32 Search Results for "Almeida, José João"

Document
Survey
DOI: 10.4230/TGDK.4.1.2
Temporal Modelling in Cultural Heritage Knowledge Graphs: Use Cases, Requirements, Evaluation, and Decision Support

Authors: Oleksandra Bruns, Jörg Waitelonis, Jeff Z. Pan, and Harald Sack

Published in: TGDK, Volume 4, Issue 1 (2026). Transactions on Graph Data and Knowledge, Volume 4, Issue 1

Abstract
Our culture, history and world are in constant motion, continuously shaped by the flow of time, evolving narratives, and shifting relationships. Capturing this temporal complexity within cultural heritage (CH) knowledge graphs is essential for preserving the dynamic nature of human heritage. However, standard RDF predicates fail to effectively model the temporal aspects of cultural data, such as changing facts, evolving relationships, and temporal concepts. Over the past two decades, a variety of RDF-based approaches have been proposed to address this limitation, yet guidance is missing on which method best suits specific CH contexts. This paper presents a systematic evaluation of temporal RDF modelling approaches from a CH perspective. Based on an analysis of real-world CH use cases, core temporal requirements are identified that reflect both modelling expressivity and practical concerns. Six prominent approaches - RDF*, tRDF, Named Graphs, Singleton Property, N-ary Relations, and 4D Fluents - are assessed across these requirements. Our findings reveal that no single solution fits all scenarios, but suitable approaches can be selected based on project-specific priorities. To support practitioners, a decision-support tool is introduced to guide them in selecting the most suitable extension for their specific needs. This work provides practical guidance for CH modelling and contributes to the broader development of temporally aware Linked Data.
Cite as

Oleksandra Bruns, Jörg Waitelonis, Jeff Z. Pan, and Harald Sack. Temporal Modelling in Cultural Heritage Knowledge Graphs: Use Cases, Requirements, Evaluation, and Decision Support. In Transactions on Graph Data and Knowledge (TGDK), Volume 4, Issue 1, pp. 2:1-2:46, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@Article{bruns_et_al:TGDK.4.1.2,
  author =	{Bruns, Oleksandra and Waitelonis, J\"{o}rg and Pan, Jeff Z. and Sack, Harald},
  title =	{{Temporal Modelling in Cultural Heritage Knowledge Graphs: Use Cases, Requirements, Evaluation, and Decision Support}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:46},
  ISSN =	{2942-7517},
  year =	{2026},
  volume =	{4},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.4.1.2},
  URN =		{urn:nbn:de:0030-drops-256871},
  doi =		{10.4230/TGDK.4.1.2},
  annote =	{Keywords: Temporal Data Representation, RDF Extensions, Cultural Heritage, Knowledge Graphs}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2025.4
Ensuring Convergence and Invariants Without Coordination

Authors: Dina Borrego, Nuno Preguiça, Elisa Gonzalez Boix, and Carla Ferreira

Published in: LIPIcs, Volume 333, 39th European Conference on Object-Oriented Programming (ECOOP 2025)

Abstract
The CAP theorem demonstrates a trade-off between consistency and availability (and, by extension, latency) in systems where network partitions are unavoidable, such as in cloud computing and local-first software. While adopting weak consistency can preserve availability, it may result in inconsistencies that compromise application correctness. Replicated data types provide a principled, coordination-free approach to guarantee convergence but do not consider application invariants. Existing methods for maintaining invariants in replicated systems either rely on coordination - undermining the benefits of weak consistency - or suffer from limited applicability. This paper introduces the No-Op framework, a generic approach for enforcing consistency without coordination while guaranteeing both convergence and invariant preservation. The core idea of the No-Op approach is to resolve conflicts among concurrent operations by prioritising one operation over the other according to programmer-defined conflict resolution policies. This prioritisation transforms the less-preferred operation into a no-side-effect operation, ensuring conflict-free execution. We formalise the model underlying the No-Op framework and introduce a replication protocol built upon it, accompanied by a formal proof of correctness for both the framework and the protocol. Furthermore, we demonstrate the framework’s applicability by showcasing the design of widely used replicated data types and the preservation of a wide range of application invariants.
Cite as

Dina Borrego, Nuno Preguiça, Elisa Gonzalez Boix, and Carla Ferreira. Ensuring Convergence and Invariants Without Coordination. In 39th European Conference on Object-Oriented Programming (ECOOP 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 333, pp. 4:1-4:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{borrego_et_al:LIPIcs.ECOOP.2025.4,
  author =	{Borrego, Dina and Pregui\c{c}a, Nuno and Gonzalez Boix, Elisa and Ferreira, Carla},
  title =	{{Ensuring Convergence and Invariants Without Coordination}},
  booktitle =	{39th European Conference on Object-Oriented Programming (ECOOP 2025)},
  pages =	{4:1--4:29},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-373-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{333},
  editor =	{Aldrich, Jonathan and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2025.4},
  URN =		{urn:nbn:de:0030-drops-232978},
  doi =		{10.4230/LIPIcs.ECOOP.2025.4},
  annote =	{Keywords: distributed systems, conflict resolution, RDTs, invariant preservation}
}
Document
Survey
DOI: 10.4230/TGDK.3.1.3
Uncertainty Management in the Construction of Knowledge Graphs: A Survey

Authors: Lucas Jarnac, Yoan Chabot, and Miguel Couceiro

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

Abstract
Knowledge Graphs (KGs) are a major asset for companies thanks to their great flexibility in data representation and their numerous applications, e.g., vocabulary sharing, Q&A or recommendation systems. To build a KG, it is a common practice to rely on automatic methods for extracting knowledge from various heterogeneous sources. However, in a noisy and uncertain world, knowledge may not be reliable and conflicts between data sources may occur. Integrating unreliable data would directly impact the use of the KG, therefore such conflicts must be resolved. This could be done manually by selecting the best data to integrate. This first approach is highly accurate, but costly and time-consuming. That is why recent efforts focus on automatic approaches, which represent a challenging task since it requires handling the uncertainty of extracted knowledge throughout its integration into the KG. We survey state-of-the-art approaches in this direction and present constructions of both open and enterprise KGs. We then describe different knowledge extraction methods and discuss downstream tasks after knowledge acquisition, including KG completion using embedding models, knowledge alignment, and knowledge fusion in order to address the problem of knowledge uncertainty in KG construction. We conclude with a discussion on the remaining challenges and perspectives when constructing a KG taking into account uncertainty.
Cite as

Lucas Jarnac, Yoan Chabot, and Miguel Couceiro. Uncertainty Management in the Construction of Knowledge Graphs: A Survey. In Transactions on Graph Data and Knowledge (TGDK), Volume 3, Issue 1, pp. 3:1-3:48, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@Article{jarnac_et_al:TGDK.3.1.3,
  author =	{Jarnac, Lucas and Chabot, Yoan and Couceiro, Miguel},
  title =	{{Uncertainty Management in the Construction of Knowledge Graphs: A Survey}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{3:1--3:48},
  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.3.1.3},
  URN =		{urn:nbn:de:0030-drops-233733},
  doi =		{10.4230/TGDK.3.1.3},
  annote =	{Keywords: Knowledge reconciliation, Uncertainty, Heterogeneous sources, Knowledge graph construction}
}
Document
Tool Paper
DOI: 10.4230/OASIcs.FMBC.2025.13
A Benchmark Framework for Byzantine Fault Tolerance Testing Algorithms (Tool Paper)

Authors: João Miguel Louro Neto and Burcu Kulahcioglu Ozkan

Published in: OASIcs, Volume 129, 6th International Workshop on Formal Methods for Blockchains (FMBC 2025)

Abstract
Recent discoveries of vulnerabilities in the design and implementation of Byzantine fault-tolerant protocols underscore the need for testing and exploration techniques to ensure their correctness. While there has been some recent effort for automated test generation for BFT protocols, there is no benchmark framework available to systematically evaluate their performance. We present ByzzBench, a benchmark framework designed to evaluate the performance of testing algorithms in detecting Byzantine fault tolerance bugs. ByzzBench is designed for a standardized implementation of BFT protocols and their execution in a controlled testing environment. It controls the nondeterminism in the concurrency, network, and process faults in the protocol execution, enabling the functionality to enforce particular execution scenarios and thereby facilitating the implementation of testing algorithms for BFT protocols.
Cite as

João Miguel Louro Neto and Burcu Kulahcioglu Ozkan. A Benchmark Framework for Byzantine Fault Tolerance Testing Algorithms (Tool Paper). In 6th International Workshop on Formal Methods for Blockchains (FMBC 2025). Open Access Series in Informatics (OASIcs), Volume 129, pp. 13:1-13:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{louroneto_et_al:OASIcs.FMBC.2025.13,
  author =	{Louro Neto, Jo\~{a}o Miguel and Kulahcioglu Ozkan, Burcu},
  title =	{{A Benchmark Framework for Byzantine Fault Tolerance Testing Algorithms}},
  booktitle =	{6th International Workshop on Formal Methods for Blockchains (FMBC 2025)},
  pages =	{13:1--13:11},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-371-3},
  ISSN =	{2190-6807},
  year =	{2025},
  volume =	{129},
  editor =	{Marmsoler, Diego and Xu, Meng},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.FMBC.2025.13},
  URN =		{urn:nbn:de:0030-drops-230406},
  doi =		{10.4230/OASIcs.FMBC.2025.13},
  annote =	{Keywords: Byzantine Fault Tolerance, BFT Protocols, Automated Testing}
}
Document
Short Paper
DOI: 10.4230/OASIcs.SLATE.2024.8
DrumLace - A Domain Specific Language (DSL) for Drum Programming (Short Paper)

Authors: André Semanas de Oliveira Araújo, José João Dias de Almeida, and Pedro Rangel Henriques

Published in: OASIcs, Volume 120, 13th Symposium on Languages, Applications and Technologies (SLATE 2024)

Abstract
In an ever expanding world of musical technology, and due to the evolution of computational power in the last decades, a subdomain emerged where software represents a tool for musicians. Within that subdomain a large variety of approaches exist that allow users to create, define, improve and analyze music. One of these approaches involves the development of text-based languages, that allows the user to define music only through text in a way that enables the development of tools which make possible the printing of the musical sheet describing the score, as well as the generation of different audio files - in WAV, MP3, or other formats - that other music software, such as software synthesizers, can use to play the described score. This project aims to develop a new language, focused on percussion instruments, that allows the description of rhythms, via text or via a visual language - made available trough a Graphic User Interface (GUI). Moreover, that new music DSL supports the use of functions applied to the rhythms and allows the generation of various outputs. This narrow focus on drum programming, as opposed to music as whole, aims at providing an easier to learn syntax, a simple to use tool and an environment open to the integration of more complex concepts presented in the world of percussion.
Cite as

André Semanas de Oliveira Araújo, José João Dias de Almeida, and Pedro Rangel Henriques. DrumLace - A Domain Specific Language (DSL) for Drum Programming (Short Paper). In 13th Symposium on Languages, Applications and Technologies (SLATE 2024). Open Access Series in Informatics (OASIcs), Volume 120, pp. 8:1-8:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{araujo_et_al:OASIcs.SLATE.2024.8,
  author =	{Ara\'{u}jo, Andr\'{e} Semanas de Oliveira and de Almeida, Jos\'{e} Jo\~{a}o Dias and Henriques, Pedro Rangel},
  title =	{{DrumLace - A Domain Specific Language (DSL) for Drum Programming}},
  booktitle =	{13th Symposium on Languages, Applications and Technologies (SLATE 2024)},
  pages =	{8:1--8:9},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-321-8},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{120},
  editor =	{Rodrigues, M\'{a}rio and Leal, Jos\'{e} Paulo and Portela, Filipe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SLATE.2024.8},
  URN =		{urn:nbn:de:0030-drops-220797},
  doi =		{10.4230/OASIcs.SLATE.2024.8},
  annote =	{Keywords: Domain Specific Languages (DSL), Visual Musical Languages, Drum Programming, Compilation}
}
Document
DOI: 10.4230/OASIcs.SLATE.2024.9
ERPL: DSL for Escape Rooms

Authors: Tiago Luís Dias da Silva and José João Almeida

Published in: OASIcs, Volume 120, 13th Symposium on Languages, Applications and Technologies (SLATE 2024)

Abstract
This article delves into the development of ERPL, a Domain-Specific Language tailored for virtual escape rooms. It explores the mechanics, technology, and architecture used in creating immersive and engaging virtual escape room experiences. Case studies demonstrate the practical application of ERPL in designing virtual escape rooms, showcasing its flexibility and effectiveness in meeting the demands of escape room creators. In conclusion, we summarize the results obtained and discuss potential future directions for the development of ERPL.
Cite as

Tiago Luís Dias da Silva and José João Almeida. ERPL: DSL for Escape Rooms. In 13th Symposium on Languages, Applications and Technologies (SLATE 2024). Open Access Series in Informatics (OASIcs), Volume 120, pp. 9:1-9:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dasilva_et_al:OASIcs.SLATE.2024.9,
  author =	{da Silva, Tiago Lu{\'\i}s Dias and Almeida, Jos\'{e} Jo\~{a}o},
  title =	{{ERPL: DSL for Escape Rooms}},
  booktitle =	{13th Symposium on Languages, Applications and Technologies (SLATE 2024)},
  pages =	{9:1--9:8},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-321-8},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{120},
  editor =	{Rodrigues, M\'{a}rio and Leal, Jos\'{e} Paulo and Portela, Filipe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SLATE.2024.9},
  URN =		{urn:nbn:de:0030-drops-220800},
  doi =		{10.4230/OASIcs.SLATE.2024.9},
  annote =	{Keywords: Escape rooms, Domain-Specific Language, Game development}
}
Document
DOI: 10.4230/OASIcs.SLATE.2024.13
Infrastructural Challenges and Good Practices in a Security Operation Center

Authors: Dimitri Alexandre da Silva, José Luís Costa, and João Rafael Almeida

Published in: OASIcs, Volume 120, 13th Symposium on Languages, Applications and Technologies (SLATE 2024)

Abstract
Organizations are facing some challenges in cybersecurity, due to the increasing of cyber threats, vulnerabilities, insufficient cybersecurity frameworks, and scarcity of proficient cybersecurity experts. The criticality of mitigating these challenges is underscored by the European Union’s Network and Information Systems (NIS) Directive. This directive is instrumental in fostering a uniformly high level of cybersecurity throughout the EU, mandating that Member States implement robust national cybersecurity strategies and collaborate effectively in responding to cyber incidents. A possible solution is the implementation of a Security Operations Center (SOC). However, SOCs are not a one-size-fits-all solution and each organization has specific needs depending on their business domain. This task can be complex, and it can be simplified when organizations can identify in the initial stages the infrastructural challenges that may emerge when implementing a SOC. In this paper, we analyzed the main considerations that should be considered when using current frameworks reviewed in the literature. We identified the core operating models that are currently in use and being deployed, and which are the best practices when designing a SOC’s infrastructure.
Cite as

Dimitri Alexandre da Silva, José Luís Costa, and João Rafael Almeida. Infrastructural Challenges and Good Practices in a Security Operation Center. In 13th Symposium on Languages, Applications and Technologies (SLATE 2024). Open Access Series in Informatics (OASIcs), Volume 120, pp. 13:1-13:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dasilva_et_al:OASIcs.SLATE.2024.13,
  author =	{da Silva, Dimitri Alexandre and Costa, Jos\'{e} Lu{\'\i}s and Almeida, Jo\~{a}o Rafael},
  title =	{{Infrastructural Challenges and Good Practices in a Security Operation Center}},
  booktitle =	{13th Symposium on Languages, Applications and Technologies (SLATE 2024)},
  pages =	{13:1--13:12},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-321-8},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{120},
  editor =	{Rodrigues, M\'{a}rio and Leal, Jos\'{e} Paulo and Portela, Filipe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SLATE.2024.13},
  URN =		{urn:nbn:de:0030-drops-220848},
  doi =		{10.4230/OASIcs.SLATE.2024.13},
  annote =	{Keywords: Eduroam, Wi-Fi, Credential stealing, Attack, Network, Security}
}
Document
Survey
DOI: 10.4230/TGDK.2.1.4
Logics for Conceptual Data Modelling: A Review

Authors: Pablo R. Fillottrani and C. Maria Keet

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
Information modelling for databases and object-oriented information systems avails of conceptual data modelling languages such as EER and UML Class Diagrams. Many attempts exist to add logical rigour to them, for various reasons and with disparate strengths. In this paper we aim to provide a structured overview of the many efforts. We focus on aims, approaches to the formalisation, including key dimensions of choice points, popular logics used, and the main relevant reasoning services. We close with current challenges and research directions.
Cite as

Pablo R. Fillottrani and C. Maria Keet. Logics for Conceptual Data Modelling: A Review. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 4:1-4:30, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{fillottrani_et_al:TGDK.2.1.4,
  author =	{Fillottrani, Pablo R. and Keet, C. Maria},
  title =	{{Logics for Conceptual Data Modelling: A Review}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:30},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.4},
  URN =		{urn:nbn:de:0030-drops-198616},
  doi =		{10.4230/TGDK.2.1.4},
  annote =	{Keywords: Conceptual Data Modelling, EER, UML, Description Logics, OWL}
}
Document
Survey
DOI: 10.4230/TGDK.2.1.1
Towards Representing Processes and Reasoning with Process Descriptions on the Web

Authors: Andreas Harth, Tobias Käfer, Anisa Rula, Jean-Paul Calbimonte, Eduard Kamburjan, and Martin Giese

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
We work towards a vocabulary to represent processes and temporal logic specifications as graph-structured data. Different fields use incompatible terminologies for describing essentially the same process-related concepts. In addition, processes can be represented from different perspectives and levels of abstraction: both state-centric and event-centric perspectives offer distinct insights into the underlying processes. In this work, we strive to unify the representation of processes and related concepts by leveraging the power of knowledge graphs. We survey approaches to representing processes and reasoning with process descriptions from different fields and provide a selection of scenarios to help inform the scope of a unified representation of processes. We focus on processes that can be executed and observed via web interfaces. We propose to provide a representation designed to combine state-centric and event-centric perspectives while incorporating temporal querying and reasoning capabilities on temporal logic specifications. A standardised vocabulary and representation for processes and temporal specifications would contribute towards bridging the gap between the terminologies from different fields and fostering the broader application of methods involving temporal logics, such as formal verification and program synthesis.
Cite as

Andreas Harth, Tobias Käfer, Anisa Rula, Jean-Paul Calbimonte, Eduard Kamburjan, and Martin Giese. Towards Representing Processes and Reasoning with Process Descriptions on the Web. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 1:1-1:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{harth_et_al:TGDK.2.1.1,
  author =	{Harth, Andreas and K\"{a}fer, Tobias and Rula, Anisa and Calbimonte, Jean-Paul and Kamburjan, Eduard and Giese, Martin},
  title =	{{Towards Representing Processes and Reasoning with Process Descriptions on the Web}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{1:1--1:32},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.1},
  URN =		{urn:nbn:de:0030-drops-198583},
  doi =		{10.4230/TGDK.2.1.1},
  annote =	{Keywords: Process modelling, Process ontology, Temporal logic, Web services}
}
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}
}
Document
Short Paper
DOI: 10.4230/OASIcs.SLATE.2023.10
Large Language Models: Compilers for the 4^{th} Generation of Programming Languages? (Short Paper)

Authors: Francisco S. Marcondes, José João Almeida, and Paulo Novais

Published in: OASIcs, Volume 113, 12th Symposium on Languages, Applications and Technologies (SLATE 2023)

Abstract
This paper explores the possibility of large language models as a fourth generation programming language compiler. This is based on the idea that large language models are able to translate a natural language specification into a program written in a particular programming language. In other words, just as high-level languages provided an additional language abstraction to assembly code, large language models can provide an additional language abstraction to high-level languages. This interpretation allows large language models to be thought of through the lens of compiler theory, leading to insightful conclusions.
Cite as

Francisco S. Marcondes, José João Almeida, and Paulo Novais. Large Language Models: Compilers for the 4^{th} Generation of Programming Languages? (Short Paper). In 12th Symposium on Languages, Applications and Technologies (SLATE 2023). Open Access Series in Informatics (OASIcs), Volume 113, pp. 10:1-10:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{s.marcondes_et_al:OASIcs.SLATE.2023.10,
  author =	{S. Marcondes, Francisco and Almeida, Jos\'{e} Jo\~{a}o and Novais, Paulo},
  title =	{{Large Language Models: Compilers for the 4^\{th\} Generation of Programming Languages?}},
  booktitle =	{12th Symposium on Languages, Applications and Technologies (SLATE 2023)},
  pages =	{10:1--10:8},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-291-4},
  ISSN =	{2190-6807},
  year =	{2023},
  volume =	{113},
  editor =	{Sim\~{o}es, Alberto and Ber\'{o}n, Mario Marcelo and Portela, Filipe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SLATE.2023.10},
  URN =		{urn:nbn:de:0030-drops-185240},
  doi =		{10.4230/OASIcs.SLATE.2023.10},
  annote =	{Keywords: programming language, compiler, large language model}
}
Document
DOI: 10.4230/OASIcs.SLATE.2022.15
Down-Translating XML: The Python Way

Authors: Alberto Simões and José João Almeida

Published in: OASIcs, Volume 104, 11th Symposium on Languages, Applications and Technologies (SLATE 2022)

Abstract
Nowadays, the most used approach to process an XML file is based on the processing of a DOM structure and a set of operations that collects or edits information in the model using some kind of selectors (usually CSS-like or XPath). Nevertheless, the process of performing a depth-first walk through the DOM, and synthesizing values, is a simple way to traverse and transform an entire XML document. In this document we discuss the details on the implementation and usage of a Python package for XML document processing based on this structure. Given the existence of similar tools for other programming languages, we will mainly focus on the used approach, that takes advantage of the Python style guides and development patterns.
Cite as

Alberto Simões and José João Almeida. Down-Translating XML: The Python Way. In 11th Symposium on Languages, Applications and Technologies (SLATE 2022). Open Access Series in Informatics (OASIcs), Volume 104, pp. 15:1-15:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{simoes_et_al:OASIcs.SLATE.2022.15,
  author =	{Sim\~{o}es, Alberto and Almeida, Jos\'{e} Jo\~{a}o},
  title =	{{Down-Translating XML: The Python Way}},
  booktitle =	{11th Symposium on Languages, Applications and Technologies (SLATE 2022)},
  pages =	{15:1--15:9},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-245-7},
  ISSN =	{2190-6807},
  year =	{2022},
  volume =	{104},
  editor =	{Cordeiro, Jo\~{a}o and Pereira, Maria Jo\~{a}o and Rodrigues, Nuno F. and Pais, Sebasti\~{a}o},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SLATE.2022.15},
  URN =		{urn:nbn:de:0030-drops-167617},
  doi =		{10.4230/OASIcs.SLATE.2022.15},
  annote =	{Keywords: XML, Python, Depth-First Processing}
}
Document
Short Paper
DOI: 10.4230/OASIcs.SLATE.2021.18
Bootstrapping a Data-Set and Model for Question-Answering in Portuguese (Short Paper)

Authors: Nuno Ramos Carvalho, Alberto Simões, and José João Almeida

Published in: OASIcs, Volume 94, 10th Symposium on Languages, Applications and Technologies (SLATE 2021)

Abstract
Question answering systems are mainly concerned with fulfilling an information query written in natural language, given a collection of documents with relevant information. They are key elements in many popular application systems as personal assistants, chat-bots, or even FAQ-based online support systems. This paper describes an exploratory work carried out to come up with a state-of-the-art model for question-answering tasks, for the Portuguese language, based on deep neural networks. We also describe the automatic construction of a data-set for training and testing the model. The final model is not trained in any specific topic or context, and is able to handle generic documents, achieving 50% accuracy in the testing data-set. While the results are not exceptional, this work can support further development in the area, as both the data-set and model are publicly available.
Cite as

Nuno Ramos Carvalho, Alberto Simões, and José João Almeida. Bootstrapping a Data-Set and Model for Question-Answering in Portuguese (Short Paper). In 10th Symposium on Languages, Applications and Technologies (SLATE 2021). Open Access Series in Informatics (OASIcs), Volume 94, pp. 18:1-18:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{carvalho_et_al:OASIcs.SLATE.2021.18,
  author =	{Carvalho, Nuno Ramos and Sim\~{o}es, Alberto and Almeida, Jos\'{e} Jo\~{a}o},
  title =	{{Bootstrapping a Data-Set and Model for Question-Answering in Portuguese}},
  booktitle =	{10th Symposium on Languages, Applications and Technologies (SLATE 2021)},
  pages =	{18:1--18:5},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-202-0},
  ISSN =	{2190-6807},
  year =	{2021},
  volume =	{94},
  editor =	{Queir\'{o}s, Ricardo and Pinto, M\'{a}rio and Sim\~{o}es, Alberto and Portela, Filipe and Pereira, Maria Jo\~{a}o},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.SLATE.2021.18},
  URN =		{urn:nbn:de:0030-drops-144355},
  doi =		{10.4230/OASIcs.SLATE.2021.18},
  annote =	{Keywords: Portuguese language, question answering, deep learning}
}
Document
Short Paper
DOI: 10.4230/OASIcs.ICPEC.2021.13
A Teaching Assistant for the C Language (Short Paper)

Authors: Rui C. Mendes and José João Almeida

Published in: OASIcs, Volume 91, Second International Computer Programming Education Conference (ICPEC 2021)

Abstract
We introduce a C tutor that can help instructors manage classes with many students learning to program in C. Nowadays, it is easy to evaluate code but it is hard to provide good feedback. We introduce a tool to help instructors provide students with feedback concerning their implementation and documentation for honing their programming skills. This tool is implemented in Python and is available at https://github.com/rcm/C_teaching_assistant.
Cite as

Rui C. Mendes and José João Almeida. A Teaching Assistant for the C Language (Short Paper). In Second International Computer Programming Education Conference (ICPEC 2021). Open Access Series in Informatics (OASIcs), Volume 91, pp. 13:1-13:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{mendes_et_al:OASIcs.ICPEC.2021.13,
  author =	{Mendes, Rui C. and Almeida, Jos\'{e} Jo\~{a}o},
  title =	{{A Teaching Assistant for the C Language}},
  booktitle =	{Second International Computer Programming Education Conference (ICPEC 2021)},
  pages =	{13:1--13:8},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-194-8},
  ISSN =	{2190-6807},
  year =	{2021},
  volume =	{91},
  editor =	{Henriques, Pedro Rangel and Portela, Filipe and Queir\'{o}s, Ricardo and Sim\~{o}es, Alberto},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ICPEC.2021.13},
  URN =		{urn:nbn:de:0030-drops-142296},
  doi =		{10.4230/OASIcs.ICPEC.2021.13},
  annote =	{Keywords: Software metrics, Documentation extractor, Domain specific language, Query language, Report generation}
}
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