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Methods in
Molecular Biology 2703
Sònia Garcia
Neus Nualart
Editors
Plant Genomic
and Cytogenetic
Databases
METHODS IN MOLECULAR BIOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, UK
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Plant Genomic and Cytogenetic
Databases
Edited by
Sònia Garcia and Neus Nualart

Botanical Institute of Barcelona, IBB (CSIC-Barcelona City Council), Barcelona, Spain
Editors
Sònia Garcia Neus Nualart
Botanical Institute of Barcelona Botanical Institute of Barcelona
IBB (CSIC-Barcelona City Council) IBB (CSIC-Barcelona City Council)
Barcelona, Spain Barcelona, Spain
ISSN 1064-3745 ISSN 1940-6029 (electronic)

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Preface
There is a myriad of online plant genomics resources, mainly due to the increasing availabil-
ity of sequencing data related to technical advances in the field of genome sequencing. The
new tools, allowing fast sequencing solutions at decreasing costs, have prompted the surge
of multiple websites offering integrated omics information. Together with sequence data,
information at the more structural level, related to chromosomes, karyotypes, or genome
size, is also relevant to our understanding of plant genome evolution. Yet, despite its utility,
such cytogenetic information seems to attract less interest or is less connected with the
overall amount of genomic data. With this in mind, this volume of Methods in Molecular
Biology series offers an updated catalogue of online plant genomics and cytogenetic
resources, which may be of interest to plant evolutionary biologists as well as to plant
breeders. The chapters describe database targets, contents, and examples of uses, aiming
to provide a practical guide to the online richness of plant genomics and cytogenetic
resources. This compilation is only about databases and does not include analytic resources,
and up to our knowledge, all reported databases are periodically updated and regularly
maintained.
The book is organized into two parts, the first one devoted to plant genomic databases
and the second to databases with a focus on cytogenetics. Part I contains eight chapters. In
Chapter 1, Daniel Arend and colleagues describe the plant phenomics and genomics
research data repository, discussing how advances in methodology and technology have
helped in the study of plant genomics and phenomics, and how this has helped with issues
like food security, biodiversity, and climate change. This data repository makes comprehen-
sive plant research data publicly available to the global research community. Chapter 2, by
Philipp E. Bayer and David Edwards, deals with pangenome graphs as a data structure to
represent genome diversity. Although pangenome graphs have been created for some
species, their visualization is challenging because of their size and complexity; here a work-
flow is presented, through the use of the tool Wheat Panache, to search and visualize wheat
pangenome graphs. The next four chapters present databases related to transposable ele-
ments (TEs), which are commonly used as evolutionary markers in genetic, genomic, and
cytogenetic approaches. In Chapter 3, Simon Gaviria-Orrego and colleagues introduce us to
the InpactorDB, a plant LTR retrotransposon reference library. This database, available
online, addresses the lack of freely available full-length and classified LTR retrotransposon
reference sequences, by collecting almost 70,000 elements that can be used to identify and
classify LTR-RTs. Chapter 4, by Asmaa H. Hassan and coauthors, presents TEMM, another
database for transposon element-based molecular markers in plants. In Chapter 5, by Doğa
Eskier and colleagues, we are introduced to PlanTEenrichment, an online database com-
prising 11 plant genomes to analyze stress-associated TEs. It provides taxonomic informa-
tion on TEs and it can inform on the enrichment values of the repeats; besides, this database
can be used by researchers with little or no experience in computational analyses to quickly
identify TEs of interest. Chapter 6, by Morad M. Mokhtar and colleagues, describes the
updated database CicerSpTEdb2.0, which now includes more accurate intact LTR-RT
elements, with annotation of internal domains belonging to species of the genus Cicer
(chickpeas), providing a valuable resource for comparative genomics of the crop Cicer
arietinum and closely related species. The following Chapter 7, by Marie C. Henniges
v
vi Preface
and Ilia J. Leitch, describes BIFloraExplorer, a taxonomic, genetic, and ecological data
resource for British and Irish vascular plants, providing a clean, curated, and taxonomically
resolved dataset that enables the study of natural ecological and evolutionary patterns and
processes within the vascular flora of Britain and Ireland. Part I is closed with Chapter 8, by
Noe Fernandez-Pozo, presenting PEATmoss, a gene expression atlas for bryophytes, with
abundant data on Physcomitrium patens and expanding to include information from Antho-
ceros agrestis and Marchantia polymorpha. PEATmoss offers visualization methods and tools
for data download and has added features including, among others, co-expression network
visualization and the ability to download replicate data.
Part II contains ten additional chapters related to cytogenetics and chromosome-related
databases. Chapter 9, by Marie C. Henniges and colleagues, deals with the plant DNA
C-values database, the most trusted and widely used resource for accessing plant genome
size data, along with information like ploidy level and chromosome number, and offering
various query and filtering options. Updated six times since its inception in 2001, the most
recent release includes data for ca. 12,300 species across various land plant and algal lineages.
In Chapter 10, another well-known database in the plant cytogenetics community is pre-
sented by Anna Rice and Itay Mayrose: the Chromosome Counts Database (CCDB).
Created in 2015, the CCDB is the central online resource for plant biologists interested in
determining and documenting chromosome numbers of extant taxa. More specific data-
bases, regarding a restricted geographical region, taxonomic group, or chromosome type or
feature, are further described. In Chapter 11, Joan Simon and colleagues present Cromo-
Cat, an online database providing karyological information on the vascular plants of the
Catalan Countries (Spain). It includes over 68,000 records belonging to more than 5000
taxa, and it has been developed for over 25 years. Chapter 12, by Kuniaki Watanabe and
John Semple, presents the Index to Plant Chromosome Numbers in Asteraceae, a resource
that has been useful for synantherologists for decades, giving information on chromosome
numbers, ploidy levels, and genome sizes for species of family Asteraceae, one of the largest
of angiosperms. The authors also take the occasion to review the processes of dysploidy,
polyploidy, and hybridization having frequently occurred throughout the family’s evolu-
tionary history. In Chapter 13, Maria Bosch and coauthors present the newly updated (and
newly online) version of the Delphineae Chromosome Database (DCDB), a resource with
karyological information on this tribe of family Ranunculaceae containing species such as
aconites or larkspurs. The DCDB provides the most accurate and complete information on
chromosome numbers, ploidy levels, and other karyological data and is intended to be useful
for research in cytotaxonomy, systematics, and evolution. Chapter 14, by Pedro Jara-Seguel
and Jonathan Urrutia-Estrada, reviews and updates the Chilean Plants Cytogenetic Data-
base, an online resource providing cytogenetic information for native and invasive plant
species in Chile. In Chapter 15, Thomas Gregor and colleagues explain to us the online data
portal “Chromosome numbers of the flora of Germany,” another resource with information
on chromosome counts, ploidy levels, and flow cytometric data (genome size), and with
over 14,000 records. Chapter 16, by Mariela A. Sader and coauthors, reviews the available
South American databases on chromosome numbers, as well as the contents of those
databases containing cytogenetic information on South American species. Chapter 17, by
Marı́a Luisa Gutiérrez and coauthors, reviews and updates B-chrom, a database on
B-chromosomes for plants, animals, and fungi, which now provides information for
ca. 3000 species. Similarly, Chapter 18, by Roi Rodrı́guez-González and collaborators,
reviews and updates the Plant Ribosomal DNA database, presenting the results of the fourth
update to the resource, contributing information on rDNA loci number, position, and
Preface vii
organization, besides other related data such as genome size or telomere type, for more than
2700 plant species.
As sequencing technologies continue to improve and more genetic, genomic, and
chromosomal information is generated, it is becoming increasingly important to have
resources like the ones described in the book you are holding. This collection of databases
can help make this wealth of information more accessible and usable for plant science
researchers.
Barcelona, Catalonia, Spain Sònia Garcia

Neus Nualart
Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
PART I GENOMIC DATABASES
1 The Plant Phenomics and Genomics Research Data Repository:

An On-Premise Approach for FAIR-Compliant Data Acquisition . . . . . . . . . . . . . 3
Daniel Arend, Uwe Scholz, and Matthias Lange
2 Investigating Pangenome Graphs Using Wheat Panache . . . . . . . . . . . . . . . . . . . . . 23
Philipp E. Bayer and David Edwards
3 InpactorDB: A Plant LTR Retrotransposon Reference Library. . . . . . . . . . . . . . . . 31
Simon Orozco-Arias, Simon Gaviria-Orrego,
Reinel Tabares-Soto, Gustavo Isaza, and Romain Guyot
4 TEMM: A Curated Data Resource for Transposon Element-Based
Molecular Markers in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Asmaa H. Hassan, Morad M. Mokhtar, and Achraf El Allali
5 PlanTEnrichment: A How-to Guide on Rapid Identification of Transposable
Elements Associated with Regions of Interest in Select Plant Genomes . . . . . . . . 59
Doğa Eskier, Alirıza Arıbaş, and Gökhan Karakülah
6 CicerSpTEdb2.0: An Upgrade of Cicer Species Transposable
Elements Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Morad M. Mokhtar, Ahmed S. Fouad, Haytham M. Abd-Elhalim,
and Achraf El Allali
7 “BIFloraExplorer”: A Taxonomic, Genetic, and Ecological Data
Resource for the Vascular Plants of Britain and Ireland . . . . . . . . . . . . . . . . . . . . . . 83
Marie C. Henniges, Andrew R. Leitch, and Ilia J. Leitch
8 PEATmoss: A Gene Expression Atlas for Bryophytes . . . . . . . . . . . . . . . . . . . . . . . . 91
Noe Fernandez-Pozo
PART II CYTOGENETICS AND CHROMOSOME-RELATED DATABASES
9 The Plant DNA C-Values Database: A One-Stop Shop

for Plant Genome Size Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Marie C. Henniges, Emmeline Johnston, Jaume Pellicer,
Oriane Hidalgo, Michael D. Bennett, and Ilia J. Leitch
10 The Chromosome Counts Database (CCDB) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Anna Rice and Itay Mayrose
11 CromoCat: Chromosome Database of the Vascular Flora
of the Catalan Countries—25 years . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Joan Simon, Maria Bosch, and Cèsar Blanché
ix
x Contents
12 An Overview to the Index to Chromosome Numbers in Asteraceae

Database: Revisiting Base Chromosome Numbers, Polyploidy,
Descending Dysploidy, and Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
John C. Semple and Kuniaki Watanabe
13 DCDB: Chromosome Database of Tribe Delphinieae (Ranunculaceae):
Structure, Exploitation, and Recent Development . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Maria Bosch, Jordi Lo pez-Pujol, Cèsar Blanché, and Joan Simon
14 Chilean Plants Cytogenetic Database: An Online Resource
for Embryophytes of the Southern Cone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Pedro Jara-Seguel and Jonathan Urrutia-Estrada
15 The Data Portal “Chromosome Numbers of the Flora of Germany”:
Progress After Five Years, Recent Developments, and Future Strategies. . . . . . . . 201
Thomas Gregor, Stefan Dressler, Sebastian Klemm,
Christiane M. Ritz, Marco Schmidt, Karsten Wesche,
Jens Wesenberg, Georg Zizka, and Juraj Paule
16 South American Plant Chromosome Numbers Databases:
The Information We Have and the Information We Lack
on the Most Plant-Diverse Continent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Mariela A. Sader, Lucas A. Costa, Gustavo Souza,
Juan D. Urdampilleta, Joan Simon, and Magdalena Vaio
17 First Update to B-Chrom: A Database on B-Chromosomes . . . . . . . . . . . . . . . . . . 227
Marı́a Luisa Gutiérrez, Roi Rodrı́guez-González, Inés Fuentes,
Francisco Gálvez-Prada, Aleš Kovařı́k, and Sònia Garcia
18 Release 4.0 of the Plant rDNA Database: A Database on Plant
Ribosomal DNA Loci Number, Their Position, and Organization:
An Information Source for Comparative Cytogenetics. . . . . . . . . . . . . . . . . . . . . . . 237
Roi Rodrı́guez-González, Marı́a Luisa Gutiérrez, Inés Fuentes,
Francisco Gálvez-Prada, Jana Sochorová, Aleš Kovařı́k, and Sònia Garcia
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Contributors
HAYTHAM M. ABD-ELHALIM • Agricultural Genetic Engineering Research Institute,

Agricultural Research Center, Giza, Egypt
DANIEL AREND • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK),
Seeland, OT Gatersleben, Germany
ALIRIZA ARIBAŞ • Bioinformatics Platform, İzmir Biomedicine and Genome Center (IBG),
İnciraltı, İzmir, Turkey
PHILIPP E. BAYER • Centre for Applied Bioinformatics and School of Biological Sciences, The
University of Western Australia, Perth, WA, Australia
MICHAEL D. BENNETT • Royal Botanic Gardens, Kew, Richmond, UK
CÈSAR BLANCHÉ • BioC (GReB, IRBio) – Laboratori de Botànica, Facultat de Farma ` cia i
Ciències de l’Alimentacio, Universitat de Barcelona, Barcelona, Catalonia, Spain
MARIA BOSCH • BioC (GReB, IRBio) – Laboratori de Botànica, Facultat de Farma ` cia i
LUCAS A. COSTA • Laboratorio de Citogenética Vegetal, Departamento de Botânica,
Universidade Federal de Pernambuco, Recife, Brazil
STEFAN DRESSLER • Department of Botany and Molecular Evolution, Senckenberg Research
Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
DAVID EDWARDS • Centre for Applied Bioinformatics and School of Biological Sciences, The
University of Western Australia, Perth, WA, Australia
ACHRAF EL ALLALI • African Genome Center, Mohammed VI Polytechnic University, Ben
Guerir, Morocco
DOĞA ESKIER • İzmir International Biomedicine and Genome Institute, Dokuz Eylül
University, İnciraltı, İzmir, Turkey; Bioinformatics Platform, İzmir Biomedicine and
Genome Center (IBG), İnciraltı, İzmir, Turkey
NOE FERNANDEZ-POZO • Plant Cell Biology, Department of Biology, University of Marburg,
Marburg, Germany; Institute for Mediterranean and Subtropical Horticulture (IHSM-
CSIC-UMA), Algarrobo-Costa, Málaga, Spain
AHMED S. FOUAD • Botany and Microbiology Department, Faculty of Science, Cairo
University, Giza, Egypt
INÉS FUENTES • Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona),
Barcelona, Catalonia, Spain; Parc de Recerca Biomèdica de Barcelona (PRBB),
Barcelona, Catalonia, Spain
FRANCISCO GÁLVEZ-PRADA • Bioscripts-Centro de Investigacion y Desarrollo de Recursos
Cientı́ficos, Sevilla, Spain
SÒNIA GARCIA • Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de Barcelona),
Barcelona, Catalonia, Spain
SIMON GAVIRIA-ORREGO • Department of Computer Science, Universidad Autonoma de
Manizales, Manizales, Caldas, Colombia
THOMAS GREGOR • Department of Botany and Molecular Evolution, Senckenberg Research
MARÍA LUISA GUTIÉRREZ • Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de
Barcelona), Barcelona, Catalonia, Spain
xi
xii Contributors
ROMAIN GUYOT • Department of Electronics and Automation, Universidad Autonoma de

Manizales, Manizales, Caldas, Colombia; Institut de Recherche pour le Développement,
CIRAD, University of Montpellier, Montpellier, France
ASMAA H. HASSAN • African Genome Center, Mohammed VI Polytechnic University, Ben
Guerir, Morocco
MARIE C. HENNIGES • Royal Botanic Gardens, Kew, Richmond, UK; School of Biological and
Behavioural Sciences, Queen Mary University of London, London, UK
ORIANE HIDALGO • Royal Botanic Gardens, Kew, Richmond, UK; Institut Botànic de
Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
GUSTAVO ISAZA • Department of Systems and Informatics, Universidad de Caldas,
Manizales, Caldas, Colombia
PEDRO JARA-SEGUEL • Departamento de Ciencias Biologicas y Quı́micas & Núcleo de
Estudios Ambientales, Facultad de Recursos Naturales, Universidad Catolica de Temuco,
Temuco, Chile
EMMELINE JOHNSTON • Royal Botanic Gardens, Kew, Richmond, UK
GÖKHAN KARAKÜLAH • İzmir International Biomedicine and Genome Institute, Dokuz Eylül
University, İnciraltı, İzmir, Turkey; Bioinformatics Platform, İzmir Biomedicine and
Genome Center (IBG), İnciraltı, İzmir, Turkey
SEBASTIAN KLEMM • Department of Botany, Senckenberg Museum of Natural History Görlitz,
Görlitz, Germany
ALEŠ KOVAŘÍK • Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno,
Czech Republic
MATTHIAS LANGE • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK),
Seeland, OT Gatersleben, Germany
ANDREW R. LEITCH • School of Biological and Behavioural Sciences, Queen Mary University
of London, London, UK
ILIA J. LEITCH • Royal Botanic Gardens, Kew, Richmond, UK
JORDI LÓPEZ-PUJOL • Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de
ITAY MAYROSE • School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv,
Israel
MORAD M. MOKHTAR • African Genome Center, Mohammed VI Polytechnic University, Ben
Guerir, Morocco
SIMON OROZCO-ARIAS • Department of Computer Science, Universidad Autonoma de
Manizales, Manizales, Caldas, Colombia; Department of Systems and Informatics,
Universidad de Caldas, Manizales, Caldas, Colombia
JURAJ PAULE • Department of Botany and Molecular Evolution, Senckenberg Research
Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany;
Botanischer Garten und Botanisches Museum Berlin, Freie Universit€ a t Berlin, Berlin,
Germany
JAUME PELLICER • Royal Botanic Gardens, Kew, Richmond, UK; Institut Botànic de
Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
ANNA RICE • School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
CHRISTIANE M. RITZ • Department of Botany, Senckenberg Museum of Natural History
Görlitz, Görlitz, Germany
ROI RODRÍGUEZ-GONZÁLEZ • Institut Botànic de Barcelona, IBB (CSIC-Ajuntament de
Contributors xiii
MARIELA A. SADER • Instituto Multidisciplinario de Biologı́a Vegetal (IMBIV), Universidad

de Cordoba – CONICET, Cordoba, Argentina
MARCO SCHMIDT • Palmengarten der Stadt Frankfurt am Main, Frankfurt am Main,
Germany
UWE SCHOLZ • Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland,
OT Gatersleben, Germany
JOHN C. SEMPLE • Department of Biology, University of Waterloo, Waterloo, ON, Canada
JOAN SIMON • BioC (GReB, IRBio) – Laboratori de Botànica, Facultat de Farma ` cia i
JANA SOCHOROVÁ • Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno,
Czech Republic
GUSTAVO SOUZA • Laboratorio de Citogenética Vegetal, Departamento de Botânica,
Universidade Federal de Pernambuco, Recife, Brazil
REINEL TABARES-SOTO • Department of Electronics and Automation, Universidad
Autonoma de Manizales, Manizales, Caldas, Colombia; Department of Systems and
Informatics, Universidad de Caldas, Manizales, Caldas, Colombia
JUAN D. URDAMPILLETA • Instituto Multidisciplinario de Biologı́a Vegetal (IMBIV),
Universidad de Cordoba – CONICET, Cordoba, Argentina
JONATHAN URRUTIA-ESTRADA • Laboratorio de Invasiones Biologicas, Facultad de Ciencias
Forestales, Universidad de Concepcion, Concepcion, Chile; Instituto de Ecologı́a y
Biodiversidad, IEB, Concepcion, Chile
MAGDALENA VAIO • Laboratorio de Evolucion y Domesticacion de las Plantas, Departamento
de Biologı́a Vegetal, Facultad de Agronomı́a, Universidad de la República, Montevideo,
Uruguay
KUNIAKI WATANABE • Department of Biology, Graduate School of Science, Kobe University,
Kobe, Japan
KARSTEN WESCHE • Department of Botany, Senckenberg Museum of Natural History Görlitz,
Görlitz, Germany; German Centre for Integrative Biodiversity Research Halle-Jena-
Leipzig, Leipzig, Germany
JENS WESENBERG • Department of Botany, Senckenberg Museum of Natural History Görlitz,
Görlitz, Germany
GEORG ZIZKA • Department of Botany and Molecular Evolution, Senckenberg Research
Part I
Genomic Databases
Chapter 1
The Plant Phenomics and Genomics Research Data

Repository: An On-Premise Approach for FAIR-Compliant
Data Acquisition
Daniel Arend, Uwe Scholz, and Matthias Lange
Abstract
The FAIR data principle as a commitment to support long-term research data management is widely
accepted in the scientific community. However, although many established infrastructures provide compre-
hensive and long-term stable services and platforms, a large quantity of research data is still hidden.
Currently, high-throughput plant genomics and phenomics technologies are producing research data in
abundance, the storage of which is not covered by established core databases. This concerns the data
volume, for example, time series of images or high-resolution hyperspectral data; the quality of data
formatting and annotation, e.g., with regard to structure and annotation specifications of core databases;
uncovered data domains; or organizational constraints prohibiting primary data storage outside institu-
tional boundaries. To share these potentially dark data in a FAIR way and master these challenges the
ELIXIR Germany/de.NBI service Plant Genomic and Phenomics Research Data Repository (PGP) imple-
ments an on-premise approach, which allows research data to be kept in place and wrapped in FAIR-aware
software infrastructure. In this chapter, the e!DAL infrastructure software and the PGP repository are
presented as best practice on how to easily setup FAIR-compliant and intuitive research data services.
Key words Research data management, FAIR principles, Digital object identifier, Plant genomics and
phenomics
1 Introduction
Plant genomics and phenomics studies benefit from methodologi-

cal and technological advances to address increasing demands on
food security, protect biodiversity and climate change [1]. However,
besides the technological advances, a key aspect is the access to a
digital data-sphere that represents the whole of plant genetic
resources as a diversity treasure. Therefore, it is essential to use
established genomic and phenomic data dissemination standards
and publish subsequent research data in sustainable and open-
access platforms.
Sònia Garcia and Neus Nualart (eds.), Plant Genomic and Cytogenetic Databases, Methods in Molecular Biology, vol. 2703,
https://doi.org/10.1007/978-1-0716-3389-2_1,
© The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023
3
4 Daniel Arend et al.
One essential cornerstone is the consequent application of

FAIR principles alongside the entire research data life cycle [2–
4]. Particularly obvious is a potential gap between data acquisition
and data management in high-throughput technologies, like in the
area of plant genomics and phenomics, which continuously pro-
duce a large amount of data. A particularly critical breaking point is
the storage of such research data, which is not covered by
community-established repositories, respectively, core databases.
Due to this, there is a high risk that many valuable datasets remain
unpublished. This in turn causes a big gap between created research
results and publicly accessible research datasets [5].
In this context, an alternative approach is to equip the data
collection facility directly with the necessary infrastructures on site.
This applies in particular to the possibility of publishing locally
stored data, that is, on-premise, according to FAIR criteria. The
following chapter describes the design and the concept of the Plant
Phenomics & Genomics Research Data Repository, following an
alternative approach providing an on-premise architecture to over-
come the mentioned challenges and making comprehensive plant
research data publicly available for the worldwide research
community.
2 Background
The Leibniz Institute of Plant Genetics and Crop Plant Research

(IPK) Gatersleben has one of the world’s largest ex situ germplasm
collections and, therefore, a large experience of over two decades of
data management of plant-related research data. Based on this
experience and demands on a sustainable data life cycle, in 2012,
the development of the e!DAL software infrastructure [6] was
initiated with the concept of an on-premise data storage infrastruc-
ture as a service to expose DOI (digital object identifiers) assigned
datasets as a base service of the IPK as a data center in the interna-
tional DataCite consortium [7]. While conceptualizing the first
draft of the underlying API specification for the infrastructure and
implementing the initial prototype, it became clear that there is the
potential for a more comprehensive software environment. In the
meanwhile, e!DAL has grown toward a generic, community-
accepted on-premise data archiving and publication infrastructure.
It is part of infrastructure programs like ELIXIR [8, 9], NFDI [10],
and institutional infrastructures [11].
2.1 Current Status of Almost all scientists in public research are obligated and willing to
Data Publication share all the data they produce with the research community. This
Infrastructures has been and is the practice in almost all cases [12]. The FAIR
principles, which stand for Findability, Accessibility, Interoperabil-
ity, and Reusability, were initially drafted by the FORCE11
The Plant Phenomics & Genomics Research Data Repository 5
workgroup in 2015 [13]. In 2016 they were finalized and pub-

lished by Wilkinson et al. [14]. Today they are widely accepted. The
research community shows an increasing awareness of the value of
FAIR-compliant data, and the principles are increasingly adopted in
several data management guidelines and funding policies [15–17].
Nevertheless, the concrete technical implementation is not a
matter of course, and many data repositories invest a lot to improve
their infrastructures for seamless integration in the data life cycle
and to acquire and share the deposited data in a FAIR manner. One
can categorize them into three classes. First, general-purpose data
repositories (I) like figshare [18], Dryad [19], or Zenodo [20] are
not focused on any specific data type. They are widely accepted and
usually, the first point of contact when sharing cross-domain data
that is not in the scope of established repositories. Next, core data
deposition databases (II) are widely accepted in the scientific com-
munity, and they usually evolved over many years and have sustain-
able funding in the background like the ELIXIR depositions
databases [21], the comprehensive resources of the European Bio-
informatics Institute (EBI) [22] or the different NCBI databases
[23]. Last but not least, there is a large group of domain-specific
repositories and databases developed and hosted by certain research
institutions (III), such as PlabiPD, GBIS, and PHIS [24].
The decisive common feature of all mentioned systems is the
method of data ingestion. Each data file is required to be uploaded
by the owner from the local storage location to the respective
system. Depending on the data granularity, such as the number of
files and subdirectories, the data volume, or the supported network
protocol, this can be very time-consuming [25] and does not even
consider various manual processes such as metadata preparation,
data formatting, and of course the actual upload process.
Repositories of category (II) provide complex submission pro-
cesses and specific metadata schema, which requires bioinformati-
cians or data stewards who are responsible and trained to operate
the specific submission pipelines and give support to researchers.
On the other hand, institutional infrastructures of category (III)
require data stewards as well as additional skilled IT staff and
computer scientists to setup, customize existing open-source solu-
tions, or develop a home-brewed infrastructure as well as budget
for maintaining the underlying storage and network infrastructure.
In some cases, the institutional repositories are too specific to
attract substantial data volume because of their mainly project-
driven development. Therefore, such repositories often have a lim-
ited lifetime due to high costs for sustainable solutions, especially
for permanent staff. The infrastructures of category (I) seem to be
an ideal alternative because they are usually very comfortable and
provide a comprehensive feature set. Nevertheless, they do not
implement rich and harmonized metadata and data to feature
integrated, linked, or big data applications, for example, to supply
comprehensive training sets for AI-based models or machine

learning algorithms. Furthermore, only a limited amount of
fee-less data storage is usually offered. This makes it necessary to
request additional budget to publish large and comprehensive
datasets, which is difficult to communicate and explain to funding
agencies, especially when the requesting institution has sufficient
in-house storage capacities but lacks a suitable infrastructure to use
it for FAIR data publication.
Consequently, researchers tend to share only condensed and
aggregated datasets and limit the re-analysis based on primary data
to support their research articles and prove their results. Even if
they are willing to share all their data in general, only a few actually
provide their data as a whole [12].
2.2 Infrastructure- As described in the previous section the existing classes of data
to-the-Data publication infrastructures have several drawbacks, which made a
Approach (I2D) complementary infrastructure concept necessary to share compre-
hensive research data. To address a multipurpose but domain spe-
cific configurable, the need to share high volume and number of
primary data files and the limitations caused by network bandwidth
and data privacy, the idea was to apply an on-premises approach
following the infrastructure-to-the-data (I2D) concept [26].
Common data publication pipelines using one or more of the
previously mentioned databases or platforms usually involve a time-
consuming data transfer by uploading the data via provided web
applications or file clients. Another shortcoming provided by many
services is the limited amount of free-of-charge storage. Such addi-
tional costs for additional storage are on top of already granted
hardware storage of institutions. However, suitable software infra-
structures to share the stored data in a FAIR-compliant way enable
the reuse of this investment and save funding for external data
hosting. Therefore the e!DAL software follows the I2D concept
by using a data publication layer to encapsulate the existing institu-
tional infrastructure and benefit from an in-house available storage
capacity. This layer acts as a broker to the data publication service of
the DataCite [7] and contains an infrastructure for submitting
research data, reviewing files and metadata, and delivering DOIs
[27]. Figure 1 shows schematically the basic idea and differences
between the data-publication-as-a-service approach and the data-
publication-on-premises approach of the I2D concept.
3 The Electronic Data Archive Library (e!DAL)
The electronic Data Archive Library or e!DAL, for short, is a

comprehensive but lightweight infrastructure software for manag-
ing and publishing research data. It combines common file-system
concepts and research data publication features. On one hand, it is
Fig. 1 Comparison of data-publication-as-a-service concept and data-publication-on-premise concept. Both

approaches feature FAIR data publication but differ in costs. The data-publication-as-a-service approach,
which is shown on the left side, costs a fee, delegates data property control, and faces capacity limits in
storage and data upload. On the right side, the data-publication-on-premise approach is presented, which
keeps the data in-house but requires the availability of a central server and storage hardware as well as the
installation of the e!DAL software
delivered as an extensible and customizable software framework,

which can be integrated and used in existing infrastructures and
frontends, and on the other hand, it delivers a stand-alone server-
client architecture to setup a data repository infrastructure. The
Plant Phenomics and Genomics Research Data Repository (e!
DAL-PGP), which is the reference implementation and is the first
productive instance based on the e!DAL infrastructure will be
described in this section. Subsequently, the software design and
the most important functions will be explained.
3.1 Software Design e!DAL is implemented in Java to feature platform-agnostic use and
and Implementation development in the JVM ecosystem. The wide distribution of the
Concept JVM ecosystem and the large developer community allows it to
implement comprehensive functions by using established libraries.
This reduces the implementation effort and is helpful for providing
stable and constant maintenance in the future. The object-oriented
API design and aspect-oriented implementation of common pat-
terns make e!DAL scalable. It consists of a modularization concept
to encapsulate functions of common concerns, like IO, network,
metadata, storage, search, etc., which are necessary to meet the
challenges and guarantee a sustainable infrastructure. The follow-
ing listing briefly mentions the functions of the e!DAL software.
• Version Management: For reproducibility reasons, tracking the
history of all stored data files and corresponding metadata is
possible. Furthermore, a strict deletion policy forbids removing
already stored datasets and allows only to mark a version chain
as closed.
• Metadata Management: To guarantee persistent data access and
readability, every data entity is annotated with a minimal set of
technical metadata, which is crucial for searching and filtering
data and support and automatic processing without the need for
semantic interpretation.
• Information Retrieval: Due to a large number of expected data

files and to provide efficient data findability, an index-based
search engine was integrated, providing enhanced functions
like a faceted search or fuzzy queries across the provided meta-
data. A standardized data harvesting interface is provided to
connect and interlink the stored data.
• Data Protection: To protect the archived data against misuse, a
fine-grained but intuitive security system is integrated, which
can protect specific data entities and define rules for single users
and groups. Additionally, a single sign-on-based authentication
was integrated to lower the barrier for the user.
• Data Publication: The major function of the infrastructure is
the sharing of research data. Therefore, a comprehensive data
publication module including an embedded and peer-review-
based data submission and publication procedure, was
integrated.
• Integrability: The overall focus of the development was on the
generality of the infrastructure in order to be universally usable,
which refers to a self-configuration of the software, an easy
setup and maintenance, as well as a user-friendly and generic
design to be easily integrated into existing workflows and tools.
The following sections describe the functional components just
mentioned in detail.
3.1.1 Version For reasons of intuitiveness, the e!DAL data structure is adapted
Management from common file-system infrastructures and consists of a hierarchy
of files and folders, which is complex enough for organizing com-
prehensive datasets but understandable by every user and compati-
ble with storage backends, like file systems, object stores or even
distributed storage. For data objects to store in a particular back-
end, any additional technical metadata is managed independently
from the concrete storage backend. This enables having a broad
range of metadata and its versioning.
An embedded version-control system features the traceability
of changes. Thereby every version is associated with a bundle of a
data entity and a set of metadata. In order to comply with the data
life cycle and to audit the complete file and metadata history the e!
DAL data structure records, every single data entity, or metadata
update results in a new version. The version-control mechanism
also prevents erasing of stored or published datasets; rather, it
creates a final version and closes the version chain by tagging it
with a “deleted” flag. This keeps all previous versions available and
prevents at the same time the creation of new versions. The
provided version control is embedded in the infrastructure design
and is automated, which makes it very intuitive for the user and
guarantees a complete tracking and auditing of ingested research
data. To achieve this, the default implementation of e!DAL extends
the classical file-system capability with the flexibility of a relational

database to manage fine grain metadata. Using object-relational
mapping techniques, e!DAL is agnostic to a concrete database
system. Thus, e!DAL can be customized to use existing database
infrastructure on site or use the embedded H2 for default as a
metadata persistence layer.
3.1.2 Metadata Besides the specific version handling, another difference of the e!
Management DAL infrastructure, in comparison to common file systems, is
integrated metadata handling. While classical file systems track
only a limited number of metadata for every data object directly
like the file owner or the file creation data, other metadata can be
only stored in separate text files or condensed in smart “self-
explaining” files names, which is not very comfortable and error-
prone. Cloud-based file stores such as object stores such as Amazon
S3 [28] overcome these shortcomings, but in practice they are not
yet rolled out in institutional storage infrastructures. The e!DAL
infrastructure solves this issue by connecting every single file or
folder version with its own set of standardized metadata. The used
schema is inspired by the DublinCore and DataCite metadata
schemata and contains a set of technical attributes, which are one
side necessary to describe the actual dataset and guarantee its long-
term readability and, on the other side, mandatory to assign a DOI
when publishing the dataset. Table 1 shows an overview about the
metadata attributes, which are provided within the e!DAL data
structure.
Table 1
Overview of the available technical attributes of the e!DAL metadata set
Attributes Description
Title A given name to the data resource
Creators Responsible people or organizations for creating the data
Contributors People or organizations contributed to the data creation
Description A brief abstract of the data content
Subjects List of specific keywords describing the data
Publisher A responsible organization for making the data available
Language The language of the data resource
Dates Linked timepoint or period of an event in the data lifecycle
Rights Information about any rights held in and over the data
Format The MIME type of the data
Size Information about the size of the data file or data set
Checksum One or more generated checksums for the data
In general, there are some recommendations but no fixed

definitions about the concrete data types which need to be used
to describe the different fields. To lower the barriers for the data
provider, e!DAL provides several data types and a mapping to
define which data type fits the different attributes. This makes the
description easier and provides a standardized schema and values.
3.1.3 Information In contrast to common file systems, which usually provide only very
Retrieval elementary search capabilities, e!DAL provides, besides the support
for data navigation following the hierarchically organized data
folder structure, an index-based search function bundle. It auto-
matically creates a full-text index over all metadata attributes and
selected content data during creating data entities, which is crucial
to make data findable within a large number of expected files. The
search is very powerful using the index and provides a comprehen-
sive set of different functions as well as settings like a faceted search
or fuzzy queries across the provided metadata.
In addition to the provided API function, e!DAL also provides
an embedded user interface (UI) component for using the compre-
hensive search functions and makes them easily usable during the
establishment of an e!DAL-based repository. A screenshot of the
search interface is shown in Fig. 2.
Fig. 2 Screenshot of the e!DAL embedded search features. Here is an example of a specific search within the
e!DAL-PGP repository is illustrated
3.1.4 Data Privacy Protecting research data is important for reusability and crucial for
the acceptance of the infrastructure by the community in general
and by users in particular. The user requests for protection against
misuse; therefore, e!DAL has an integrated and fine-granular access
control system with sensible methods already on a low API level.
Executing code is owned by a particular subject, which can be a
trusted digital identity resulting from an authentication process.
This could be, for example, access principal bound to, a user name,
email, or a user group. It is assigned within a single-sign-on authen-
tication process when initiating a session to the e!DAL infrastruc-
ture. This supports local authentication services such as logins of
the operating system as well as OAuth or SAML-based AAI like
federated AAI, Google, ORCID, or others. To lower the barrier, an
authentication module based on the ELIXIR AAI [29] allows many
researchers to use their existing institutional identity provider to
log in without implementing proprietary user management. This
features a trusted infrastructure and is comfortable for the user,
decreasing the effort to host an e!DAL-based infrastructure.
Besides the capability to define access rules and protect specific
methods on stored datasets, another important aspect of data secu-
rity and reusability is a transparent and reliable definition of the
permissions and licenses for data reuse. This legal and authorization
information can be stored in the metadata set and can be therefore
defined for every single version of a stored data entity if necessary.
Due to the generic character of the infrastructure and the diversity
of the research data, there is no concrete license fixed. Nevertheless,
for the provided graphical user interface (GUI) of the embedded
submission tool, which is described in the next section, the license
model of the Creative Commons (CC) was integrated, and one of
the seven provided CC licenses can be selected, because they are
suitable for a broad field of research data.
3.1.5 Data Publication Generally, it is impossible to embed comprehensive research data

directly into a research article. Either because they are way too big
or because there is no suitable graphical representation to show
them in an article. Thus, the authors add additional links to make
the data accessible. Usually, this is encoded as proprietary IDs of
core databases or URLs. To make these stable and long-term
resolvable, it is necessary to support globally unique and persistent
identifiers (PUIDs), which are widely accepted and fulfill interna-
tional standards because this is crucial to ensure that research data is
citable. Furthermore, this enables credit to the data producer and
curator. A central resolver service ensures the long-term resolvabil-
ity of a PUID to a valid URL. A specific interface in e!DAL was
designed to bind to PUID services. For the reference implementa-
tion, a connection to the DataCite REST API was implemented to
mint DOIs. Obviously, DOIs and PUIDs, in general, are immuta-
ble and represent scientific publications, which makes it necessary
Fig. 3 Integrated data review and approval process. The flow chart on the left side explains the data
submission and review procedure. Thereby the communication between the reviewers and the infrastructure,
as well as the data producers, is handled via email with embedded action links on the right side. The decisions
of the reviewers during the approval process were evaluated using a decision matrix, which is also shown on
the right side
that the assignment is permitted and controlled by a responsible

publisher. Therefore, a customizable, peer-review-inspired approval
workflow was designed. The workflow is schematically shown in
Fig. 3, and it allows the evaluation of data publication requests by a
hierarchy of reviewer decisions encoded as a decision matrix.
This process is embedded in the publication module of e!DAL
and can be customized for any connected PUID service. It is
necessary to pass the datasets and their corresponding metadata
through an internal review process before being published to guar-
antee a sustainably described data annotation and prevent legal
violations. For the default configuration, two reviewer groups are
distinguished. The scientific reviewers have scientific expertise in
the author’s research area and are asked to evaluate the dataset for
scientific data quality. The administrative reviewers are responsible
to check for publication rights and potential conflicts with respect
to intellectual property and patent regulations of the authors and
affiliated institutions. Each data submission triggers a notification
for the reviewers, who then exclusively or collaboratively decide to
permit or reject it. The reviewer’s ratings are combined with a
configurable decision matrix to make a final decision. The default
matrix, which is also shown in Fig. 3, lets a scientific reviewer or

their assistant decide for rejection or acceptance. The administrative
reviewer may confirm their decisions or draw a veto that rejects the
entire submission. This procedure increases the data quality and
prevents accidentally publishing secret information. The default
configuration is intuitive and guarantees performant processing,
but it can also be customized to reflect further institutional policies.
After approval by the reviewers, a DOI is assigned as a permanent
reference for data sharing. To make the process intuitive and as fast
as possible for data providers and reviewers, the workflow is based
on an asynchronous email notification system with reminders.
In order to make the data submission and the mentioned
approval process usable, an intuitive and embedded GUI for data
description and submission was developed and embedded.
The publication process is initiated by the data and metadata
submission tool, as shown in Fig. 4. This comprises an upload of
the dataset and mandatory technical metadata, like a title, key-
words, and a suitable license. Some of them, for example, file size,
Fig. 4 Graphical user interface of the desktop version of the data submission tool for the e!DAL-PGP repository
file type, or file format, will be automatically determined. Further-

more, the tool supports and enables the reuse of metadata typed in
previous sessions during the use of the system. Optionally the data
submitter may define an embargo date to hide the public access to
the content page, which provides access to the dataset at a defined
time point, which is useful when the dataset is subject to certain
project restrictions.
In order to mimic known submission processes, the design and
handling of the graphical user interface reuse design patterns
known from scientific journals or research conferences. After the
data upload process to the connected e!DAL-based repository is
completed, and the reviewers are notified of the publication request
by an email that includes a preview URL with restricted access to
the submitted files and metadata.
In case the data submission was rejected, the requesting user is
informed and asked to revise the dataset and metadata. After a
successful review, the author is notified and can confirm the sub-
mission to finally assign the DOI or alternatively discard the sub-
mission if any change is necessary. The released DOI will be
registered and sent out with an additional email. Alternatively, the
author can wait to assign a DOI and use the temporary preview link
from the notification, for example, to provide access to the
reviewers of a manuscript.
3.1.6 Integrability The overall goal during the conceptualization of e!DAL and the
development of the reference implementation provided a flexible
and generic infrastructure. In concrete, this means it should not
only be easy to use but rather also configurable and maintainable
with low effort. This is crucial to be able to integrate the infrastruc-
ture in diverse existing workflows and solutions for supporting
researchers in their daily work.
Therefore, e!DAL is implemented in Java, which is still one of
the most popular programming languages and is widely used in the
life science community. Furthermore, it allows it to be used plat-
form independent. e!DAL supports stand-alone and client-server
architectures and can be integrated into Java applications as an
embedded local archive or as a central archiving system. Thus
several applications or project-specific central repositories can be
easily operated. All needed and previously described components
are already fully embedded within the infrastructure and the refer-
ence implementation. To setup e!DAL no additional technology
like a database, an indexing engine, or a web server is needed. No
specific knowledge is required because the setup of e!DAL is more
or less self-configuring. To initiate a local or a central instance, the
user needs to provide several general connection parameters, which
is required to connect the system with different online services like
DataCite for assigning DOIs, and some organizational parameter
which are needed to use the full functionality like the reviewer’s
email addresses for the embedded approval process. The compre-
hensive set of diverse login modules, which is already integrated,
facilitates the usage of the infrastructure.
3.2 Software Quality Besides the generic character of the e!DAL infrastructure and their
and Sustainable reference implementation as e!DAL-PGP repository at IPK Gate-
Documentation rsleben, another important aspect during the development was to
guarantee high software quality and usability, resulting in diverse
challenges in reusing existing software [30]. Therefore, the quality
of research software is important and is getting increasingly
focused, which also results in several approaches and recommenda-
tions for maintainable, reusable, and high-quality research
software [31].
Following lessons learned in the past decade of active software
development in research projects, published studies [32], and
guidelines for software development [33] are used to guarantee
the quality and sustainability of the e!DAL software stack, One
focus was to set the platform independency, which was addressed
by implementing e!DAL in Java. Furthermore, we consequently
used the opportunity to use open-source libraries, which extend the
native Java API, to avoid home-brewed code. There is a huge
community that maintains comprehensive libraries. Therefore the
reference implementation of e!DAL consequently used several
established libraries and frameworks like Hibernate [34] for object
persistence, AspectJ [35] for performant code-weaving and Lucene
[36] for the search engine. This supports the use of current, best-
performing code and prevents wasting time on developing error-
prone code for core components such as security, database connec-
tion, search functionality, or user management. Furthermore,
JVM-based code is widely used in the bioinformatics community
to develop graphical user interfaces, algorithms, data management
infrastructures, and web apps.
Furthermore, parallel to the development of the API and the
core code, a comprehensive test suite based on JUnit was created,
guaranteeing a permanent quality and performance evaluation dur-
ing the development. Obviously, the comprehensive functionality
results in a large amount of code and embedded libraries, which
requires to application build and dependency management tools to
maintain the infrastructure in the long term and the regular release
of stable versions. To meet these challenges, the development and
release process is mastered using Gradle Build Management. It
allows fast and specific build cycles by supporting multi-core sys-
tems, which makes it possible to run a large set of unit tests in
parallel. The different components of the e!DAL infrastructure is
thereby organized in a multi-build project, which contains the main
API components, including the reference implementation and the
components for the server-client architecture, which is directly
based on this core implementation. The whole project is stored in a

GIT repository on BitBucket [37], and furthermore, every release
is published in Maven Central as an artifact [38], which allows
embedding the library easily using build management tools like
Maven or Gradle.
The next important aspect is to improve the acceptance of the
e!DAL infrastructure is comprehensive software documentation for
experienced developers as well as sample code and training material
for casual programmers, who usually have a basic programming
knowledge. A comprehensive source code documentation is col-
lected in a JavaDoc and automatically created during every release
process. It is published as a bundle with the above-mentioned
artifact and is also available on the project website [39]. The latter
also provides different usage examples as code snippets, which help
get started with the software and show how to set up and
conFig. own repository instances. Furthermore, some video tutor-
ials, presentation recordings, and associated publications are avail-
able to lower the initial barriers to digging into the e!DAL
infrastructure. The website is automatically updated during the
comprehensive release process.
4 Plant Phenomics and Genomics Research Data Repository
Based on the previously described e!DAL software infrastructure,

in 2015, the first productive repository which follows the I2D
approach, was released at the IPK Gatersleben to address the chal-
lenging data publication needs within the German Plant Phenotyp-
ing Network (DPPN). The now institutional operated “Plant
Phenomics and Genomics Research Data Repository” (e!DAL-
PGP) features the full potential of the IPKs capabilities as DataCite
data center for assigning DOIs. Initially, it was limited to just IPK
users as an intuitive solution to publish their diverse and large plant-
related research datasets. After several successful data publications
and some slight improvements, the submission was promptly
extended by integrating the ELIXIR AAI [29] and supporting
external submissions.
The e!DAL-PGP repository covers in particular cross-domain
datasets, which are not supported to get published in other public
repositories for reasons of data volume or data domain, such as
phenotyping images, genotyping data, visualizations of morpho-
logical models, and data from mass spectrometry, as well as software
and related documents. In doing so, in mid-2022 e!DAL-PGP
provides 250 data records that can be referenced via DOIs and
annotated with technical metadata. These datasets comprise over
1.5 million files with an overall volume of >4.8 TB, as shown in
Fig. 5.
Fig. 5 Overview of the data access statistics and development of the data stock provided by the e!DAL-PGP
repository. The left diagram shows the increasing number of stored datasets separated by number of files and
overall volume. The right diagram shows the overall volume of downloaded data and the number of different
user accesses to the published datasets
To ensure data findability and accessibility, e!DAL-PGP pro-

vides content pages (see Fig. 6) for every dataset containing JSON-
LD formatted metadata and is therefore harvestable through web
crawler services like Google or Microsoft, which follow the Schema.
org recommendations [40] for structured data.
To support scientists in disseminating their research data e!
DAL-PGP is accepted as a recommended institutional repository
for the journals such as Scientific Data (Nature Publishing Group),
GigaScience (Oxford Academic), and others. Furthermore, it is
registered in re3data.org [41], FAIRsharing.org [42], OpenAIRE
[43], and DataCite [7]. The benefits of this wide support of data
discovery enabling technologies and data publication, in general,
are proven by the constantly increasing number of data accesses. By
mid-2022, e!DAL-PGP delivered 900 TB of data, and the provided
datasets have been accessed by 180,000 unique clients.
5 Summary
This chapter presented the design principles of an infrastructure-to-

the-data approach (I2D) to implement a “on-premises’‘data man-
agement and data publication approach. A proof of principle was
given by the presented e!DAL infrastructure. It is a comprehensive
infrastructure and compliant with the FAIR data principles. The
development was driven by the claim to provide a flexible setup and
easy integration into existing infrastructures and the daily research
process. The described I2D concept differs from generic publica-
tion platforms like figshare, DRYAD, or Zenodo. Their business
model is based on considerable client investments depending on
the needed storage and additional data transfer time. In case of an
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— Ja ochorilaiset, herra kuningas, sanoi poppamies. — Niin, he
ovat kanssasi, vaikka heitä hallitseva muukalainen onkin sandilaisia.
— Se asia vaatii miettimistä, sanoi kuningas, — mutta meidän

täytyy kuitenkin liikkua nopeasti, sillä Sandi tulee pian takaisin. Hän
lähti jo kolme päivää sitten, ja rattaallinen vene kulkee nopeasti.
Sananviejiä tuli ja meni koko sen päivän. Viisi kertaa kuningas

nousi levoltaan vastaanottamaan tietoja ja vastaamaan kysymyksiin.
Isisiläiset olivat hermostuksissaan; he pelkäsivät Sandia.
Vannoiko kuningas kuoleman nimessä, että jos suunnitelma

menisi myttyyn, hän sanoisi Sandille pakottaneensa isisiläiset
mukaan uhkauksin ja peloituksin? Ngombilaisilia oli Sandin
perheeseen kuuluva kuningatar; pitikö heidän tappaa hänet? Hänellä
oli rakastaja, joka voisi hyvin pian hänet murhata, kun kerran hänellä
oli pääsy kuningattaren majaan.
— Älkää tappako häntä, lähetti Toloni sanan, — sillä tiedän hänet

hyvin kauniiksi. Hän saakoon majan minun majani varjossa.
Pikkuisisiläiset olivat kärsimättömiä. Heidän maassaan oli kaksi

lähetysasemaa; oliko ne poltettava?
— Nämä ovat pikku asioita, sanoi kuningas Toloni. — Ensin

meidän tulee saada Sandi käsiimme, ja hänet me uhraamme vanhan
tavan mukaan. Sitten toiset asiat ovat pieniä ja vähäpätöisiä.
Sinä iltana, kun pimeys tuli ja hänen mitään tietämättömät

miehensä istuivat ja rupattelivat tuleen ääressä — suuria tulevia
tapahtumia eivät aavistaneet eivätkä tietäneet muut kuin Tolonin
neuvonantajat ja eräiden toisten heimojen päämiehet — soi lokali
soinnukkaasti kylän ulkolaidoilla.
Kuningas kuuli majansa merkkirummun äänen ja tunsi sen

äänestä, että se vastasi jollekin kaukaiselle rummulle.
Majansa edessä, kädet kummallakin korvallisillaan, kuningas

kuunteli.
Kolme pärrytystä, nousevia ja laskevia, hidas kalistus, pärrytys,

lyönti ja vielä pärrytys.
Se merkitsi Sandia — nopea Sandi, tulinen Sandi, yllättävä Sandi,

oikeudenjakaja Sandi.
Kaukainen rumpu ilmaisi kaikki nämä luonteelliset maininnat.
Kahdesti kaukainen lokali kertoi Sandin nimen, sitten pitkä

pärrytys, lyhyt pärrytys ja hiljaisuus.
Taas — pitkä pärrytys, lyhyt pärrytys — hiljaisuus.
— Sandi kuolee!
Tolonin ääni oli terävä ja riemukas.
— Kuulkaa! kuiskasi hän.
Metallinsointuisia lyöntejä, joihin liittyi säännöttömiä, matalia ääniä

— se merkitsi arabialaista.
— Tap-tap-tap-tap.
Oli ammuttu paljon.

Sitten tuli jälleen Sandersin nimi — pitkä pärrytys, lyhyt pärrytys ja
hiljaisuus.
Tolonin rummuttaja lähetti viestiä edelleen. Koko yön pitkin ja

poikin maata viestiä kerrattiin, kunnes se tuli villien maiden rajoille,
jossa Sandi oli tuntematon ja viesti mahdoton ymmärtää.
— Kaikki jumalat ja paholaiset ovat kanssani, sanoi Akasavan

kuningas.
— Nyt on aika.
Vuoteeseensa ojentautuneena Sanders Abibun ja pienen

käsipeilin avulla korjasi vauriotaan.
Hänen saamansa haava oli kaikkein pienimpiä. Kuula oli sattunut

taskussa olevaan teräsketjukukkaroon ja kimmonnut siitä vieden
kappaleen lihaa vasemmasta kyynärvarresta ja mennyt sitten sen
hytin kattoon, jonka edessä hän oli seisonut.
Hän ei ollut kärsinyt minkäänlaista vahinkoa lukuunottamatta

kyljen ruhjevammaa ja käden pikku haavaa. Abibu sitoi molemmat
paikat, ja asia olisi ollut lopussa, sillä Sanders oli terve mies.
Mutta seuraava aamu tapasi hänet kuumeisena vuoteessa.

Käsivarsi oli paisunut kaksi kertaa paksummaksi kuin se oli ennen
ollut, ja sitä särki. Sanders epäili kuulan olleen myrkytetyn ja oli
luultavasti oikeassa. Hän ei saanut asiaa valmiiksi pohdituksi, sillä
kuvernöörinvirasto ei kiinnittänyt sellaisiin pikkuasioihin
minkäänlaista huomiota. Oli selvitettävä ikävä juttu silinterihatusta.
Oliko Sandersin pidettävä kruunaustilaisuuden
laivastokatsastuksessa silinteriä vai eikö? Kuvernöörinvirasto oli
ankara, mutta Sanders oli myöskin päättäväinen.
— Minulla on kauhea päänsärky, ja te vaaditte minua panemaan
silinterin, Teidän Ylhäisyytenne, sanoi hän kiukuissaan ja puhkesi
kyyneliin.
Se ei ollut ensinkään Sandersille ominaista, ja hän tunsi, ettei se

ollut hänelle ensinkään ominaista, niin että suurilla
voimainponnistuksilla hän palautui takaisin todellisuuteen.
Hän makasi hytissään. Päätä ja käsivartta särki kovasti. Hänen

kasvonsa olivat tuskasta hiessä, ja kieli oli kuin nahanpala.
Vuoteen vieressä kyykkivä Abibu nousi, kun Sanders avasi

silmänsä.
— Mihin menet? kysyi Sanders.
— Jumalanaisen luo, joka antaa lääkettä, sanoi Abibu näöltään

tunteettomana. — Sillä luulen, että sinä kuolet, ja minä tahdon kirjan,
että olen tehnyt kaiken oikein.
— Varovainen pentele, mutisi Sanders ja vaipui jälleen

tajuttomaksi.
Herätessään jälleen hän ei kuullut laivan rattaan iskuja. Oli

tavattoman tyyntä ja helppoa herätä. Hän makasi isossa huoneessa
pienellä vuoteella, ja lakanat olivat puhdasta liinaa — jota ne eivät
olleet hänen laivallaan.
Vuoteen vieressä pöydällä oli iso maljakko täynnä sinisiä kukkia, ja

tuoksu oli omituinen.
Ei voi sanoa hänen tunteneen paikkaa, koska hän ei milloinkaan

käynyt nti Glandynnen makuuhuoneessa; mutta hän muisteli
hämärästi jonkun sanoneen aikovansa viedä hänet tytön luo. Hänen
ensimmäinen tietoinen tunteensa oli, että hän tunsi olevansa
jollekulle vaivaksi, ja toiseksi hän ajatteli omaa tilaansa.
Hän käänsi päätänsä hitaasti nähdäkseen särkevän käden. Häntä

ei olisi ihmetyttänyt, vaikka olisi havainnut sen olevan poissa. Se oli
vielä paikallaan, ja hän huokasi helpotuksesta. Se oli myöskin jo
melkein tavallisen kokoinen.
Hän koetti liikuttaa vahingoittuneen käden sormia ja huomasi

suureksi ilokseen, ettei se ollut ollenkaan vaikeata eikä tehnyt
kipeätä.
Sitten Ruth Glandynne tuli sisään — kaunis näky mustassa

maassa.
Tyttö hymyili, heristi varoittavasti sormeaan, kohensi hiukan tyynyä

ja istuutui hänen viereensä.
— Mitä Akasavassa on tapahtunut? kysyi Sanders äkkiä. Se tuli

noin vain ilman aikojaan; hän ei ollut edes ajatellutkaan Akasavaa,
mutta jokin aiheutti kysymyksen.
Tyttö näki hänen kasvojensa äkkiä käyvän vakaviksi.
— Eiköhän — eiköhän teidän ole parempi olla ajattelematta

akasavalaisia, sammalsi hän. — Teidän täytyy pysyä hyvin hiljaa.
— Minun täytyy tietää, sanoi Sanders.
Hänen äänensä oli hiljainen ja heikko, mutta tyttö tiesi, että olipa
seuraus mikä tahansa, hänen piti kertoa.
Sanders makasi hiljaa silmät ummessa hänen puhuessaan ja
hänen lopetettuaan makasi vaiti — niin hiljaa, että tyttö luuli hänen
pyörtyneen.
Sitten Sanders avasi silmänsä.
— Lähettäkää sana Ochoriin, sanoi hän, — ja pyytäkää päällikkö

Bosamboa luokseni.
*****
Bosambo ei ollut hullu. Hän oli elänyt sivistyneiden ihmisten

parissa ja puhui englantia, ja hän oli hankkinut toimeentulonsa
varkaana varkaiden keskellä.
Hän tunsi Akasavan tapahtumat. Siellä oli kapina kehittymässä —

ja joukko ihmisiä, jotka olivat asettuneet vastustamaan kapinaa oli
lakaistu pois maan pinnalta. Myöskin Isisi oli yhtynyt yleiseen
liikkeeseen, oli tappanut osan kansalaisistaan ja pakottanut
bolenzilaiset valtaansa.
Bosambo oli saanut kehoituksen totella kuningas Tolonia, ja hän

lähetti takaisin sanan, joka oli helposti ymmärrettävä ja jyrkkä. Häntä
eivät häiritsisi tungettelut viikon päiviin. Hänen ja Akasavan välillä oli
asema, jolla Sandi makasi — kuolevana, kaikkien laskelmien
mukaan, mutta varmasti siellä. Ja lähetysaseman rannassa oli
»Zaire» ja puoli komppaniaa hausoja, puhumattakaan kahdesta
suuresta tykistä.
Mutta vaikka Bosambo ei välittänytkään maailman itsevaltiaasta

kuninkaasta, joksi Toloni itseään sanoi, niin Ochorissa oli miehiä,
jotka muistaen Bosambon suuren ruoskan ja hänen valmiutensa sen
käyttöön keskustelivat Tolonin kanssa, ja Bosambo tiesi, että puolet
ochorilaisista oli puoliksi valmiina kapinaan.
Mutta hän ei vielä säikähtänyt — se liikutti häntä vähemmän kuin

toinen seikka.
— Elämäni valo ja sieluni ilo, sanoi hän vaimolle, joka oli hänen
olkikattoisen haareminsa kaunistus. — Jos Sandi kuolee, niin uskolla
ei ole mitään merkitystä, sillä olen rukoillut kaikkia jumalia,
profeettoja ja herroja Markusta, Luukasta ja Johannasta — ja Pyhää
äitiä, josta Maristveljet minulle kertoivat; olen rukoillut ristejä ja ju-jua
ja uhrannut vuohen ja kanan Ochorin jumalan edessä.
— Mahomet, sanoi nainen, — kaikki tämä on pahasta, sillä ei ole

kuin yksi Jumala.
— Hän palkitsee minun pyrkimykseni hänen etsinnäkseen, virkkoi

Bosambo miettivänä. — Mutta jos Sandi paranee, niin kiitän kaikkia
jumalia, sillä muuten loukkaan häntä, joka pelasti herrani.
Hänen asemansa oli vaikea, hän tiesi sen. Juuri edellisenä yönä
hän oli siepannut Tolonin salaisen lähetin, joka oli tullut Ochoriin
kehoittamaan heitä hyökkäämään Sandin miesten kimppuun
pohjoisesta päin ja ajamaan heitä kapinoivan kuninkaan odottavia
legioonia kohti. Bosambo otti mieheltä selville koko viestin, ennen
kuin lopetti hänet.
Seurasi vielä kaksi tuskallisen odotuksen päivää. Eräs chorilainen

päämies, jolle oli luvattu heimon päällikkyys, koetti jouduttaa
tapahtumain kehitystä ja ryömi eräänä iltana Bosambon majaan
saadakseen tarvitsemansa paikan avoimeksi.
Bosambo, joka odotti häntä, nuiji hänet tajuttomaksi äkkiä ja
tehokkaasti, kiskoi hänet yön pimeydessä joen rantaan ja heitti hänet
veteen naru kaulassa ja kivi narun päässä.
Se vei asian päätökseen eräässä suhteessa, sillä kaivaten

päällikköään hänen kannattajansa tulivat Bosambolta vaatimaan,
että mies oli annettava heille. Heidän päällikkönsä vastaus oli
tehokas. Puhujana toiminut mies kantoi Bosambon äkkipikaisuuden
merkkiä hautaan asti. Miten asiat olisivat kehittyneet, on vaikea
arvata, mutta Sandin kutsu saapui Bosambolle, ja hän kutsui
kansansa koolle.
— Menen Sandin luo, sanoi hän heille, — Sandin, joka on minun

herrani ja teidän ja lisäksi minun sukulaiseni, niin kuin tiedätte. Ja
jätän tänne kansan, joka on kiittämätön ja turmeltunut. Sanon teille
nyt, että minun poissaollessani teidän tulee pysyä työssänne ettekä
saa tehdä pahaa — ette saa seurata hullujen neuvoja ja omien
juonienne pyyteitä — sillä palatessani minä rankaisen nopeasti; ja
jos joku on tottelematon minulle, niin puhkaisen hänen silmänsä ja
heitän hänet metsän petojen raadeltavaksi. Teen tämän Iwan kautta,
joka on kuolema.
Minkä jälkeen Bosambo läksi lähetysasemalle ottaen mukaansa

päävaimonsa ja viisikymmentä sotilasta.
Hän tuli Sandin luo neljänkymmenenkahdeksan tunnin kuluttua

siitä, kun komissaari oli lähettänyt kutsun, ja kyykötti herransa
vuoteen vieressä.
— Bosambo, sanoi Sandi, — olen ollut hyvin sairas ja olen vieläkin

liian heikko nousemaan. Ja minun maatessani täällä Toloni,
Akasavan kuningas, on noussut kapinaan ja hänen kanssaan koko
maakunta.
— Herra, on niin kuin sanot, myönsi Bosambo.
— Aikanaan tulee paljon valkeita miehiä, sanoi Sandi, — ja he

syövät tämän hullun kuninkaan; mutta siihen mennessä tulee paljon
kärsimyksiä ja monta viatonta ihmistä surmataan. Olen lähettänyt
hakemaan sinua, koska luotan sinuun.
— Herra, sanoi Bosambo, — olen varas ja alhainen mies, ja minun

sydämeni on ylpeä siitä, että nojaat minuun.
Sandi huomasi Bosambon äänen vavahtelevan ja tiesi hänet

vilpittömäksi.
— Sen vuoksi, oi päällikkö, olen pannut sinut sijalleni, sillä olet

tottunut sotaan. Ja annan sinulle laivani ja sotamiesteni
päällikkyyden, ja sinä teet niin kuin on paras.
Bosambo hypähti äänettömästi jaloilleen ja seisoi vuoteen

vieressä jännittyneenä ja suorana. Hänen silmissään oli outo kiilto.
— Herra Sandi, sanoi hän matalalla äänellä, — puhutko totta, että

minä — hän löi molemmin nyrkein leveään rintaansa — minä olen
sinun sijassasi?
— Juuri niin, sanoi Sandi.
Bosambo oli vati hetken, sitten hän avasi suunsa puhuakseen,

pidättäytyi, kääntyi ja läksi huoneesta sanaakaan sanomatta.
Mikä ei ollut Bosambon tapaista.

Hänen tuloonsa oli valmistauduttu. Abibu seisoi porraslankun
päässä ja teki kunniaa.
— Olen sinun miehesi, päällikkö, sanoi hän.
Bosambo katsoi häneen.
— Abibu, hän sanoi, — en valehtele, kun sanon, että olen samaa

uskoa kuin sinäkin, ja Allahin ja hänen Profeettansa kautta aion
tehdä, mikä on paras Sandille, meidän herrallemme.
— Niin toivomme molemmat, sanoi Abibu.
Bosambon valmistelut tehtiin hiljaisuudessa.
Hän lähetti puolet sotilaistaan lähetysasemalle vartioimaan

Sandia, ja heidän kanssaan meni kaksikymmentä hausaa kersantin
johtamina.
— Nyt käymme katsomassa kuningas Tolonia, sanoi hän.
Akasavan kuningas istui neuvottelussa. Hänen voimansa olivat

leiriytyneet Ngombin rajoille, ja savuava kylä puhui vastarinnasta ja
tappiosta — sillä Ngombi oli viime hetkessä kieltäytynyt liitosta, ja
rakastaja, joka oli ottanut suostutellakseen kuningattaren ja
pystymättä suostuttelemaan oli ryhtynyt tehokkaampiin
toimenpiteisiin, oli epäonnistunut.
Kuningatar ilmoitti hänen epäonnistumisensa lähettämällä hänen

päänsä
Tolonille.
Eivät edes tiedot, että Sandi oli kuolemansairas, järkyttäneet
heidän vastarintaansa. Mahdollisesti nuorella kuningattarella oli oma
kunnianhimonsa.
Kuninkaan neuvottelu oli vakava.
— Näyttää kuin ngombilaiset olisi syötävä kylä kylältä, sanoi hän,

— sillä koko tämä maa on minun kanssani heitä lukuunottamatta. Ja
tämä kuningatar taas tulee surulliseksi.
Hänen joukkonsa olivat hyökkäysmatkan päässä Ngombin

kuningattaresta. Hänen legioonansa lähenivät tuomittua kaupunkia.
Yön tullessa hän oli aivan lähellä sitä, ja seuraavana aamuna Toloni
valloitti kaupungin äkkirynnäköllä, ja siitä tuli verinen leikki.
He veivät kuningattaren kuninkaan päämajaan, ja seurasi suuri

tanssi.
Kymmenkunnan nuotion ääressä kuningas istui oikeutta.
Tyttö — hän oli ehkä hieman enemmän — seisoi hänen edessään

alasti riisuttuna ja katseli kuninkaan silmiin pelottomasti.
— Nainen, sanoi tämä, — tänä iltana sinä kuolet.
Tyttö ei vastannut.
— Tapan sinut tulella ja kidutuksella! sanoi Toloni ja kertoi hänelle,

miten hän tulisi kuolemaan.
Toloni istui leikkauksin koristetulla tuolillaan puun alla. Hän oli

alasti, mutta toisella olkapäällä oli leopardinnahka, ja hänen julmat
silmänsä kimalsivat ennakolta siitä nautinnosta, jonka tyttö hänelle
tuottaisi.
Tämä puhui tyynesti.
— Jos minä kuolen tänään ja sinä kuolet huomenna, oi kuningas,

mitä on yksi päivä? Sillä Sandi tulee sotilaineen.
— Sandi on kuollut, sanoi kuningas nopeasti. Hän oli juonut

runsaasti maissiolutta, jota alkuasukkaat valmistavat. — Ja jos hän
eläisi…
Hän kuuli heikkoa suhinaa, joka tuli kimeämmäksi, kunnes se oli

aivan ulvontaa. Se meni vinkuen hänen päänsä yli ja hävisi.
Hän ponnahti epävarmasti jaloilleen.
— Se oli henki, mutisi hän, sitten…
Suhina tuli jälleen — tällä kertaa miehet ulvoivat. Jokin sattui

puuhun pirstoen kuoren.
Taivaalle levisi aamun heikko ja kaamea kajastus, hetkessä

maailma muuttui harmaaksi, ja saattoi nähdä, että vastapäistä rantaa
kierteli »Zaire».
Kun kuningas katsoi, hän näki salaman välähtävän laivalta, kuuli

tulevan ammuksen ulvonnan ja totesi vaaran.
Hän antoi kiireisen käskyn, ja rykmentti juoksi rannalle, johon

kanootit oli kiskottu. Ne eivät olleet siellä. Niitä vartioimaan jätetyt
miehet makasivat kuin nukkuen rannalla, mutta kanootit olivat
keskellä jokea viiden mailin päässä, ja virta kuljetti niitä poispäin.
Bosambon miehet olivat yöllä tulleet joen poikki.
Tolonin kukistumisen tarina on lyhyt. Ahdistettuna saarelle joen

keskelle ja »Zairen» kauaskantavien tykkien nujertamana Toloni
antautui.
Hänet tuotiin »Zairelle».
Bosambo kohtasi hänet komentosillalla.
— No, Bosambo! sanoi Toloni. — Olen tullut tapaamaan Sandia.
— Näet minut, joka olen kuin herramme, sanoi Bosambo.
Toloni sylki kannelle.
— Kun orja istuu kuninkaan paikalla, niin vain orjat häntä kuulevat,
siteerasi hän Joen sananpartta.
— Kuninkaalla on vain yksi pää, ja orjankin veri on punaista, oli

Bosambolla vastaus valmiina. — Ja huomaan, Toloni, sinun olevan
liian täynnä elämää, jotta herrani voisi olla onnellinen. Mutta ensin
sinun on kerrottava, miten on käynyt Ngombin kuningattaren.
— Hän kuoli, sanoi Toloni huolettomasti, — hän kuoli hyvin äkkiä.
Bosambo tähysti häntä. Se oli Sandersin tähyilemisen jäljittelyä, ja

Ochorin päällikkö osasi jäljitellä.
— Sinun on kerrottava, miten hän kuoli.
Kuninkaan kasvoissa saattoi havaita värähdyksiä.
— Otin häntä kurkusta, sanoi hän hiljaa.

— Tällä tavoin? sanoi Bosambo, ja hänen suuri kätensä tarttui
kuninkaan vahvaan kaulaan.
— Sillä tavoin! haukotteli kuningas. — Ja minä pistin häntä

veitsellä, ah!
— Tällä tavoin? sanoi Bosambo.
Kahdesti hänen pitkä leveäteräinen veitsensä kohosi ja putosi, ja

kuningas vaipui värähtäen kannelle.
*****
Sandi oli kyllin voimissaan tullakseen rannalle »Zairea» vastaan

sen palatessa — kyllin voimissaan, vaikkakin komeuden
sokaisemana tervehtimään Bosamboa, jolla oli taivaansininen,
kullallakirjailtu viitta ja korkea nukkavieru hattu.
Bosambo sipsutteli porraslankkua pitkin heiluttaen

messinkihelaista keppiä ja laulaen laulua, jota Rannikon krulaiset
laulavat, kun ovat saaneet palkkansa ja joutuvat maihin laivastaan.
Hän oli kovin kaunisteltu — hänen hiuksissaan oli sulkia, ja

helminauha helminauhan vieressä riippui hänen kaulassaan.
— Olen tappanut Tolonin, sanoi hän, — aivan kuin herranikin olisi

tehnyt — hän käänsi kasvonsa minusta poispäin ja sanoi, että »on
kunniallista kuolla sinun sylissäsi, Bosambo», ja hän päästeli
tämäntapaisia ääniä…
Ja Bosambo matki ihmeteltävästi.
— Jatka, sanoi Sandi nopeasti.

— Myöskin olen lähettänyt isisiläiset ja akasavalaiset kotiinsa
odottamaan sinun ylhäisyytesi tuomiota, niin kuin olisit itsekin tehnyt,
herra.
Sandi nyökkäsi.
— Entä nämä? kysyi hän osoittaen päällikön koristuksia.
— Nämä minä varastin Tolonin leiristä, sanoi Bosambo.
— Nämä ja muita esineitä, sillä palvelin hallitusta ja herraani, jatkoi

hän käyden yksinkertaiseksi. — Se on valkeiden miesten tapa, kuten
sinun ylhäisyytesi tietää.
LÄHETYSSAARNAAJA
Tämä on moraalinen tarina. Voitte mennä mustiin maihin oppimaan

moraalia ja saada ihmissyöjiltä mitä luotettavimpia siveyssääntöjä.
Sillä ihmissyöjät ovat suuressa määrin tarkkoja, erittäin häveliäitä —
vaikkakin tavallisen Bogran alkuasukkaan valokuva voi antaa aihetta
yhteen ja toiseen ajatukseen — puhtaita puheissa ja tavoissa. Jos
he syövätkin ihmisiä, niin se johtuu siitä, että he pitävät
senlaatuisesta lihasta. He eivät ole parempia eivätkä pahempia kuin
kasvissyöjät, jotka myöskin tarkoin valikoivat syötävänsä.
Alkuasukkailla on omat tapansa, ja he noudattavat perheperinteitä.
Kaksi veljestä eli Isisin maassa pienessä kylässä, ja kun heidän

isänsä kuoli, niin he lähtivät maailmalle hakemaan onneaan. Toisen
nimi oli Mkamdina ja toisen nimi Mkairi. Mkamdina, joka oli
rohkeampi, meni rajan yli Suuren kuninkaan alueelle ja myi siellä
itsensä orjuuteen.
Niihin aikoihin Suuri kuningas oli hyvin suuri ja hyvin vanha; niin
suuri, että mikään brittiläinen kuvernööri ei uskaltanut muuta kuin
pyytää häntä olemaan harjoittamatta julmuuksia.
Tämä Mkamdina oli älykäs nuorukainen, hyvin taitava ja sieti hyvin
pitkälle haukkumisia. Hänellä oli hovimiehen kaikki ominaisuudet. Ei
ole sen vuoksi ihmeteltävää, että hän saavutti aseman kuninkaan
perheessä, istui hänen oikealla puolellaan aterialla ja meni naimisiin
kuninkaan mielitietyn kanssa, jonka tämä hylkäsi.
Hän tuli rikkaaksi ja voimakkaaksi, oli kuninkaan pääministeri

valliten elämää ja kuolemaa tämän poissaollessa. Hän valikoi
herransa tanssitytöt, ja kun hänellä oli niissä asioissa hyvä maku,
hän sai hyvän palkinnon.
Niin hän eli onnellisena, mahtavana ja tyytyväisenä.
Toinen veli, Mkairi, ei ollut yhtä onnekas. Hän asettui pieneen

kylään Henkien putouksen lähelle ja köyhänä miehenä, pystymättä
hankkimaan muuta kuin yhden vaimon, hän uutterasti raivasi
maatilkkua. Siihen hän kylvi työteliäästi, korjasi hyvän sadon ja myi
tuotteensa saaden hiukan voittoa.
Hän kuuli veljensä menestyksestä, ja kerran, huolimatta Sandersin

käskyistä, Suuren kuninkaan pääministerin maalattu kanootti tuli
komeasti jokea myötävirtaan, tuoden lahjoja köyhälle veljelle.
Sanders kuuli tästä ollessaan tarkastusmatkalla ja meni

katsomaan
Mkairia.
— Herra, niin on asia, sanoi mies alakuloisesti. — Suuret lahjat

sain veljeltäni, joka on orja. Suolaa ja viljaa ja keihäänkärkiä hän
lähetti minulle.
Sanders katsoi ympärilleen ja näki köyhän pellon, jonka mies oli
muokannut.
— Ja kuitenkaan, Mkairi, sanoi hän, — tämä ei ole rikkaan miehen

puutarha, enkä näe sinulla hienoja vaatteita enkä vaimoja, joita saat
suolalla.
— Herra, sanoi mies, — lähetin lahjat takaisin, sillä sydäntäni

särkee se, että veljeni on orja ja minä olen vapaa; ja antaisin elämäni
voidakseni maksaa hänen hintansa.
Hän kertoi Sandersille lähettäneensä miehen kysymään, mikä

hinta oli, ja Sanders sattui olemaan itse paikalla, kun Suuri kuningas
huvikseen lähetti sanan, että hinta oli kymmenentuhatta matakoa —
matako oli messinkiputki.
Seitsemän vuotta — pitkiä, piinallisia, kärsimyksentäyteisiä,

vaivalloisia vuosia — Mkairi muokkasi maataan, myi ja osti, antoi
myöten ja tinki, kunnes hänellä oli kymmenentuhatta matakoa. Nämä
hän pani kanoottiinsa ja meni sen maan rajoille, jossa Suuri
kuningas hallitsi, ja tuli siten veljensä ja veljensä herran eteen.
Suuri kuningas nauroi, mutta veli ei nauranut, sillä hän kiukustui

veljensä yksinkertaisuudesta.
— Mene takaisin putkinesi, sanoi hän. Hän istui suurenmoisessa

majassaan ympärillään nauravat vaimot ja orjat. — Ota putkesi,
Mkairi veljeni, ja tiedä, että on parempi olla orja kuninkaan majassa
kuin vapaa mies, joka tonkii peltoja.
Ja Mkairi palasi maahansa sydän kipeänä.

Kolme viikkoa myöhemmin Suuri kuningas kuoli. Nyt ilmenee
tämän lyhyen tarinan moraalinen puoli. Sillä tavan mukaan, kun
Suuri kuningas makasi paareillaan, otettiin Suuren pääorja — ja se
orja oli Mkamdina — ja häneltä leikattiin pää, jotta hänen ruumiinsa
voitaisiin asettaa palvelemaan herransa sielun tarpeita toisessa
maailmassa.
Ja Suuren kuninkaan poika hallitsi hänen sijastaan ja kuoli

aikanaan väkivaltaisesti.
— Tuossa tarinassa on hyvän pyhäkoulukertomuksen perustus,

sanoi hausakapteeni.
— Hm, murahti Sanders, joka ei ollut ensinkään halunnut antaa

aihetta sellaisiin tarinoihin.
— Eriskummallinen pentele, tuo vanha kuningas, sanoi hausa

miettiväisenä, — ja poika oli vielä eriskummallisempi. Sinä hirtit
hänet jostain syystä, vai miten?
— Olen sen unohtanut, sanoi Sanders lyhyesti. — Jos sinun

helvetilliset joukkosi olisivat suolansa arvoiset, ei tarvitsisi ketään
hirttää. Mikä se on?
Hänen palvelijansa seisoi hausapäällikön majan ovella.
— Herra, tässä on kirja, sanoi mies.
Sanders otti mieheltä tahritun kirjekuoren. Siinä oli osoite arabian

kukkaiskielellä:
Herra komissaarille. Joka on kaupungissa siellä, missä joki on

levein lähellä merta. Kaksi lipputankoa pystyssä ja paljon sotilaita
näkyvissä. Mene nopeasti ja Jumala olkoon kanssasi.
— Kuka tämän toi?
— Eräs arabialainen, sanoi mies, — joka on kaupitellut ylimaassa.
Sanders repi kirjeen auki. Hän silmäsi ensin nimikirjoitusta kirjeen

yläkulmassa ja huomasi sen olevan Ahmedin, hänen salaisen
palveluskuntansa luotettavan päällikön.
Sanders luki kirjeen sivuuttaen kukkivan johdannon, jossa Ahmed

pyysi kohtaloa ja sen valtuutettuja asiamiehiä tuomaan onnea
komissaarin huoneelle.
On hyvä, että saan kertoa sinulle tämän, vaikkakin minun on

kätkettävä
silmäni puhuessani sinun perheeseesi kuuluvasta naisesta.
(Sanders ei ollut milläänkään harhaiskusta, joka yhdisti viattoman

naislähetyssaarnaajan nimen hänen omaansa.)
Tästä jumalanaisesta, joka parhaillaan on Joella, kuuluu monta

tarinaa, joista jotkin tietävät hänen itkevän öisin, koska kukaan
akasavalainen ei tunnusta jumalataikaa.
Ja olen kuullut erään isisiläisen naisen, joka on hänen

palvelijansa, kertovan, että tämä jumalanainen menisi takaisin
omaan maahansa, mutta hän on vain häpeissään, kun niin harvat
ovat oppineet Jumalaa. Hänellä on myöskin kuumetta. Lähetän
tämän erään arabialaisen myötä, ystäväni Ahmedin, joka on viisi
päivää etsinyt Akasavassa miestä, joka on varastanut vuohia.
Sanders nauroi avuttomana.

Full Chapter Plant Genomic and Cytogenetic Databases Methods in Molecular Biology 2703 Sonia Garcia PDF

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Full Chapter Plant Genomic and Cytogenetic Databases Methods in Molecular Biology 2703 Sonia Garcia PDF

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Plant Genomic and Cytogenetic

Databases Methods in Molecular

Plant Proteomics Methods and Protocols Methods in

Eukaryotic Genomic Databases Martin Kollmar

Plant Genetics and Molecular Biology Rajeev K. Varshney

Plant Micronutrient Use Efficiency: Molecular and

Molecular Approaches in Plant Biology and Environmental

Cancer Cytogenetics Methods and Protocols Methods in

Neurobiology Methods and Protocols Methods in Molecular

Xylem Methods and Protocols Methods in Molecular

For further volumes:

Sònia Garcia and Neus Nualart

ISSN 1064-3745 ISSN 1940-6029 (electronic)

Paper in this product is recyclable.

Barcelona, Catalonia, Spain Sònia Garcia

PART I GENOMIC DATABASES

1 The Plant Phenomics and Genomics Research Data Repository:

PART II CYTOGENETICS AND CHROMOSOME-RELATED DATABASES

9 The Plant DNA C-Values Database: A One-Stop Shop

12 An Overview to the Index to Chromosome Numbers in Asteraceae

HAYTHAM M. ABD-ELHALIM • Agricultural Genetic Engineering Research Institute,

ROMAIN GUYOT • Department of Electronics and Automation, Universidad Autonoma de

MARIELA A. SADER • Instituto Multidisciplinario de Biologı́a Vegetal (IMBIV), Universidad

The Plant Phenomics and Genomics Research Data

Plant genomics and phenomics studies benefit from methodologi-

One essential cornerstone is the consequent application of

The Leibniz Institute of Plant Genetics and Crop Plant Research

workgroup in 2015 [13]. In 2016 they were finalized and pub-

comprehensive training sets for AI-based models or machine

3 The Electronic Data Archive Library (e!DAL)

The electronic Data Archive Library or e!DAL, for short, is a

Fig. 1 Comparison of data-publication-as-a-service concept and data-publication-on-premise concept. Both

delivered as an extensible and customizable software framework,

• Information Retrieval: Due to a large number of expected data

the classical file-system capability with the flexibility of a relational

In general, there are some recommendations but no fixed

3.1.5 Data Publication Generally, it is impossible to embed comprehensive research data

that the assignment is permitted and controlled by a responsible

matrix, which is also shown in Fig. 3, lets a scientific reviewer or

file type, or file format, will be automatically determined. Further-

based on this core implementation. The whole project is stored in a

4 Plant Phenomics and Genomics Research Data Repository

Based on the previously described e!DAL software infrastructure,

To ensure data findability and accessibility, e!DAL-PGP pro-

This chapter presented the design principles of an infrastructure-to-

— Se asia vaatii miettimistä, sanoi kuningas, — mutta meidän

Sananviejiä tuli ja meni koko sen päivän. Viisi kertaa kuningas

Vannoiko kuningas kuoleman nimessä, että jos suunnitelma

— Älkää tappako häntä, lähetti Toloni sanan, — sillä tiedän hänet

Pikkuisisiläiset olivat kärsimättömiä. Heidän maassaan oli kaksi

— Nämä ovat pikku asioita, sanoi kuningas Toloni. — Ensin

Sinä iltana, kun pimeys tuli ja hänen mitään tietämättömät

Kuningas kuuli majansa merkkirummun äänen ja tunsi sen

Majansa edessä, kädet kummallakin korvallisillaan, kuningas

Kolme pärrytystä, nousevia ja laskevia, hidas kalistus, pärrytys,

Se merkitsi Sandia — nopea Sandi, tulinen Sandi, yllättävä Sandi,

Kaukainen rumpu ilmaisi kaikki nämä luonteelliset maininnat.

Kahdesti kaukainen lokali kertoi Sandin nimen, sitten pitkä

Taas — pitkä pärrytys, lyhyt pärrytys — hiljaisuus.

Tolonin ääni oli terävä ja riemukas.

— Kuulkaa! kuiskasi hän.

Metallinsointuisia lyöntejä, joihin liittyi säännöttömiä, matalia ääniä

Oli ammuttu paljon.