3 Search Results for "Splendiani, Andrea"

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
Vision
DOI: 10.4230/TGDK.1.1.10
Multilingual Knowledge Graphs and Low-Resource Languages: A Review

Authors: Lucie-Aimée Kaffee, Russa Biswas, C. Maria Keet, Edlira Kalemi Vakaj, and Gerard de Melo

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
There is a lack of multilingual data to support applications in a large number of languages, especially for low-resource languages. Knowledge graphs (KG) could contribute to closing the gap of language support by providing easily accessible, machine-readable, multilingual linked data, which can be reused across applications. In this paper, we provide an overview of work in the domain of multilingual KGs with a focus on low-resource languages. We review the current state of multilingual KGs along with the different aspects that are crucial for creating KGs with language coverage in mind. Special consideration is given to challenges particular to low-resource languages in KGs. We further provide an overview of applications that yield multilingual KG information as well as downstream applications reusing such multilingual data. Finally, we explore open problems regarding multilingual KGs with a focus on low-resource languages.
Cite as

Lucie-Aimée Kaffee, Russa Biswas, C. Maria Keet, Edlira Kalemi Vakaj, and Gerard de Melo. Multilingual Knowledge Graphs and Low-Resource Languages: A Review. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 10:1-10:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{kaffee_et_al:TGDK.1.1.10,
  author =	{Kaffee, Lucie-Aim\'{e}e and Biswas, Russa and Keet, C. Maria and Vakaj, Edlira Kalemi and de Melo, Gerard},
  title =	{{Multilingual Knowledge Graphs and Low-Resource Languages: A Review}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{10:1--10:19},
  ISSN =	{2942-7517},
  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.1.1.10},
  URN =		{urn:nbn:de:0030-drops-194845},
  doi =		{10.4230/TGDK.1.1.10},
  annote =	{Keywords: knowledge graphs, multilingual, low-resource languages, review}
}
Document
DOI: 10.4230/DagSemProc.05441.3
Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper)

Authors: Andrea Splendiani

Published in: Dagstuhl Seminar Proceedings, Volume 5441, Managing and Mining Genome Information: Frontiers in Bioinformatics (2006)

Abstract
Studying biological organisms at the systems level is a complex task. Computational approaches require structured representations of existing biological knowledge. This necessity has prompted the development of formal representations of specific areas of knowledge, resulting in ontologies such as Gene Ontology and BioPAX. However, only part of this formalized knowledge is exploited for the interpretation of experimental data. Specifically, it is common to use the association between entities and annotations, like genes and functions, while the structure of the annotation is not considered beyond some common features as inheritance. This is partly due to a lack of tools and methods that bridge resources related to ontologies to the ones related to data analysis. Here we present a platform that merges a semantic web toolkit with a widely adopted modular tool for systems biology investigation. We demonstrate how in this environment it is possible to query ontologies not only as a list of annotations but as a knowledge base from which new information can be derived. We also show how this knowledge can be integrated with biological data.
Cite as

Andrea Splendiani. Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper). In Managing and Mining Genome Information: Frontiers in Bioinformatics. Dagstuhl Seminar Proceedings, Volume 5441, pp. 1-24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{splendiani:DagSemProc.05441.3,
  author =	{Splendiani, Andrea},
  title =	{{Semantic browsing of pathway ontologies and biological networks with RDFScape (working paper)}},
  booktitle =	{Managing and Mining Genome Information: Frontiers in Bioinformatics},
  pages =	{1--24},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5441},
  editor =	{Jacek Blazewicz and Johann Christoph Freytag and Martin Vingron},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05441.3},
  URN =		{urn:nbn:de:0030-drops-4746},
  doi =		{10.4230/DagSemProc.05441.3},
  annote =	{Keywords: Pathways, Semantic Web, Ontologies, Microarrays}
}
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