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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Graphs with Free Software</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Simon Bin</string-name>
          <email>sbin@informatik.uni-leipzig.de</email>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Claus Stadler</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Norman Radtke</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Kurt Junghanns</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Sabine Gründer-Fahrer</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Institute for Applied Informatics (InfAI)</institution>
          ,
          <addr-line>Leipzig</addr-line>
        </aff>
      </contrib-group>
      <abstract>
        <p>We present an Open Source base platform for theCoyPu knowledge graph project in the resilience domain. We report on our experiences with several tools which are used to create, maintain, serve, view and explore a modular large-scale knowledge graph, as well as the adaptions that were necessary to enable frictionless interaction from both performance and usability perspectives. For this purpose, several adjustments had to be made. We provide a broad view of diferent programs which are of relevance to this domain. We demonstrate that while it is already possible to achieve good results with free software, there are still several pain points that need to be addressed. Resolution of these issues is often not only a matter of configuration but requires modification of the source code as well.</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>1. Introduction</title>
      <p>Semantic knowledge graphs (KGs) nowadays not only have become a key asset for search
engines but are at the centre of numerous applications, for instance, in data analytics, question
answering, recommendation systems, and decision support.</p>
      <p>Current interest from research communities as well as industries and administration rests on
the capability of KGs to capture comprehensive machine-readable knowledge in application
scenarios and their strengths in integrating, managing and exploiting information from
heterogeneous data sources at scale. One especially interesting application scenario for KGs is crisis
and resilience research. Semantic KGs can play a crucial role in increasing transparency of, for
instance, economic value chains and in understanding the complex mechanisms of crisis factors
at a global level.</p>
      <p>
        Although methodologies and strategies for building knowledge graphs vary based on the
specific conditions and requirements of individual use cases, the creation, utilisation, and
maintenance of KGs involve several common necessities and corresponding implementation
phases. These processes have been discussed for more than twenty years [
        <xref ref-type="bibr" rid="ref1 ref2 ref3 ref4">1, 2, 3, 4</xref>
        ]. While
general approaches for KG development and maintenance are proposed, limited guidance
regarding the selection of eficient tools for implementing these methodologies is available.
CEUR
      </p>
      <p>
        Knowledge graph engineering must address additional challenges in today’s rapidly evolving
landscape. Firstly, contemporary knowledge graphs should adhere to Linked Open Data
requirements, such as the FAIR [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ] data principles (Findable, Accessible, Interoperable, and Reusable)
and the 5-star Open Data Model.1 These standards ensure that the resulting knowledge graphs
can be easily discovered, understood, and integrated with other datasets, promoting data sharing
and collaboration across various domains. Secondly, knowledge graph engineering projects
often involve teams with diverse backgrounds and expertise levels in ontology authoring.
Consequently, the tools used for KG engineering must cater to both ontology experts and
domain-specific specialists, facilitating efective real-time collaboration and allowing all team
members to contribute meaningfully to the development and maintenance of the knowledge
graph.
      </p>
      <p>We aim to create a knowledge graph-based platform for managing and exploring supply chain
data. The platform will ofer customised views for scientists, engineers, and decision-makers to
foster collaboration and interaction with the knowledge graph. Our goal is to enable users to
analyse complex data, make informed decisions, and contribute to a resilient economy.</p>
    </sec>
    <sec id="sec-2">
      <title>2. Related work</title>
      <p>
        Recent studies [
        <xref ref-type="bibr" rid="ref10 ref6 ref7 ref8 ref9">6, 7, 8, 9, 10</xref>
        ] have shown that there are many diferent approaches for
building specific KGs. Limitations are often faced regarding the approaches’ scalability, metadata
and ontology management, entity resolution and fusion, incremental updates, and quality
assurance [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ].
      </p>
      <p>While certain commercial tools like metaphactorya or the Enterprise Knowledge Graph
Platformb claim to ofer comprehensive, all-in-one solutions, free and open-source alternatives
often only address specific aspects. Consequently, users seeking to employ free and open-source
tools must combine multiple applications and platforms to arrive at a complete knowledge
graph platform.</p>
      <p>
        When embarking on the creation of a custom stack for knowledge graph and ontology
engineering, a valuable starting point for discovering relevant tools are link collections. Two
notable lists in this domain include the Awesome Knowledge Graph2 and the Awesome Semantic
Web3 repositories on GitHub. However, it is crucial to be aware that despite being curated,
these lists may still sufer from link rot, leading to outdated or non-functional resources. The
previously popular list hosted on the W3C website4 is rather outdated, with only 4 out of
21 listed tools still operable at the time of writing in the category of “RDF or OWL browser”
(LodViewc, Rhizomer [
        <xref ref-type="bibr" rid="ref12 ref38">12</xref>
        ], Structured Data Linter, and VocBench [
        <xref ref-type="bibr" rid="ref13">13</xref>
        ]). Refer to Table 1 for an
overview of the tools mentioned in this paper.
      </p>
      <sec id="sec-2-1">
        <title>1https://5stardata.info/ 2https://github.com/totogo/awesome-knowledge-graph 3https://github.com/semantalytics/awesome-semantic-web 4https://www.w3.org/2001/sw/wiki/Category:RDF_or_OWL_Browser</title>
        <p>T-Box</p>
        <sec id="sec-2-1-1">
          <title>Widoco</title>
          <p>View
Source</p>
        </sec>
        <sec id="sec-2-1-2">
          <title>Protégé</title>
          <p>OWL
RDFS</p>
          <p>RDF</p>
          <p>Shacl
DALICC
Apache Jena Fuseki
A-Box</p>
        </sec>
        <sec id="sec-2-1-3">
          <title>Ontodia Linked Data Viewer tarql RPT</title>
        </sec>
      </sec>
    </sec>
    <sec id="sec-3">
      <title>3. Solution and other tools</title>
      <p>In the following, we will show how we tackle the previous concerns with free and open-source
tools. Our solution and the utilised tools are shown inFigure 1.</p>
      <p>
        Ontology authoring. Part of creating knowledge graphs involves creating a schema
(ontology) for your data. We used the venerable Protégé [
        <xref ref-type="bibr" rid="ref14">14</xref>
        ] for this purpose. We looked but failed
to find other comparable OWL 5 authoring tools. While working on the ontology together with
the partners, we found the best working approach to discuss one step of ontology evolution in
a group and then designate one person to implement the change. Afterwards, the change could
be reviewed on a source code control system. For the latter, it should also be ensured that all
engineers are using the same version of Protégé, this will ensure that the textual diference of
changes to the ontology is minimal and limited to the actual changes implemented.
whenever the ontology files are changed in the Git source code repository on GitLab.6
ult on ‹https://schema.coypu.org/›. We have created a pipeline that updates our documentation
5Web Ontology Language, https://www.w3.org/TR/owl2-overview/
6Source code for the pipeline script ongitlab.com/coypu-project/coy-ontologyin the supplements folder
n
o
i
t
a
c
i
f
i
c
e
y
g
o
n
O
      </p>
      <p>another organization.
p Term status
S
tlo has super-classes</p>
      <p>Company c
identity militiasc
t
Simofan Bin et al. CEUR Workshop Proceedings
r
D IRI: https://schema.coypu.org/global#Customer</p>
      <p>CoyPu graph: Not currently in use
An organization that sources something needed such as a product or service from
IRI: https://schema.coypu.org/global#IdentityMilitias
Term status
Term rationale</p>
      <p>CoyPu graph: In use, distinct subjects: 7977
CoyPu graph: ---USED BUT NOT IN
ONTOLOGY--back to ToC or Class ToC</p>
      <p>
        1–13
back to ToC or Class ToC
in the ontology, whereas the term “Customer” is contained in the ontology but not (yet) used
in the knowledge graph. Calculation of the usage statistics is done using the RDF Processing
Toolkit (RPT)g with a set of VoID [
        <xref ref-type="bibr" rid="ref17">17</xref>
        ]-generating SPARQL queries.7
      </p>
      <p>Automated pipelines that run automatically whenever changes to your ontology are
committed to a source code control system, require integration with the source code control system.
There are two common ways to realise pipelines. One is to use the platform-specific CI/CD
pipelines,8 the other is using a Webhook event9 to trigger the start of an external pipeline.</p>
      <p>
        To further increase the quality of our ontology, we have started to implement RDFUnit 1[
        <xref ref-type="bibr" rid="ref8">8</xref>
        ]
rules that check the ontology details and version. Another standard with growing adoption
is the Shapes Constraint Language (SHACL),10 which might be validated for example using
pySHACL [
        <xref ref-type="bibr" rid="ref19">19</xref>
        ] or Jena SHACLh.
      </p>
      <p>Mapping structured data to RDF data.</p>
      <sec id="sec-3-1">
        <title>A big part of our knowledge graph is not our</title>
        <p>original creation, but rather the mapping and integration, combination, and refinement of
existing data sources. Most of the data sources we used are structured data, for example in
XML, GML, JSON, CSV formats or data returned by Web APIs. Other parts of the data were
also extracted and semantified from unstructured or semi-structured data like news articles.</p>
        <p>
          Several diferent tools were used by the diferent project partners, for example Tarql i, RPT or
Morph-KGC [
          <xref ref-type="bibr" rid="ref20">20</xref>
          ]. Each tool was chosen by the familiarity of the expert user and applicability
to the data source that is to be mapped. Tarql for instance is an excellent choice to map CSV
to RDF. RPT on the other hand can easily process CSV, JSON, and XML input files as well as
web APIs and remote services using SPARQL, and Morph-KGC can map CSV or connect to SQL
databases using RML.
such functions using either JavaScript or Java annotations1.1 We also tested some commercial
web-form based mapping editor, but found it to be rather cumbersome when having to edit and
refine the mappings compared to a good old programmers’ text editor.
        </p>
        <p>
          Further tools used by our partners include Named entity recognition from text using
Falcon 2.0 [
          <xref ref-type="bibr" rid="ref24">24</xref>
          ] as well as many custom-written programs.12 For some of these, the Python RDFLibj
was a popular choice when producing RDF data.
        </p>
        <p>
          Dereference and visualise the Graph. In our experience in the CoyPu project, we found
it extremely helpful to grasp the Semantic Web concepts when the IRIs are dereferenceable,
i.e. you can open the IRIs of your graph entities in the browser. Users and experts alike want
to see and understand what is “in” the graph. The classes and properties are dereferenceable
through the use of Widoco and publishing the ontology documentation at the same location
as the Ontology IRI. To make the data dereferenceable and browseable, tools like Trifid k and
LodView can be used. It was easy to start Trifid with the Docker image provided by the authors.
However, the default view is a bit bland. There is a great overview of tools presented in [
          <xref ref-type="bibr" rid="ref25">25</xref>
          ],
but we found that at the time of writing only LodView and Trifid were still available.
9https://progrium.github.io/blog/2007/05/03/web-hooks-to-revolutionize-the-web/
11https://docs.oracle.com/javase/6/docs/technotes/guides/language/annotations.html
12https://docs.coypu.org/ExternalRepositories.html
        </p>
        <p>Linked Data Viewer
Greece
+
−
▨ rdf: type
▨ geo: hasGeometry</p>
        <p>Leaflet | © OpenStreetMap
https://data.coypu.org/country/GRC
▨ : country/GRC/geometry
▨ : country/GRC/geometry/boundary
Resolve labels en</p>
        <p>Calculate inferences
Local Browsing | Explore | Link
▨ rdfs: label</p>
        <p>Greece @en</p>
        <p>Our solution for IRI dereferencing (see Figure 3) is built on top of the Trifid rendering
componentl. Compared to Trifid, we have extended the code for full client-side querying,
a map widget for resources with geospatial data, rendering of inverse relations (similar to
LodView), source attribution (useful to know which data set the entity is from), lazy pagination
for many property values, label resolution and language switching, colour cards for
namespaces and optional inferencing. Furthermore, we support browser-based authentication for
password-protected graph databases.</p>
        <p>
          To make the graph explorable and the graph-based nature understandable, we have found the
Ontodia Graph Explorer (see Figure 4) [
          <xref ref-type="bibr" rid="ref26">26</xref>
          ]. It allows one to interactively add existing entities
from the knowledge graph to a drawing area on the screen, and will automatically add the links
between entities. It can also show the Ontology schema in a tree fashion and will show a list
of instances of the selected ontology class. We refined the graph explorer with a geo-spatial
map widget and the possibility to hide obstructive properties. Further, we included meta-data
schema and concept schema in the class tree. As a convenience, we have also integrated a link
into the Linked Data Viewer which will add the current entity to the graph explorer, and we
have made it possible to share created knowledge graph diagrams with other users through
custom links.
        </p>
        <p>Country
C Russia
has country location</p>
        <p>External%2FOtherForces, StateForces</p>
        <p>E Police Forces of Russia (2000-) F…
A Ukraine</p>
        <p>Administrative…</p>
        <p>has actor</p>
        <p>T Tgheinogmetry
IRI: https://data.coypu.org/event/acled/8005488/geometry
has country location</p>
        <p>Attack, Conflict, Event</p>
        <p>A Attack - Ukraine - Simferopol
IRI: https://data.coypu.org/event/acled/8005488
comment
+
−</p>
        <p>hasGeometry
Leaflet | © OpenStreetMap contributors</p>
        <p>On 11 May 2021, the
Russian Federal
Security Service shot
dead an Uzbek
national in Simferopol
district, Crimea,
during searches.</p>
        <p>Human rights activists
condemned police
b t lit
map13 map widget, it is possible to present and verify the SPARQL results of geospatial data
and numeric data easily.</p>
        <p>Documentation and Dataset catalogue.</p>
        <p>To provide project documentation, we make use of
Just the Docsm. The documentation can be written in Markdown in our source control system
and is then deployed on ‹https://docs.coypu.org/› using a pipeline. The configuration has been
extended with a “Try it!” link on SPARQL queries,14 so that these can be tried out directly on
the Jena Fuseki User Interface.</p>
        <p>
          Additionally, a tabular listing of our data catalogue content is published at h‹ttps://datasets.
coypu.org/› by automatically executing SPARQL queries on our knowledge graph and rendering
the result to Markdown. This is done by feeding the SPARQL CSV output [
          <xref ref-type="bibr" rid="ref31">31</xref>
          ] into csvlookn.
        </p>
        <p>
          The data catalogue itself is hand-created in RDF/Turtle format and collects all the details about
13https://www.openstreetmap.org, implemented with Leaflet: https://leafletjs.com/
14https://gitlab.com/coypu-project/skynet/platform-exhibits/-/tree/main/just-the-docs
the externally sourced data that is being used in the CoyPu project. This includes licensing
information, links to the data source, the target RDF graph where this data set is loaded and a
link to the Data Licenses Clearance Center [
          <xref ref-type="bibr" rid="ref32">32</xref>
          ]15 (DALICC) licence where available. We plan
to record further meta-data into our catalogue, such as the tools involved in transforming the
original data into RDF data.
        </p>
        <p>The DALICC ofers a RESTful web service that supports automated clearance of rights thus
supporting the legally secure and time-eficient re-utilisation of third-party data sources . The
service is also named DALICC and the source code can be found on GitHub. It is possible
to run your own instance of DALICC but some features like the usage of a remote SPARQL
endpoint are missing at the moment. We also consider extending the service with a feature
that helps to examine the rights and permission of data, derived from multiple datasets (e.g.
via SPARQL queries).</p>
        <p>Hosting and serving the knowledge graph.</p>
      </sec>
      <sec id="sec-3-2">
        <title>We use Apache Jena [33] Fuseki backed by</title>
        <p>Apache Jena TDB2, both combined making a full-fledged SPARQL Endpoint for scripts and
programs to work with. Getting started is mostly straightforward, for a simple deployment you
can download the Apache Jena Fuseki release and start it (Java is required).</p>
        <p>
          Extensive customisation has been added to our Jena Fuseki. First of all, we configured
geospatial16 and Lucene [
          <xref ref-type="bibr" rid="ref34">34</xref>
          ] text index in Fuseki.17 The endpoint for the Graph Store Protoco1l8
was moved from the Fuseki-default to a/data sub-path, to stop inadvertent dumps of the full
graph. The endpoint has been access-restricted using Apache Shiro that is included in Fuseki19
(we hope to make it publicly available at a later date).
        </p>
        <p>
          We identified a performance bottleneck involving SPARQL FROM queries and implemented a
FROM-as-GRAPH filter for Jena. Concerning the geospatial data, we added GeoSPARQL functions
such as lat, lon (to access the latitude and longitude of a point),centroid and aggUnion
(from the upcoming GeoSPARQL 1.1 standard [
          <xref ref-type="bibr" rid="ref35">35</xref>
          ]) and simplifyDp (to simplify a geometry)
or lineMerge20 functions, which we have suggested to the Open Geospatial Consortium for
consideration. Additionally, the geospatial index was reprogrammed to work on a per-graph
level rather than on the whole data set, and we also implemented a Fuseki service to recompute
the geo-index of individual graphs at run-timeo. The initial loading time of the index was
also heavily improved due to a custom serialisation format. To aid in RDFS21 reasoning and
owl:sameAs [
          <xref ref-type="bibr" rid="ref36">36</xref>
          ] resolution, we have implemented two new SPARQL-SERVICE based RDFS
and sameAs inferencers. They are also conveniently exposed in our linked data viewer (see
Dereference and visualise the Graph). These additional functions are implemented in our JenaXp
extension modules for Apache Jena.
16https://jena.apache.org/documentation/geosparql/geosparql-assembler
17https://jena.apache.org/documentation/query/text-query.html#text-dataset-assembler
18https://www.w3.org/TR/sparql11-http-rdf-update/
19https://jena.apache.org/documentation/fuseki2/fuseki-security.html
Server Infrastructure. The knowledge graph and the associated processes cannot
conveniently operate on free resources. To deploy our knowledge graph, we have a physical server
with 250 GiB main memory, of which the Apache Jena Fuseki server is using 50 GiB. According
to one of the Jena maintainers2,2 per TDB2 database approx. 2 GiB heap should be assigned
(we have configured 10 databases). We have configured the Java heap space to 32 GiB 23 (after
having experimented with smaller values, but those were found insuficient when executing
larger CONSTRUCT or UPDATE queries).
        </p>
        <p>The on-disk database files take currently 200 GiB of disk space, which amounts to 700 million
(7 ⋅ 108) triples spread across 39 graphs. For the spatial index for GeoSPARQL, 300 MiB of disk
space is used for our 4 million (4 ⋅ 106) geometries. The database files are stored on 4 SATA QLC
SSDs operating in a software RAID. Fuseki is accessing the database files using memory-mapped
I/O. Scanning through the whole index takes 200 seconds and scanning the whole literal table
takes 50 minutes.</p>
        <p>To create the initial database, we used RPT to convert all the output from our various mapping
tools into N-Quads format and then thexloader script included in Fuseki. We did this after
testing all the various loaders provided by Fuseki and determining that this script works best for
our hardware/configuration. Altogether, it takes 8 hours for our system to convert the source
RDF files into a Fuseki TDB2 database. The break-down is as follows: 3h 20m for mapping the
data, 4h 20m for loading into TDB2, 1 minute to calculate the statistics for the query optimiser,
7 minutes to calculate the geospatial index for GeoSPARQL queries, 20 minutes to calculate a
Lucene index for full-text search on the RDFS labels and just short of 1 minute to reload the
database. (All times, sizes, and triple counts are approximate.)24</p>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>4. Conclusion</title>
      <p>Many free and open-source software components have been created by the community when it
comes to knowledge graph serving and preparation. Nevertheless, it can be challenging to set
up the individual software components and configure them in the right way to work together.
We had to manually configure nearly all of the components, which requires a diverse skill set
ranging from Docker, YAML, JSON, and Bash, to SPARQL, JavaScript, and Java.</p>
      <p>The remaining pain points are the long loading times and the query performance for more
complex SPARQL queries as well as missed automatic optimisations when using the full-text
search. Other issues could be improved, such as the per-graph Geo-index, but could be further
enhanced for example by implementing a self-updating geo-index.</p>
      <p>
        We gave impulses to heavily optimise the speed of certain specific queries such as the named
graph list27 and raised other issues as we met them. Other improvements have been contributed
22https://lists.apache.org/thread/43vo5pdgfy0mst2pl6ppyyf65bwf7yb2
23java -Xmx command line flag
24An initial stumbling block for us was that the server was originally provided to the project with a ZFS RAID-1
iflesystem [
        <xref ref-type="bibr" rid="ref37">37</xref>
        ] on Ubuntu. Despite database-specific tuning 25 we were unable to make it work satisfactorily. The
system Input-output load became unbearably high so we had to reinstall the system using the ext426 filesystem.
25https://openzfs.github.io/openzfs-docs/Performance%20and%20Tuning/Workload%20Tuning.html
26https://www.kernel.org/doc/Documentation/filesystems/ext4.txt
27https://github.com/apache/jena/pull/1655
directly by us, such as speed-ups for certain path query patterns, geospatial queries, or a whole
new bulk SPARQL service and cache implementation. Yet other improvements such as the
per-graph geo-index are still work-in-progress in our fork of Apache Jena, or part of our JenaX
extension modules for Apache Jena. We plan to upstream our changes if possible, and to provide
a docker compose file for easy reproducing of the set-up described in this paper.
      </p>
    </sec>
    <sec id="sec-5">
      <title>Acknowledgments</title>
      <p>The authors acknowledge the financial support by the Federal Ministry for Economic Afairs
and Energy of Germany in the project Coypu (project number 01MK21007[A-L]).</p>
      <p>Commercial
metaphactory
Enterprise Knowledge
Graph Platform
TopBraid Composer Authoring</p>
      <p>Free software</p>
      <p>Authoring
franz.com/agraph/tbc
BSD-3-Clause
Authoring</p>
      <p>BSD-2-Clause
Mapping+</p>
      <p>
        Apache-2.0
b
[
        <xref ref-type="bibr" rid="ref18">18</xref>
        ]+
[
        <xref ref-type="bibr" rid="ref19">19</xref>
        ]+
h+
c+
k+
j+
p+
      </p>
      <p>VocBench
Protégé
Version 5.6.1
Widoco
Version 1.4.17
pyLODE
YASGUI
GeoYASGUI</p>
      <p>Repository / Website
Docu.</p>
      <p>Docu.</p>
      <p>Docu.</p>
      <p>Docu.</p>
      <p>Docu.</p>
      <p>NER</p>
      <p>Deref.</p>
      <p>Explore
Explore
Explore
Explore
Explore
Explore</p>
      <p>Apache-2.0</p>
      <p>GPL-3.0 /
BSD-3-Clause</p>
      <p>MIT
MIT</p>
      <p>MIT
BSD-2-Clause</p>
      <p>Apache-2.0
Apache-2.0</p>
      <p>MIT
Apache-2.0</p>
      <p>MIT
BSD-3-Clause
Apache-2.0</p>
    </sec>
  </body>
  <back>
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