Class: Bundle¶
A bundle representing a set of genome annotation files, organised in sub-collections. Metadata has been harmonised in line with the "FAIRification of Genomic Annotations" data model.
URI: https://w3id.org/fga-wg/schema/bundle/Bundle
classDiagram
class Bundle
click Bundle href "../Bundle/"
Bundle : analyses
Bundle --> "*" Analysis : analyses
click Analysis href "../Analysis/"
Bundle : bundle_metadata
Bundle --> "1" BundleMetadata : bundle_metadata
click BundleMetadata href "../BundleMetadata/"
Bundle : donors
Bundle --> "*" Donor : donors
click Donor href "../Donor/"
Bundle : experiments
Bundle --> "*" Experiment : experiments
click Experiment href "../Experiment/"
Bundle : file_collections
Bundle --> "*" FileCollection : file_collections
click FileCollection href "../FileCollection/"
Bundle : files
Bundle --> "*" File : files
click File href "../File/"
Bundle : samples
Bundle --> "*" Sample : samples
click Sample href "../Sample/"
Bundle : studies
Bundle --> "*" Study : studies
click Study href "../Study/"
Example¶
Example JSON
{
"bundle_metadata": {
"bundle_deposit": {
"deposit_first_created": "2025-07-01T12:36:00Z",
"deposit_id": "doi:10.1234/zenodo.12345678",
"deposit_last_changed": "2025-07-01T12:36:00Z",
"deposit_versioned_id": "doi:10.1234/zenodo.12345679"
},
"bundle_description": "The metadata contents of the International Human Epigenome Consortium (IHEC) data portal, harmonised to follow the metadata model developed by the \"FAIRification of Genomic Annotations WG\" in the Research Data Alliance (RDA), enhanced with metadata from original sources.",
"bundle_input_sources": [
{
"inputsource_external_ref": "https://epigenomesportal.ca/ihec/",
"qualified_relation": "prov:wasDerivedFrom"
}
],
"bundle_label": "IHEC data portal metadata, harmonised to the FGA-WG model.",
"bundle_ontology_versions": [
{
"namespace": "edam",
"ontology_url": "http://edamontology.org/EDAM.owl",
"versioned_ontology_url": "http://edamontology.org/EDAM_1.21.owl"
},
{
"namespace": "cl",
"ontology_url": "http://purl.obolibrary.org/obo/cl.owl",
"versioned_ontology_url": "http://purl.obolibrary.org/obo/cl/releases/2020-05-21/cl.owl"
},
{
"namespace": "efo",
"ontology_url": "http://www.ebi.ac.uk/efo/efo.owl",
"versioned_ontology_url": "http://www.ebi.ac.uk/efo/releases/v3.21.0/efo.owl"
},
{
"namespace": "ncit",
"ontology_url": "http://purl.obolibrary.org/obo/ncit.owl",
"versioned_ontology_url": "http://purl.obolibrary.org/obo/ncit/releases/2020-07-17/ncit.owl"
},
{
"namespace": "obi",
"ontology_url": "http://purl.obolibrary.org/obo/obi.owl",
"versioned_ontology_url": "http://purl.obolibrary.org/obo/obi/2020-04-23/obi.owl"
},
{
"namespace": "so",
"ontology_url": "http://purl.obolibrary.org/obo/so.owl",
"versioned_ontology_url": "http://purl.obolibrary.org/obo/so/2020-08-20/so.owl"
},
{
"namespace": "uberon",
"ontology_url": "http://purl.obolibrary.org/obo/uberon.owl",
"versioned_ontology_url": "http://purl.obolibrary.org/obo/uberon/releases/2020-06-30/uberon.owl"
}
]
},
"analyses": [
{
"analysis_description": "ENCODE3 ChIP-seq pipeline on GRCH38 with replicated peak calling using MACS.",
"analysis_external_id": "encode:ENCAN718KHT",
"analysis_id": "analysis:ENCAN718KHT",
"analysis_input_sources": [
{
"biological_replicate_labels": [
"1",
"2"
],
"inputsource_ref": "experiment:ENCSR000DPJ",
"qualified_relation": "prov:wasInformedBy",
"technical_replicate_labels": [
"1_1",
"2_1"
]
},
{
"biological_replicate_labels": [
"1",
"2"
],
"date_of_retrieval": "2016-04-19",
"inputsource_external_ref": "https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15",
"qualified_relation": "https://bioschemas.org/FormalParameter",
"technical_replicate_labels": [
"1_1",
"2_1"
]
}
],
"analysis_label": "ENCODE3 ChIP-seq pipeline, GRCH38, replicated peak calling",
"analysis_main_tool": "biotools:macs",
"analysis_main_tool_version": "2.10",
"analysis_protocol": "https://www.encodeproject.org/documents/7009beb8-340b-4e71-b9db-53bb020c7fe2/@@download/attachment/ChIP-seq_pipeline_overview.pdf",
"analysis_study_ref": "study:S-EPMC7391744",
"analysis_type": {
"id": "edam:operation_3222",
"label": "Peak calling"
},
"analysis_workflow": "encode:ENCPL272XAE"
}
],
"donors": [
{
"donor_external_id": "biosamples:SAMN04284578",
"donor_id": "donor:ENCDO001AAA",
"sex": {
"id": "CARO:0000027",
"label": "male organism"
},
"species_taxon": {
"id": "NCBITaxon:9606",
"label": "Homo sapiens"
}
}
],
"experiments": [
{
"antibody_target": {
"id": "SO:0001707",
"label": "H3K9Me3"
},
"assay_type": {
"id": "obi:OBI_0000716",
"label": "ChIP-seq assay"
},
"biological_processes": [
{
"id": "GO:0140999",
"label": "histone H3K4 trimethyltransferase activity"
}
],
"design_description": "https://www.encodeproject.org/documents/92cd1386-ccad-450a-b5a6-ad49983e7e3f/@@download/attachment/wgEncodeUwHistone.release5.html.pdf",
"experiment_external_id": "encode:ENCSR000DPJ",
"experiment_id": "experiment:ENCSR000DPJ",
"experiment_label": "H3K9me3 ChIP-seq on human AG04450",
"experiment_samples": [
{
"biological_replicate_labels": [
"1",
"2"
],
"inputsource_ref": "sample:ENCBS004ENC",
"qualified_relation": "prov:used",
"technical_replicate_labels": [
"1_1",
"2_1"
]
}
],
"experiment_study_ref": "study:E-GEOD-35583",
"instrument": {
"id": "obi:OBI_0002128",
"label": "Illumina Genome Analyzer"
},
"library_layout": {
"id": "obi:OBI_0000736",
"label": "single fragment library"
},
"molecule_type": {
"id": "SO:0000991",
"label": "genomic_DNA"
}
}
],
"file_collections": [
{
"deposit_versioned_ref": "doi:10.1234/zenodo.12345679",
"filecollection_contact": {
"contact_id": "bioproject:PRJNA234466",
"email": "info@ihec-epigenomes.org",
"name": "International Human Epigenome Consortium"
},
"filecollection_description": "ENCODE dataset in the International Human Epigenome Consortium (IHEC) data portal, enhanced with metadata from the ENCODE data portal.",
"filecollection_id": "filecollection:ihec_encode",
"filecollection_input_sources": [
{
"inputsource_external_ref": "https://epigenomesportal.ca/ihec/grid.html?build=2020-10&assembly=4&institutions=4",
"qualified_relation": "prov:wasDerivedFrom",
"version": "2020-10"
},
{
"inputsource_external_ref": "https://www.encodeproject.org",
"qualified_relation": "prov:hadPrimarySource"
}
],
"filecollection_label": "IHEC data portal: ENCODE dataset"
}
],
"files": [
{
"access_methods": [
{
"access_method": "https",
"access_url": {
"url": "https://epigenomesportal.ca/tracks/ENCODE/hg38/87234.ENCODE.ENCBS004ENC.H3K9me3.peak_calls.bigBed"
}
},
{
"access_method": "https",
"access_url": {
"url": "https://www.encodeproject.org/files/ENCFF323LCS/@@download/ENCFF323LCS.bigBed"
}
},
{
"access_method": "s3",
"access_url": {
"url": "s3://encode-public/2016/11/13/efd4e74e-7875-4d13-9630-0085bc834f18/ENCFF323LCS.bigBed"
}
},
{
"access_method": "https",
"access_url": {
"url": "https://encode-public.s3.amazonaws.com/2016/11/13/efd4e74e-7875-4d13-9630-0085bc834f18/ENCFF323LCS.bigBed"
}
},
{
"access_method": "https",
"access_url": {
"url": "https://datasetencode.blob.core.windows.net/dataset/2016/11/13/efd4e74e-7875-4d13-9630-0085bc834f18/ENCFF323LCS.bigBed?sv=2019-10-10&si=prod&sr=c&sig=9qSQZo4ggrCNpybBExU8SypuUZV33igI11xw0P7rB3c%3D"
}
}
],
"checksums": [
{
"checksum": "535bc9628a1c5e5215226f9996e4eaca",
"checksum_type": "md5"
}
],
"created_time": "2016-11-13T17:42:04.385801+00:00",
"data_content": "replicated peaks",
"drs_uri": "drs://drs.example.org/ENCFF323LCS",
"file_description": "H3K9me3 ChIP-seq replicated peaks on human (hg38) AG04450 (Fibroblast derived cell line).",
"file_external_id": "encode:ENCFF323LCS",
"file_id": "file:ENCFF323LCS",
"file_input_sources": [
{
"biological_replicate_labels": [
"1",
"2"
],
"inputsource_ref": "analysis:ENCAN718KHT",
"qualified_relation": "prov:wasGeneratedBy",
"technical_replicate_labels": [
"1_1",
"2_1"
]
}
],
"file_label": "H3K9me3 ChIP-seq replicated peaks, GRCh38, AG04450",
"file_name": "87234.ENCODE.ENCBS004ENC.H3K9me3.peak_calls.bigBed",
"file_size": 5359719,
"file_type": {
"id": "edam:format_3004",
"label": "bigBed"
},
"file_version": "efd4e74e-7875-4d13-9630-0085bc834f18",
"filecollection_refs": [
"collection:ihec_encode"
],
"genome_assembly": "ga4gh:SC.EiFob05aCWgVU_B_Ae0cypnQut3cxUP1",
"mime_type": "application/octet-stream",
"quality_assessments": [
{
"assessment_details_url": "https://www.encodeproject.org/histone-chipseq-quality-metrics/70ae08dc-3edc-437f-a0a5-378c72e6269b/",
"assessment_method": "histone-chipseq-quality-metrics",
"assessment_values": {
"frip": 0.2931669095906483,
"nreads": 21018235,
"nreads_in_peaks": 6161851
}
}
],
"run_provenance": "encode:ENCAN718KHT",
"sequence_features": [
{
"id": "SO:0001707",
"label": "H3K9Me3"
}
],
"track_geometry": {
"elements_circular": false,
"elements_overlapping": false,
"has_edges": false,
"has_gaps": true,
"has_lengths": true,
"has_names": true,
"has_strands": false,
"has_values": true,
"lengths_constant": false,
"value_type": "multiple"
},
"updated_time": "2016-11-13T17:42:04.385801+00:00"
}
],
"samples": [
{
"biospecimen_classification": "cell line",
"cell_line": {
"id": "CLO:0034832",
"label": "AG04450 cell"
},
"donor_age": "W12",
"donor_clinical_information": "apparently healthy",
"donor_development_stage": {
"id": "UBERON:0000323",
"label": "late embryo"
},
"donor_organism_ref": "donor:ENCDO001AAA",
"organism_tissue": {
"id": "UBERON:0002048",
"label": "lung"
},
"other_biospecimen": [
{
"id": "UBERON:0002384",
"label": "connective tissue"
},
{
"id": "CL:0002320",
"label": "connective tissue cell"
},
{
"id": "CL:0000057",
"label": "fibroblast"
},
{
"id": "UBERON:0000925",
"label": "endoterm"
},
{
"id": "UBERON:0001004",
"label": "respiratory system"
}
],
"phenotype": {
"id": "PATO:0000461",
"label": "normal"
},
"sample_description": "Homo sapiens AG04450 cell line",
"sample_external_id": "encode:ENCBS004ENC",
"sample_id": "sample:ENCBS004ENC",
"sample_label": "Homo sapiens AG04450 cell line",
"sampling_protocol": "https://www.encodeproject.org/documents/3ed29dac-da67-47be-91b0-c9cad6a1b791/@@download/attachment/AG04450_Stam_protocol.pdf"
}
],
"studies": [
{
"project_external_ref": "bioproject:PRJNA63441",
"publications": [
"https://doi.org/10.1038/s41467-020-14743-w"
],
"study_abstract": "ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, and whole-genome STARR-seq on a number of data-rich ENCODE cell types. A key aspect of this annotation is comprehensive and experimentally derived networks of both transcription factors and RNA-binding proteins (TFs and RBPs). Cancer, a disease of system-wide dysregulation, is an ideal application for such a network-based annotation. Specifically, for cancer-associated cell types, we put regulators into hierarchies and measure their network change (rewiring) during oncogenesis. We also extensively survey TF-RBP crosstalk, highlighting how SUB1, a previously uncharacterized RBP, drives aberrant tumor expression and amplifies the effect of MYC, a well-known oncogenic TF. Furthermore, we show how our annotation allows us to place oncogenic transformations in the context of a broad cell space; here, many normal-to-tumor transitions move towards a stem-like state, while oncogene knockdowns show an opposing trend. Finally, we organize the resource into a coherent workflow to prioritize key elements and variants, in addition to regulators. We showcase the application of this prioritization to somatic burdening, cancer differential expression and GWAS. Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns, CRISPR-based editing, and luciferase assays demonstrate the value of the ENCODE resource.",
"study_contact": {
"contact_id": "orcid:0000-0002-9746-3719",
"email": "mark@gersteinlab.org",
"name": "Mark Gerstein"
},
"study_external_id": "biostudies:S-EPMC7391744",
"study_id": "study:S-EPMC7391744",
"study_title": "An integrative ENCODE resource for cancer genomics"
}
]
}
Slots¶
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| bundle_metadata | 1 BundleMetadata |
Top-level metadata about the bundle of genomic annotation files. | direct |
| donors | * Donor |
Information about the donors or complete organisms from which the samples were taken. | direct |
| experiments | * Experiment |
Information about sequencing experiments that have been carried out to generate the files. | direct |
| files | * File |
Information about particular genome annotation (and other relevant) files. | direct |
| file_collections | * FileCollection |
Information about collections of files contained in this dataset, each collection defined according to some selection criteria. | direct |
| analyses | * Analysis |
Information about computational processing and analyses that have been carried out to generate the files. | direct |
| samples | * Sample |
Information about the biospecimens/samples used as raw material for lab experiments. | direct |
| studies | * Study |
The scientific studies, i.e. units of research, within which experiments and/or analyses have been carried out. | direct |
Identifier and Mapping Information¶
Schema Source¶
- from schema: https://w3id.org/fga-wg/schema/bundle
Mappings¶
| Mapping Type | Mapped Value |
|---|---|
| self | https://w3id.org/fga-wg/schema/bundle/Bundle |
| native | https://w3id.org/fga-wg/schema/bundle/Bundle |
LinkML Source¶
Direct¶
name: Bundle
description: A bundle representing a set of genome annotation files, organised in
sub-collections. Metadata has been harmonised in line with the "FAIRification of
Genomic Annotations" data model.
from_schema: https://w3id.org/fga-wg/schema/bundle
slots:
- bundle_metadata
- donors
- experiments
- files
- file_collections
- analyses
- samples
- studies
Induced¶
name: Bundle
description: A bundle representing a set of genome annotation files, organised in
sub-collections. Metadata has been harmonised in line with the "FAIRification of
Genomic Annotations" data model.
from_schema: https://w3id.org/fga-wg/schema/bundle
attributes:
bundle_metadata:
name: bundle_metadata
description: Top-level metadata about the bundle of genomic annotation files.
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
owner: Bundle
domain_of:
- Bundle
range: BundleMetadata
required: true
inlined: true
donors:
name: donors
description: Information about the donors or complete organisms from which the
samples were taken.
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
owner: Bundle
domain_of:
- Bundle
range: Donor
multivalued: true
inlined: true
inlined_as_list: true
experiments:
name: experiments
description: Information about sequencing experiments that have been carried out
to generate the files.
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
owner: Bundle
domain_of:
- Bundle
range: Experiment
multivalued: true
inlined: true
inlined_as_list: true
files:
name: files
description: Information about particular genome annotation (and other relevant)
files.
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
owner: Bundle
domain_of:
- Bundle
range: File
multivalued: true
inlined: true
inlined_as_list: true
file_collections:
name: file_collections
description: Information about collections of files contained in this dataset,
each collection defined according to some selection criteria.
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
owner: Bundle
domain_of:
- Bundle
range: FileCollection
multivalued: true
inlined: true
inlined_as_list: true
analyses:
name: analyses
description: Information about computational processing and analyses that have
been carried out to generate the files.
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
owner: Bundle
domain_of:
- Bundle
range: Analysis
multivalued: true
inlined: true
inlined_as_list: true
samples:
name: samples
description: Information about the biospecimens/samples used as raw material for
lab experiments.
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
owner: Bundle
domain_of:
- Bundle
range: Sample
multivalued: true
inlined: true
inlined_as_list: true
studies:
name: studies
description: The scientific studies, i.e. units of research, within which experiments
and/or analyses have been carried out.
from_schema: https://w3id.org/fga-wg/schema/bundle
rank: 1000
owner: Bundle
domain_of:
- Bundle
range: Study
multivalued: true
inlined: true
inlined_as_list: true