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Ontological interpretation of biomedical database content

Filipe Santana da Silva, Ludger Jansen, Fred Freitas, Stefan Schulz
2017 Journal of Biomedical Semantics  
We address this problem by grounding implicit and explicit database content in a formal-ontological framework.  ...  The result is a seamless representation of database structure, content and annotations as OWL models.  ...  LJ has written and contributed to the ontological basics of the manuscript, as well as reviewed and commented on content and organization.  ... 
doi:10.1186/s13326-017-0127-z pmid:28651575 pmcid:PMC5485580 fatcat:6wn2a2px3rbjfh2yzi6vli5t2i

Ontological interpretation of biomedical database annotations

Filipe Santana, Ludger Jansen, Fred Freitas, Stefan Schulz
2016 Workshop on Ontologies and Data in Life Sciences  
We explore the options for an ontology-based integration and interpretation of database content of individuals, defined classes, dispositions and a combination of these.  ...  Motivation: In general, the meaning of biological database records is not sufficiently specified from an ontological point of view.  ...  a subclass of Methionine synthase, defined as Methionine synthase that is part of an organism of the type Rattus Ontological interpretation of biomedical database annotations Filipe Santana da Silva  ... 
dblp:conf/odls/SantanaJFS16 fatcat:jr6jumq42vgavax3n4ssa66eau

Thematic series on biomedical ontologies in JBMS: challenges and new directions

Robert Hoehndorf, Melissa Haendel, Robert Stevens, Dietrich Rebholz-Schuhmann
2014 Journal of Biomedical Semantics  
The aim of the series is to disseminate the latest developments in research on biomedical ontologies and provide a venue for publishing newly developed ontologies, updates to existing ontologies as well  ...  As ontologies are becoming a central part of biological and biomedical research, a communication channel to publish frequent updates and latest developments on them would be an advantage.  ...  Representing ontologies The annotation of research data using an ontology enables integration of data both within a database and across multiple databases [1] .  ... 
doi:10.1186/2041-1480-5-15 pmid:24602198 pmcid:PMC4006457 fatcat:v5kignpyjrhxniirpbuxnylnsq

Biomedical ontologies: a functional perspective

D. L. Rubin, N. H. Shah, N. F. Noy
2007 Briefings in Bioinformatics  
She is a member of the Protege group and of the National Center on Biomedical Ontology, where she works on tools for ontology management, including versioning, mapping and modularization of ontologies  ...  Shah is a research scientist at the Stanford Center for Biomedical Informatics group and member of the National Center for Biomedical Ontology.  ...  Acknowledgements This work was supported by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health.  ... 
doi:10.1093/bib/bbm059 pmid:18077472 fatcat:z3orlk75yzherjf37i3nehqlmm

Imaging Informatics: Toward Capturing and Processing Semantic Information in Radiology Images

S. Napel, D. L. Rubin
2010 IMIA Yearbook of Medical Informatics  
image information for decision support to improve radiologist interpretation performance.  ...  of ontologies to describe radiology reports and images, (2) structured reporting and image annotation methods to make image semantics explicit and machine-accessible, and (3) applications that use semantic  ...  and mining biomedical databases [80] .  ... 
doi:10.1055/s-0038-1638686 fatcat:6iu5bwe675emdnizsub5rwyqvu

Logical Axiomatization of the Evidence & Conclusion Ontology (ECO) by Integrating External Ontology Classes

Rebecca Tauber, Marcus C. Chibucos
2017 International Conference on Biomedical Ontology  
The Evidence & Conclusion Ontology (ECO) and the Ontology for Biomedical Investigations (OBI) began a loose collaboration, i.e. talking, in 2011.  ...  Mapping semantically equivalent classes across ontologies is a crucial step toward increasing interoperability and is necessary to enable the leveraging of existing external ontologies during ontology  ...  Ultimately researchers use evidence to support a variety of conclusions. In the biomedical realm, one such conclusion might be the interpretation that a protein has a particular function.  ... 
dblp:conf/icbo/TauberC17 fatcat:r7dgzyja4zhcno5stuem3pfha4

Current status of biomedical ontologies: Developments in 2007

Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang
2008 2008 2nd IEEE International Conference on Digital Ecosystems and Technologies  
' between what are called 'concepts', and serving primarily the purposes of information extraction from on-line biomedical literature and databases.  ...  This paper discusses features of biomedical ontologies that allow true information integration in biomedical domain.  ...  The Center is developing two major repositories of biomedical content: (1) Open Biomedical Ontologies (OBO), a comprehensive, online library of open-content ontologies and controlled terminologies, and  ... 
doi:10.1109/dest.2008.4635220 fatcat:xwovgpwagrfw7ka57fccs5cw4q

National Center for Biomedical Ontology [chapter]

Mark A. Musen
2013 Encyclopedia of Systems Biology  
the cornerstone of software for bridging systems, domains, and resources. 2 Ontologies are the foundation of all semantic technologies in e-science, and are a critical component of multi-disciplinary  ...  In biomedicine, one of the most fruitful approaches has been to use software tools and knowledge resources known as ontologies-machineprocessable descriptions of scientific domains-that can promote the  ...  We have created the system as the nexus of an online community of ontology developers and ontology users who use BioPortal to view, to comment on, and to discuss the content of biomedical ontologies (  ... 
doi:10.1007/978-1-4419-9863-7_1515 fatcat:3fb7uzhelvgdzlcbmuaekggtyu

National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge

Daniel L. Rubin, Suzanna E. Lewis, Chris J. Mungall, Sima Misra, Monte Westerfield, Michael Ashburner, Ida Sim, Christopher G. Chute, Margaret-Anne Storey, Barry Smith, John Day-Richter, Natalya F. Noy (+1 others)
2006 Omics  
and communicate best practices of ontology development to the biomedical community.  ...  of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate,  ...  ACKNOWLEDGMENTS We would like to acknowledge the enormous contributions of all the talented members of our Center, ͗http://bioontology.org/overview-team.html͘.  ... 
doi:10.1089/omi.2006.10.185 pmid:16901225 fatcat:s6m4gcw645fwrhnkc4zky7bav4

Current Status of Biomedical Ontologies: Developments in 2006

Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang
2007 2007 Inaugural IEEE-IES Digital EcoSystems and Technologies Conference  
The paper is compilation of several biomedical ontologies like Gene Ontology, Protein Ontology, etc. that have developed serving primarily the purposes of information extraction from on-line biomedical  ...  This paper discusses features of biomedical ontologies that allow true information integration in biomedical domain.  ...  The Center is developing two major repositories of biomedical content: (1) Open Biomedical Ontologies (OBO), a comprehensive, online library of open-content ontologies and controlled terminologies, and  ... 
doi:10.1109/dest.2007.372042 fatcat:v4ej54x67fgi7jj6qep5vby2xu

The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research

Lauren Chan, Nicole Vasilevsky, Anne Thessen, Julie McMurry, Melissa Haendel
2021 Database: The Journal of Biological Databases and Curation  
In particular, we will focus on the application of biomedical ontologies and their potential to improve the standardization and interoperability of nutrition terminologies and relationships between nutrition  ...  and other biomedical disciplines such as disease and phenomics.  ...  Micronutrient content Average weight/volume Downloaded from https://academic.oup.com/database/article/doi/10.1093/database/baab003/6119904 by guest on 07 February 2021  ... 
doi:10.1093/database/baab003 pmid:33494105 pmcid:PMC7833928 fatcat:l6jywwjkgncvtb6kxoou2c5swy

Evaluation of research in biomedical ontologies

R. Hoehndorf, M. Dumontier, G. V. Gkoutos
2012 Briefings in Bioinformatics  
the objective evaluation and comparison of research results in applied ontology.  ...  We propose that results in applied ontology must be evaluated within their domain of application, based on some ontology-based task within the domain, and discuss quantitative measures which would facilitate  ...  Furthermore, the content of the ontology can be evaluated similarly to database content evaluation [109].  ... 
doi:10.1093/bib/bbs053 pmid:22962340 pmcid:PMC3888109 fatcat:lyepy5en5vfpzgbq6uaaxr7aiu

Ontology-Based Knowledge Representation of Experiment Metadata in Biological Data Mining [chapter]

Carl Dahlke, Richard Scheuermann, Patrick Dunn, David Karp, Jamie Lee, Herb Hagler, Jennifer Cai, Barry Smith, Burke Squires, Yu Qian, Megan Kong, Jeff Wiser
2009 Chapman & Hall/CRC Data Mining and Knowledge Discovery Series  
, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant  ...  In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled  ...  , free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant  ... 
doi:10.1201/9781420086850.ch21 fatcat:wglqpy4ozvg77cgwy2k52w57cy

Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge

Sirarat Sarntivijai, Alexander D. Diehl, Yongqun He
2017 BMC Bioinformatics  
This is an established approach in data-driven ontologies such as the Experimental Factor Ontology (EFO), and the Ontology for Biomedical Investigation (OBI).  ...  This CELLS workshop also provided a venue for panel discussions of innovative solutions as well as challenges in the development and applications of biomedical ontologies to represent and analyze experimental  ...  We have identified the area where the use of biomedical ontologies can aid effective data annotation for the scMap tool and Stemformatics database to extend the analysis/content of the resources to other  ... 
doi:10.1186/s12859-017-1976-2 pmid:29322916 pmcid:PMC5763506 fatcat:r7y4wcuw6jezvbxfy2ovo6jfh4

Interpretation errors related to the GO annotation file format

Dilvan A Moreira, Nigam H Shah, Mark A Musen
2007 AMIA Annual Symposium Proceedings  
The Gene Ontology (GO) is the most widely used ontology for creating biomedical annotations. GO annotations are statements associating a biological entity with a GO term.  ...  These statements comprise a large dataset of biological knowledge that is used widely in biomedical research.  ...  The GO is the most widely used biomedical ontology for annotation of genes and proteins as well as analysis of high throughput datasets -especially microarray data 1 .  ... 
pmid:18693894 pmcid:PMC2655813 fatcat:p43q3b6f6jhvbgtljk42nehh2a
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