ISO/TS 23494-1
(Main)Biotechnology — Provenance information model for biological material and data — Part 1: Design concepts and general requirements
Biotechnology — Provenance information model for biological material and data — Part 1: Design concepts and general requirements
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© ISO 2023 – All rights reserved
ISO/DTS.2 23494-1:20222023(E)
Date: 2023-01-05
ISO/TC 276/WG 5
Date: 2022-12-05
Secretariat: DIN
Biotechnology— Provenance information model for biological
material and data — Part 1: Design concepts and general
requirements
DTS.2 stage
---------------------- Page: 1 ----------------------
ISO/DTS.2 23494-1:2023(E)
© ISO 2023
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of
this publication may be reproduced or utilized otherwise in any form or by any means, electronic or
mechanical, including photocopying, or posting on the internet or an intranet, without prior written
permission. Permission can be requested from either ISO at the address below or ISO’s member body in the
country of the requester.ISO Copyright Office
CP 401 • CH-1214 Vernier, Geneva
Phone: + 41 22 749 01 11
Email: copyright@iso.org
Website: www.iso.org
Published in Switzerland.
ii © ISO 2023 – All rights reserved
---------------------- Page: 2 ----------------------
ISO/DTS.2 23494-1:2023(E)
Contents
Foreword ................................................................................................................................................................iv
Introduction ........................................................................................................................................................... v
1 Scope .......................................................................................................................................................... 1
2 Normative references .......................................................................................................................... 1
3 Terms and definitions .......................................................................................................................... 1
4 Requirements and recommendations on provenance information management ........ 4
4.1 Provenance information generation .............................................................................................. 4
4.2 Provenance information availability and findability ............................................................... 6
4.3 Provenance information accessibility ........................................................................................... 6
4.4 Requirements for the computer infrastructure ......................................................................... 6
Bibliography .......................................................................................................................................................... 8
© ISO 2023 – All rights reserved iii---------------------- Page: 3 ----------------------
ISO/DTS.2 23494-1:2023(E)
Foreword
ISO (the International Organization for Standardization) is a worldwide federation of national standards
bodies (ISO member bodies). The work of preparing International Standards is normally carried out
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work. ISO
collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO documents should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www.iso.org/directives).Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of any
patent rights identified during the development of the document will be in the Introduction and/or on
the ISO list of patent declarations received (see www.iso.org/patents).Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO’s adherence to the World
Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT), see
www.iso.org/iso/foreword.html.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
complete listing of these bodies can be found at www.iso.org/members.html.iv © ISO 2023 – All rights reserved
---------------------- Page: 4 ----------------------
ISO/DTS.2 23494-1:2023(E)
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 to
1[1] 2[2]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) and
[3][4]TRANSFoRm projects in several papers [1], [2 ).
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, the 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 for complex data processing workflows to extract biologically relevant
information. This trend is particularly evident in next-generation sequencing (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
datasets,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. This includesThese 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 belowas follows:
http://openprovenance.org/http://www.w3.org/TR/prov-dm/
© ISO 2023 – All rights reserved v
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ISO/DTS.2 23494-1:2023(E)
— Retrospectiveretrospective evaluation of experimental results and data analysis with respect to the
influence of Standard Operating Procedures (standard operating procedures (SOPs) and workflow
parameters.;— Qualityquality monitoring of biological materials and data entered in a workflow or analysis pipeline
(e.g.,. against reference ranges and tolerances).;— Automationautomation of quality control procedures (e.g.,. comparisons between different
pipelines).;— Profilingprofiling of sample and data analysis to identify bottlenecks.;
— Assessmentassessment 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 standarddocument will be complemented by appropriate vertical standards for specific
fields (e.g.,. collection of biological material, data generation, and 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 standarddocument.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 herein 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 nonrepudiability.non-repudiability. 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.Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights other than those in the patent database. ISO shall not be held responsible for identifying any
or all such patent rights.vi © ISO 2023 – All rights reserved
---------------------- Page: 6 ----------------------
TECHNICAL SPECIFICATION ISO/DTS.2 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
lifecyclelife 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, analyzing,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.This standard does not touch legal, governmental, or organizational regulations or ethical rules.
NOTE International, national, or regional regulations or requirements can also apply to specific topics covered
in this document.2 Normative references
There are no normative references in this document.
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=_en3 Terms and definitions
For the purposes of this document, the following terms and definitions apply.
ISO and IEC maintain terminologicalterminology databases for use in standardization at the following
addresses:© ISO 2023 – All rights reserved 1
---------------------- Page: 7 ----------------------
ISO/DTS.2 23494-1:2023(E)
— ISO Online browsing platform: available at https://www.iso.org/obp
— IEC Electropedia: available at https://www.electropedia.org/
3.1
automatic
pertaining to a process or equipment that, under specified conditions, functions without human
intervention[SOURCE: ISO/IEC 2382:2015, 2121282]
common provenance model
3.2
CPM
Common Provenance Model
extension of PROV-DM (3.12) for generating, maintaining, and provisioning provenance information
(3.13) on biological material and data3.3
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, 3.1.6.3.4 3
described object
physical or digital object, which is being documented by provenance information (3.5 13)
3.4finalization event
time instance, at which generated and assembled provenance information (3.13) is transformed into
finalized provenance information (3.5)3.6 5
finalized provenance information
provenance information (3.13) transformed into a representation specified by the Common Provenance
Model (CPM)common provenance model (3.1), and which is prepared to be conserved or archived and
which is considered as being immutableNOTE Note 1 to entry: Finalized provenance information is a subset of provenance information.
3.7 6interoperability
capability to communicate, execute programs, or transfer data among various functional units in a
manner that requires the user to have little or no knowledge of the unique characteristics of those units
[SOURCE: ISO/IEC 20944-1:2013, 3.6.1.24]3.8 7
2 © ISO 2023 – All rights reserved
---------------------- Page: 8 ----------------------
ISO/DTS.2 23494-1:2023(E)
machine-readable
pertaining to data in a form that can be automatically input to a computer
[SOURCE: ISO/IEC/IEEE 24765:2017, 3.2300], modified — Example deleted.]
3.9 8
opaque provenance component
part of the finalized provenance information (3.5) that is findable but not directly accessible and is stored
as an opaque object at the respective responsible subject (3.15)3.10 9
persistent identifier
unique identif
...
FINAL
TECHNICAL ISO/DTS
DRAFT
SPECIFICATION 23494-1
ISO/TC 276
Biotechnology — Provenance
Secretariat: DIN
information model for biological
Voting begins on:
2023-01-20 material and data —
Voting terminates on:
Part 1:
2023-03-17
Design concepts and general
requirements
RECIPIENTS OF THIS DRAFT ARE INVITED TO
SUBMIT, WITH THEIR COMMENTS, NOTIFICATION
OF ANY RELEVANT PATENT RIGHTS OF WHICH
THEY ARE AWARE AND TO PROVIDE SUPPOR TING
DOCUMENTATION.
IN ADDITION TO THEIR EVALUATION AS
Reference number
BEING ACCEPTABLE FOR INDUSTRIAL, TECHNO-
ISO/DTS 23494-1:2023(E)
LOGICAL, COMMERCIAL AND USER PURPOSES,
DRAFT INTERNATIONAL STANDARDS MAY ON
OCCASION HAVE TO BE CONSIDERED IN THE
LIGHT OF THEIR POTENTIAL TO BECOME STAN-
DARDS TO WHICH REFERENCE MAY BE MADE IN
NATIONAL REGULATIONS. © ISO 2023
---------------------- Page: 1 ----------------------
ISO/DTS 23494-1:2023(E)
FINAL
TECHNICAL ISO/DTS
DRAFT
SPECIFICATION 23494-1
ISO/TC 276
Biotechnology — Provenance
Secretariat: DIN
information model for biological
Voting begins on:
material and data —
Voting terminates on:
Part 1:
Design concepts and general
requirements
COPYRIGHT PROTECTED DOCUMENT
© ISO 2023
All rights reserved. Unless otherwise specified, or required in the context of its implementation, no part of this publication may
be reproduced or utilized otherwise in any form or by any means, electronic or mechanical, including photocopying, or posting on
the internet or an intranet, without prior written permission. Permission can be requested from either ISO at the address below
or ISO’s member body in the country of the requester.RECIPIENTS OF THIS DRAFT ARE INVITED TO
ISO copyright office
SUBMIT, WITH THEIR COMMENTS, NOTIFICATION
OF ANY RELEVANT PATENT RIGHTS OF WHICH
CP 401 • Ch. de Blandonnet 8
THEY ARE AWARE AND TO PROVIDE SUPPOR TING
CH-1214 Vernier, Geneva
DOCUMENTATION.
Phone: +41 22 749 01 11
IN ADDITION TO THEIR EVALUATION AS
Reference number
Email: copyright@iso.org
BEING ACCEPTABLE FOR INDUSTRIAL, TECHNO-
ISO/DTS 23494-1:2023(E)
Website: www.iso.org
LOGICAL, COMMERCIAL AND USER PURPOSES,
DRAFT INTERNATIONAL STANDARDS MAY ON
Published in Switzerland
OCCASION HAVE TO BE CONSIDERED IN THE
LIGHT OF THEIR POTENTIAL TO BECOME STAN-
DARDS TO WHICH REFERENCE MAY BE MADE IN
© ISO 2023 – All rights reserved
NATIONAL REGULATIONS. © ISO 2023
---------------------- Page: 2 ----------------------
ISO/DTS 23494-1:2023(E)
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© ISO 2023 – All rights reserved
---------------------- Page: 3 ----------------------
ISO/DTS 23494-1:2023(E)
Foreword
ISO (the International Organization for Standardization) is a worldwide federation of national standards
bodies (ISO member bodies). The work of preparing International Standards is normally carried out
through ISO technical committees. Each member body interested in a subject for which a technical
committee has been established has the right to be represented on that committee. International
organizations, governmental and non-governmental, in liaison with ISO, also take part in the work.
ISO collaborates closely with the International Electrotechnical Commission (IEC) on all matters of
electrotechnical standardization.The procedures used to develop this document and those intended for its further maintenance are
described in the ISO/IEC Directives, Part 1. In particular, the different approval criteria needed for the
different types of ISO documents should be noted. This document was drafted in accordance with the
editorial rules of the ISO/IEC Directives, Part 2 (see www.iso.org/directives).Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. ISO shall not be held responsible for identifying any or all such patent rights. Details of
any patent rights identified during the development of the document will be in the Introduction and/or
on the ISO list of patent declarations received (see www.iso.org/patents).Any trade name used in this document is information given for the convenience of users and does not
constitute an endorsement.For an explanation of the voluntary nature of standards, the meaning of ISO specific terms and
expressions related to conformity assessment, as well as information about ISO’s adherence to
the World Trade Organization (WTO) principles in the Technical Barriers to Trade (TBT), see
www.iso.org/iso/foreword.html.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
complete listing of these bodies can be found at www.iso.org/members.html.© ISO 2023 – All rights reserved
---------------------- Page: 4 ----------------------
ISO/DTS 23494-1:2023(E)
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;© ISO 2023 – All rights reserved
---------------------- Page: 5 ----------------------
ISO/DTS 23494-1:2023(E)
— 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-repudiability. 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.© ISO 2023 – All rights reserved
---------------------- Page: 6 ----------------------
TECHNICAL SPECIFICATION ISO/DTS 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 = _en3 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/
© ISO 2023 – All rights reserved
---------------------- Page: 7 ----------------------
ISO/DTS 23494-1:2023(E)
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 data3.2
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)
3.4finalization event
time instance, at which generated and assembled provenance information (3.13) is transformed into
finalized provenance information (3.5)3.5
finalized provenance information
provenance information (3.13) transformed into a representation specified by the common provenance
model (3.1), and which is prepared to be conserved or archived and which is considered as being
immutableNote 1 to entry: Finalized provenance information is a subset of provenance information.
3.6interoperability
capa
...
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