Ewas Atlas Tools#

Configuration File: ewas_atlas_tools.json Tool Type: Local Tools Count: 5

This page contains all tools defined in the ewas_atlas_tools.json configuration file.

Available Tools#

EWASAtlas_get_probe (Type: EWASAtlasTool)#

Get every curated epigenome-wide association study (EWAS) result reported for one Illumina CpG pr…

EWASAtlas_get_probe tool specification

Tool Information:

  • Name: EWASAtlas_get_probe

  • Type: EWASAtlasTool

  • Description: Get every curated epigenome-wide association study (EWAS) result reported for one Illumina CpG probe from EWAS Atlas: the traits it was associated with, direction of the methylation change, the study and PubMed ID, plus the probe’s hg19 position, CpG-island context and nearby genes. Example: probe_id=’cg05575921’ (AHRR, the strongest known smoking-methylation signal, 100+ associations). Source: EWAS Atlas (NGDC/CNCB), curated independently of the EWAS Catalog, so it is the fallback when EWASCatalog_* tools fail (ewascatalog.org has answered HTTP 503 since at least 2026-10-05).

Parameters:

  • probe_id (string) (required) Illumina 450K/EPIC CpG probe ID, e.g. ‘cg05575921’.

  • limit ([‘integer’, ‘null’]) (optional) Max associations to return, 1-500. Default 50.

Example Usage:

query = {
    "name": "EWASAtlas_get_probe",
    "arguments": {
        "probe_id": "example_value"
    }
}
result = tu.run(query)

EWASAtlas_get_publication (Type: EWASAtlasTool)#

Get the epigenome-wide association studies (EWAS) that EWAS Atlas curated from one publication, b…

EWASAtlas_get_publication tool specification

Tool Information:

  • Name: EWASAtlas_get_publication

  • Type: EWASAtlasTool

  • Description: Get the epigenome-wide association studies (EWAS) that EWAS Atlas curated from one publication, by PubMed ID: title, DOI, date, and for each study the reported trait, probes with direction and p-value, and cohorts. Example: pmid=’29535343’.

Parameters:

  • pmid (string) (required) PubMed ID, e.g. ‘29535343’.

  • limit ([‘integer’, ‘null’]) (optional) Max associations per study to return, 1-1000. Default 50.

Example Usage:

query = {
    "name": "EWASAtlas_get_publication",
    "arguments": {
        "pmid": "example_value"
    }
}
result = tu.run(query)

EWASAtlas_get_study (Type: EWASAtlasTool)#

Get one curated epigenome-wide association study (EWAS) from EWAS Atlas by its study ID: reported…

EWASAtlas_get_study tool specification

Tool Information:

  • Name: EWASAtlas_get_study

  • Type: EWASAtlasTool

  • Description: Get one curated epigenome-wide association study (EWAS) from EWAS Atlas by its study ID: reported trait, case/control groups, the probes it reported with direction and p-value, and each cohort’s size, tissue, platform and demographics. Study IDs (ES#####) come from EWASAtlas_get_probe, EWASAtlas_search_by_gene or EWASAtlas_get_publication. Example: study_id=’ES00033’ (body mass index).

Parameters:

  • study_id (string) (required) EWAS Atlas study ID, e.g. ‘ES00033’.

  • limit ([‘integer’, ‘null’]) (optional) Max associations to return, 1-1000. Default 100.

Example Usage:

query = {
    "name": "EWASAtlas_get_study",
    "arguments": {
        "study_id": "example_value"
    }
}
result = tu.run(query)

EWASAtlas_search_by_gene (Type: EWASAtlasTool)#

Find the CpG probes annotated to a gene in EWAS Atlas and the curated epigenome-wide association …

EWASAtlas_search_by_gene tool specification

Tool Information:

  • Name: EWASAtlas_search_by_gene

  • Type: EWASAtlasTool

  • Description: Find the CpG probes annotated to a gene in EWAS Atlas and the curated epigenome-wide association study (EWAS) results reported for each, with a count of the most frequently reported traits across the gene. Probes are ordered by how many associations they have. Example: gene_symbol=’AHRR’. Heavily studied genes take 10-20 s. Source: EWAS Atlas (NGDC/CNCB), curated independently of the EWAS Catalog, so it is the fallback when EWASCatalog_* tools fail (ewascatalog.org has answered HTTP 503 since at least 2026-10-05).

Parameters:

  • gene_symbol (string) (required) HGNC gene symbol, e.g. ‘AHRR’ or ‘F2RL3’.

  • limit ([‘integer’, ‘null’]) (optional) Max probes to return, 1-500. Default 50.

  • max_associations_per_probe ([‘integer’, ‘null’]) (optional) Max associations listed under each probe, 1-200. Default 10 (association_count always gives the full number).

Example Usage:

query = {
    "name": "EWASAtlas_search_by_gene",
    "arguments": {
        "gene_symbol": "example_value"
    }
}
result = tu.run(query)

EWASAtlas_search_by_region (Type: EWASAtlasTool)#

List the CpG probes with curated epigenome-wide association study (EWAS) results inside a genomic…

EWASAtlas_search_by_region tool specification

Tool Information:

  • Name: EWASAtlas_search_by_region

  • Type: EWASAtlasTool

  • Description: List the CpG probes with curated epigenome-wide association study (EWAS) results inside a genomic window (GRCh37/hg19, at most 1 Mb) from EWAS Atlas, with the traits reported for each probe and the most frequent traits in the window. Example: chromosome=’5’, start=373000, end=374000 (the AHRR smoking locus). A 1 Mb window takes about 20 s. Source: EWAS Atlas (NGDC/CNCB), curated independently of the EWAS Catalog, so it is the fallback when EWASCatalog_* tools fail (ewascatalog.org has answered HTTP 503 since at least 2026-10-05).

Parameters:

  • chromosome (string) (required) Chromosome: 1-22, X or Y (‘chr’ prefix accepted).

  • start (integer) (required) Window start, GRCh37/hg19, 1-based.

  • end (integer) (required) Window end, GRCh37/hg19. end - start must be at most 1,000,000.

  • limit ([‘integer’, ‘null’]) (optional) Max probes to return, 1-500. Default 50.

  • max_associations_per_probe ([‘integer’, ‘null’]) (optional) Max associations listed under each probe, 1-200. Default 10 (association_count always gives the full number).

Example Usage:

query = {
    "name": "EWASAtlas_search_by_region",
    "arguments": {
        "chromosome": "example_value",
        "start": 10,
        "end": 10
    }
}
result = tu.run(query)