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The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources

Catia Pesquita, João D Ferreira, Francisco M Couto, Mário J Silva
2014 Journal of Biomedical Semantics  
Results: The EPO follows the OBO Foundry guidelines and uses the Basic Formal Ontology (BFO) as an upper ontology.  ...  Although several ontologies cover some of the subdomains of epidemiology, we identified a lack of semantic resources for epidemiology-specific terms.  ...  The authors are grateful to Mélanie Courtot for her comments and guidance on tailoring the Epidemiology Ontology to OBO Foundry principles.  ... 
doi:10.1186/2041-1480-5-4 pmid:24438387 pmcid:PMC3926306 fatcat:f42nbyfg3fd6rcwxxh6ek2d2oy

Collecting Community-Based Mappings in an Ontology Repository [chapter]

Natalya F. Noy, Nicholas Griffith, Mark A. Musen
2008 Lecture Notes in Computer Science  
This metadata may include information provided by ontology authors, such as ontologies' scope and intended use; feedback provided by users such as their experiences in using the ontologies or reviews of  ...  More specifically, we develop a model for representing mappings collected from the user community and the metadata associated with the mapping.  ...  Acknowledgments This work was supported by the National Center for Biomedical Ontology, under roadmapinitiative grant U54 HG004028 from the National Institutes of Health.  ... 
doi:10.1007/978-3-540-88564-1_24 fatcat:crz7sk632jdkbaqyqrlbj4xjuu

Distributed Biomedical Terminology Development: From Experiments to Open Process

C. G. Chute
2010 IMIA Yearbook of Medical Informatics  
Nevertheless, several projects, including the Gene Ontology and the new revision of the International Classification of Disease (ICD-11) hold promise.  ...  example on the order of Wikipedia is yet extant.  ...  Acknowledgements This work was supported in part by the National Center for Biomedical Ontology, N01-HG04028. Dr.  ... 
doi:10.1055/s-0038-1638690 fatcat:q6ngwv23avdslehajt2vnvefyq

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  ...  terms in the National Cancer Institute (NCI) Thesaurus.  ... 
doi:10.1007/978-1-4419-9863-7_1515 fatcat:3fb7uzhelvgdzlcbmuaekggtyu

The ontology life cycle: Integrated tools for editing, publishing, peer review, and evolution of ontologies

Natalya Noy, Tania Tudorache, Csongor Nyulas, Mark Musen
2010 AMIA Annual Symposium Proceedings  
as Protégé; and publish it on a Web server or in an ontology library, such as BioPortal, in order to share it with the community; they use the tools provided by the library or mailing lists and bug trackers  ...  In this paper, we present a set of tools that bring the ontology editing and publishing closer together, in an integrated platform for the entire ontology lifecycle.  ...  Furthermore, ontologies are becoming so large in their coverage (e.g., NCI Thesaurus with 80,000 concepts) that no single centralized group of people can develop them effectively and many organizations  ... 
pmid:21347039 pmcid:PMC3041389 fatcat:mrbl2tfiure2pgandmj3jsb644

Application and evaluation of automated semantic annotation of gene expression experiments

L. French, S. Lane, T. Law, L. Xu, P. Pavlidis
2009 Bioinformatics  
We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data.  ...  The most errorprone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision.  ...  Many other ontologies or terminologies have these references and could be used in our system such as the Gene Ontology (Ashburner et al., 2000) , Medical Subject Headings (MeSHs), the NCI Thesaurus (  ... 
doi:10.1093/bioinformatics/btp259 pmid:19376825 pmcid:PMC2687992 fatcat:tc4ru66rfvgfxluz62lok6v7hi

Accessing and integrating data and knowledge for biomedical research

A Burgun, O Bodenreider
2008 IMIA Yearbook of Medical Informatics  
We analyzed the requirements for effective knowledge repositories and studied issues in the integration of biomedical knowledge.  ...  Using examples form the biomedical literature, we identified new trends in biomedical research and their impact on bioinformatics.  ...  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:18660883 pmcid:PMC2553094 fatcat:buqnlvjixvfwdlblwug6hyajzy

Accessing and Integrating Data and Knowledge for Biomedical Research

O. Bodenreider, A. Burgun
2008 IMIA Yearbook of Medical Informatics  
We analyzed the requirements for effective knowledge repositories and studied issues in the integration of biomedical knowledge.  ...  High-quality, integrated ontologies and knowledge bases serve as a source of prior knowledge used in combination with traditional data mining techniques and contribute to the development of more effective  ...  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-0038-1638588 fatcat:75nhlolnare4vfqehvoiowelqm

Biomedical Semantic Resources for Drug Discovery Platforms [chapter]

Ali Hasnain, Dietrich Rebholz-Schuhmann
2017 Lecture Notes in Computer Science  
Since the data sources are publicly available, the amount of content can be measured giving an overview on the accessible content but also on the state of the data representation in comparison to the existing  ...  The biomedical research community is providing large-scale data sources to enable knowledge discovery from the data alone, or from novel scientific experiments in combination with the existing knowledge  ...  Biological Activities, (iv) Disease Specific Databases for Prevention, and the (v) Literature databases.  ... 
doi:10.1007/978-3-319-70407-4_34 fatcat:2bzddzat5zdcrinfwd6m4xqlai

Informatics and standards for nanomedicine technology

Dennis G. Thomas, Fred Klaessig, Stacey L. Harper, Martin Fritts, Mark D. Hoover, Sharon Gaheen, Todd H. Stokes, Rebecca Reznik-Zellen, Elaine T. Freund, Juli D. Klemm, David S. Paik, Nathan A. Baker
2011 Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology  
There are several issues to be addressed concerning the management and effective use of information (or data), generated from nanotechnology studies in biomedical research and medicine.  ...  These data are large in volume, diverse in content, and are beset with gaps and ambiguities in the description and characterization of nanomaterials.  ...  Center for Biomedical Ontology for their support of nanomedicine informatics through the NCBO Bioportal, Resource Index, and caOBR.  ... 
doi:10.1002/wnan.152 pmid:21721140 pmcid:PMC3189420 fatcat:x4nlyhsdxrgxtcq7ihabv3pwsy

Knowledge-based Biomedical Data Science 2019 [article]

Tiffany J. Callahan, Ignacio J. Tripodi Computational Bioscience Program, Department of Pharmacology, University of Colorado Denver Anschutz Medical Campus
2019 arXiv   pre-print
Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating  ...  Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs.  ...  The supplemental material has been submitted in a separate word document titled: Supplementtal_Material.docx.  ... 
arXiv:1910.06710v1 fatcat:kvz5k643zvhpdiq67blc2v33wi

Dependencies between ontology design parameters

C. Maria Keet
2010 International Journal of Metadata, Semantics and Ontologies  
Ontology development methodologies provide scenarios, but they do not address the dependencies between the permutations at the different stages in the development process.  ...  The parameters considered are: nine main purpose(s) of the ontology, reuse of the three main types of ontologies, eight different ways for bottom-up ontology development, eight ontology languages, and  ...  There are many terminologies and thesauri and a few of them are being adapted for the Semantic Web, such as the NCI Thesaurus 8 .  ... 
doi:10.1504/ijmso.2010.035550 fatcat:lhnye6za7rdvrnvukiv4pyjyx4

Ontologies and Knowledge Graphs in Oncology Research

Marta Contreiras Silva, Patrícia Eugénio, Daniel Faria, Catia Pesquita
2022 Cancers  
We also review the most commonly used ontologies and newly developed ones.  ...  The complexity of cancer research stems from leaning on several biomedical disciplines for relevant sources of data, many of which are complex in their own right.  ...  The immense potential of ontologies and the knowledge graph paradigm to support cancer research data management and analysis is increasingly recognized by the oncology research community as an essential  ... 
doi:10.3390/cancers14081906 pmid:35454813 pmcid:PMC9029532 fatcat:t6erzohmvnextkix4infnk7kza

Detecting Role Errors in the Gene Hierarchy of the NCI Thesaurus

Hua Min, Barry Cohen, Michael Halper, Marc Oren, Yehoshua Perl
2008 Cancer Informatics  
In light of this, an auditing methodology tailored to the characteristics of the NCI Thesaurus's (NCIT's) Gene hierarchy is presented.  ...  The Gene hierarchy is of particular interest to the NCIT's designers due to the primary role of genomics in current cancer research.  ...  Acknowledgment We would like to thank Gilberto Fragoso, Frank Hartel, and Larry Wright of the NCI for their assistance and insights.  ... 
doi:10.4137/cin.s440 fatcat:iennbaalrze33n4zcjq5i7rqpq

The ACGT Master Ontology and its applications – Towards an ontology-driven cancer research and management system

Mathias Brochhausen, Andrew D. Spear, Cristian Cocos, Gabriele Weiler, Luis Martín, Alberto Anguita, Holger Stenzhorn, Evangelia Daskalaki, Fatima Schera, Ulf Schwarz, Stelios Sfakianakis, Stephan Kiefer (+3 others)
2011 Journal of Biomedical Informatics  
This included the careful study of best practices, design principles and evaluation methods for ontology design, maintenance, implementation, and versioning, as well as for use on the part of domain experts  ...  While the available data in the life sciences has recently grown both in amount and quality, the full exploitation of it is being hindered by the use of different underlying technologies, coding systems  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support. The authors thank two anonymous reviewers for valuable comments.  ... 
doi:10.1016/j.jbi.2010.04.008 pmid:20438862 pmcid:PMC5755590 fatcat:r5o5r66xazh7dfxh4pfzchb46m
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