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Bioenergy Research Center Data Schema

This schema defines the structure for biomolecular and -omics datasets, capturing essential metadata including investigators, affiliations, data citation, organism details, analysis type, and more. These are datasets generated by the Bioenergy Research Centers (BRCs), including CABBI, CBI, GLBRC, and JBEI.

URI: https://w3id.org/brc/brc_schema

Name: brc_schema

Classes

Class Description
BRCOrganization An organization involved in the dataset
Dataset A body of structured information describing some topic or topics of interest
DatasetCollection Container class for defining a collection of datasets
Funding Funding source for the dataset
Individual An individual involved in the dataset
        Contributor An individual who contributed to the dataset in some manner, not necessarily ...
MediaFile Metadata about a particular file or off-site resource associated with a datas...
MediaSet Metadata about a group of files associated with this dataset
OntologyAnnotation A structured reference to an ontology term used to annotate a dataset
Organism An organism studied in the dataset
Plasmid Description of plasmid or other molecular vector features
RelatedItem A related publication or item, including cited publications

Slots

Slot Description
abstract "A brief abstract summarizing the dataset
access_limitations Access limitation codes associated with this media set
active Indicates whether the dataset is active or inactive
additional_brcs Additional Bioenergy Research Center affiliations
affiliation Affiliation of the individual
alert Indicates whether availability of the dataset has encountered some inconsiste...
analysisType The type of analysis performed on the dataset
awardNumber Award number from the funding entity
awardTitle Title of the award
awardURI URI for the award
backbone Name of the backbone of the plasmid, e
bibliographicCitation Citation for the dataset
brc The primary Bioenergy Research Center affiliation
canonical_name Canonical label used for this term in its source ontology
category Category of the dataset
checksum Checksum value for the file, if known
conference_date Date or date range for the conference
conference_information General conference information related to the dataset
conference_location Location of the conference
conference_title Title of the conference
conference_type Code representing the type of conference-related work
contributors Contributors to the dataset who are not necessarily authors
contributorType The contribution type
country_publication Human-readable country of publication, if available
country_publication_code Country code for the publication venue, if applicable
creator List of creators involved in the dataset, where one must be the primary conta...
dataset_url URL for the dataset landing page
datasetName "Name of a overall dataset to which this data entry belongs
datasets List of datasets in the collection
datasetType High-level type of the main content of the dataset
date The date the dataset was created or published
date_added Date the media set was first created
date_file_added Date this media file was created
date_file_updated Date this media file was last modified
date_updated Date the media set was most recently modified
date_valid_end Date when the media association ended, if applicable
description A detailed description of the dataset
document_page_count Number of pages detected in the media set, if applicable
duration_seconds Duration in seconds for audio-visual media
email Email address of the individual
file_size_bytes File size in bytes, if applicable
files Files associated with this media set
funding Funding source(s) for the dataset
fundingOrganization Details of the funding entity
has_related_ids "Related identifiers for the dataset
host Host organism for the plasmid, e
id Unique identifier for the dataset, assigned prior to inclusion in bioenergy
identifier Unique identifier for the dataset
issue Issue number for a journal or other venue, if applicable
journal_issn International Standard Serial Number for the journal, if known
journal_license_url URL for information regarding the journal license
journal_name Name of the journal publishing this information
journal_open_access_flag Indicates whether the journal is open access
journal_type Specific sub-type of the journal article
keywords Keywords associated with the dataset
media Media bundles and file-package metadata associated with the dataset
media_file_id Unique identifier for this media file
media_id Unique identifier for this media set
media_source Primary source of the media set
media_title Optional title for the media set
media_type Type code for this media file
mime_type MIME type description for the primary media content
name Name of the individual
NCBITaxID NCBI taxonomy ID for the organism
ontology_annotations Structured ontology term annotations that align this dataset with controlled ...
orcid ORCID for the individual
organizationName Name of the organization
ori Origin of replication for the plasmid, e
osti_id OSTI record identifier linked to this media set, if any
parent_media_file_id Identifier of the parent media file, if this file is derived
parentOrganization Higher-level parent of this organization
pdf_version PDF version, if this file is a PDF
pdfa_conformance PDF/A conformance level, if applicable
pdfa_part PDF/A part number, if applicable
pdfua_part PDF/UA part number, if applicable
plasmid_features Description of plasmid features, if applicable
preferred_name Preferred display name for this ontology annotation in BRC metadata
primaryContact Indicates if the individual is a primary contact
promoters Promoters for the plasmid, e
publication_date_text Textual representation of the publication date, if used
publisher_information Publisher-specific information, if applicable
relatedItem Related publications or items
relatedItemIdentifier Identifier or URL for the related item
relatedItemType Type of the related item, e
replicates_in Organism(s) in which the plasmid replicates
repository The repository where the dataset is stored
revision Revision number of this media set
ror_id ROR identifier for the organization
schema_version Version of the schema used for the collection
scientificName Scientific name of the organism
selection_markers Selection markers for the plasmid, e
species Species information for the organism(s) studied
strains Name of one or more strains of the organism
subtitle_tracks Number of subtitle tracks for audio-visual media
term_id Ontology term identifier in CURIE format, such as BERVO:8000232
theme High-level theme areas for the dataset
title The title of the dataset
topic High-level topic area for the dataset
url Local file name or off-site URL
video_tracks Number of video tracks for audio-visual media
volume Volume number for a journal or book, if applicable
wikidata_id Wikidata identifier for the organization

Enumerations

Enumeration Description
AnalysisType Type of analysis performed on the dataset
BRCEnum Bioenergy Research Center affiliation
CitedItemType Type of cited item, e
ContributorTypeCodes The type of contribution
DatasetThemeEnum High-level theme area for the dataset
DatasetTopicEnum High-level topic area for the dataset
DatasetTypeCodes High-level type of the main content of the dataset, following OSTI categories
RepositoryEnum Repository where the dataset is stored

Types

Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
RorIdentifier Identifier from Research Organization Registry
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE
WikidataIdentifier Identifier from Wikidata open knowledge base

Subsets

Subset Description
Deprecated These repositories are deprecated and may have been replaced by newer reposit...
GeneralPurpose These repositories are general-purpose data repositories, suitable for a wide...
Metabolomics These repositories specialize in metabolomics data, such as small molecule pr...
Proteomics These repositories specialize in proteomics data, such as mass spectrometry a...
RequiresLoginAll These repositories require a login to access and download any data
RequiresLoginForDownload These repositories allow public access to view metadata about datasets, but r...
RequiresLoginSome These repositories may require a login to access and download some data, depe...
Sequence These repositories specialize in sequence data, such as genomic, transcriptom...
Structure These repositories specialize in structural data, such as protein structures ...
Text These repositories specialize in text-based data, such as protocols, publicat...