ISO/TS 23494-1:2023

TECHNICAL ISO/TS
SPECIFICATION 23494-1
First edition
2023-04
Biotechnology — Provenance
information model for biological
material and data —
Part 1:
Design concepts and general
requirements
Reference number
© ISO 2023
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ii
Contents Page
Foreword .iv
Introduction .v
1 Scope . 1
2 Normative references . 1
3 Terms and definitions . 1
4 Requirements and recommendations on provenance information management .3
4.1 Provenance information generation . 3
4.2 Provenance information availability and findability . 5
4.3 Provenance information accessibility . 6
4.4 Requirements for the computer infrastructure . 6
Bibliography . 7
iii
Foreword
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This document was prepared by Technical Committee ISO/TC 276, Biotechnology.
A list of all parts in the ISO 23494 series can be found on the ISO website.
Any feedback or questions on this document should be directed to the user’s national standards body. A
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iv
Introduction
Research in life sciences has undergone significant changes during recent years, evolving away from
individual projects confined to small research groups to transnational consortia covering a wide
range of techniques and expertise. The exchange of research data and biological materials has become
essential for the research in life sciences and biotechnology, and consequently interoperability and
quality measures of data have become imperative.
At the same time several reports addressing the quality of research papers in life sciences uncovered
an alarming number of ill-founded claims. The reasons for the deficiencies are diverse, with insufficient
quality and documentation of the biological material used being the major issue.
Hence there is urgent need for standardized and comprehensive documentation of the whole workflow
from the collection, generation, processing and analysis of the biological material to data analysis and
statistics. This provenance information serves as a quality indicator and provides information on the
reliability thus enabling transparency and comparability of research results.
The purpose of these documents is the standardization of provenance information management for the
biotechnology domain in a way that allows for meaningful data integration. To this end, provenance
information needs to be prepared in a way that enables interoperability between prevailing tools for
data generation, processing and analysis. While in information technology well-established approaches
[1] [2]
to provenance information management in general are available (e.g. OPM or W3C PROV ), the
implementation for the biotechnology domain and related fields in particular is still a pending issue (as
discussed in the results from the Electronic Health Records Systems for Clinical Research (EHR4CR)
[3][4]
and TRANSFoRm projects in several papers ).
Since data in biotechnology mostly originate from analysis of biological material, it is essential that
the provenance information covers the entire process chain, from the source of biological material,
throughout processing and analysis of the material, generation, and processing of the data to final
analysis and interpretation. With the increasing adoption of data-intensive technologies, such as
next-generation sequencing (NGS), high-throughput mass spectrometry as used for proteomics or
metabolomics, or high-throughput microscopy in digital pathology, and their impact on data collection
strategies, consistent and comprehensive documentation of data provenance has become a necessity.
In fact, experimental designs in life sciences have moved from individual experiments with a limited
amount of data towards pipelines generating a vast volume of raw digital data using massively parallel
acquisition systems demanding complex data processing workflows to extract biologically relevant
information. This trend is particularly evident in NGS, where the actual data acquisition device at the
wet lab-digital interface (i.e. the sequencer) is completely oblivious to the details of the experiment
being performed, with all the specialization pushed to the protocols used by the sample preparation
procedure and to the software pipelines processing the data. Software pipelines are continuously
changing due to the evolution of analytical algorithms and reference data sets, which is having a
significant effect on result concordance.
In addition, particular issues, relevant to scientific domains utilizing biological material and data
obtained from humans, must be considered. These include aspects of data privacy, ethics or management
of identities. Notably, issues such as withdrawal of an informed consent or communication of incidental
findings require the implementation of appropriate mechanisms.
The major objectives for collecting and storing provenance information are summarized as follows:
— retrospective evaluation of experimental results and data analysis with respect to the influence of
standard operating procedures (SOPs) and workflow parameters;
— quality monitoring of biological materials and data entered in a workflow or analysis pipeline (e.g.
against reference ranges and tolerances);
— automation of quality control procedures (e.g. comparisons between different pipelines);
— profiling of sample and data analysis to identify bottlenecks;
v
— assessment of fitness for purpose of biological materials and data for the intended use.
To achieve these objectives, a digitally processable description of provenance information is required.
This overarching document will be complemented by appropriate vertical standards for specific fields
(e.g. collection of biological material, data generation, processing of biological material and data). The
basic requirements contained in this document do not impose any limitations to future, domain-specific
standards based on this document.
The standardization of provenance information requires the conceptualization and essential
specifications for the generation, management, provisioning and maintenance as described in this
document. Not covered in this document are additional fundamental components such as a generic
model for provenance information and extensions common to all kinds of provenance information,
ensuring security, privacy and non-repudiation. For particular domains in biotechnology, detailed
specifications building on a common provenance model are required, covering provenance information
describing:
— the life cycle of biological materials, including acquisition, processing, transport and storage.
— the data generation by analytical methods.
— the data processing and analysis in computational workflows.
This document provides definitions for relevant terms used and specifies fundamental requirements
for provenance information generation, management and provisioning.
vi
TECHNICAL SPECIFICATION ISO/TS 23494-1:2023(E)
Biotechnology — Provenance information model for
biological material and data —
Part 1:
Design concepts and general requirements
1 Scope
This document specifies a general concept for a provenance information model for biological material
and data and requirements for provenance data interoperability and serialization.
The provenance information model covers any information relevant to the quality and fitness for
purpose of the biological material generated throughout the preanalytical phase of the materials life
cycle from collection to analysis, data originating from analytical procedures applied to the biological
material and results from further mathematical processing of the data.
This document is applicable to organizations, authorities and industries that are:
a) collecting, processing or distributing biological material for research;
b) generating, collecting, analysing or storing data on biological material.
This document does not apply to biological material and data used for other than research or in fields
that are regulated by national, regional or international laws, such as medical diagnosis and therapy or
food production.
NOTE International, national, or regional regulations or requirements can also apply to specific topics
covered in this document.
2 Normative references
The following documents are referred to in the text in such a way that some or all of their content
constitutes requirements of this document. For dated references, only the edition cited applies. For
undated references, the latest edition of the referenced document (including any amendments) applies.
United Nations Treaty Collection. Nagoya Protocol on Access to Genetic Resources and the Fair and
Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity
[online]. Available from: https:// treaties .un .org/ pages/ ViewDetails .aspx ?src = IND & mtdsg _no = XXVII -8
-b & chapter = 27 & clang = _en
3 Terms and definitions
For the purposes of this document, the following terms and definitions apply.
ISO and IEC maintain terminology databases for use in standardization at the following addresses:
— ISO Online browsing platform: available at https:// www .iso .org/ obp
— IEC Electropedia: available at https:// www .electropedia .org/
3.1
common provenance model
CPM
extension of PROV-DM (3.12) for generating, maintaining and provisioning provenance information
(3.13) on biological material and data
3.2
described activity
activity performed on a described object (3.3)
Note 1 to entry: Examples for activities performed on physical objects can be biobanking activities as specified
in ISO 20387:2018, 3.6. Examples for activities performed on digital objects can be data analytics as specified in
ISO/IEC 20546:2019, 3.1.6.
3.3
described object
physical or digital object which is being documented by provenance information (3.13)
3.4
finalization event
time instance, at which generated and assembled provenance information (3.13) is transformed into
...