cac-c948-45d1-b258-8d564738635f', '_constrainedBy': 'https://bluebrain.github.io/nexus/schemas/unconstrained.json', '_project': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/projects/dke/myverycoolproj', '_rev': 1, '_deprecated': False, '_createdAt': '2021-02-13T19:47:14.465959Z', '_createdBy': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/realms/bbp/users/sy', '_updatedAt': '2021-02-13T19:47:14.465959Z', '_updatedBy': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/realms/bbp/users/sy', '_incoming': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F635b6cac-c948-45d1-b258-8d564738635f/incoming', '_outgoing': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F635b6cac-c948-45d1-b258-8d564738635f/outgoing'}, {'score': 0.7779727, '@id': 'https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/9203e600-98de-42fe-aacc-152411970b5c', '@type': 'http://schema.org/SoftwareAgent', 'name': 'random name 02b7437e-c1f7-401c-990f-cc09cab93125', 'version': '0.0.1', '_self': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F9203e600-98de-42fe-aacc-152411970b5c', '_constrainedBy': 'https://bluebrain.github.io/nexus/schemas/unconstrained.json', '_project': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/projects/dke/myverycoolproj', '_rev': 1, '_deprecated': False, '_createdAt': '2021-02-13T19:47:15.100153Z', '_createdBy': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/realms/bbp/users/sy', '_updatedAt': '2021-02-13T19:47:15.100153Z', '_updatedBy': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/realms/bbp/users/sy', '_incoming': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F9203e600-98de-42fe-aacc-152411970b5c/incoming', '_outgoing': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F9203e600-98de-42fe-aacc-152411970b5c/outgoing'}, {'score': 0.7800082, '@id': 'https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/1e4bd1b0-e0dd-4cd7-9aad-70133eed6955', '@type': 'http://schema.org/SoftwareAgent', 'name': 'random name 02b7437e-c1f7-401c-990f-cc09cab93125', 'version': '0.0.1', '_self': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F1e4bd1b0-e0dd-4cd7-9aad-70133eed6955', '_constrainedBy': 'https://bluebrain.github.io/nexus/schemas/unconstrained.json', '_project': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/projects/dke/myverycoolproj', '_rev': 1, '_deprecated': False, '_createdAt': '2021-02-13T19:47:12.880466Z', '_createdBy': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/realms/bbp/users/sy', '_updatedAt': '2021-02-13T19:47:12.880466Z', '_updatedBy': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/realms/bbp/users/sy', '_incoming': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F1e4bd1b0-e0dd-4cd7-9aad-70133eed6955/incoming', '_outgoing': 'https://staging.nexus.ocp.bbp.epfl.ch/v1/resources/dke/myverycoolproj/_/https%3A%2F%2Fsandbox.bluebrainnexus.io%2Fv1%2Fresources%2Fdke%2Fmyverycoolproj%2F_%2Fhttps%3A%2F%2Fbbp.epfl.ch%2Fdke%2Fkgforge_tests%2F1e4bd1b0-e0dd-4cd7-9aad-70133eed6955/outgoing'}])
!ls ../../configurations/entitylinking-resolver/entitylinking-mapper-es.hjson
../../configurations/entitylinking-resolver/entitylinking-mapper-es.hjson
type(result)
list
result
[Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/cde04474-e9a1-4f36-8426-f6c6e316e9d0', type='http://schema.org/SoftwareAgent', score=0.67232597), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/c5c2d542-b589-45c5-9572-08978af21d84', type='http://schema.org/SoftwareAgent', score=0.67268145), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/0fc1e9cd-b67c-4876-acb9-8df458d63feb', type='http://schema.org/SoftwareAgent', score=0.68226916), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/96773bbd-0f02-4469-8388-01ed3979805a', type='http://schema.org/SoftwareAgent', score=0.68565005), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/1647a417-8f7a-46e0-99b4-21ce0b27e44a', type='http://schema.org/SoftwareAgent', score=0.6860905), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/df95cc4c-b99b-4e08-a8e8-b4a4fe722485', type='http://schema.org/SoftwareAgent', score=0.69775426), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/635b6cac-c948-45d1-b258-8d564738635f', type='http://schema.org/SoftwareAgent', score=0.69894576), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/9203e600-98de-42fe-aacc-152411970b5c', type='http://schema.org/SoftwareAgent', score=0.7779727), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/1e4bd1b0-e0dd-4cd7-9aad-70133eed6955', type='http://schema.org/SoftwareAgent', score=0.7800082), Resource(_last_action=None, _validated=False, _synchronized=False, _store_metadata=None, id='https://sandbox.bluebrainnexus.io/v1/resources/dke/myverycoolproj/_/https://bbp.epfl.ch/dke/kgforge_tests/0befef0a-134a-455f-8244-c09940fffee0', type='http://schema.org/SoftwareAgent', score=1.0)]
forge.as_dataframe(result)
id | type | score | |
---|---|---|---|
0 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.672326 |
1 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.672681 |
2 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.682269 |
3 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.685650 |
4 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.686091 |
5 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.697754 |
6 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.698946 |
7 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.777973 |
8 | https://sandbox.bluebrainnexus.io/v1/resources... | http://schema.org/SoftwareAgent | 0.780008 |
!ls ../../configurations/entitylinking-resolver/entitylinking-mapper.hjson
../../configurations/entitylinking-resolver/entitylinking-mapper.hjson
b = forge.resolve("somatosensory", scope="ontology", target="terms", strategy=ResolvingStrategy.ALL_MATCHES)
[{'id': 'http://api.brain-map.org/api/v2/data/Structure/1070', 'type': 'Class', 'label': 'Primary somatosensory area, barrel field, layer 5', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-bfd5', 'prefLabel': 'Primary somatosensory area, barrel field, layer 5', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1086', 'type': 'Class', 'label': 'Primary somatosensory area, trunk, layer 4', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-tr4', 'prefLabel': 'Primary somatosensory area, trunk, layer 4', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1090', 'type': 'Class', 'label': 'Supplemental somatosensory area, layer 5', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSs5', 'prefLabel': 'Supplemental somatosensory area, layer 5', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1094', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 4', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll4', 'prefLabel': 'Primary somatosensory area, lower limb, layer 4', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1102', 'type': 'Class', 'label': 'Primary somatosensory area, mouth, layer 6a', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-m6a', 'prefLabel': 'Primary somatosensory area, mouth, layer 6a', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1111', 'type': 'Class', 'label': 'Primary somatosensory area, trunk, layer 5', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-tr5', 'prefLabel': 'Primary somatosensory area, trunk, layer 5', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/1128', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 5', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll5', 'prefLabel': 'Primary somatosensory area, lower limb, layer 5', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/113', 'type': 'Class', 'label': 'Primary somatosensory area, lower limb, layer 2/3', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-ll2/3', 'prefLabel': 'Primary somatosensory area, lower limb, layer 2/3', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/2', 'type': 'Class', 'label': 'Primary somatosensory area, mouth, layer 6b', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-m6b', 'prefLabel': 'Primary somatosensory area, mouth, layer 6b', 'subClassOf': 'nsg:BrainRegion'}, {'id': 'http://api.brain-map.org/api/v2/data/Structure/201', 'type': 'Class', 'label': 'Primary somatosensory area, barrel field, layer 2/3', 'isDefinedBy': 'http://bbp.epfl.ch/neurosciencegraph/ontologies/mba', 'notation': 'SSp-bfd2/3', 'prefLabel': 'Primary somatosensory area, barrel field, layer 2/3', 'subClassOf': 'nsg:BrainRegion'}]
forge.as_dataframe(b)
id | type | label | definition | isDefinedBy | notation | prefLabel | subClassOf | |
---|---|---|---|---|---|---|---|---|
0 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, barrel field, layer 5 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-bfd5 | Primary somatosensory area, barrel field, layer 5 | nsg:BrainRegion | |
1 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, trunk, layer 4 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-tr4 | Primary somatosensory area, trunk, layer 4 | nsg:BrainRegion | |
2 | http://api.brain-map.org/api/v2/data/Structure... | Class | Supplemental somatosensory area, layer 5 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSs5 | Supplemental somatosensory area, layer 5 | nsg:BrainRegion | |
3 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, lower limb, layer 4 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-ll4 | Primary somatosensory area, lower limb, layer 4 | nsg:BrainRegion | |
4 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, mouth, layer 6a | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-m6a | Primary somatosensory area, mouth, layer 6a | nsg:BrainRegion | |
5 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, trunk, layer 5 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-tr5 | Primary somatosensory area, trunk, layer 5 | nsg:BrainRegion | |
6 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, lower limb, layer 5 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-ll5 | Primary somatosensory area, lower limb, layer 5 | nsg:BrainRegion | |
7 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, lower limb, layer 2/3 | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-ll2/3 | Primary somatosensory area, lower limb, layer 2/3 | nsg:BrainRegion | |
8 | http://api.brain-map.org/api/v2/data/Structure/2 | Class | Primary somatosensory area, mouth, layer 6b | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-m6b | Primary somatosensory area, mouth, layer 6b | nsg:BrainRegion | |
9 | http://api.brain-map.org/api/v2/data/Structure... | Class | Primary somatosensory area, barrel field, laye... | http://bbp.epfl.ch/neurosciencegraph/ontologie... | SSp-bfd2/3 | Primary somatosensory area, barrel field, laye... | nsg:BrainRegion |
print(forge.resolve("female", scope="terms", type="Class"))
Resolving a resource for EPFL
in the entities.
epfl = forge.resolve("Malcher Lopez", scope="agent", strategy=ResolvingStrategy.ALL_MATCHES)
[{'id': 'https://bbp.epfl.ch/neurosciencegraph/data/persons/287b93c3-40f9-42d2-9d77-b16bc536eb8a', 'type': ['Person', 'Agent'], 'familyName': 'Malcher Lopez', 'givenName': 'Renato', 'name': None}]
type(epfl)
kgforge.core.resource.Resource
forge.as_dataframe([epfl])
id | type | familyName | givenName | |
---|---|---|---|---|
0 | https://bbp.epfl.ch/neurosciencegraph/data/per... | [Person, Agent] | Malcher Lopez | Renato |
print(epfl)
{ id: https://bbp.epfl.ch/neurosciencegraph/data/persons/287b93c3-40f9-42d2-9d77-b16bc536eb8a type: [ Person Agent ] familyName: Malcher Lopez givenName: Renato }
p = forge.resolve("Malcher Lopez", scope="agent", target="agents")
[{'id': 'https://bbp.epfl.ch/neurosciencegraph/data/persons/287b93c3-40f9-42d2-9d77-b16bc536eb8a', 'type': ['Agent', 'Person'], 'familyName': 'Malcher Lopez', 'givenName': 'Renato', 'name': None}]
print(forge.resolve("EPFL", scope="entities", type="Organization"))
Different strategies can be used to resolve terms.
In the following example, the missing 'e' at the end is intended for the demonstration.
text = "mal"
The default applied strategy is strategy=ResolvingStrategy.BEST_MATCH
.
print(forge.resolve(text, scope="terms"))
print(forge.resolve(text, scope="terms", strategy=ResolvingStrategy.EXACT_MATCH))
The result list is ordered by matching relevance.
results = forge.resolve(text, scope="terms", strategy=ResolvingStrategy.ALL_MATCHES, limit=3)
type(results)
len(results)
type(results[0])
print(*results, sep="\n")