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Documents authored by Jiménez-Ruiz, Ernesto

Artifact
Software
DOI: 10.4230/artifacts.22938
KG2Tables

Authors: Nora Abdelmageed, Ernesto Jiménez-Ruiz, Oktie Hassanzadeh, and Birgitta König-Ries

Abstract
Cite as

Nora Abdelmageed, Ernesto Jiménez-Ruiz, Oktie Hassanzadeh, Birgitta König-Ries. KG2Tables (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@misc{dagstuhl-artifact-22938,
   title = {{KG2Tables}}, 
   author = {Abdelmageed, Nora and Jim\'{e}nez-Ruiz, Ernesto and Hassanzadeh, Oktie and K\"{o}nig-Ries, Birgitta},
   note = {Software (visited on 2025-04-11)},
   url = {https://github.com/fusion-jena/KG2Tables},
   doi = {10.4230/artifacts.22938},
}
Document
Resource Paper
DOI: 10.4230/TGDK.3.1.1
KG2Tables: A Domain-Specific Tabular Data Generator to Evaluate Semantic Table Interpretation Systems (Resource Paper)

Authors: Nora Abdelmageed, Ernesto Jiménez-Ruiz, Oktie Hassanzadeh, and Birgitta König-Ries

Published in: TGDK, Volume 3, Issue 1 (2025). Transactions on Graph Data and Knowledge, Volume 3, Issue 1

Abstract
Tabular data, often in the form of CSV files, plays a pivotal role in data analytics pipelines. Understanding this data semantically, known as Semantic Table Interpretation (STI), is crucial but poses challenges due to several factors such as the ambiguity of labels. As a result, STI has gained increasing attention from the community in the past few years. Evaluating STI systems requires well-established benchmarks. Most of the existing large-scale benchmarks are derived from general domain sources and focus on ambiguity, while domain-specific benchmarks are relatively small in size. This paper introduces KG2Tables, a framework that can construct domain-specific large-scale benchmarks from a Knowledge Graph (KG). KG2Tables leverages the internal hierarchy of the relevant KG concepts and their properties. As a proof of concept, we have built large datasets in the food, biodiversity, and biomedical domains. The resulting datasets, tFood, tBiomed, and tBiodiv, have been made available for the public in the ISWC SemTab challenge (2023 and 2024 editions). We include the evaluation results of top-performing STI systems using tFood Such results underscore its potential as a robust evaluation benchmark for challenging STI systems. We demonstrate the data quality level using a sample-based approach for the generated benchmarks including, for example, realistic tables assessment. Nevertheless, we provide an extensive discussion of KG2Tables explaining how it could be used to create other benchmarks from any domain of interest and including its key features and limitations with suggestions to overcome them.
Cite as

Nora Abdelmageed, Ernesto Jiménez-Ruiz, Oktie Hassanzadeh, and Birgitta König-Ries. KG2Tables: A Domain-Specific Tabular Data Generator to Evaluate Semantic Table Interpretation Systems (Resource Paper). In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 1, pp. 1:1-1:28, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{abdelmageed_et_al:TGDK.3.1.1,
  author =	{Abdelmageed, Nora and Jim\'{e}nez-Ruiz, Ernesto and Hassanzadeh, Oktie and K\"{o}nig-Ries, Birgitta},
  title =	{{KG2Tables: A Domain-Specific Tabular Data Generator to Evaluate Semantic Table Interpretation Systems}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:28},
  ISSN =	{2942-7517},
  year =	{2025},
  volume =	{3},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.3.1.1},
  URN =		{urn:nbn:de:0030-drops-230104},
  doi =		{10.4230/TGDK.3.1.1},
  annote =	{Keywords: Semantic Table Interpretation (STI), Knowledge Graph (KG), STI Benchmark, Food, Biodiversity, Biomedical}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
Survey
DOI: 10.4230/TGDK.1.1.11
How Does Knowledge Evolve in Open Knowledge Graphs?

Authors: Axel Polleres, Romana Pernisch, Angela Bonifati, Daniele Dell'Aglio, Daniil Dobriy, Stefania Dumbrava, Lorena Etcheverry, Nicolas Ferranti, Katja Hose, Ernesto Jiménez-Ruiz, Matteo Lissandrini, Ansgar Scherp, Riccardo Tommasini, and Johannes Wachs

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
Openly available, collaboratively edited Knowledge Graphs (KGs) are key platforms for the collective management of evolving knowledge. The present work aims t o provide an analysis of the obstacles related to investigating and processing specifically this central aspect of evolution in KGs. To this end, we discuss (i) the dimensions of evolution in KGs, (ii) the observability of evolution in existing, open, collaboratively constructed Knowledge Graphs over time, and (iii) possible metrics to analyse this evolution. We provide an overview of relevant state-of-the-art research, ranging from metrics developed for Knowledge Graphs specifically to potential methods from related fields such as network science. Additionally, we discuss technical approaches - and their current limitations - related to storing, analysing and processing large and evolving KGs in terms of handling typical KG downstream tasks.
Cite as

Axel Polleres, Romana Pernisch, Angela Bonifati, Daniele Dell'Aglio, Daniil Dobriy, Stefania Dumbrava, Lorena Etcheverry, Nicolas Ferranti, Katja Hose, Ernesto Jiménez-Ruiz, Matteo Lissandrini, Ansgar Scherp, Riccardo Tommasini, and Johannes Wachs. How Does Knowledge Evolve in Open Knowledge Graphs?. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 11:1-11:59, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{polleres_et_al:TGDK.1.1.11,
  author =	{Polleres, Axel and Pernisch, Romana and Bonifati, Angela and Dell'Aglio, Daniele and Dobriy, Daniil and Dumbrava, Stefania and Etcheverry, Lorena and Ferranti, Nicolas and Hose, Katja and Jim\'{e}nez-Ruiz, Ernesto and Lissandrini, Matteo and Scherp, Ansgar and Tommasini, Riccardo and Wachs, Johannes},
  title =	{{How Does Knowledge Evolve in Open Knowledge Graphs?}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{11:1--11:59},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.11},
  URN =		{urn:nbn:de:0030-drops-194855},
  doi =		{10.4230/TGDK.1.1.11},
  annote =	{Keywords: KG evolution, temporal KG, versioned KG, dynamic KG}
}
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