25,276 research outputs found
Helping scientists integrate and interact with biomedical data
Tese de mestrado, Bioinformática e Biologia Computacional , 2021, Universidade de Lisboa, Faculdade de CiênciasFor the past decades, the amount and complexity of biomedical data available have increased and far
exceeded the human capacity to process it. To support this, knowledge graphs and ontologies have been
increasingly used, allowing semantic integration of heterogeneous data within and across domains. However, the independent development of biomedical ontologies has created heterogeneity problems, with the
design of ontologies with overlapping domains or significant differences.
Automated ontology alignment techniques have been developed to tackle the semantic heterogeneity
problem, by establishing meaningful correspondences between entities of two ontologies. However, their
performance is limited, and the alignments they produce can contain erroneous, incoherent, or missing
mappings. Therefore, manual validation of automated ontology alignments remains essential to ensure
their quality.
Given the complexity of the ontology matching process, is important to provide visualization and a user
interface with the necessary features to support the exploration, validation, and edition of alignments.
However, these aspects are often overlooked, as few alignment systems feature user interfaces enabling
alignment visualization, fewer allow editing alignments, and fewer provide the functionalities needed to
make the task seamless for users.
This dissertation developed VOWLMap — an extension for the standalone web application, WebVOWL
— for visualizing, editing, and validating biomedical ontology alignments. This work extended the Visual
Notation for OWL Ontologies (VOWL), which defines a visual representation for most language constructs of OWL, to support graphical representations of alignments and restructured WebVOWL to load
and visualize alignments. VOWLMap employs modularization techniques to facilitate the visualization
of large alignments, while maintaining the context of each mapping, and offers a dynamic visualization
that supports interaction mechanisms, including direct interaction with and editing of graph representations. A user study was conducted to evaluate the usability and performance of VOWLMap, having
obtained positive feedback with an excellent score in a standard usability questionnaire
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Results of the ontology alignment evaluation initiative 2019
The Ontology Alignment Evaluation Initiative (OAEI) aims at comparing ontology matching systems on precisely defined test cases. These test cases can be based on ontologies of different levels of complexity (from simple thesauri to expressive OWL ontologies) and use different evaluation modalities (e.g., blind evaluation, open evaluation, or consensus). The OAEI 2019 campaign offered 11 tracks with 29 test cases, and was attended by 20 participants. This paper is an overall presentation of that campaign
Git4Voc: Git-based Versioning for Collaborative Vocabulary Development
Collaborative vocabulary development in the context of data integration is
the process of finding consensus between the experts of the different systems
and domains. The complexity of this process is increased with the number of
involved people, the variety of the systems to be integrated and the dynamics
of their domain. In this paper we advocate that the realization of a powerful
version control system is the heart of the problem. Driven by this idea and the
success of Git in the context of software development, we investigate the
applicability of Git for collaborative vocabulary development. Even though
vocabulary development and software development have much more similarities
than differences there are still important differences. These need to be
considered within the development of a successful versioning and collaboration
system for vocabulary development. Therefore, this paper starts by presenting
the challenges we were faced with during the creation of vocabularies
collaboratively and discusses its distinction to software development. Based on
these insights we propose Git4Voc which comprises guidelines how Git can be
adopted to vocabulary development. Finally, we demonstrate how Git hooks can be
implemented to go beyond the plain functionality of Git by realizing
vocabulary-specific features like syntactic validation and semantic diffs
Save up to 99% of your time in mapping validation
Identifying semantic correspondences between different vocabularies has been recognized as a fundamental step towards achieving interoperability. Several manual and automatic techniques have been recently proposed. Fully manual approaches are very precise, but extremely costly. Conversely, automatic approaches tend to fail when domain specific background knowledge is needed. Consequently, they typically require a manual validation step. Yet, when the number of computed correspondences is very large, the validation phase can be very expensive. In order to reduce the problems above, we propose to compute the minimal set of correspondences, that we call the minimal mapping, which are sufficient to compute all the other ones. We show that by concentrating on such correspondences we can save up to 99% of the manual checks required for validation
OntoMaven: Maven-based Ontology Development and Management of Distributed Ontology Repositories
In collaborative agile ontology development projects support for modular
reuse of ontologies from large existing remote repositories, ontology project
life cycle management, and transitive dependency management are important
needs. The Apache Maven approach has proven its success in distributed
collaborative Software Engineering by its widespread adoption. The contribution
of this paper is a new design artifact called OntoMaven. OntoMaven adopts the
Maven-based development methodology and adapts its concepts to knowledge
engineering for Maven-based ontology development and management of ontology
artifacts in distributed ontology repositories.Comment: Pre-print submission to 9th International Workshop on Semantic Web
Enabled Software Engineering (SWESE2013). Berlin, Germany, December 2-5, 201
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