Resolving Strategies¶

Example on how to use resolving strategies

In [1]:

import os
import json

from kgforge.core import KnowledgeGraphForge
from kgforge.specializations.resources import Dataset

In [2]:

import getpass
TOKEN = getpass.getpass()

In [3]:

BUCKET = "dke/kgforge"
forge = KnowledgeGraphForge("../use-cases/prod-forge-nexus.yml",
 bucket=BUCKET,
 token=TOKEN
 )

List available resolvers¶

In [4]:

forge.resolvers(output='dict')

Out[4]:

{'agent': {'agents': {'bucket': 'bbp/agents', 'filters': None}},
 'ontology': {'terms': {'bucket': 'neurosciencegraph/datamodels',
   'filters': None},
  'CellType': {'bucket': 'neurosciencegraph/datamodels',
   'filters': {'subClassOf*.id': 'BrainCellType'}},
  'BrainRegion': {'bucket': 'neurosciencegraph/datamodels',
   'filters': {'subClassOf*.id': 'BrainRegion'}},
  'Species': {'bucket': 'neurosciencegraph/datamodels',
   'filters': {'has_rank.id': 'http://purl.obolibrary.org/obo/NCBITaxon_species'}},
  'Strain': {'bucket': 'neurosciencegraph/datamodels',
   'filters': {'has_rank.id': 'http://purl.obolibrary.org/obo/NCBITaxon_strain'}}}}

In [5]:

case_insensitive = forge.resolve('Pv+', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH')

In [6]:

exact = forge.resolve('PV+', scope='ontology', strategy='EXACT_MATCH')

In [7]:

assert case_insensitive == exact

Try with a similar string, but other characters¶

In [8]:

similar = forge.resolve('pv-', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH')

In [9]:

similar1 = forge.resolve('pv:', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH')

In [10]:

assert similar is None
assert similar1 is None

Combine spaces and other characters¶

In [11]:

print(forge.resolve('229_l6 it ctx', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH'))

{
    id: https://bbp.epfl.ch/ontologies/core/ttypes/229_L6_IT_CTX
    type: Class
    label: 229_L6 IT CTX
    subClassOf:
    [
        https://bbp.epfl.ch/ontologies/core/ttypes/L4_5_6_IT_Car3
        https://bbp.epfl.ch/ontologies/core/celltypes/NeuronTranscriptomicType
    ]
}

In [12]:

print(forge.resolve('264_L5/6 np CTX', scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH'))

{
    id: https://bbp.epfl.ch/ontologies/core/ttypes/264_L5_6_NP_CTX
    type: Class
    label: 264_L5/6 NP CTX
    subClassOf:
    [
        https://bbp.epfl.ch/ontologies/core/ttypes/L5_6_NP_CTX
        https://bbp.epfl.ch/ontologies/core/celltypes/NeuronTranscriptomicType
    ]
}

Resolve from a specific ontology¶

This is particularly useful when two entities have a similar acronym like the example below, where there is a brain region called BAC, and a electrical cell type labelled bAC.

Without any specification, it will return the first result in the list of matches (no priority or ranking).

List available ontologies to resolve from¶

In [5]:

list(forge.resolvers(output='dict')['ontology'].keys()) # terms is for resolving accross all ontologies

Out[5]:

['terms', 'CellType', 'BrainRegion', 'Species', 'Strain']

In [14]:

from kgforge.core.commons.strategies import ResolvingStrategy

print(forge.resolve("bAC", scope="ontology", target="terms", 
                    strategy=ResolvingStrategy.EXACT_CASE_INSENSITIVE_MATCH))

{
    id: http://uri.interlex.org/base/ilx_0738199
    type: Class
    label: bAC
    notation: bAC
    prefLabel: Burst accommodating electrical type
    subClassOf:
    [
        nsg:EType
        bmo:NeuronElectricalType
    ]
}

In [15]:

print(forge.resolve("bAC", scope="ontology", target="CellType", strategy="EXACT_CASE_INSENSITIVE_MATCH"))

{
    id: http://uri.interlex.org/base/ilx_0738199
    type: Class
    label: bAC
    notation: bAC
    prefLabel: Burst accommodating electrical type
    subClassOf:
    [
        nsg:EType
        bmo:NeuronElectricalType
    ]
}

In [16]:

print(forge.resolve("bAC", scope="ontology", target="BrainRegion", strategy="EXACT_CASE_INSENSITIVE_MATCH"))

{
    id: http://api.brain-map.org/api/v2/data/Structure/287
    type: Class
    label: Bed nucleus of the anterior commissure
    isDefinedBy: http://bbp.epfl.ch/neurosciencegraph/ontologies/core/brainregion
    notation: BAC
    prefLabel: Bed nucleus of the anterior commissure
    subClassOf: nsg:BrainRegion
}

In [6]:

print(forge.resolve("rat", scope="ontology", target="Species", strategy="EXACT_CASE_INSENSITIVE_MATCH"))

{
    id: http://purl.obolibrary.org/obo/NCBITaxon_10116
    type: Class
    label: Rattus norvegicus
    altLabel: rat
    atlasRelease:
    {
        id: https://bbp.epfl.ch/neurosciencegraph/data/4906ab85-694f-469d-962f-c0174e901885
    }
    subClassOf:
    [
        nsg:Species
        NCBITaxon:10114
    ]
}

In [7]:

print(forge.resolve("Wistar", scope="ontology", target="Strain", strategy="EXACT_CASE_INSENSITIVE_MATCH"))

{
    id: http://www.ebi.ac.uk/efo/EFO_0001342
    type: Class
    label: Wistar
    altLabel:
    [
        Rats, Wistar
        Wistar rat
        Wistar rats
    ]
    atlasRelease:
    {
        id: https://bbp.epfl.ch/neurosciencegraph/data/4906ab85-694f-469d-962f-c0174e901885
    }
    subClassOf: NCBITaxon:10116
}

Ensuring one label¶

In [18]:

resource = forge.resolve("AOB_MC", scope="ontology", target="terms", strategy="EXACT_MATCH")
assert isinstance(resource.label, str)

In [19]:

excitatory = forge.resolve("exc", scope='ontology', strategy='EXACT_CASE_INSENSITIVE_MATCH')
assert isinstance(excitatory.label, str)

In [20]:

print(excitatory)

{
    id: https://neuroshapes.org/ExcitatoryNeuron
    type: Class
    label: Excitatory Neuron
    notation: Exc
    prefLabel: Excitatory Neuron
    subClassOf: bmo:NeurotransmitterType
}