ISO 20691:2022
Biotechnology — Requirements for data formatting and description in the life sciences
This document specifies requirements for the consistent formatting and documentation of data and corresponding metadata (i.e. data describing the data and its context) in the life sciences, including biotechnology, and biomedical, as well as non-human biological research and development. It provides guidance on rendering data in the life sciences findable, accessible, interoperable and reusable (F-A-I-R).
This document is applicable to manual or computational workflows that systematically capture, record or integrate data and corresponding metadata in the life sciences for other purposes.
This document provides formatting requirements for both primary experimental or procedural data obtained manually and machine derived data. This document also describes requirements for storing, sharing, accessing, interoperability and reuse of data and corresponding metadata in the life sciences.
This document specifies requirements for large quantities of data systematically obtained from automated high throughput workflows in the life sciences, as well as requirements for large-scale and small-scale data sets obtained by other life science technologies and manual data capture.
This document is applicable to many domains in biotechnology and the life sciences including, but not limited to: basic/applied research in all domains of the life sciences, and industrial, medical, agricultural, or environmental biotechnology (excluding for diagnostic or therapeutic purposes), as well as methodology-driven domains, such as genomics (including massive parallel sequencing, metagenomics, epigenomics and functional genomics), transcriptomics, translatomics, proteomics, metabolomics, lipidomics, glycomics, enzymology, immunochemistry, synthetic biology, systems biology, systems medicine and related fields.
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Foreword
Introduction
1 Scope
2 Normative references
3 Terms and definitions
4 Recommendations and requirements for the description of entities and concepts in life science data
4.1 General
4.2 Recommended ubiquitous identifier scheme for biological and conceptual entities
4.2.1 URI provisions
4.2.2 IRI provisions
4.2.3 Relationship between URI and IRI
4.3 Formatting data and contextual descriptive data (metadata) for biological entities and concepts
4.3.1 General
4.3.2 Version control
4.3.3 Arbitrary Limits
4.3.4 Character sets
4.3.5 Machine readability
4.3.6 Knowledge representation
5 Technical and organizational recommendations and requirements for data formats
5.1 General
5.2 Organizational responsibilities
5.3 Documentation
5.4 Versioning and change log
5.5 Compatibility
5.6 Extensibility
5.7 Compression
5.8 Structural and control elements
5.9 Requirements for data types within formats
5.9.1 General
5.9.2 Encoding of numerical quantity values
5.9.3 Encoding of character strings
5.9.4 Encoding of sequence data
5.9.5 Time data
5.9.6 Boolean data
5.9.7 Biological Imaging data
5.10 Consistency and compatibility
5.11 Data integrity
5.12 Format validation
5.13 Data provenance
6 Semantic recommendations and requirements for data formats
6.1 General
6.2 Minimum consensus information for annotation of biological data
6.2.1 General
6.2.2 Species
6.2.3 Sex
6.2.4 Age
6.2.5 Organ
6.2.6 Tissue
6.2.7 Cell type
6.2.8 Identifiable objects
6.2.9 Identifiable processes
6.2.10 Manipulated entities
6.2.11 Analytical, experimental and computational technology
6.2.12 Biological or analytical question
6.2.13 Technology-specific data
6.3 Syntax and reification
7 Requirements for terminologies and ontologies suitable for annotation of biological data
7.1 General
7.2 Requirements for biological ontologies
7.2.1 Maintainer
7.2.2 Maintenance of the ontology
7.2.3 Ontology syntax
7.2.4 Linking to other ontologies and term reuse
7.2.5 Licensing and attribution
7.2.6 Stable URIs and versioning information
7.2.7 Community involvement
7.2.8 Language
8 Requirements for domain specific data standards
8.1 General
8.2 Specific requirements for domain specific data standards
8.2.1 Maintainer
8.2.2 Maintenance of the data standard
8.2.3 Data standard syntax
8.2.4 Linking to other data standards
8.2.5 Licensing and attribution
8.2.6 Stable URIs and versioning information
8.2.7 Community involvement
8.2.8 Language
9 Requirements for data repositories for biological data
9.1 General
9.2 Requirements for data repositories of biological data
9.2.1 Maintainer
9.2.2 Maintenance of the repository
9.2.3 Repository structure
9.2.4 Linking to other repositories
9.2.5 Licensing and attribution
9.2.6 Stable URIs and versioning information
9.2.7 Data visibility
9.2.8 Community involvement
9.2.9 Language
Annex A (informative) Examples of common formats for life science data
Annex B (informative) Minimum reporting standards for data, models and metadata
Bibliography
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Foreword
Introduction
1 Scope
2 Normative references
3 Terms and definitions
4 Recommendations and requirements for the description of entities and concepts in life science data
4.1 General
4.2 Recommended ubiquitous identifier scheme for biological and conceptual entities
4.2.1 URI provisions
4.2.2 IRI provisions
4.2.3 Relationship between URI and IRI
4.3 Formatting data and contextual descriptive data (metadata) for biological entities and concepts
4.3.1 General
4.3.2 Version control
4.3.3 Arbitrary Limits
4.3.4 Character sets
4.3.5 Machine readability
4.3.6 Knowledge representation
5 Technical and organizational recommendations and requirements for data formats
5.1 General
5.2 Organizational responsibilities
5.3 Documentation
5.4 Versioning and change log
5.5 Compatibility
5.6 Extensibility
5.7 Compression
5.8 Structural and control elements
5.9 Requirements for data types within formats
5.9.1 General
5.9.2 Encoding of numerical quantity values
5.9.3 Encoding of character strings
5.9.4 Encoding of sequence data
5.9.5 Time data
5.9.6 Boolean data
5.9.7 Biological Imaging data
5.10 Consistency and compatibility
5.11 Data integrity
5.12 Format validation
5.13 Data provenance
6 Semantic recommendations and requirements for data formats
6.1 General
6.2 Minimum consensus information for annotation of biological data
6.2.1 General
6.2.2 Species
6.2.3 Sex
6.2.4 Age
6.2.5 Organ
6.2.6 Tissue
6.2.7 Cell type
6.2.8 Identifiable objects
6.2.9 Identifiable processes
6.2.10 Manipulated entities
6.2.11 Analytical, experimental and computational technology
6.2.12 Biological or analytical question
6.2.13 Technology-specific data
6.3 Syntax and reification
7 Requirements for terminologies and ontologies suitable for annotation of biological data
7.1 General
7.2 Requirements for biological ontologies
7.2.1 Maintainer
7.2.2 Maintenance of the ontology
7.2.3 Ontology syntax
7.2.4 Linking to other ontologies and term reuse
7.2.5 Licensing and attribution
7.2.6 Stable URIs and versioning information
7.2.7 Community involvement
7.2.8 Language
8 Requirements for domain specific data standards
8.1 General
8.2 Specific requirements for domain specific data standards
8.2.1 Maintainer
8.2.2 Maintenance of the data standard
8.2.3 Data standard syntax
8.2.4 Linking to other data standards
8.2.5 Licensing and attribution
8.2.6 Stable URIs and versioning information
8.2.7 Community involvement
8.2.8 Language
9 Requirements for data repositories for biological data
9.1 General
9.2 Requirements for data repositories of biological data
9.2.1 Maintainer
9.2.2 Maintenance of the repository
9.2.3 Repository structure
9.2.4 Linking to other repositories
9.2.5 Licensing and attribution
9.2.6 Stable URIs and versioning information
9.2.7 Data visibility
9.2.8 Community involvement
9.2.9 Language
Annex A (informative) Examples of common formats for life science data
Annex B (informative) Minimum reporting standards for data, models and metadata
Bibliography