open_targets.evidence_europepmc

Python

In [1]:

import bedrock_bio as bb

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

df = rel.limit(5).pl()  # Polars
df = rel.limit(5).df()  # Pandas
df.head()

Out[1]:

	id	targetFromSourceId	diseaseFromSourceMappedId	datasourceId	datatypeId	resourceScore	literature	textMiningSentences	pmcIds	publicationYear	qualityControls	diseaseId	targetId	publicationDate	evidenceDate	score	version
0	000092b275b75d97ab2fb377374bdb9acae99dae	ENSG00000213921	MONDO_0017361	europepmc	literature	4.0	[38036973]	[{'dEnd': 36, 'dStart': 33, 'section': 'abstra...	[PMC10691010]	2023	[]	MONDO_0017361	ENSG00000213921	2023-11-30	2023-11-30	0.04	26.09
1	0000fa7936a8cf5a3779f797a902e3ae6518e8d7	ENSG00000104518	EFO_0007006	europepmc	literature	2.0	[39684254]	[{'dEnd': 205, 'dStart': 195, 'section': 'disc...	[PMC11640976]	2024	[]	EFO_0007006	ENSG00000104518	2024-11-22	2024-11-22	0.02	26.09
2	00023e66dea210f9dcb9d105c1aa34c96b7e87bd	ENSG00000189077	MONDO_0006573	europepmc	literature	3.0	[PPR311142]	[{'dEnd': 239, 'dStart': 226, 'section': 'abst...	<NA>	2021	[]	MONDO_0006573	ENSG00000189077	2021-04-12	2021-04-12	0.03	26.09
3	00029df95ff72e1db05c0461b14cbb882816efc0	ENSG00000112715	MONDO_0005070	europepmc	literature	2.0	[32156035]	[{'dEnd': 175, 'dStart': 170, 'section': 'othe...	[PMC7151145]	2020	[]	MONDO_0005070	ENSG00000112715	2020-03-07	2020-03-07	0.02	26.09
4	0003ef8cbf2ff1048a2e5f4a672d1670dd77b19c	ENSG00000004846	MONDO_0004948	europepmc	literature	6.0	[22044138]	[{'dEnd': 208, 'dStart': 205, 'section': 'abst...	<NA>	2011	[]	MONDO_0004948	ENSG00000004846	2011-12-07	2011-12-07	0.06	26.09

R

In [1]:

library(bedrockbio)

lf <- load_table("open_targets.evidence_europepmc")
df <- head(lf, 5) |> collect()

head(df)

Out[1]:

Sample output (5 rows, showing 8 of 17 columns)
   id                       | targetFromSourceId | diseaseFromSourceMappedId | datasourceId | datatypeId | resourceScore | publicationYear | diseaseId
   ------------------------ | ------------------ | ------------------------- | ------------ | ---------- | ------------- | --------------- | -------------
0  000092b275b75d97ab2fb37… | ENSG00000213921    | MONDO_0017361             | europepmc    | literature | 4             | 2023            | MONDO_0017361
1  0000fa7936a8cf5a3779f79… | ENSG00000104518    | EFO_0007006               | europepmc    | literature | 2             | 2024            | EFO_0007006
2  00023e66dea210f9dcb9d10… | ENSG00000189077    | MONDO_0006573             | europepmc    | literature | 3             | 2021            | MONDO_0006573
3  00029df95ff72e1db05c046… | ENSG00000112715    | MONDO_0005070             | europepmc    | literature | 2             | 2020            | MONDO_0005070
4  0003ef8cbf2ff1048a2e5f4… | ENSG00000004846    | MONDO_0004948             | europepmc    | literature | 6             | 2011            | MONDO_0004948

Description

Disease-target evidence derived from literature mining provided by Europe PMC [Target-Disease]

Partitions

Not partitioned.

Schema

Column	Type	Description
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
datasourceId	TEXT	Identifer of the evidence source
datatypeId	TEXT	Type of the evidence
resourceScore	DOUBLE	Score provided by datasource indicating strength of target-disease association
literature	TEXT[]	List of PubMed or preprint reference identifiers
textMiningSentences	STRUCT(dEnd BIGINT, dStart BIGINT, section TEXT, tEnd BIGINT, tStart BIGINT, text TEXT)[]	Sentences of a publication supporting the disease/target relationship
pmcIds	TEXT[]	List of PubMed Central identifiers of full text publication
publicationYear	BIGINT	Year of publication
qualityControls	TEXT[]	Evidence quality flags
diseaseId	TEXT	Open Targets disease identifier
targetId	TEXT	Open Targets target 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
version	TEXT	Open Targets Platform release version (major.minor), e.g. 26.09. Added during ingest.