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Biomedical ontologies: a functional perspective

D. L. Rubin, N. H. Shah, N. F. Noy
2007 Briefings in Bioinformatics  
In fact, bio-ontologies are beginning to proliferate in step with accruing biological data.  ...  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

Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase

Erik Segerdell, Virgilio G Ponferrada, Christina James-Zorn, Kevin A Burns, Joshua D Fortriede, Wasila M Dahdul, Peter D Vize, Aaron M Zorn
2013 Journal of Biomedical Semantics  
The XAO, now with 1313 defined anatomical and developmental stage terms, has been integrated with Xenbase expression and anatomy term searches and it enables links between various data types including  ...  The Xenopus Anatomy Ontology (XAO) reflects the anatomy and embryological development of Xenopus.  ...  We thank Chris Mungall and Melissa Haendel for advice on ontology improvements, best practices, and version control, and Melissa Haendel for comments on the manuscript.  ... 
doi:10.1186/2041-1480-4-31 pmid:24139024 pmcid:PMC3816597 fatcat:x54xjgsz25hwvc7imkwx2aoysi

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

O Bodenreider
2008 IMIA Yearbook of Medical Informatics  
Examples of applications are taken from operational systems and the biomedical literature, with a bias towards recent journal articles.  ...  The ontologies under investigation in this survey include SNOMED CT, the Logical Observation Identifiers, Names, and Codes (LOINC), the Foundational Model of Anatomy, the Gene Ontology, RxNorm, the National  ...  Several biomedical search engines exploit MeSH and the UMLS to provide access to the biomedical literature, including SAPHIRE [81] , Essie [82] and Textpresso [83] , as well as web resources for consumers  ... 
pmid:18660879 pmcid:PMC2592252 fatcat:axl74koixzbffmfi6m3txvlwqu

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

O. Bodenreider
2008 IMIA Yearbook of Medical Informatics  
Examples of applications are taken from operational systems and the biomedical literature, with a bias towards recent journal articles.  ...  Results The ontologies under investigation in this survey include SNOMED CT, the Logical Observation Identifiers, Names, and Codes (LOINC), the Foundational Model of Anatomy, the Gene Ontology, RxNorm,  ...  Several biomedical search engines exploit MeSH and the UMLS to provide access to the biomedical literature, including SAPHIRE [81] , Essie [82] and Textpresso [83] , as well as web resources for consumers  ... 
doi:10.1055/s-0038-1638585 fatcat:r7vz4bruq5fpxa5nhhgcxohd2e

AN ANATOMICAL ONTOLOGY FOR AMPHIBIANS

ANNE M. MAGLIA, JENNIFER L. LEOPOLD, L. ANALÍA PUGENER, SUSAN GAUCH
2006 Biocomputing 2007  
Further demonstrating the importance of anatomical ontologies was the recent National Center for Biomedical Ontology-sponsored workshop † to bring researchers together to discuss issues associated with  ...  There are several challenges to developing an ontology for amphibian anatomy. First, the separate anatomical lexicons must be reconciled.  ...  to the search term in the ontology.  ... 
doi:10.1142/9789812772435_0035 fatcat:v45d6jb4fvh3vnokygaqlgrhnu

A Maximum-Entropy approach for accurate document annotation in the biomedical domain

George Tsatsaronis, Natalia Macari, Sunna Torge, Heiko Dietze, Michael Schroeder
2012 Journal of Biomedical Semantics  
In this paper we address this issue for the biomedical domain and present a new automated and robust method, based on a Maximum Entropy approach, for annotating biomedical literature documents with MeSH  ...  A fundamental step in these approaches is the annotation of documents with ontology concepts, which can also be seen as a classification task.  ...  CONCLUSIONS AND FUTURE WORK In this work we introduced a novel approach for annotating documents of the biomedical literature with concepts from the MeSH ontology.  ... 
doi:10.1186/2041-1480-3-s1-s2 pmid:22541593 pmcid:PMC3337257 fatcat:ftaxggw2cjebvd26epq26ofn6i

Building a biomedical ontology recommender web service

Clement Jonquet, Mark A Musen, Nigam H Shah
2010 Journal of Biomedical Semantics  
Methods We present the Biomedical Ontology Recommender web service.  ...  The number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use.  ...  Acknowledgements This work is supported by NIH grant U54 HG004028 in support of the National Center for Biomedical Ontology.  ... 
doi:10.1186/2041-1480-1-s1-s1 pmid:20626921 pmcid:PMC2903720 fatcat:d7mxashoyjhsbphqqlpsi3ugxq

An ontology for Xenopus anatomy and development

Erik Segerdell, Jeff B Bowes, Nicolas Pollet, Peter D Vize
2008 BMC Developmental Biology  
The ontology is available for download at the Open Biomedical Ontologies Foundry http:// obofoundry.org.  ...  Its robust developmental map will enable powerful database searches and data analyses. We encourage community recommendations for updates and improvements to the ontology.  ...  We also thank Chris Mungall for his guidance in joining the OBO Foundry, Mark Gibson for help with Phenote, and Naoto Ueno for the images in Figure 2 .  ... 
doi:10.1186/1471-213x-8-92 pmid:18817563 pmcid:PMC2561031 fatcat:dqxvjryvujd5xplm2sansy75oi

HuPSON: the human physiology simulation ontology

Michaela Gündel, Erfan Younesi, Ashutosh Malhotra, Jiali Wang, Hui Li, Bijun Zhang, Bernard de Bono, Heinz-Theodor Mevissen, Martin Hofmann-Apitius
2013 Journal of Biomedical Semantics  
It is meant to foster a more rapid uptake of semantic technologies in the modelling and simulation domain, with particular focus on the VPH domain.  ...  The ontology is based on the Basic Formal Ontology, and adheres to the MIREOT principles; the constructed ontology has been evaluated via structural features, competency questions and use case scenarios  ...  The ontology is suited to link the mathematics and algorithmics behind biomedical simulations and the communication dealing with simulation experiments.  ... 
doi:10.1186/2041-1480-4-35 pmid:24267822 pmcid:PMC4177144 fatcat:zjjzvomhdvhlnpt3n4hrczcgvu

Phenotype ontologies: the bridge between genomics and evolution

P MABEE, M ASHBURNER, Q CRONK, G GKOUTOS, M HAENDEL, E SEGERDELL, C MUNGALL, M WESTERFIELD
2007 Trends in Ecology & Evolution  
Here, we suggest that evolutionary and genomics databases can be developed to exchange and use information through shared phenotype and anatomy ontologies.  ...  By contrast, model organism studies have been enhanced by ontologies shared among genomic databases.  ...  G.V.G. is supported by the National Center for Biomedical Ontology (NIH: 1-U54-HG004028-01). We thank Adam Amsterdam and Nancy Hopkins for use of the image in Figure 2 .  ... 
doi:10.1016/j.tree.2007.03.013 pmid:17416439 fatcat:lub7w3xaxbghhcf7ygb7c2o36a

Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data

Terry F. Hayamizu, Richard A. Baldock, Martin Ringwald
2015 Mammalian Genome  
Mouse anatomy ontologies provide standard nomenclature for describing normal and mutant mouse anatomy, and are essential for the description and integration of data directly related to anatomy such as  ...  We report on recent ontology enhancements, describe the current status, and discuss future plans for mouse anatomy ontology development and application in integrating data resources.  ...  to the new version of the mouse developmental anatomy ontology, and for help with the figures presented in this paper.  ... 
doi:10.1007/s00335-015-9584-9 pmid:26208972 pmcid:PMC4602063 fatcat:bydou3vkfzd37itvnzt7ehuqg4

Speeding Up Iterative Ontology Alignment using Block-Coordinate Descent

U. Thayasivam, P. Doshi
2014 The Journal of Artificial Intelligence Research  
Several algorithms exist for automatically aligning ontologies with diverse levels of performance.  ...  As biomedicine represents a key application domain for ontologies, we introduce a comprehensive biomedical ontology testbed for the community in order to evaluate alignment algorithms.  ...  These ontologies are primarily being used to annotate biomedical data and literature in order to facilitate improved information exchange.  ... 
doi:10.1613/jair.4366 fatcat:hecqxsh2pzgmrer3uy7gl3j7ya

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio

Ceri E Van Slyke, Yvonne M Bradford, Monte Westerfield, Melissa A Haendel
2014 Journal of Biomedical Semantics  
The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish  ...  Results: The ZFA models anatomy and development with a subclass hierarchy, a partonomy, and a developmental hierarchy and with relationships to the ZFS that define the stages during which each anatomical  ...  Since ZFA classes are required for literature annotation, the ZFA editors add classes to the ontology as they are described in the literature, through discussion and coordination within the larger anatomy  ... 
doi:10.1186/2041-1480-5-12 pmid:24568621 pmcid:PMC3944782 fatcat:bmhhm3n4dzfuba3tkwnkfzoee4

Towards Visualizing the Alignment of Large Biomedical Ontologies [chapter]

Catia Pesquita, Daniel Faria, Emanuel Santos, Jean-Marc Neefs, Francisco M. Couto
2014 Lecture Notes in Computer Science  
It allows non-expert users to easily align biomedical ontologies, offering a wide selection of matching strategies and algorithms, with a particular focus on the use of external background knowledge.  ...  Recent developments in ontology alignment techniques, including our AgreementMakerLight system, have been successful in matching very large biomedical ontologies.  ...  However, there are also opportunities within the biomedical domain such as the abundance of scientific literature or the availability of many related biomedical ontologies.  ... 
doi:10.1007/978-3-319-08590-6_10 fatcat:ebzacwiuvrde7p22ymxnghknle

The Xenbase literature curation process

Jeff B. Bowes, Kevin A. Snyder, Christina James-Zorn, Virgilio G. Ponferrada, Chris J. Jarabek, Kevin A. Burns, Bishnu Bhattacharyya, Aaron M. Zorn, Peter D. Vize
2013 Database: The Journal of Biological Databases and Curation  
This may involve examining anatomy ontologies for other vertebrates such as mouse or zebrafish or through consultation with other ontology development teams such as National Center for Biomedical Ontology  ...  The Xenopus literature corpus contains >42 000 papers with 1500 new papers added per year.  ... 
doi:10.1093/database/bas046 pmid:23303299 pmcid:PMC3540419 fatcat:6kpdiqi74jdirh5ptf6zn4kbsq
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