8 research outputs found
Validation Framework for RDF-based Constraint Languages
In this thesis, a validation framework is introduced that enables to consistently execute RDF-based constraint languages on RDF data and to formulate constraints of any type. The framework reduces the representation of constraints to the absolute minimum, is based on formal logics, consists of a small lightweight vocabulary, and ensures consistency regarding validation results and enables constraint transformations for each constraint type across RDF-based constraint languages
Short papers of the 10th Conference on Cloud Computing, Big Data & Emerging Topics
Compilaci贸n de los short papers presentados en las 10mas Jornadas de Cloud Computing, Big Data & Emerging Topics (JCC-BD&ET2022), llevadas a cabo en modalidad h铆brida durante junio de 2021 y organizadas por el Instituto de Investigaci贸n en Inform谩tica LIDI (III-LIDI) y la Secretar铆a de Posgrado de la Facultad de Inform谩tica de la UNLP, en colaboraci贸n con universidades de Argentina y del exterior.Facultad de Inform谩tic
Scaling the development of large ontologies : identitas and hypernormalization
PhD ThesisDuring the last decade ontologies have become a fundamental part of the life sciences
to build organised computational knowledge. Currently, there are more than
800 biomedical ontologies hosted by the NCBO BioPortal repository. However, the
proliferation of ontologies in the biomedical and biological domains has highlighted
a number of problems. As ontologies become large, their development and maintenance
becomes more challenging and time-consuming. Therefore, the scalability of
ontology development has become problematic. In this thesis, we examine two new
approaches that can help address this challenge.
First, we consider a new approach to identi ers that could signi cantly facilitate the
scalability of ontologies and overcome some related issues with monotonic, numeric
identi ers while remaining semantics-free. Our solutions are described, along with
the Identitas library, which allows concurrent development, pronounceability and
error checking. The library integrated into two ontology development environments,
Prot eg e and Tawny-OWL. This thesis also discusses the ways in which current ontological
practices could be migrated towards the use of this scheme.
Second, we investigate the usage of the hypernormalisation, patternisation and programatic
approaches by asking how we could use this approach to rebuild the Gene
Ontology (GO). The aim of the hypernormalisation and patternisation techniques
is to allow the ontology developer to manage its maintainability and evolution. To
apply this approach we had to analyse the ontology structure, starting with the
Molecular Function Ontology (MFO). The MFO is formed from several large and
tangled hierarchies of classes, each of which describe a broad molecular activity.
The exploitation of the hypernormalisation approach resulted in the creation of a
hypernormalised form of the Transporter Activity (TA) and Catalytic Activity (CA)
hierarchies, together they constitute 78% of all classes in MFO. The hypernormalised
structure of the TA and CA are generated based on developed higher-level patterns
and novel content-speci c patterns, and exploit ontology logical reasoners. The gen-
erated ontologies are robust, easy to maintain and can be developed and extended
freely. Although, there are a variety of ontologies development tools, Tawny-OWL is
a programmatic interactive tool for ontology creation and management and provides
a set of patterns that explicitly support the creation of a hypernormalised ontology.
Finally, the investigation of the hypernormalisation highlighted inconsistent classi-
cations and identi cation of signi cant semantic mismatch between GO and the
Chemical Entities of Biological Interest (ChEBI). Although both ontologies describe
the same real entities, GO often refers to the form most common in biology, while
ChEBI is more speci c and precise. The use of hypernormalisation forces us to
deal with this mismatch, we used the equivalence axioms created by the GO-Plus
ontology.
To sum up, to address the scalability and ease development of ontologies we propose a
new identi er scheme and investigate the use of the hypernormalisation methodology.
Together, the Identitas and the hypernormalisation technique should enable the
construction of large-scale ontologies in the future.Northern Borders University, Saudi Arabia