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Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Larisa N Soldatova, Susanna-Assunta Sansone, Michel Dumontier, Nigam H Shah
2012 Journal of Biomedical Semantics  
Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more  ...  electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open  ...  Acknowledgements As editors of this supplement, we thank all the authors who submitted papers, the Program Committee members and the reviewers for their excellent work.  ... 
doi:10.1186/2041-1480-3-s1-i1 pmid:22541591 pmcid:PMC3337261 fatcat:zxzw6ar4bvajlnd6a5eaonufiy

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

O. Bodenreider
2008 IMIA Yearbook of Medical Informatics  
the National Cancer Institute Thesaurus, the International Classification of Diseases, the Medical Subject Headings (MeSH) and the Unified Medical Language System (UMLS).  ...  Barriers to the use of ontologies in biomedical applications are discussed.Geissbuhler A, Kulikowski C, editors. IMIA Year book of Medical Informatics 2008.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1055/s-0038-1638585 fatcat:r7vz4bruq5fpxa5nhhgcxohd2e

Biomedical ontologies in action: role in knowledge management, data integration and decision support

O Bodenreider
2008 IMIA Yearbook of Medical Informatics  
Cancer Institute Thesaurus, the International Classification of Diseases, the Medical Subject Headings (MeSH) and the Unified Medical Language System (UMLS).  ...  Barriers to the use of ontologies in biomedical applications are discussed.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
pmid:18660879 pmcid:PMC2592252 fatcat:axl74koixzbffmfi6m3txvlwqu

ONBIRES: Ontology-Based Biological Relation Extraction System

Minlie Huang, Xiaoyan Zhu, Shilin Ding, Hao Yu, Ming Li
2005 Proceedings of the 4th Asia-Pacific Bioinformatics Conference  
This framework is unified and able to extract several kinds of relations such as gene-disease, gene-gene, and protein-protein interactions etc.  ...  In this paper, we present an ontology-based framework of biological relation extraction system.  ...  We also would like to thank Xiaozhe Li and Zhiyuan Liu for coding programs and converting data from several publicly available external resources.  ... 
doi:10.1142/9781860947292_0036 fatcat:tdkpedv6ojdbroe3vcscdpo7pq

Infectious Disease Ontology [chapter]

Lindsay Grey Cowell, Barry Smith
2009 Infectious Disease Informatics  
The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information.  ...  We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases.  ...  The GO and other ontologies are used for annotation of genes and gene products in a variety of databases relevant to infectious disease research.  ... 
doi:10.1007/978-1-4419-1327-2_19 fatcat:ouv6gfucszfcpdh5mlifysopne

Desiderata for an ontology of diseases for the annotation of biological datasets

Olivier Bodenreider, Anita Burgun
2009 Nature Precedings  
There is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets.  ...  The four ontologies most closely aligned with our desiderata are Disease Ontology, SNOMED CT, NCI thesaurus and UMLS.  ...  Acknowledgements This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1038/npre.2009.3531.1 fatcat:qnc7y44w6bhwvp64yjxqvzwxzy

The Landscape of Disease and Phenotype Ontologies [article]

Nicole Vasilevsky
2022 Zenodo  
A compliation of disease and phenotype terminologies and ontologies. Last updated 2021-10-22.  ...  Medical Subject Headings (MeSH) thesaurus is a controlled and hierarchically-organized vocabulary produced by the National Library of Medicine.  ...  Medical Subject Headings (MeSH) Medical Subject Headings (MeSH) Description: Description: Website: Website: https://meshb.nlm.nih.gov/search Use Cases: Website: Open: Open: Yes NCIt)is a reference terminology  ... 
doi:10.5281/zenodo.6299897 fatcat:ryvbudptq5gtno2b7ntlhbnbcm

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

Cynthia L. Smith, Janan T. Eppig
2012 Mammalian Genome  
In this review we describe the MP as it presently exists, its application to phenotype annotations, the relationship of the MP to other ontologies, and the integration of the MP within large-scale phenotyping  ...  Using the ontology structure, data are retrieved inclusively, i.e., data annotated to chosen terms and to terms subordinate in the hierarchy.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s)  ... 
doi:10.1007/s00335-012-9421-3 pmid:22961259 pmcid:PMC3463787 fatcat:ygcz5rtafnbo7a7exo764r5vsu

Quantitative Imaging Biomarker Ontology (QIBO) for Knowledge Representation of Biomedical Imaging Biomarkers

Andrew J. Buckler, M. Ouellette, J. Danagoulian, G. Wernsing, Tiffany Ting Liu, Erica Savig, Baris E. Suzek, Daniel L. Rubin, David Paik
2013 Journal of digital imaging  
We have demonstrated that QIBO can be used to annotate imaging experiments with standardized terms in the ontology and to generate hypotheses for novel imaging biomarker-disease associations.  ...  This advances the goal of developing applications to (1) improve precision and recall of storage and retrieval of quantitative imaging-related data using standardized terminology; (2) streamline the discovery  ...  We would also like to acknowledge Yi Liu of the Biomedical Informatics Program at Stanford University annotating linked terms in QIBO shared with Disease Ontology.  ... 
doi:10.1007/s10278-013-9599-2 pmid:23589184 pmcid:PMC3705004 fatcat:czuz7iswincb7bf2dump4whrca

Representing virus-host interactions and other multi-organism processes in the Gene Ontology

R. E. Foulger, D. Osumi-Sutherland, B. K. McIntosh, C. Hulo, P. Masson, S. Poux, P. Le Mercier, J. Lomax
2015 BMC Microbiology  
Methods: To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology.  ...  The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms.  ...  Acknowledgements The authors would like to thank Amelia Ireland and the PAMGO Consortium, especially Candace Colmer, Michelle Gwinn-Giglio and Trudy Torto-Alalibo for work developing the original set of  ... 
doi:10.1186/s12866-015-0481-x pmid:26215368 pmcid:PMC4517558 fatcat:m4yomtx7hnhtdkzi63w2pgrmae

e-Science and the Semantic Web: A Symbiotic Relationship [chapter]

Carole Goble, Oscar Corcho, Pinar Alper, David De Roure
2006 Lecture Notes in Computer Science  
It is about harvesting and harnessing the "collective intelligence" of the scientific community.  ...  The Semantic Web is an extension of the current Web in which information is given well-defined meaning to facilitate sharing and reuse, better enabling computers and people to work in cooperation.  ...  Acknowledgements The authors express their thanks to their many colleagues in the e-Science programme and beyond.  ... 
doi:10.1007/11894841_3 fatcat:6aavv7okzba2vblbh5g6gp5z6y

e-Science and the Semantic Web: A Symbiotic Relationship [chapter]

Carole Goble, Oscar Corcho, Pinar Alper, David De Roure
2006 Lecture Notes in Computer Science  
It is about harvesting and harnessing the "collective intelligence" of the scientific community.  ...  The Semantic Web is an extension of the current Web in which information is given well-defined meaning to facilitate sharing and reuse, better enabling computers and people to work in cooperation.  ...  Acknowledgements The authors express their thanks to their many colleagues in the e-Science programme and beyond.  ... 
doi:10.1007/11893318_1 fatcat:c65dar7f3vdwdco5zpmqy2d5me

Combining Concept Annotation and Pattern Structures for Guiding Ontology Mapping

Pierre Monnin, Amedeo Napoli, Adrien Coulet
2018 International Joint Conference on Artificial Intelligence  
In this paper, we combine Concept Annotation with the formalism of Pattern Structures and we consider multiple annotation possibilities, i.e., multiple annotations for one concept and computing the annotation  ...  We illustrate our approach and its interest with two use cases: (i) suggesting mappings between ontology classes and (ii) finding specific classes frequently associated as domain and range of a predicate  ...  Acknowledgments This work is supported by the PractiKPharma project, founded by the French National Research Agency (ANR) under Grant No.: ANR-15-CE23-0028, and by the Snowball Inria Associate Team.  ... 
dblp:conf/ijcai/MonninNC18 fatcat:vgsc7nrs6ngl7m33aj2syofkzq

Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs)

Warren A Cheung, BF Ouellette, Wyeth W Wasserman
2012 BMC Bioinformatics  
MEDLINE W /PubMed W indexes over 20 million biomedical articles, providing curated annotation of its contents using a controlled vocabulary known as Medical Subject Headings (MeSH).  ...  The reliability of MeSHOP annotations is assessed based on the capacity to re-derive the subset of the Gene Ontology annotations with equivalent MeSH terms.  ...  Acknowledgement The authors are grateful to Drs. Leon French, Paul Pavlidis and Raf Podowski for comments and discussion on the research and Joseph Yamada for help with the website. Funding  ... 
doi:10.1186/1471-2105-13-249 pmid:23017167 pmcid:PMC3564935 fatcat:kzqloymanvhihgtrd5swvp57em

New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models

P. N. Schofield, J. P. Sundberg, R. Hoehndorf, G. V. Gkoutos
2011 Briefings in Functional Genomics  
The focus of his research is the application of ontologies for large-scale data analysis in biomedicine and their use for translational research. Georgios V.  ...  He has developed a number of biomedical ontologies and his research focuses on the association of genotype to phenotype, translational research and the discovery of novel disease genes and drugs.  ...  The intermediate framework may be a network or terminology such as Unified Medical Language System (UMLS) [36] or Medical Subject Headings (MeSH), or in recent approaches may make the use of the semantic  ... 
doi:10.1093/bfgp/elr031 pmid:21987712 pmcid:PMC3189694 fatcat:xgppdrqndvba5ppmijvqhkuraa
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