Datasets

fanta.bio

Website

fanta.bio (Functional genome ANnotations with Transcriptional Activities) is a database of functional genome annotations focused on cis-regulatory elements, such as promoters and enhancers. It integrates regulatory elements identified using CAGE data and their transcriptional activities across cell and tissue types with transcription factor binding sites and genomic variants to support studies of gene regulation.

Dataset specifications

Tags
Genome Human Expression
Provenance Original
Registration Submitted
Data provider
  • Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences
Creator
  • Takeya KasukawaRiken Center for Integrative Medical Sciences, Riken
  • Hideya KawajiResearch Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science
  • Yuki MoriyaNational Institute of Genetics
Issued 2026-09-03
Licenses
  • https://creativecommons.org/licenses/by-sa/4.0/deed.en
Version Ver. 1.2.1
Download /website/download/#fantabio
SPARQL Endpoint https://rdfportal.org/primary/sparql

Dataset statistics

Triples
630117311
Subjects
179827083
Properties
21
Objects
184580098
Classes
19

SPARQL example queries

Example 1

Run on Endpoint 
# Retrieve cis-regulatory elements associated with a given gene symbol
# Example: ALDH2 in humans

PREFIX fantao: <http://fanta.bio/ontology/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX tax: <http://identifiers.org/taxonomy/>

SELECT DISTINCT ?cre ?cre_id ?cre_name ?activity_class
WHERE {
  VALUES ?symbol { "ALDH2" }

  ?cre a fantao:CisRegulatoryElement ;
       obo:RO_0002162 tax:9606 ;
       dct:identifier ?cre_id ;
       rdfs:label ?cre_name ;
       sio:SIO_000395 ?regulated_entity .

  ?regulated_entity rdfs:label ?symbol .

  OPTIONAL {
    VALUES ?activity_class { fantao:PLA fantao:ELA }
    ?cre a ?activity_class .
  }
}
ORDER BY ?cre_id ?activity_class

Example 2

Run on Endpoint 
# Retrieve cis-regulatory elements overlapping a genomic interval
# Example: chromosome 12, positions 111766000–111767000, GRCh38

PREFIX fantao: <http://fanta.bio/ontology/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>

SELECT DISTINCT ?cre ?cre_id ?cre_name ?begin ?end
WHERE {
  VALUES (?reference ?query_start ?query_end) {
    (<http://identifiers.org/hco/12/GRCh38> 111766000 111767000)
  }

  ?cre a fantao:CisRegulatoryElement ;
       dct:identifier ?cre_id ;
       rdfs:label ?cre_name ;
       faldo:location ?location .

  ?location faldo:begin ?begin_position ;
            faldo:end ?end_position .

  ?begin_position faldo:position ?begin ;
                  faldo:reference ?reference .

  ?end_position faldo:position ?end ;
                faldo:reference ?reference .

  FILTER(?begin <= ?query_end && ?end >= ?query_start)
}
ORDER BY ?begin ?end ?cre_id

Example 3

Run on Endpoint 
# Retrieve ChIP-Atlas annotations and supporting experiments for a CRE
# Return antigen names, external IDs, experiment IDs, and Q-scores

PREFIX fanta: <http://fanta.bio/cre/>
PREFIX fantao: <http://fanta.bio/ontology/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sio: <http://semanticscience.org/resource/>

SELECT DISTINCT
  ?antigen_symbol ?antigen ?experiment_id ?experiment_link ?q_score
WHERE {
  VALUES ?cre { fanta:FCHS_104205 }

  ?cre fantao:hasOverlappedAnnotation ?annotation .

  ?annotation a fantao:ChipAtlasAntigen ;
              rdfs:label ?antigen_symbol ;
              rdfs:seeAlso ?antigen ;
              fantao:hasExperiment ?experiment .

  ?experiment dct:identifier ?experiment_id ;
              rdfs:seeAlso ?experiment_link ;
              sio:SIO_000216 ?measurement .

  ?measurement a fantao:Qscore ;
               sio:SIO_000300 ?q_score .
}
ORDER BY ?antigen_symbol DESC(?q_score) ?experiment_id

Example 4

Run on Endpoint 
# Retrieve nearest-TSS annotations for CREs associated with a given gene
# Distances are reported in base pairs as stored in the dataset

PREFIX fantao: <http://fanta.bio/ontology/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX tax: <http://identifiers.org/taxonomy/>

SELECT DISTINCT ?cre_id ?cre_name ?transcript ?distance
WHERE {
  VALUES ?symbol { "ALDH2" }

  ?cre a fantao:CisRegulatoryElement ;
       obo:RO_0002162 tax:9606 ;
       dct:identifier ?cre_id ;
       rdfs:label ?cre_name ;
       sio:SIO_000395 ?regulated_entity ;
       fantao:hasTSS ?tss .

  ?regulated_entity rdfs:label ?symbol .

  ?tss a fantao:NearestTSS ;
       sio:SIO_000216 ?measurement .

  ?measurement a fantao:TSSDistance ;
               sio:SIO_000300 ?distance .

  OPTIONAL { ?tss rdfs:seeAlso ?transcript . }
}
ORDER BY ?cre_id ?distance ?transcript

Example 5

Run on Endpoint 
# Retrieve FANTOM5 CAGE peaks overlapping a given cis-regulatory element

PREFIX fanta: <http://fanta.bio/cre/>
PREFIX fantao: <http://fanta.bio/ontology/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?cre_id ?cre_name ?cage_peak_id ?cage_peak_name
WHERE {
  VALUES ?cre { fanta:FCHS_104205 }

  ?cre dct:identifier ?cre_id ;
       rdfs:label ?cre_name ;
       fantao:hasOverlappedAnnotation ?annotation .

  ?annotation a fantao:Fantom5CagePeak ;
              dct:identifier ?cage_peak_id ;
              rdfs:label ?cage_peak_name .
}
ORDER BY ?cage_peak_id

Schema diagram

Schema diagram for fantabio
Schema diagram for fantabio