Publications Referencing NCBO

The information on this page was extracted from Google Scholar and then manually curated to remove non-meaningful references (such as references to NCBO appearing solely in a "related work" section).

Publication Reference Context Highlights
A. C. Mauer, E. M. Barbour, N. A. Khazanov, N. Levenkova, S.A. Mollah and B.S.Coller Creating an Ontology Based Human Phenotyping System: The Rockefeller University Bleeding History Experience Clinical and Translational Science 2009, Volume 2, Issue 5; 382-385 Publish Ontology After completion, the BHO was made publicly available on BioPortal (http://bioportal.bioontology. org/visualize/38563) to allow others to comment on it and offer suggestions for improvement and updating.
A. F. Guidry, J. L. Walson and N. F. Abernethy  Linking information systems for HIV care and research in Kenya Proceedings of the 1st ACM International Health Informatics Symposium 2010; 531-535 Access Ontologies In order to include an example ontology in the sample, we searched the BioPortal [12] website which facilitates the sharing of ontologies in the biomedical community. A search using the keywords "patient identifier"returned three ontologies: RadLex, RadLex in OWL (Web Ontology Language) and Logical Observation Identifier Names and Codes (LOINC) [13]. LOINC was not included in this study due to its specialized focus on laboratory results. RadLex and RadLex in OWL's patient identifying information were identical, hence they were treated as a single source for our purposes. RadLex provided six patient identifier fields. This information can be seen in Table 1, following this discussion.
Okhmatovskaia, W. Chapman, N. Collier, J. Espino and D. Buckeridge SSO: The syndromic surveillance ontology A.  Proceedings of the International Society for Disease Surveillance  2009 Publish Ontology  
A. Ruttenberg, T. Clark, W. Bug, M. Samwald, O. Bodenreider, H. Chen, D. Doherty, K. Forsberg, Y. Gao and V. Kashyap Advancing translational research with the Semantic Web  BMC Bioinformatics  2007, Volume 8, Supplement 3; S2 Benefit from Outreach  
B. S. Coller Thinking Globally, Acting Locally: Rockefeller University's Enterprising CTSA Work Clinical and Translational Science  2008, Volume 1, Issue 3; 190-191 Publish Ontology  
C. Fonseca, M. Backhaus, J. Do Chung, W. Tao, P. Medrano-Gracia, B. Cowan, P. Hunter, J. Finn, K. Shivkumar and J. Lima  The cardiac atlas project: rationale, design and procedures Statistical Atlases and Computational Models of the Heart  2010; 36-45

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Collect Comments on Ontology

The standardized classification and description of CAP data elements (CV images and derived morphological information including contours and parametric geometry descriptions) will occur through registration of an information model and associated semantic annotations, expressed in the Web Ontology Language (OWL) [15], at the National Center for Biomedical Ontologies (NCBO) [16]. This will allow grid-enabled tools to query and access data of the correct type, and databases to declare what type of data are available. Data and derived results from several studies can be labeled and col- lated in a standardized manner to achieve meta or subgroup analyses via the use of ex- isting domain ontologies, such as the Foundational Model of Anatomy (FMA) for ana- tomical data [17] and the Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) for clinical terms [18]. Where gaps occur, suggested terms will be proposed based on feedback from the radiological and cardiological communities via online resources such as the NCBO BioPortal [16] and WebProtégé [19].
D. E. Avrin and A. E. Flanders  Annual Report from the RSNA Radiology Informatics Committee for 2009 Radiographics  2010, Volume 30; 7-11 Publish Ontology  
D. G. Thomas, R. V. Pappu and N. A. Baker NanoParticle Ontology for cancer nanotechnology research Journal of Biomedical Informatics  2011, Volume 44, Issue 1; 59-74 Publish Ontology  
D. S. DeLuca, E. Beisswanger, J. Wermter, P. A. Horn, U. Hahn and R. Blasczyk MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining Bioinformatics  2009, Volume 25, Issue 16; 2064-70 Publish Ontology  
E. Antezana, M. Egana, W. Blonde, R. Stevens, B. De Baets, V. Mironov and M. Kuiper The Cell Cycle Ontology: an application ontology supporting the study of cell cycle control ICBO 2009 Publish Ontology  
H. P. Kang, C. D. Borromeo, J. J. Berman and M. J. Becich The tissue microarray OWL schema: An open-source tool for sharing tissue microarray data Journal of Pathology Informatics  2010, Volume 1; 9 Publish Ontology  
H. S. Low, C. J. O. Baker, A. Garcia and M. R. Wenk An OWL-DL Ontology for Classification of Lipids    ICBO 2009 Publish Ontology  
H. Yu, S. Taduri, J. Kesan, G. Lau and K. H. Law  Retrieving information across multiple, related domains based on user query and feedback: application to patent laws and regulations Proceedings of the 4th International Conference on Theory and Practice of Electronic Governance 2010; 143-151 Access Ontologies  
I. N. Sarkar  Leveraging Biomedical Ontologies and Annotation Services to Organize Microbiome Data from Mammalian Hosts American Medical Informatics Association (AMIA) Annual Symposium Proceedings 2010; 717-721 Annotate Text Organize mamallian knowledge
J. A. Turner, J. L. V. Mejino, J. F. Brinkley, L. T. Detwiler, H. J. Lee, M. E. Martone and D. L. Rubin Application of neuroanatomical ontologies for neuroimaging data annotation Frontiers in Neuroinformatics  2010, Volume 4; 10 Publish Ontology  
J. A. Turner, J. L. V. Mejino, J. F. Brinkley, L. T. Detwiler, H. J. Lee, M. E. Martone and D. L. Rubin.  IN Neuroinformatics Journal Info  2011 Publish Ontology  
J. Greenberg, R. Deshmukh, L. Huang, J. Mostafa, L. La Vange, E. Carretta and W. O Neal  The COPD Ontology and Toward Empowering Clinical Scientists as Ontology Engineers Journal of Library Metadata  2010, Volume 10; 173-187 Benefit from Outreach  
J. L. Fink, P. Fernicola, R. Chandran, S. Parastatidis, A. Wade, O. Naim, G. B. Quinn and P. E. Bourne Word add-in for ontology recognition: semantic enrichment of scientific literature BMC Bioinformatics  2010, Volume 11; 103-110 Access Ontologies Integrating ontologies in the tool
J. Malone, E. Holloway, T. Adamusiak, M. Kapushesky, J. Zheng, N. Kolesnikov, A. Zhukova, A. Brazma and H. Parkinson Modeling sample variables with an Experimental Factor Ontology Bioinformatics  2010, Volume 26, Issue 8; 1112-1118

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Search Resources

Since EFO is used to annotate data in ArrayExpress and also provides multiple mappings to other ontologies, it is possible to query data through BioPortal using ontology class names and return annotated data from multiple resources via the BioPortal's Resources facility, for example, pathway data from Reactome.
J. Malone, T. Adamusiak, E. Holloway, M. Kapushesky and H. Parkinson   Developing an Ontology from the Application Up CiteSeer 2010 Access Ontologies This way it is easy to map data annotated with EFO to data annotated with the many other bioontology efforts. The process of adding these mappings has been automated and wraps around BioPortal REST services to automatically follow all definition_citation properties from EFO into relevant ontologies, pulling in synonyms and definitions.
J. P. Kesan, H. Yu, S. Taduri, G. Lau and K. H. Law Developing a Comprehensive Patent Related Information Retrieval Tool Journal of Theoretical and Applied Electronic Commerce Research  2010, Volume 4, Issue 1; 1-15 Access Ontologies  
J. Pathak, P. D. J. Wang and M. S. S. K. R. Li  eleMAP: An Online Tool for Harmonizing Data Elements using Standardized Metadata Registries and Biomedical Vocabularies  AMIA Annual Symposium Proceedings 2010; 1214 Access Ontologies For querying biomedical vocabularies, we used RESTful Web services from BioPortal. 
J. Peace. The use of ontology to represent nursing knowledge about family health history and facilitate automated search for clinical practice guidelines The University of Wisconsin-Madison 2009 Publish Ontology  
 L. Young, S. W. Tu, L. Tennakoon, D. Vismer, V. Astakhov, A. Gupta, J. S. Grethe, M. E. Martone, A. K. Das and M. J. McAuliffe  Ontology driven data integration for autism research  22nd IEEE International Symposium 2009; 1-7 Publish Ontology  
M. Backhaus, J. D. Chung, B. R. Cowan, C. G. Fonseca, W. Tao and A. A. Young The Cardiac Atlas Project: Towards a Map of the Heart  Patient-Specific Modeling of the Cardiovascular System  2010; 113-129 Publish Ontology Plans to use Webprotege
M. Brochhausen, A. D. Spear, C. Cocos, G. Weiler, L. Martin, A. Anguita, H. Stenzhorn, E. Daskalaki, F. Schera and U. Schwarz  The ACGT Master Ontology and its applications-Towards an ontology-driven cancer research and management system  Journal of Biomedical Informatics  2010, Volume 44, Issue 1; 8-25 Publish Ontology  
M. Dumontier, B. Andersson, C. Batchelor, C. Denney and C. Domarew  The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bench to bedside  Journal of Biomedical Semantics 2010, Volume 2, Supplement 2; S1

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Create Mappings

To establish the TMO as a global ontology, we created 223 class equivalence mappings (using owl:equivalentClass) from 60 TMO classes to 201 target classes from 40 ontolo- gies (see Table 2). Initially identified using the NCBO Bio- portal and UMLS, each mapping was manually validated.
M. E. Martone, J. Tran, W. W. Wong, J. Sargis, L. Fong, S. Larson, S. P. Lamont, A. Gupta and M. H. Ellisman The cell centered database project: an update on building community resources for managing and sharing 3D imaging data Journal of Structural Biology  2008, Volume 161, Issue 3; 220-231 Publish Ontology  
M. J. Yoder, I. MikÛ, K. C. Seltmann, M. A. Bertone, A. R. Deans and C. S. Moreau A gross anatomy ontology for Hymenoptera PloS One  2010, Volume 5, Issue 12; e15991 Publish Ontology  
M. N. Knowlton, T. Li, Y. Ren, B. R. Bill, L. Ellis and S. C. Ekker A PATO-compliant zebrafish screening database(MODB): management of morpholino knockdown screen information  BMC Bioinformatics  2008, Volume 9; 7 Access Ontologies This defects ontology was developed in conjunction with ZFIN to model the current status of Phenotypic Attribute Trait Ontology (PATO) developed by the National Center for Biomedical Ontology (NCBO) [30]. To facilitate the use of this common language, MODB users assess phenotypes using defect descriptions linked to current PATO terminology (Figure 4). Initially, PATO was designed to describe a defect observed in an anatomical structure (the entity, e.g. tail) using a trait (e.g. relative length) and attribute of that trait (e.g. short length). This system has subsequently been replaced with an entity and quality designation (e.g. tail, short length). MODB's defects ontology contains the latter version of PATO. When no PATO term exists to adequately describe the defect observed, a proposed term is submitted to NCBO via ZFIN to assist in the development of a cross-species phenotypic ontology.
M. Roos, S. Bechhofer, J. Zhao, P. Missier, D. Newman, D. De Roure and M. Marshall  A linked data approach to sharing workflows and workflow results Proceedings of the 4th International Conference on Leveraging Applications of Formal Methods, Verification, and Validation  2010, Volume 1; 340-354 Access Ontologies For example, four ontologies were chosen for case studies in genomics from the almost 200 publicly shared models that are available via the National Centre for Biomedical Ontologies (NCBO; [15])
M. Samwald and H. Stenzhorn Establishing a distributed system for the simple representation and integration of diverse scientific assertions  Journal of Biomedical Semantics  2010, Volume 1, Supplement 1; S5 Annotate Text Adding a 'tag recommender' function to the aTag generator by integrating the Open Biomedical Annotator web service [36] of NCBO.
M. Samwald and H. Stenzhorn   Simple, ontology-based representation of biomedical statements through fine-granular entity tagging and new web standards 12th Knowledge in Biology Workshop 2009 Annotate Text  
O. Daramola and S. FatumoDeveloping Ontology Support for Human Malaria Control Initiatives  ICBO  2009 Publish Ontology  
P. Ciccarese, E. Wu, G. Wong, M. Ocana, J. Kinoshita, A. Ruttenberg and T. Clark The SWAN biomedical discourse ontology Journal of biomedical informatics  2008, Volume 41, Issue 5; 739-751 Benefit from Outreach  
P. D. Thomas, H. Mi, G. E. Swan, C. Lerman, N. Benowitz, R. F. Tyndale, A. W. Bergen and D. V. Conti A systems biology network model for genetic association studies of nicotine addiction and treatment  Pharmacogenetics and Genomics  2009, Volume 19, Issue 7; 538-551 Publish Ontology  
P. Missier, S. Sahoo, J. Zhao, C. Goble and A. Sheth Janus: from workflows to semantic provenance and linked open data Provenance and Annotation of Data and Processes  2010 Access Ontologies To model semantic provenance in Janus, we re-use the classes defined in four public on- tologies listed at NCBO, namely the BioPAX, National Cancer Institute The- saurus, Foundational Model of Anatomy (FMA), and the Sequence ontologies, while the fifth ontology, OWL Time11 is available from the W3C.
P. Topalis, E. Mitraka, I. Bujila, E. Deligianni, E. Dialynas, I. Siden-Kiamos, M. Troye-Blomberg and C. Louis IDOMAL: an ontology for malaria  Malaria Journal  2010, Volume 9; 230 Publish Ontology  
 R. D. Shankar, S. B. Martins, M. O'Connor, D. B. Parrish and A. K. Das An ontology-based architecture for integration of clinical trials management applications American Medical Informatics Association Annual Sympsium Proceedings 2007; 661-665 Publish Ontology The Epoch ontologies are publicly accessible from the Open Biomedical Ontologies (OBO) library hosted by the National Center for Biomedical Ontology (NCBO)
R. Shankar, H. Parkinson, T. Burdett, E. Hastings, J. Liu, M. Miller, R. Srinivasa, J. White, A. Brazma and G. Sherlock Annotare -a tool for annotating high-throughput biomedical investigations and resulting data  Bioinformatics  2010, Volume 26, Issue 19; 2470-2471 Access Ontologies Use of ontologies in the tool; . Annotare also supports an ontology widget that is enabled with ontology look-up services of the NCBO Bioportal (http://bioportal.bioontology.org/). The widget allows users to search for and use appropriate terms from many ontologies, such as the MGED Ontology (Whetzel, 2006).
S. Kohler, M. H. Schulz, P. Krawitz, S. Bauer, S. Dolken, C. E. Ott, C. Mundlos, D. Horn, S. Mundlos and P. N. Robinson Clinical diagnostics in human genetics with semantic similarity searches in ontologies The American Journal of Human Genetics  2009, Volume 85, Issue 4; 457-464 Publish Ontology  
S. Kundu, M. Itkin, D. A. Gervais, V. N. Krishnamurthy, M. J. Wallace, J. F. Cardella, D. L. Rubin and C. P. Langlotz  The IR Radlex Project: an interventional radiology lexicon -a collaborative project of the Radiological Society of North America and the Society of Interventional Radiology  Journal of Vascular and Interventional Radiology  2009, Volume 20, Supplement 7; S275-S277 Publish Ontology  
S. S. Sahoo, R. Barga, A. Sheth, K. Thirunarayan and P. Hitzler Kno. e. sis Center PrOM: A Semantic Web Framework for Provenance Management in Science Wright State University  2009, Technical Report Publish Ontology ProPreO and the Parasite Experiment ontology are listed at NCBO
S. W. Tu, M. Peleg, S. Carini, M. Bobak, J. Ross, D. Rubin and I. Sim A practical method for transforming free-text eligibility criteria into computable criteria Journal of Biomedical Informatics  2010, Volume 44, Issue 2; 239-250 Annotate Text ERGO annotations
T. Y. Kim, A. Coenen and N. Hardiker A quality improvement model for healthcare terminologies Journal of Biomedical Informatics  2010, Volume 43, Issue 6; 1036-1043 Publish Ontology  
W. C. Cheng, M. L. Tsai, C. W. Chang, C. L. Huang, C. R. Chen, W. Y. Shu, Y. S. Lee, T. H. Wang, J. H. Hong and C. Y. Li  Microarray meta-analysis database(M 2 DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database BMC Bioinformatics  2010, Volume 11; 421 Access Ontologies This research manually extracted relative information from the free-text description of each sample, then iden- tified accurate terms and unified the synonyms via the Bioportal [35], Ontology Lookup Service (OLS) [36] and NCI Enterprise Vocabulary Services (EVS). 
W. J. Bug, G. A. Ascoli, J. S. Grethe, A. Gupta, C. Fennema-Notestine, A. R. Laird, S. D. Larson, D. Rubin, G. M. Shepherd and J. A. Turner The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience  Neuroinformatics  2008, Volume 6, Issue 3; 175-194

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Access Ontologies

To create more human friendly viewing environments, both NIFSTD and BIRNLex have been uploaded into the NCBO BioPortal
W. M. Dahdul, J. G. Lundberg, P. E. Midford, J. P. Balhoff, H. Lapp, T. J. Vision, M. A. Haendel, M. Westerfield and P. M. Mabee The Teleost Anatomy Ontology: Anatomical representation for the genomics age Systematic Biology  2010, Volume 59, Issue 4; 369-383 Publish Ontology  
Y. He and Z. Xiang Bioinformatics analysis of Brucella vaccines and vaccine targets using VIOLIN Immunome research  2010, Volume 6, Supplement 1; S5 Publish Ontology  
V. M. Bedell, S. E. Westcot and S. C. Ekker Lessons from morpholino-based screening in zebrafish  Briefings in Functional Genomics Oxford Journals 2011, Volume 10, Issue 4; 181-188 Access Ontologies  
M. Evangelia, D. Taibi, D. Giordano, S. Dietze, H. Q. Yu, P. Bamidis, C. Bratsas and L. Woodham Connecting medical educational resources to the Linked Data cloud: the mEducator RDF Schema, store and API  Linked Learning 2011: 1st International Workshop on eLearning Approaches for the Linked Data Age, 8th Extended Semantic Web Conference (ESWC2011)  2011 Access Ontologies  
B. Hidasi and C. Gaspar-Papanek ShiftTree: An Interpretable Model-Based Approach for Time Series Classification Machine Learning and Knowledge Discovery in Databases Springer 2011 Access Ontologies  
O. Ivchenko, E. Younesi, M. Shahid, A. Wolf, B. Muller and M. Hofmann-Apitius PLIO: an ontology for formal description of protein-ligand interactions  Bioinformatics Oxford Journals 2011, Volume 27, Issue 12; 1684-1690 Access Ontologies  
C. S. G. Khoo, J. C. Na, V. W. Wang and S. Chan Developing an Ontology for Encoding Disease Treatment Information in Medical Abstracts  DESIDOC Journal of Library & Information Technology  2011 Access Ontologies  
R. D. King, M. Liakata, C. Lu, S. G. Oliver and L. N. Soldatova  On the formalization and reuse of scientific research  Journal of The Royal Society Interface The Royal society 2011, Volume 8, Issue 63; 1440-1448 Access Ontologies  
R. Kontchakov, C. Lutz, D. Toman, F. Wolter and M. Zakharyaschev The combined approach to ontology-based data access  International Joint Conference on Aritifical Intelligence AAAI Press 2011 Search Resources  
A. C. Mauer, N. A. Khazanov, N. Levenkova, S. Tian, E. M. Barbour, C. Khalida, J. N. Tobin and B. S. Coller  Impact of sex, age, race, ethnicity and aspirin use on bleeding symptoms in healthy adults Journal of Thrombosis and Haemostasis  2011, Volume 9, Issue 1; 100-108 Publish Ontology  
R. M. H. Merks, M. Guravage, D. Inze and G. T. S. Beemster VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development Plant Physiology  2011, Volume 155, Issue 2; 656-666 Publish Ontology  
 I. Nikolova and G. Angelova Identifying Relations between Medical Concepts by Parsing UMLS Definitions Conceptual Structures for Discovering Knowledge  2011 Access Ontologies  
S. Park, J. S. Yang, Y. E. Shin, J. Park, S. K. Jang and S. Kim Protein localization as a principal feature of the etiology and comorbidity of genetic diseases Molecular Systems Biology  2011, Volume 7; 494 Access Ontologies  
D. L. Rubin, A. Flanders, W. Kim, K. M. Siddiqui and C. E. Kahn Ontology-Assisted Analysis of Web Queries to Determine the Knowledge Radiologists Seek  Journal of Digital Imaging  2011, Volume 24, Issue 1; 160-164 Publish Ontology  
S. Schenk, R. Dividino and S. Staab Using provenance to debug changing ontologies Web Semantics: Science, Services and Agents on the World Wide Web  2011 Access Ontologies  
J. A. Turner and A. R. Laird The Cognitive Paradigm Ontology: Design and Application Neuroinformatics  2011 [Epub ahead of print] Publish Ontology  
J. Vanschoren, H. Blockeel, B. Pfahringer and G. Holmes Experiment databases. A new way to share, organize and learn from experiments  Machine learning  2011 Access Ontologies  
 K. Wolstencroft, S. Owen, M. Horridge, O. Krebs, W. Mueller, J. L. Snoep, F. du Preez and C. Goble RightField: embedding ontology annotation in spreadsheets Bioinformatics Oxford Journals 2011, Volume 27, Issue 14; 2021-2022 Access Ontologies  
A. Zhavoronkov and C. R. Cantor Methods for Structuring Scientific Knowledge from Many Areas Related to Aging Research PloS One  2011, Volume 6, Issue 7; E22597 Access Ontologies