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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. As of version 0.1.4, this schema imports the LinkML version of the E-Link schema (see osti_schema.yaml) to promote further interoperability with OSTI records.

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

Name: brc_schema

Classes

Class Description
Affiliation An affiliation for a person, such as an organization or institution
AuditLog Indicates status and information about back-end processing on a given metadat...
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
Geolocation
Identifier Values of various identifying numbers, such as DOE contract number, product n...
Individual An individual involved in the dataset
        Contributor An individual who contributed to the dataset in some manner, not necessarily ...
MediaFile Metadata information pertaining to a particular media resource associated wit...
MediaSet Metadata about files associated with this product
Organism An organism studied in the dataset
Organization Describes a particular organization associated with the bibliographic record
OrganizationIdentifier One or more identifying numbers or references associated with this organizati...
Person Information about a particular person involved in the production or maintenan...
Plasmid Description of plasmid or other molecular vector features
Point
Record Defines the bibliographic metadata about a particular work or record
Records A list of Record metadata
RelatedIdentifier Identifies other resources that are related in some manner to this record
RelatedItem A related publication or item, including cited publications

Slots

Slot Description
access_limitation_other Additional information about access/distribution limitation for this record, ...
access_limitations Access/distribution limitation codes to describe the distribution rules and l...
active Indicates whether the dataset is active or inactive
added_by E-Link user ID that initially entered this record
added_by_email E-Link account email address initially entering this record
added_by_name E-Link user name initially entering this record
added_by_user_id Indicates the E-Link USER ID that attached this MEDIA FILE
additional_brcs Additional Bioenergy Research Center affiliations
affiliation Affiliation of the individual
affiliations List of any affiliations for this person
alert Indicates whether availability of the dataset has encountered some inconsiste...
analysisType The type of analysis performed on the dataset
announcement_codes List of announcement codes for this record
audit_date Timestamp of the operation detailed in this audit log
audit_logs Listing of any audit logs of actions taken and worker interactions performed ...
availability Describes record's availibility information
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
checksum Calculated hash or checksum value of the physical file as applicable, from me...
collection_type Indicates the OSTI collection type originally creating this record
conference_information "Describes the conference pertaining to this record, if any; usually name and...
conference_type Code representing the type of conference-related work of this record
contract_award_date Date contract for this record was awarded
contributor_type Indicate the contribution made by this Organization
contributors Contributors to the dataset who are not necessarily authors
contributorType The contribution type
country_publication_code Country of publication for this record
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 this media set was first created
date_file_added Indicates the date and time this media file was created
date_file_updated Indicates the last date and time this media file was modified
date_metadata_added Date record first entered the OSTI system
date_metadata_updated Date of this revision of the record
date_submitted_to_osti_first Date record was first submitted to OSTI for publication
date_submitted_to_osti_last Most recent date record information was submitted to OSTI
date_updated Date this media set was most recently modified
date_valid_end If present, date and time when media association was removed or replaced
description A detailed description of the dataset
descriptors List of descriptor codes for this record
document_page_count Number of pages, if applicable, found in the processing of this file
doe_funded_flag Indicates if the record is primarily DOE-funded
doi The DOI for this record, if any
doi_infix "Any customized infix value for the DOI used when generating a DOI reference
duration_seconds For audio-visual media, the duration of the resource in seconds
edit_reason Value provided by user editing a record describing the reason for the edit
edit_source Value determined based on type of edit and user performing the association
edited_by OSTI user ID making this revision of the metadata record
edited_by_email E-Link user email address that created this revision of the metadata record
edited_by_name E-Link user name that created this revision of the metadata record
edition Edition number, as applicable to Books or other products
email Email address of the individual
file_size_bytes If local file, the file size in bytes
files Array of all files, including original submission of file or URL along with a...
first_name First (or 'Given') name of the person
format_information Information about the format of the product, including any operating system o...
funding Funding source(s) for the dataset
fundingOrganization Details of the funding entity
geolocations List of geolocation references for this record
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
identifiers List of identifying numbers related to this record
issue Issue number for journals or other applicable products if any
journal_license_url URL for information regarding the journal license for information
journal_name Name of journal publishing this information
journal_open_access_flag Indicates if the journal article is available in an open access journal, indi...
journal_type Specific sub-type of the journal article
keywords Keywords associated with the dataset
label Optional place name for this location or set of geolocation points
languages Language codes for this record
last_name Last (or 'Family') name of this person
latitude Latitude of this point in the geolocation; limited to -90 to 90, inclusive
longitude Longitude of this point in the geolocation; limited to -180 to 180, inclusive
media Listing of any media and files associated with this record, along with variou...
media_embargo_sunset_date Indicates date on which the document embargo ends, if applicable
media_file_id Unique identifier for a given MEDIA FILE
media_id Unique ID for this MEDIA SET
media_location Indicates if this media set's main content is LOCAL or OFF-SITE
media_source Indicates the initial primary source of the media set
media_title Optional title provided for the given media set
media_type Indicates TYPE of media file, detected or set during media processing
messages One or more messages pertaining to the action taken or results of worker proc...
middle_name Middle name or initial of the person
mime_type MIME type description of the file content of this media file
name Name of the individual
NCBITaxID NCBI taxonomy ID for the organism
opn_addressee For OpenNET records, the addressee information
opn_declassified_date For OpenNET records, the date information was declassified
opn_declassified_status For OpenNET records, status of declassification of information
opn_document_categories For OpenNET records, list of any document categories pertaining to this recor...
opn_document_location
opn_fieldoffice_acronym_code
orcid ORCID for the individual
organizationName Name of the organization
organizations List of organizations related to this record
ori Origin of replication for the plasmid, e
osti_id Unique identifier for OSTI record, only required for updates
osti_user_id OSTI-assigned identifier for this person, if any
other_information Information useful to include in published announcements which is not suited ...
ouo_release_date Date of OUO access limitation expiration if applicable
paper_flag Indicates if OSTI has or had a paper copy of this product
parent_media_file_id If non-zero, indicates unique MEDIA FILE ID this MEDIA FILE is derived from
parentOrganization Higher-level parent of this organization
patent_assignee The holder of property rights to a patent
patent_file_date Date patent was filed with US Patent Office
patent_priority_date
pdf_version For PDF media files, indicates the version of PDF
pdfa_conformance For PDF media that is PDF/A compliant, the conformance level, generally A, B,...
pdfa_part For PDF media that is PDF/A compliant, the level of compliance, as a value be...
pdfua_part For PDF media that is PDF/UA compliant, its compliance level, generally 1 or ...
pdouo_exemption_number Exception number for PDOUO access limitation records
persons List of persons (authors, contributors, etc
phone Contact phone number for this person, if available
plasmid_features Description of plasmid features, if applicable
points
primaryContact Indicates if the individual is a primary contact
processing_exceptions If present, the reason why media processing failed, or description of problem...
product_size Information regarding physical size of media or report, if applicable
product_type
product_type_other Additional information for 'OTHER' product types
promoters Promoters for the plasmid, e
prot_data_other Information regarding why the information is protected if not a CRADA product
prot_flag Indicates the type of protected data described by this record
prot_release_date The date on which data protections for this record will end
publication_date Date of publication of this record
publication_date_text String representation of the publication date (e
publisher_information Publisher-specific information if applicable
records List of records in the collection
related_doc_info Additional information regarding the document
related_identifiers List of related identifiers connected to this record
relatedItem Related publications or items
relatedItemIdentifier Identifier or URL for the related item
relatedItemType Type of the related item, e
relation
released_to_osti_date Date record information was released to OSTI, as entered by releasing officia...
releasing_official_comments Any comments made by the releasing official on the record
replicates_in Organism(s) in which the plasmid replicates
report_period_end_date
report_period_start_date
report_type_other Detail information about 'Other' report types
report_types The type(s) of information or frequency of reporting of information in this r...
repository The repository where the dataset is stored
revision Revision number (sequence) for this record
ror_id ROR identifier for the organization
sbiz_flag Indicates if this metadata is SBIR or STTR related
sbiz_phase A three-character field constrained to 'I', 'II', 'IIA', 'IIB', or 'III' indi...
sbiz_previous_contract_number The previous SBIR/STTR contract number if a Phase III SBIR/STTR report
sbiz_release_date Date data protections on this SBIR/STTR record will expire
schema_version Version of the schema used for the collection
scientificName Scientific name of the organism
selection_markers Selection markers for the plasmid, e
site_ownership_code Code of the DOE site submitting this document
site_unique_id Site-specified unique accession number for this record
site_url (DATASET product type only) The URL of the data set landing page, containing ...
source_edit_type Value determined by submission type for each edit or revision of a record
source_input_type Value determined by submission type at record creation time
species Species information for the organism(s) studied
status Indicates state or notification level of worker action detailed in this audit...
subject_category_code Set two-character subject category code values for this record
subject_category_code_legacy Any legacy or historical subject category codes for this report
subtitle_tracks Indicates the number of subtitle tracks for audio-visual media
title The title of the dataset
type Identify the type of this related identifier
url Either the file name for local files, or URL path to off-site resource
url_type Indicates if the file is LOCALLY HOSTED ('L') or OFF-SITE URL ('O')
value The value of the identifier
video_tracks Indicates the number of video tracks in audio-visual media
volume A volume number as applicable, usually for journals or books
wikidata_id Wikidata identifier for the organization
workflow_status Workflow status of current revision of record

Enumerations

Enumeration Description
AccessLimitationsEnum Access limitation codes to describe the distribution rules and limitations fo...
AnalysisType Type of analysis performed on the dataset
BRCEnum Bioenergy Research Center affiliation
CitedItemType Type of cited item, e
CollectionTypeEnum The OSTI collection type originally creating this record
ContributorType Describes the type of contribution to the work
ContributorTypeCodes The type of contribution
DatasetTypeCodes High-level type of the main content of the dataset, following OSTI categories
GeolocationType
IdentifierType Describe the type of identifier
MediaLocationEnum Indicates if a media file is stored locally or off-site
OrganizationIdentifierType Describe the type of identifier
OrganizationType Indicates type of organization
PersonType Indicates type of person
ProductType Define the type of product represented by this metadata information
RelatedIdentifierType Identify the type of this related identifier
RelationType Indicates the relationship between this identifier and the source record
RepositoryEnum Repository where the dataset is stored
WorkflowStatusEnum The workflow status of the record

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
RequiresLogin These repositories require a login to access data