Ontology, Ontologies, and Science

Merrill, Gary H.

doi:10.1007/s11245-011-9091-x

Cited by 7 publications

(3 citation statements)

References 14 publications

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“…EDAM is founded on logic, and on relevance and utility to the bioinformatics community. This is in accordance with Lord and Stevens (2010), Merrill (2010, 2011) and Rzhetsky and Evans (2011) that all indicate, using separate sets of arguments, that it is the relevance of scientific ontologies with respect to their practical applications that is more important than an imposed metaphysical ideology. EDAM concepts are not concepts existing only in minds of the EDAM authors, but common notions shared within the bioinformatics community.…”

Section: Methodssupporting

confidence: 78%

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

et al. 2013

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Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required.Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations.Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl.Contact: jison@ebi.ac.uk

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Section: Methodssupporting

confidence: 78%

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

et al. 2013

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“…The initial workstream, which sought to propose an evidence-based nomenclature of Cannabis products, turned out to be insoluble before a first address of existing terms and concepts from the perspectives of the philosophies of science and language. Ontology, both traditionally as a metaphysical address of the nature and essence of 'things' and, in its modern understanding, as an applied discipline of knowledge management (Merrill, 2011) provided methodological guidance in this regard. 'The big task for the new "ontology"' as Smith (2003) notes, 'derives from what we might call the Tower of Babel problem.…”

Section: Methodsmentioning

confidence: 99%

‘Cannabis’ ontologies I: Conceptual issues with Cannabis and cannabinoids terminology

Riboulet-Zemouli¹

2020

Drug Science, Policy and Law

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Objective Identify a coherent nomenclature for Cannabis sativa L. derived products and their analogues. Design Research undertaken in parallel to the three-year assessment of Cannabis derivatives by the World Health Organisation. The scope is limited to Cannabis products intended for human incorporation (internal and topical consumption). Primarily embedded in pharmacognosy, the study incorporates a wide range of scholarly and grey literature, folk knowledge, archives, pharmacopœias, international law, field pharmacy, clinical and herbal medicine data, under a philosophical scrutiny. Generic and Cannabis-specific nomenclatural frames are compared to determine the extent to which they coincide or conflict. Results All lexica reviewed use weak, ambiguous, or inconsistent terms. There is insufficient scientific basis for terms and concepts related to Cannabis at all levels. No sound classification exists: current models conflict by adopting idiosyncratic, partial, outdated, or utilitarian schemes to arrange the extraordinarily numerous and diverse derivatives of the C. sativa plant. In law and policy, no clear or unequivocal boundary between herbal and non-herbal drugs, nor natural and synthetic cannabinoids was found; current nomenclatures need updates. In science, the botanical Cannabis lexicon overlooks parthenocarpy, and wide disagreement remains as to the taxonomy and systematics of the plant; chemical research should address differences in kinds between synthetic cannabinoids; pharmacopœias include little information related to Cannabis, and disagree on broader classes of herbal medicines, virtually failing to embrace many known Cannabis medicines. Since existing products and compounds fail to be categorised in an evidence-based manner, confusions will likely increase as novel cannabinoid compounds, genetic and biotechnological modifications surge. Conclusions The lack of clarity is comprehensive: for patients, physicians, and regulators. This study proposes an update of terms at several levels. It points at gaps in morphological descriptions in botany and pharmacognosy and a need for a metaphysical address of cannabinoids. Methods of obtention are identified as a common criterion to distinguish products; the way forward suggests a mutually exclusive nomenclatural pattern based on the smallest common denominator of obtention methods. In the context of a swelling number of Cannabis products being consumed (be it via medical prescription, adult-use, ‘hemp’ foodstuff and cosmetics, or other purposes), this study can assist research, contribute to transparent labelling of products, consumer safety and awareness, pharmacovigilance, medical standards of care, and an update of prevention and harm reduction approaches. It can also better inform regulatory policies surrounding C. sativa, its derivatives, and other cannabinoid-containing products.

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“…Focus of the study In Figure 4.1, the philosophical stance or ontology of empirical realism could be applied to the areas of penetrating damp problem and concrete housing construction where there is no overlap with other areas. Idealist ontology would be relevant to the house owners, experts and culture because it highlights the meaning of an existing phenomenon as the critical question for human beings (Merrill, 2011). This study assumes that the reality of the issue of dampness in domestic concrete houses in the Green Mountain area of Libya is interpreted by the stakeholders' perceptions, knowledge and experiences.…”

Section: Ontologymentioning

confidence: 99%

An AHP damp penetration model for concrete houses: Green Mountain, Libya

Laeirj¹

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The Green Mountain region of Libya experiences a persistent housing problem with regard to damp, regardless of the quality of the design, materials used, the construction practice and policy. This investigation into the factors influencing the performance of concrete housing to combat penetrating damp identified a broad range of factors: technical, managerial, economic, socio-cultural design and climatic issues. Consideration was given to specific national factors impacting on housing design and construction such as housing policy. The applicability of factors was confirmed by primary data collected from a householder questionnaire and a photographic observation survey of the condition of damp houses. Primary data were combined with secondary data in order to develop a more complete picture of the phenomenon under investigation. The analytical hierarchy process (AHP) technique was applied to construct an evaluation hierarchy of factors affecting the performance of houses in a Albeida city in North Eastern Libya. Factors were weighted and evaluated through interviews of construction professionals and self-build house owners. Results were integrated using the mathematical technique of AHP and a model of the most significant factors proposed. While the technique has been widely applied in various construction disciplines as a multiple criteria decision making technique, this study is the first to apply the technique as an analytical tool for understanding in depth a specific problem of construction and housing rather than for deciding a course of action. The results show that the issue mainly affects middle income and poor householders. Construction and socioeconomic design factors are the major causes of the presence of penetrating damp, together with the financial constraints of the owners. Surprisingly, management and climatic factors have less impact on the occurrence of damp. The model was subsequently validated in a sample of houses suffering from penetrating damp in Massa. This indicated that caution should be exercised regarding the application of AHP to the owners' judgments and the transferability of results. Whilst the findings of this research can assist decision makers in similar situations to identify appropriate assessment criteria for the construction of future housing projects, further investigation into the applicability of AHP in comparison with other methods is recommended. IV Acknowledgements I am most grateful to Allah Almighty for providing me with the patience and making it possible to produce this piece of work. I am also thankful to many people for their help and assistance, both directly and indirectly.

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Ontology, Ontologies, and Science

Cited by 7 publications

References 14 publications

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

‘Cannabis’ ontologies I: Conceptual issues with Cannabis and cannabinoids terminology

An AHP damp penetration model for concrete houses: Green Mountain, Libya

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