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
---------------------- Page: 5 ----------------------
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=_en
3 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 data
3.3
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)

3.4
finalization 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 immutable

NOTE Note 1 to entry: Finalized provenance information is a subset of provenance information.

3.7 6
interoperability

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 = _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/
© 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 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

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

immutable

Note 1 to entry: Finalized provenance information is a subset of provenance information.

3.6
interoperability
capa
...

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