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Enabling Ontology Based Semantic Queries in Biomedical Database Systems

Shuai Zheng, Fusheng Wang, James Lu, Joel Saltz
2012 Proceedings of the ... ACM International Conference on Information & Knowledge Management. ACM International Conference on Information and Knowledge Management  
The problem may be largely attributed to the mismatch between the models of the ontologies and the databases, and the mismatch between the query interfaces of the two systems.  ...  DBOntoLink is adaptable to different ontologies through customizations and supports major biomedical ontologies hosted at the NCBO BioPortal.  ...  Acknowledgments This research is supported in part by PHS Grant UL1RR025008 from the CTSA program, R01LM009239 from the NLM, and NCI Contract No. HHSN261200800001E.  ... 
pmid:23404054 pmcid:PMC3567445 fatcat:3zkcvoz4cjcztjpam5pro4okp4

Community of Learners: Ontological and non-ontological projects

Eugene Matusov, Katherine von Dyuke, Sohyun Han
2013 Outlines : Critical Social Studies  
We will consider two ontological COL projects into: narrowly dialogic and polyphonic.  ...  Our analysis reveals two major types of "Community of Learners" (COL) projects: instrumental and ontological.  ...  And we're going to go back to math class. And they're like, ohhhhh!!!  ... 
doi:10.7146/ocps.v14i1.6062 fatcat:tgsrl4b4yfhzvcs3xtr2burtlu

Dependencies between ontology design parameters

C. Maria Keet
2010 International Journal of Metadata, Semantics and Ontologies  
Development and use of ontologies is increasing, but hampered by new challenges, such as determining which ontologies to reuse and which language to use.  ...  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  ...  Biological databases as well as databases at the back-end of content management systems have a mixture of the two so that some database data have to be imported into the ontology as concepts (OWL classes  ... 
doi:10.1504/ijmso.2010.035550 fatcat:lhnye6za7rdvrnvukiv4pyjyx4

Ontologies for clinical and translational research: Introduction

Barry Smith, Richard H. Scheuermann
2011 Journal of Biomedical Informatics  
We are grateful for the support of the National Institutes of Health and of the National Human Genome Research Institute through the NIH Roadmap for Medical Research Grant 1 U 54 HG004028 and through conference  ...  Acknowledgments The majority of the contributions to this issue are based on papers presented at the first International Conference on Biomedical Ontology held in Buffalo, NY in July 2009.  ...  chemical entity ontology in GO.  ... 
doi:10.1016/j.jbi.2011.01.002 pmid:21241822 pmcid:PMC4896064 fatcat:27z33vylvrcrbaqcadzvnbjjvu

Comparative GO: A Web Application for Comparative Gene Ontology and Gene Ontology-Based Gene Selection in Bacteria

Mario Fruzangohar, Esmaeil Ebrahimie, Abiodun D. Ogunniyi, Layla K. Mahdi, James C. Paton, David L. Adelson, Randen Lee Patterson
2013 PLoS ONE  
Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically.  ...  The primary means of classifying new functions for genes and proteins relies on Gene Ontology (GO), which defines genes/ proteins using a controlled vocabulary in terms of their Molecular Function, Biological  ...  Controller part contains all the logic regarding handling user HTTP requests and sending back response to user and also it orchestrates Model and View operations.  ... 
doi:10.1371/journal.pone.0058759 pmid:23536820 pmcid:PMC3594149 fatcat:5bt6fzbuvje4bnfxhg3gxu7ile

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

David P Hill, Nico Adams, Mike Bada, Colin Batchelor, Tanya Z Berardini, Heiko Dietze, Harold J Drabkin, Marcus Ennis, Rebecca E Foulger, Midori A Harris, Janna Hastings, Namrata S Kale (+7 others)
2013 BMC Genomics  
We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally  ...  The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes.  ...  molecules extracted from plants, terpenoids are those molecules that have been derived from terpene molecules by chemical modification and so forth.  ... 
doi:10.1186/1471-2164-14-513 pmid:23895341 pmcid:PMC3733925 fatcat:ts753ihc5fdrjjz4akrcmaejga

The Complexity of Ontology-Based Data Access with OWL 2 QL and Bounded Treewidth Queries

Meghyn Bienvenu, Stanislav Kikot, Roman Kontchakov, Vladimir V. Podolskii, Vladislav Ryzhikov, Michael Zakharyaschev
2017 Proceedings of the 36th ACM SIGMOD-SIGACT-SIGAI Symposium on Principles of Database Systems - PODS '17  
For OMQs with arbitrary ontologies and bounded-leaf CQs, NDL-rewritings are constructed and evaluated in LOGCFL.  ...  OMQs with a fixed ontology (of infinite depth) is NP-complete for tree-shaped and LOGCFL for bounded-leaf CQs.  ...  Y atom takes us one step closer to a (prior to the first Y Y , we may go back and forth on the extra P -edge leaving from h(y)).  ... 
doi:10.1145/3034786.3034791 dblp:conf/pods/BienvenuKKPRZ17 fatcat:pq2pdscf5zbzzkzn3lzqif2dlu

An ontology-based MicroRNA knowledge sharing and acquisition framework

Jingshan Huang, Xingyu Lu, Dejing Dou, William T. Gerthoffer, Jiangbo Dang, Judith A. Blake, Ming Tan
2012 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops  
(ii) According to the global metadata model defined in ontologies, heterogeneous data sources were annotated and seamlessly integrated and stored into a central Resource Description Framework (RDF) data  ...  (i) We developed the very first domain-specific ontologies in the miRNA field, Ontology for MIcroRNA Target (OMIT).  ...  Note that the system was designed so that the user can easily go back and forth along links among ontological concept instances. D.  ... 
doi:10.1109/bibmw.2012.6470228 dblp:conf/bibm/HuangLDGDBT12 fatcat:ypbj6jwotbgtbmjtusmbrqrzhi

Ontology-based fusion of sensor data and natural language

Erik Thomsen, Barry Smith
2018 Applied Ontology  
See also Smith, Kusnierczyk, Schober, and Ceusters (2006) and Ceusters and Manzoor (2010) . 2 In Basic Formal Ontology this level comprises Continuant and Occurrent.  ...  In the BFO-conformant ontology we used for our project, there are four dimensions covering time, space, object and process.  ...  More generally, human analysts know how to go back and forth between names of the instances existing in their respective domains of expertise and descriptions of these instances linking them to background  ... 
doi:10.3233/ao-180203 fatcat:c5zkof6bivcdpgh2szc2y6zlm4

Thesauri and ontologies in digital libraries

Dagobert Soergel
2005 Proceedings of the 5th ACM/IEEE-CS joint conference on Digital libraries - JCDL '05  
It will touch on cross-database and cross-language searching as natural extensions of these functions.  ...  , and hierarchy) for topic clarification and hierarchic query term expansion).  ...  Introduction (v.1), Tables (v.1), Schedules (v.2+3), Relative Index (v.4), Manual (v.5) Need to go back forth between schedules and manual, otherwise reasonably helpful. 5.1.2 Display of conceptual  ... 
doi:10.1145/1065385.1065526 dblp:conf/jcdl/Soergel05 fatcat:zpmxl5d3qjaldawhnm7d57xrpa

OntoMate: a text-mining tool aiding curation at the Rat Genome Database

Weisong Liu, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jeff De Pons, Melinda R. Dwinell, Mary Shimoyama
2015 Database: The Journal of Biological Databases and Curation  
The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data.  ...  OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD.  ...  Funding This work was supported by the National Heart, Lung and Blood Institute on behalf of the National Institutes of Health (HL064541 and HL094271).  ... 
doi:10.1093/database/bau129 pmid:25619558 pmcid:PMC4305386 fatcat:tu5j3s7rujf2ngqe2m4rhwj6rq

Ontologies: principles, methods and applications

Mike Uschold, Michael Gruninger
1996 Knowledge engineering review (Print)  
Various issues are a ected by the choice of whether to go bottom-up, top-down, or middle out.  ...  After motivating their need, we clarify just what ontologies are and what purposes they serve.  ...  Austin Tate drew our attention to the existence of the Work ow Management Coalition and links between this, PIF and the KRSL planning ontology.  ... 
doi:10.1017/s0269888900007797 fatcat:iymubzfterbwrptlq7fmrqnt2e

Mapping between the OBO and OWL ontology languages

Syed Tirmizi, Stuart Aitken, Dilvan A Moreira, Chris Mungall, Juan Sequeda, Nigam H Shah, Daniel P Miranker
2011 Journal of Biomedical Semantics  
Conclusions: Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge.  ...  OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content.  ...  Also, we thank Smriti Ramakrishnan for her help in the development and deployment of the OBO OWL transformation web service.  ... 
doi:10.1186/2041-1480-2-s1-s3 pmid:21388572 pmcid:PMC3105495 fatcat:f2c4ttwjifhwdj4zocqb2nv4ay

Information Carriers and Identification of Information Objects: An Ontological Approach [article]

Martin Doerr, Yannis Tzitzikas
2012 arXiv   pre-print
This is a fundamental problem since curators and archivists would like to formally record the decisions of what has to be preserved over time and to decide (or verify) whether a migration (transformation  ...  Even though library and archival practice, as well as Digital Preservation, have a long tradition in identifying information objects, the question of their precise identity under change of carrier or migration  ...  The CIDOC CRM ontology (ISO 21127:2006) is a core ontology of 80 classes and 132 relations describing the underlying semantics of over a hundred database schemata and structures from all museum disciplines  ... 
arXiv:1201.0385v2 fatcat:vts4rrtd7falddp6afdsztwrze

The Cell Cycle Ontology: An application ontology for the representation and integrated analysis of the cell cycle process

Erick Antezana, Mikel Egana, Ward Blonde, Aitzol Illarramendi, Inaki Bilbao, Bernard De Baets, Robert Stevens, Vladimir Mironov, Martin Kuiper
2009 Genome Biology  
The Cell Cycle Ontology ( is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process.  ...  Cell Cycle Ontology is enabled by semantic web technologies, and is accessible via the web for browsing, visualizing, advanced querying, and computational reasoning.  ...  Acknowledgements We acknowledge Dany Cuyt, Alan Ruttenberg and the OpenLink Virtuoso community for their support while setting up the Virtuoso  ... 
doi:10.1186/gb-2009-10-5-r58 pmid:19480664 pmcid:PMC2718524 fatcat:bg4y5k6d7vgspn7j6jdkpqca4i
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