The Ecology of Ontologies in the Public Domain

Baker, Christopher J. O.; Warren, Robert H.; Haarslev, Volker; Butler, Gregory

doi:10.5840/monist200790438

“…This is not untypical. The same usage pattern was previously identified as the most frequent in previous studies of larger numbers of ontologies randomly selected from the internet and representing a variety of subject domains [12]. The FungalWeb ontology also displayed this pattern indicating that it is not much different from the majority of other bio-ontologies which demonstrate relatively little implicit knowledge.…”

Section: Ontology Evaluationsupporting

confidence: 75%

“…Our ontology was evaluated on the following criteria: occurrences of multiple inheritances, the number of children per concept, depth, and use of OWL tags that store implicit knowledge. Furthermore we compared the FungalWeb ontology to 50 publicly available bio-ontologies [12], in order to assess how amenable it is to knowledge discovery in the context of other ontologies in the same general domain. Our initial analysis involved the simple enumeration of the OWL and RDFS tags in our ontology and 50 other bio-ontologies.…”

Section: Ontology Evaluationmentioning

confidence: 99%

“…Also of particular relevance to knowledge discovery is the inclusion of implicit knowledge about a domain within ontologies such that reasoning tools can make non-obvious discoveries. It remains a difficult challenge to make use of the full expressivity of OWL and recent studies [12] have indicated that few ontologies make full use of OWL tags. We have produced an ontological frame of predominantly explicit knowledge that provides fungal enzymologists with semantic access to knowledge relevant to their studies.…”

Section: Fungalweb Challengesmentioning

confidence: 99%

See 1 more Smart Citation

Semantic web infrastructure for fungal enzyme biotechnologists

Baker

¹

,

Shaban-Nejad

²

,

Su

³

et al. 2006

Journal of Web Semantics

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The FungalWeb Ontology aims to support the data integration needs of enzyme biotechnology from inception to product roll. Serving as a knowledgebase for decision support, the conceptualization seeks to link fungal species with enzymes, enzyme substrates, enzyme classifications, enzyme modifications, enzyme related intellectual property, enzyme retail and applications. The ontology, developed in the OWL language, is the result of the integration of numerous biological database schemas, web accessible text resources and components of existing ontologies. We assess the quantity of implicit knowledge in the Fungal Web ontology by analyzing the range of tags in the OWL files and along with other description logic (DL) computable metrics of the ontology, contrast it with other publicly available bio-ontologies. Thereafter we demonstrate how the FungalWeb Ontology supports its broad remit required in fungal biotechnology by (i) suggesting semantic queries typical of a fungal enzymologist involved in product development, (ii) presenting application scenarios, and (iii) presenting the conceptualizations of the ontological frame able to support these scenarios. Recognizing the complexity of the ontology query process for the non-technical manager we introduce a simplified query tool, Ontologent Interative Query (OntoIQ) that allows the user to browse and build queries from a selection of query patterns. The OntoIQ interface supports users not familiar with writing DL syntax allowing them access to the ontology with expressive description logic and automated reasoning tools. Finally we discuss the challenges encountered during the development of semantic infrastructure for fungal enzyme biotechnologists.

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“…Where ontologies or parts of ontologies have been imported to new ontologies this can be identified by reviewing ontology files for imports with different URLs to reveal which parts of an ontology are from other conceptualizations. Some studies have sought to elucidate such artifacts [39] with varying degrees of success.…”

Section: Disease Surveillance Ontologiesmentioning

confidence: 99%

Applied Ontologies for Global Health Surveillance and Pandemic Intelligence

Baker

¹

,

Manir

²

,

Brenas

³

et al. 2020

Preprint

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Global health surveillance and pandemic intelligence rely on the systematic collection and integration of data from diverse distributed and heterogeneous sources at various levels of granularity. These sources include data from multiple disciplines represented in different formats, languages, and structures posing significant integration challenges This article provides an overview of challenges in data driven surveillance. Using Malaria surveillance as a use case we highlight the contribution made by emerging semantic data federation technologies that offer enhanced interoperability, interpretability and explainability through the adoption of ontologies. The paper concludes with a focus on the relevance of these technologies for ongoing pandemic preparedness initiatives.

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Semantic Web Infrastructure for Fungal Enzyme Biotechnologists

Baker

¹

,

Shaban-Nejad

²

,

Su

³

et al. 2006

Self Cite

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The FungalWeb Ontology aims to support the data integration needs of enzyme biotechnology from inception to product roll. Serving as a knowledgebase for decision support, the conceptualization seeks to link fungal species with enzymes, enzyme substrates, enzyme classifications, enzyme modifications, enzyme related intellectual property, enzyme retail and applications. The ontology, developed in the OWL language, is the result of the integration of numerous biological database schemas, web accessible text resources and components of existing ontologies. We assess the quantity of implicit knowledge in the Fungal Web ontology by analyzing the range of tags in the OWL files and along with other description logic (DL) computable metrics of the ontology, contrast it with other publicly available bio-ontologies. Thereafter we demonstrate how the FungalWeb Ontology supports its broad remit required in fungal biotechnology by (i) suggesting semantic queries typical of a fungal enzymologist involved in product development, (ii) presenting application scenarios, and (iii) presenting the conceptualizations of the ontological frame able to support these scenarios. Recognizing the complexity of the ontology query process for the non-technical manager we introduce a simplified query tool, Ontologent Interative Query (OntoIQ) that allows the user to browse and build queries from a selection of query patterns. The OntoIQ interface supports users not familiar with writing DL syntax allowing them access to the ontology with expressive description logic and automated reasoning tools. Finally we discuss the challenges encountered during the development of semantic infrastructure for fungal enzyme biotechnologists.

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The Ecology of Ontologies in the Public Domain

Cited by 3 publications

References 17 publications

Semantic web infrastructure for fungal enzyme biotechnologists

Semantic web infrastructure for fungal enzyme biotechnologists

Applied Ontologies for Global Health Surveillance and Pandemic Intelligence

Semantic Web Infrastructure for Fungal Enzyme Biotechnologists

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