Survey-based naming conventions for use in OBO Foundry ontology development

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data

Relations in biomedical ontologies

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena

Survey-based naming conventions for use in OBO Foundry ontology development

<p>Abstract</p> <p>Background</p> <p>A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion.</p> <p>Results</p> <p>We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies.</p> <p>Conclusion</p> <p>Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data.</p

Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data

IgA nephropathy and liver disease / by Jane Lomax-Smith

Bibliography: leaves 331-381xxiv, 381 leaves : ill ; 31 cm.Thesis (Ph.D.)--University of Adelaide, Dept. of Pathology 198

Higher education base funding review: final report

This report defines enduring principles to underpin the long-term funding of Australian higher education as well as specific recommendations and options for a reformed funding model. Australia’s future social and economic development depends on having an educated and highly skilled community, delivering creativity, innovation and improved productivity. Australian universities contribute to society by leading public debate, enhancing civic and cultural life and enriching our self-awareness by the expansion of knowledge. In addition, universities contribute to the economy by supporting the development of effective graduates, driving regional economies and improving the national accounts by virtue of their research and development as well as their onshore and offshore education activities. Their regional success and global impact enhances our national standing and assists in globalising the national economy. An effective and highly performing university sector is essential to achieving these goals and base funding to universities from the Australian Government and student contributions provides the largest source of revenue to universities. Australian universities are institutions with highly complex goals and operations. They demonstrate strong international links but are also responsive to national and regional priorities. The sector is diverse but needs to operate in a legislatively controlled framework; it must focus on excellence yet also have a wide reach. Australian universities are accountable to Government but receive much of their funding from non-government sources and are autonomous institutions. To ensure they contribute to innovation, productivity and a civil society, our universities undertake teaching that is informed by scholarship, as well as research which is collaborative and global in its significance and often capable of commercialisation. The evidence available to the Higher Education Base Funding Review Panel (the Panel) showed that the Australian university sector was well managed and had adapted to changing circumstances to become more efficient and productive, such that it is now able to use any additional funding effectively. The trust of the community and government investment over many decades has been and continues to be justified. Australia’s higher education system has been responsive to government initiatives and has diversified its income sources. The diverse system includes areas of research excellence, high-quality and innovative teaching, and a widespread focus on equity. Our national system is well regarded at home, respected internationally and a source of national pride. Nevertheless, specific local issues, changing policy settings and rapid global changes have the potential to pose significant risks to the quality and effectiveness of Australian universities. The Government has acted swiftly in response to the Knight Review of the Student Visa Program to support international enrolments in universities. However, the Panel noted ongoing concern in the sector about the potential for emerging international issues to erode Australia’s competitive advantage in the international higher education market. There are pressures on operating costs and infrastructure, reflecting the dramatic changes in the sector over the last two decades; a period marked by far more than just expansion. Across the sector the stresses were seen to be largely similar, reflecting changes in student and employer expectations, technological change, teaching reforms including online delivery and an increasing emphasis on work-integrated learning. Put simply, despite productivity gains and allowing for institutional decisions about priorities, the costs have not just risen, but also the nature of the institutions has changed during the decades on either side of the millennium

Interdyscyplinarne perspektywy rozwoju, integracji i zastosowań ontologii poznawczych (Przełożył Przemysław Nowak)

Przedstawiamy ostatnie postępy w rozwoju ontologii poznawczych i omawiamy trzy wyzwania dla skoordynowanego rozwoju i zastosowań tych zasobów. Wyzwaniem_1 jest przyjęcie zestandaryzowanej definicji procesów poznawczych. Opisujemy trzy możliwości i rekomendujemy jedną, spójną z tradycyjnym ujęciem w naukach poznawczych i biomedycznych. Wyzwaniem_2 jest harmonizacja [harmonization]. Luki i niezgodności w reprezentacjach muszą być usunięte, tak żeby zasoby mogły być połączone w celu oznaczania i interpretacji danych multimodalnych. Na koniec, wyzwaniem_3 jest przetestowanie użyteczności tych zasobów dla szeroko zakrojonej anotacji danych, zapytań i przeszukiwania oraz integracji i odkrywania wiedzy. Podczas gdy definicje terminów są tes- towane i poprawiane, harmonizacja powinna umożliwiać skoordynowane aktualizacje pomiędzy ontologiami. Jednak prawdziwym testem dla tych definicji będzie przyjęcie ich przez całą wspólnotę, która sprawdzi, czy wspierają one poprawne wnioskowania o danych psychologicznych i neu- ronaukowych.Przedstawiamy ostatnie postępy w rozwoju ontologii poznawczych i omawiamy trzy wyzwania dla skoordynowanego rozwoju i zastosowań tych zasobów. Wyzwaniem_1 jest przyjęcie zestandaryzowanej definicji procesów poznawczych. Opisujemy trzy możliwości i rekomendujemy jedną, spójną z tradycyjnym ujęciem w naukach poznawczych i biomedycznych. Wyzwaniem_2 jest harmonizacja [harmonization]. Luki i niezgodności w reprezentacjach muszą być usunięte, tak żeby zasoby mogły być połączone w celu oznaczania i interpretacji danych multimodalnych. Na koniec, wyzwaniem_3 jest przetestowanie użyteczności tych zasobów dla szeroko zakrojonej anotacji danych, zapytań i przeszukiwania oraz integracji i odkrywania wiedzy. Podczas gdy definicje terminów są testowane i poprawiane, harmonizacja powinna umożliwiać skoordynowane aktualizacje pomiędzy ontologiami. Jednak prawdziwym testem dla tych definicji będzie przyjęcie ich przez całą wspólnotę, która sprawdzi, czy wspierają one poprawne wnioskowania o danych psychologicznych i neu- ronaukowych.

Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies.

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data