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Keywords: ontologies
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Journal Article
The limits of waste as a resource: a critique and a proposition towards a new scalar imagination for the circular economy model
Stylianos Zavos and Olli Pyyhtinen
Cambridge Journal of Regions, Economy and Society, Volume 17, Issue 3, November 2024, Pages 683–697, https://doi.org/10.1093/cjres/rsae013
Published: 09 May 2024
... and propose that the potential of a sustained circular economy promise requires a novel scalar imagination attentive to its multiple co-constituted spatialities, social relations and fluid materials. waste resources circular economy scales flat ontologies ‘The benefits of the circular economy...
Journal Article
Making head and neck cancer clinical data Findable-Accessible-Interoperable-Reusable to support multi-institutional collaboration and federated learning
Varsha Gouthamchand and others
BJR|Artificial Intelligence, Volume 1, Issue 1, January 2024, ubae005, https://doi.org/10.1093/bjrai/ubae005
Published: 06 March 2024
... as described above, using the Radiomics Ontology. 28 For this working proof, we only hand-picked 5 radiomics features of interest identified in previous studies of prognostic performance and vulnerabilities 29 , 30 ; there was no radiomics feature selection...
Journal Article
BioLORD-2023: semantic textual representations fusing large language models and clinical knowledge graph insights
François Remy and others
Journal of the American Medical Informatics Association, Volume 31, Issue 9, September 2024, Pages 1844–1855, https://doi.org/10.1093/jamia/ocae029
Published: 27 February 2024
.... Conclusion In this article, we introduced BioLORD-2023, a state-of-the-art model for STS and BCR designed for the clinical domain. natural language processing machine learning knowledge bases biological ontologies semantics ADAM VLAIO O&O HBC.2020.3234 This article introduces several novel...
Journal Article
Normalization of drug and therapeutic concepts with Thera-Py
Matthew Cannon and others
in
JAMIA Open
JAMIA Open, Volume 6, Issue 4, December 2023, ooad093, https://doi.org/10.1093/jamiaopen/ooad093
Published: 08 November 2023
... of available therapeutic ontologies continues to increase, the need for harmonized cross-resource mappings is becoming increasingly apparent. This study creates harmonized concept mappings that enable the linking together of like-concepts despite source-dependent differences in data structure or semantic...
Journal Article
Stated preference methods and STI policy studies: a foreground approach
Víctor Gómez-Valenzuela
Research Evaluation, Volume 32, Issue 2, April 2023, Pages 171–187, https://doi.org/10.1093/reseval/rvad022
Published: 28 August 2023
..., and reproduction in any medium, provided the original work is properly cited. Ontologies refer to those structured theories, paradigms, and conceptual corps that, at different resolution levels, provide explanations of the problems' causality and the interactions of the different elements or constituents...
Journal Article
Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience
Tarcisio Mendes de Farias and others
in
GigaScience
GigaScience, Volume 12, 2023, giad058, https://doi.org/10.1093/gigascience/giad058
Published: 17 August 2023
... define alignments with plain English—implying not machine-ready to be read; programming languages—specific-purpose adaptors/translators; the OWL—Web Ontology Language (e.g., owl:sameAs, owl:equivalentClass) [ 30 ]; SKOS—Simple Knowledge Organization System vocabulary (e.g., skos:closeMatch) [ 31 ]; SWRL...
Journal Article
Automated detection of causal relationships among diseases and imaging findings in textual radiology reports
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Ronnie A Sebro and Charles E Kahn
Journal of the American Medical Informatics Association, Volume 30, Issue 10, October 2023, Pages 1701–1706, https://doi.org/10.1093/jamia/ocad119
Published: 28 June 2023
... (disorders and imaging findings) of the Radiology Gamuts Ontology (RGO). Entities that occurred in fewer than 25 patients were excluded. A Bayesian network structure-learning algorithm was applied at P < 0.05 threshold: edges were evaluated as possible causal relationships. RGO and/or physician...
Journal Article
FEATURED
The case for expressing nursing theories using ontologies
Elizabeth E Umberfield and others
Journal of the American Medical Informatics Association, Volume 30, Issue 11, November 2023, Pages 1865–1867, https://doi.org/10.1093/jamia/ocad095
Published: 12 June 2023
... to represent the knowledge of communities . Inf Organ 2009 ; 19 ( 4 ): 199 – 217 . 12 Guarino N , Oberle D , Staab S. What is an ontology? In: Staab S , Studer R , editors. Handbook on Ontologies . Berlin, Heidelberg : Springer ; 2009 : 1 – 17 . (International...
Journal Article
FEATURED
Rare disease research resources at the Rat Genome Database
Mary L Kaldunski and others
in
Genetics
Genetics, Volume 224, Issue 4, August 2023, iyad078, https://doi.org/10.1093/genetics/iyad078
Published: 29 April 2023
.... Leveraging these resources for rare disease mechanism discovery, and potentially the discovery of new treatment modalities, will help further clinical progress for those afflicted with these diseases. RGD’s data and tools are globally accessible. rare diseases Rat Genome Database ontologies Fig. 3...
Journal Article
FAIR data station for lightweight metadata management and validation of omics studies
Bart Nijsse and others
in
GigaScience
GigaScience, Volume 12, 2023, giad014, https://doi.org/10.1093/gigascience/giad014
Published: 06 March 2023
... to build searchable metadata databases of similar projects and can assist in ENA metadata submission of sequence data. The FAIR Data Station is available at https://fairbydesign.nl . FAIR metadata MIxS standards ENA submission tool semantic web ontologies NWO 10.13039/501100003246 Wageningen...
Journal Article
La inclusión relacional: examining neoliberal tensions, relational opportunities, and fixed understandings in diversity, equity, and inclusion work in the Global South
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Astrid M Villamil and others
Human Communication Research, Volume 49, Issue 2, April 2023, Pages 158–169, https://doi.org/10.1093/hcr/hqad011
Published: 01 March 2023
... of Organization (CCO) as an informing paradigm, this study proposed to understand institutional DEI as interconnected communicative practices of relational ontology. In addition, this study constituted an effort to recognize novel contours that delink knowledge from hegemonic North Atlantic and Eurocentric...
Journal Article
Transforming and evaluating the UK Biobank to the OMOP Common Data Model for COVID-19 research and beyond
Vaclav Papez and others
Journal of the American Medical Informatics Association, Volume 30, Issue 1, January 2023, Pages 103–111, https://doi.org/10.1093/jamia/ocac203
Published: 13 October 2022
.... The transformed UK Biobank resource is a valuable tool that can enable federated research, like COVID-19 studies. electronic health records medical ontologies phenotyping OMOP common data model European Health Data & Evidence Network Innovative Medicines Initiative 2 Joint Undertaking 806968...
Journal Article
Handling inconsistency in partially preordered ontologies: the Elect method
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Sihem Belabbes and others
Journal of Logic and Computation, Volume 31, Issue 5, July 2021, Pages 1356–1388, https://doi.org/10.1093/logcom/exab024
Published: 22 April 2021
..., the ICAR semantics involves a closure operation on the initial ABox before computing the repairs and intersecting them. Both IAR and ICAR are tractable, whereas AR and CAR are computationally expensive, even for lightweight ontology logics such as DL-Lite. It is also known that AR and CAR are more...
Journal Article
1619: The Danger of a Single Origin Story
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Michelle M Wright
American Literary History, Volume 32, Issue 4, Winter 2020, Pages e1–e12, https://doi.org/10.1093/alh/ajaa027
Published: 28 November 2020
... ones. 1619 Project African American culture Black queer and Black feminist representation Black epistemologies Black ontologies African American history African Diaspora In 2009, Nigerian author Chimamanda Ngozi Adichie gave a now-famous TED Talk entitled “The Danger of a Single Story,” arguing...
Journal Article
Phexpo: a package for bidirectional enrichment analysis of phenotypes and chemicals
Christopher Hawthorne and others
in
JAMIA Open
JAMIA Open, Volume 3, Issue 2, July 2020, Pages 173–177, https://doi.org/10.1093/jamiaopen/ooaa023
Published: 06 July 2020
.... Abbreviations: HPO: Human Phenotype Ontology; FDR: false discovery rate. Corresponding Author: Guillermo López-Campos, PhD, Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; g.lopezcampos@qub.ac.uk 11 01 2020 13 03 2020 21 05...
Journal Article
Development of the Gender, Sex, and Sexual Orientation ontology: Evaluation and workflow
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Clair A Kronk and Judith W Dexheimer
Journal of the American Medical Informatics Association, Volume 27, Issue 7, July 2020, Pages 1110–1115, https://doi.org/10.1093/jamia/ocaa061
Published: 17 June 2020
... (Medical Subject Headings), and National Cancer Institute Thesaurus). Results We published version 2 of the Gender, Sex, and Sexual Orientation (GSSO) ontology with over 10 000 entries with definitions, a readable hierarchy system, and over 14 000 database mappings. Over 70% of terms had no mapping...
Journal Article
The road towards data integration in human genomics: players, steps and interactions
Anna Bernasconi and others
Briefings in Bioinformatics, Volume 22, Issue 1, January 2021, Pages 30–44, https://doi.org/10.1093/bib/bbaa080
Published: 04 June 2020
... as evaluate the computational environments that they provide to follow up data integration by means of visualization and analysis tools. data integration genomics metadata interoperability genomic databases bio-ontologies In recent years, benefiting from high-throughput technologies [ 1 ], increasing...
Journal Article
Evaluation of ontology structural metrics based on public repository data
Manuel Franco and others
Briefings in Bioinformatics, Volume 21, Issue 2, March 2020, Pages 473–485, https://doi.org/10.1093/bib/bbz009
Published: 04 February 2019
... and distributed under the terms of the Oxford University Press, Standard Journals Publication Model ( https://dbpia.nl.go.kr/journals/pages/open_access/funder_policies/chorus/standard_publication_model ) Abstract The development and application of biological ontologies have increased significantly in recent...
Journal Article
Integrating ontologies of human diseases, phenotypes, and radiological diagnosis
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Michael T Finke and others
Journal of the American Medical Informatics Association, Volume 26, Issue 2, February 2019, Pages 149–154, https://doi.org/10.1093/jamia/ocy161
Published: 08 January 2019
...:https://dbpia.nl.go.kr/journals/pages/open_access/funder_policies/chorus/standard_publication_model ) Abstract Mappings between ontologies enable reuse and interoperability of biomedical knowledge. The Radiology Gamuts Ontology (RGO)—an ontology of 16 918 diseases, interventions, and imaging observations—provides...
Journal Article
Bioinformatics methodologies for coeliac disease and its comorbidities
Eugenio Del Prete and others
Briefings in Bioinformatics, Volume 21, Issue 1, January 2020, Pages 355–367, https://doi.org/10.1093/bib/bby109
Published: 16 November 2018
... two terms, according to a given ontology. Many methods are based on the annotation statistics of their common ancestor terms, i.e. on the information content of each term. In this work, the connections among the terms (genes, GO and DO) are more important than single comparisons. The Wang method fits...
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