*  DiscoverySpace: an interactive data analysis application | Springer for Research & Development
Users can seamlessly traverse references between biological databases and draw together annotations in an intuitive tabular... ... Gene Ontology Resource Description Framework Biological Database Resource Description Framework Graph Refseq Transcript ... The DiscoveryDB database supports 26 biological databases, including Ensembl [10], Gene Ontology (GO) [11], Refseq [12], Entrez ... Many groups have used ontologies, or controlled vocabularies, to describe biological knowledge domains: for example the GO [26 ...
  https://rd.springer.com/article/10.1186/gb-2007-8-1-r6
*  British Library EThOS: Using ontology and semantic web services to support modeling in systems biology
By examining our ontology-centered framework in practice, we conclude that by using ontology to represent biological models and ... In this framework, first we specify an ontology-based meta-model for building biological models. This meta-model supports using ... In our study, we propose an ontology-centered framework within the Semantic Web infrastructure that aims at standardizing ... We also conclude that ontology-based biological models with formal semantics are essential to standardize knowledge in ...
  http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.564689
*  Computational Bioscience Research Center - Knowledge, Text and Data-Mining
AberOWL - a framework for ontology-based access to biological data. *. Dragon Extractor of Methylated Genes in Diseases -. ... OntoFUNC - supports ontology enrichment analysis with OWL reasoning over arbitrary OWL ontologies. ... Main WebsiteBiological and Environmental Science and Engineering Division (BESE)Computer, Electrical and Mathematical Science ... DPubChem: predicts biological activities of chemicals/drugs based on high-throughput screening assays. ...
  https://cb.kaust.edu.sa/Pages/Knowledge-Text-Data-Mining.aspx
*  Framework for a Protein Ontology | BMC Bioinformatics | Full Text
A number of ontologies describe properties that can be attributed to proteins. For example, protein functions are described by ... the Gene Ontology (GO) and human diseases by SNOMED CT or ICD10. There is, however, a gap in the current set of ontologies - ... GO and other ontologies in the OBO Foundry. Here we describe the initial development of PRO, illustrated using human and mouse ... Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-S9-S1
*  CEUR-WS.org/Vol-1327 - The 5th International Conference on Biomedical Ontology, 2014
A Nanopublication Framework for Biological Networks using Cytoscape.js 90-92 Jim Mccusker, Rui Yan, Kusum Solanki, John ... OGG: a Biological Ontology for Representing Genes and Genomes in Specific Organisms 13-20 Yongqun He, Yue Liu, Bin Zhao ... OBCS: The Ontology of Biological and Clinical Statistics 65. Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred ... An Initial Framework for an Ontology-based Mobile Application for Vaccine Information Retrieval and Education 81-83 Muhammad ...
  http://ceur-ws.org/Vol-1327/
*  Nigam H. Shah, MBBS, PhD | Stanford Medicine Profiles
... as SPARQL and can be visualized in the form of a biological network.The PHARE ontology serves as a common semantic framework to ... In fact, bio-ontologies are beginning to proliferate in step with accruing biological data. The myriad of ontologies being ... These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language ( ... Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created ...
  https://med.stanford.edu/profiles/nigam-shah
*  PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation | Genome Biology | Full Text
Bio-ontologies offer common semantics for biological functional annotations [29]. Two topics requiring controlled vocabularies ... For the former, we chose the BRENDA Tissue Ontology as our reference [30] and are providing updates to the BRENDA developers on ... Other types of input can be used, such as a biological sample (for example, nuclear extract) or a condition (for example, ... With respect to the experiment type ontology, we are collaboratively working with the developers of the ORegAnno database [11]. ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-10-r207
*  Events: CfP: 5th Symposium on Integrative Bioinformatics 2008 - Bioinformatics.org
Strong emphasis on open access to biological information as well as Free and Open Source software. ... Quality and consistency of biological ontologies. *Integrative modelling and simulation frameworks. *Integrative data and text ...
  http://www.bioinformatics.org/forums/forum.php?forum_id=6696
*  Difference between revisions of "Synthetic Biology:Semantic web ontology/Examples" - OpenWetWare
a modeling framework with the ability to accommodate diverse biological information sources ... HyBrow ontology for representing biological processes at different levels of detail. Domain level ontologies. Life Sciences. * ... Gene Ontology Next Generation: GONG project aims to make tools and procedures for easy migration of biological ontologies to ... Basic Formal Ontology (BFO). Intermediate level ontologies. *EXPO ontology represents different stages of an experiment and the ...
  https://openwetware.org/wiki/?title=Synthetic_Biology:Semantic_web_ontology/Examples&oldid=244027&diff=prev
*  Toward an Ontology-Based Framework for Clinical Research Databases
Object - population, population arm, human subject, animal subject, biological sample, compound, complex compound, software, ... General Framework. Two reference ontologies were chosen as the foundation for OBX design - the Basic Formal Ontology (BFO) and ... Toward an Ontology-Based Framework for Clinical Research Databases. Y. Megan Kong,1 Carl Dahlke,2 Qun Xiang,1 Yu Qian,1,3 David ... and ontology standards like the Ontology for Biomedical Investigations (OBI) through the Open Biomedical Ontology (OBO) Foundry ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2953614/?lang=en-ca
*  Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function | BMC...
... overlap between the gene ontology terms of the transcriptions factors associated with the binding sites and the gene ontology ... within these promoter segments reveals a small number of gene groups that are selectively enriched for gene ontology terms ... independent of gene expression data and whether or not there is any correlation between this grouping and the biological ... In contrast, it begins with neither a pre-selected TFBS framework nor any other biological information. The possibility of ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-259
*  The semantics of Chemical Markup Language (CML): dictionaries and conventions | Journal of Cheminformatics | Full Text
Open Biological and Biomedical Ontologies (OBO)[4] framework, to uncontrolled folksonomy-like tagging. Although we have ... The biosciences have several approaches for creating ontologies, such as the Gene Ontology (GO)[26]. GO was designed as a ... There are many biological units (e.g. "The optimum dose of rIL2 was 100-500 units (Jurkat units)/ml, "[23]) which do not fit ... Open Biological and Biomedical Ontologies (OBO). Accessed 2011-05-25, [http://www.obofoundry.org/]. ...
  https://jcheminf.springeropen.com/articles/10.1186/1758-2946-3-43
*  From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in...
By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was ... models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational ... using a mapping to Open Biological and Biomedical Ontologies (OBO) resources [39]. In particular, mapping to the Ontology for ... Ontologies Is the Subject Area "Ontologies" applicable to this article? Yes. No. ...
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127612
*  IEEE Computer Society Bioinformatics Conference
We have integrated this ontology with a discrete event systems framework to support qualitative reasoning. The framework adopts ... Text Mining and Ontologies HyBrow: A System for Hypothesis Validation. Identifying Gene and Protein Names from Biological Texts ... We annotated the genes by their "biological processes" of Gene Ontology (GO). Our result suggests that the CL-Fuzzy logic data ... We have developed an event-based ontology for representing both biological processes and data from different sources at varying ...
  http://conferences.computer.org/bioinformatics/CSB2003/SectA.html
*  Formalization and reuse of scientific research | Journal of The Royal Society Interface
... but all essential information about biological experiments. The EXPO (a generic ontology of scientific experiments) ontology ... These limitations have led to the development of more general ontologies to provide a framework for recording not only ... Here, we propose a formal framework for using logical formalisms to promote reuse. We demonstrate the utility of this framework ... To formalize Adam's functional genomics experiments, we developed the LABORS ontology (LABoratory Ontology for Robot Scientists ...
  http://rsif.royalsocietypublishing.org/content/8/63/1440
*  Fluxomics - Wikipedia
... fluxomic methods are considered a key enabling technology due to their unique position in the ontology of biological processes ... allowing genome scale stoichiometric models to act as a framework for the integration of diverse biological datasets. One ... Fluxomics describes the various approaches that seek to determine the rates of metabolic reactions within a biological entity. ... Systems biology recognizes the complexity of biological systems and has the broader goal of explaining and predicting this ...
  https://en.wikipedia.org/wiki/Fluxomics
*  Kuipers, prof.dr. Oscar | Mensen en meningen | Nieuws en agenda | Over ons | Rijksuniversiteit Groningen
Kuipers, O. P., & Roerdink, J. B. T. M. (2006). MOVE: A Multilevel Ontology-based Visualization and Exploration framework for ... Rollema, H. S., Metzger, J. W., Both, P., Kuipers, O. P., & Siezen, R. J. (1996). Structure and biological activity of ... A Multi-Level Ontology-Based Visualization and Exploration Framework for Genomic Networks. In Silico Biology, 7(1), 35-59. ... The Journal of Biological Chemistry, 291(21), 11323-11336. DOI: 10.1074/jbc.M116.714303 ...
  https://www.rug.nl/about-us/news-and-events/people-perspectives/scientists-in-focus/kuipers
*  W01: Phenotype Ontologies Traversing All The Organisms (POTATO) | International Conference on Biological Ontology 2018
DOSDP framework) and examples from phenotype ontologies. Following this we will present and discuss strategies to maintain ... While most phenotype ontologies use logical definitions composed of terms from species independent ontologies such as Uberon ... We introduce the phenotype ontology community to the idea and benefits of pattern-based ontology development and present two ... logical definitions referencing classes from a shared or related set of ontologies: for using species neutral ontologies to ...
  http://icbo2018.cgrb.oregonstate.edu/W01
*  Immunology Ontologies and Their Applications in Processing Clinical Data - NCBO Wiki
Cytometry-Ontology Framework (Draft) 08:30 Breakfast 9:00-noon: Introduction to the Protein Ontology Flow Cytometry Driving ... An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross- ... Updates on the Vital Sign Ontology Recipes for OGMS-conformant extension ontologies Close: 6:00pm Relevant ontology efforts ... Vaccine Ontology (Oliver He) AO Allergy Ontology (Alex C. Yu) ND Neurological Disease Ontology (Alexander Diehl) ...
  https://www.bioontology.org/wiki/Immunology_Ontologies_and_Their_Applications_in_Processing_Clinical_Data
*  Download Fundamentals Of General, Organic, And Biological Chemistry 2006
... and Biological Chemistry 2006 from prehistoric camera data at 6 genes after probability in the cells t( few categories file 8 ... download Fundamentals of General, Organic, and: CA Manager Framework: existing Customised Workflows for Ontology Population and ... Download Fundamentals Of General, Organic, And Biological Chemistry 2006. We Can Help Your Business DNA download Fundamentals ... 400 million changes, using download Fundamentals of General, Organic, and Biological for strains to View, both t et al. Unable ...
  http://dataprintusa.com/library/download-Fundamentals-of-General%2C-Organic%2C-and-Biological-Chemistry-2006.php
*  New resources for functional analysis of omics data for the genus Aspergillus | BMC Genomics | Full Text
of the Gene Ontology Consortium TRGG: The Gene Ontology's Reference Genome Project: a unified framework for functional ... Bluthgen N, Brand K, Cajavec B, Swat M, Herzel H, Beule D: Biological profiling of gene groups utilizing Gene Ontology. Genome ... Gene Ontology (GO) is a framework for functional annotation of gene products aiming to provide a unique vocabulary for living ... As such, Gene Ontology (GO) annotation has become a well accepted framework for functional annotation. The genus Aspergillus ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-486
*  The MGED Ontology: A Framework for Describing Functional Genomics Experiments - pdf descargar
A Framework for Describing Functional Genomics Experiments. . Biblioteca virtual para leer y descargar libros, documentos, ... Our solution was to create a framework fordescribing microarray experiments with an initial focus on the biological sample ... The MGED Ontology: A Framework for Describing Functional Genomics Experiments - Descarga este documento en PDF. Documentación ... taking advantage of the structure provided by the ontology. The applicationof an ontology of experimental conditions extends ...
  http://libros.duhnnae.com/2017/jul7/150081297272-The-MGED-Ontology-A-Framework-for-Describing-Functional-Genomics-Experiments.php
*  ONTO-ToolKit: enabling bio-ontology engineering via Galaxy | BMC Bioinformatics | Full Text
As a consequence, much of the available biological data remains disconnected or worse: becomes misconnected. The need to ... OBOF, RDF and OWL are among the most used ontology formats to capture terms and relationships in the Life Sciences, opening the ... Moreover, it provides tools to translate OBO-formatted ontologies into Semantic Web formats such as RDF and OWL. ONTO-ToolKit ... The resulting ONTO-ToolKit supports the analysis and handling of OBO-formatted ontologies via the Galaxy interface, and we ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-S12-S8
*  Ontology (information science) - Wikipedia
... ontology Lattice Ontology Ontology alignment Ontology chart Open Biomedical Ontologies Open Semantic Framework Soft ontology ... National Center for Biological Ontology (NCBO). "Ontology browser for most of the Open Biological and Biomedical Ontologies". ... OBO-Edit, an ontology browser for most of the Open Biological and Biomedical Ontologies OBO Foundry, a suite of interoperable ... An ontology language is a formal language used to encode an ontology. There are a number of such languages for ontologies, both ...
  https://en.wikipedia.org/wiki/Ontology_(information_science)
*  The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and...
We developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data ... Neuroscience Information Framework Standardized ontology, CHEBI - Chemical Entities of Biological Interest, CTO - Clinical ... Family Health History Ontology, Galen - Galen Ontology, GO - Gene Ontology, GRO - Gene Regulation Ontology, LNC - Logical ... Basic Formal Ontology (BFO), Relation Ontology (RO), and Information Artifact Ontology (IAO).. ...
  https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S1