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bedrock.bio

open_targets.evidence_impc

import bedrock_bio as bb

rel = bb.load_table('open_targets.evidence_impc')

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()
targetId id targetFromSourceId diseaseFromSourceMappedId targetInModelMgiId diseaseFromSourceId biologicalModelGeneticBackground biologicalModelAllelicComposition diseaseFromSource resourceScore ... datasourceId datatypeId qualityControls diseaseId publicationDate evidenceDate score directionOnTrait directionOnTarget version
0 ENSG00000125965 000515759568498d1e5370d217149960aa85cd84 ENSG00000125965 MONDO_0015229 MGI:95688 OMIM:615986 involves: BALB/cJ Gdf5<bp-3J>/Gdf5<bp-3J> Bardet-Biedl Syndrome 9 46.29 ... impc animal_model [] MONDO_0015229 1977-07-01 1977-07-01 0.4629 risk LoF 26.09
1 ENSG00000159216 002849358288947298dcf009ab3173c8f4a31566 ENSG00000159216 MONDO_0007572 MGI:99852 OMIM:263400 involves: 129S4/SvJae * C57BL/6J Runx1<tm1Sata>/Runx1<tm1Sata> Erythrocytosis, Familial, 2 50.74 ... impc animal_model [] MONDO_0007572 1996-01-01 1996-01-01 0.5074 risk LoF 26.09
2 ENSG00000158813 002bcbc2c5acb85324a843b40a476b69e435e9b8 ENSG00000158813 MONDO_0018094 MGI:1195272 OMIM:193510 involves: 129 Eda<Ta-J>/Y Waardenburg Syndrome, Type 2A 48.72 ... impc animal_model [] MONDO_0018094 2023-02-11 2023-02-11 0.4872 risk LoF 26.09
3 ENSG00000125965 002e2b5df0b3efce02f76348c45ed17f0f0f933b ENSG00000125965 MONDO_0015437 MGI:95688 ORPHA:1445 Swiss albino stock Gdf5<bp>/Gdf5<bp> Ring Chromosome 21 Syndrome 45.85 ... impc animal_model [] MONDO_0015437 1966-01-01 1966-01-01 0.4585 risk LoF 26.09
4 ENSG00000102678 002ea0b8f26cb9ba95eafa67c84ac0a186875341 ENSG00000102678 MONDO_0010243 MGI:104723 ORPHA:2571 involves: C57BL/6J Fgf9<Aca12>/Fgf9<+> X-Linked Immunoneurologic Disorder 42.59 ... impc animal_model [] MONDO_0010243 2011-08-17 2011-08-17 0.4259 risk LoF 26.09

Description

Section titled “Description”

Disease-target evidence based on mouse knock-out models, where mouse phenotypes are mapped to human diseases by PhenoDigm algorithm.

Data provided by IMPC [Target-Disease]

Partitions

Section titled “Partitions”

Not partitioned.

Schema

Section titled “Schema”
Column Type Description
targetId TEXT Open Targets target identifier
id TEXT Identifer of the disease/target evidence
targetFromSourceId TEXT Target ID in resource of origin (accepted sources include Ensembl gene ID, Uniprot ID, gene symbol), only capital letters are accepted
diseaseFromSourceMappedId TEXT Mapped Open Targets disease identifier
targetInModelMgiId TEXT Target MGI ID in animal model [bioregistry:mgi]
diseaseFromSourceId TEXT Disease identifier from the original source
biologicalModelGeneticBackground TEXT Genetic background of the model organism
biologicalModelAllelicComposition TEXT Allelic composition of the model organism
diseaseFromSource TEXT Disease label from the original source
resourceScore DOUBLE Score provided by datasource indicating strength of target-disease association
targetInModel TEXT Target name/synonym in animal model
targetInModelEnsemblId TEXT Target Ensembl ID in animal model [bioregistry:ensembl]
diseaseModelAssociatedModelPhenotypes STRUCT(id TEXT, label TEXT)[] Phenotypes observed in genetically modified animal models
diseaseModelAssociatedHumanPhenotypes STRUCT(id TEXT, label TEXT)[] Human phenotypes equivalent to those observed in animal models
literature TEXT[] List of PubMed or preprint reference identifiers
biologicalModelId TEXT Identifier of the biological model (eg. in MGI)
datasourceId TEXT Identifer of the evidence source
datatypeId TEXT Type of the evidence
qualityControls TEXT[] Evidence quality flags
diseaseId TEXT Open Targets disease identifier
publicationDate TEXT Date of the earliest publication supporting the evidence
evidenceDate TEXT Earliest data for the evidence
score DOUBLE Score of the evidence reflecting the strength of the disease/target relationship
directionOnTrait TEXT Predicted direction of effect on the trait
directionOnTarget TEXT Gain or loss of function effect of the evidence on the target resulting from genetic variants, pharmacological modulation, or other perturbations
version TEXT Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.