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Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights

Matthew H. Brush, Jie Zheng, Yongqun He, Sirarat Sarntivijai, Bjoern Peters, Alexander D. Diehl, Christian J. Stoeckert Jr., Melissa A. Haendel
2013 International Conference on Biomedical Ontology  
At present, several ontologies within the OBO Foundry library contain modeling that relates to the types, production, and biological attributes of cell lines and cultures. These include the Cell  ...  The in vitro culture of animal cells has long served as an experimentally amenable model for investigating cellular phenomena that occur in metazoan organisms.  ...  To address these issues, a working group comprised of representatives from each of these efforts was formed to harmonize modeling of experimentally cultured cells in accordance with OBO Foundry principles  ... 
dblp:conf/icbo/BrushZHSPDSH13 fatcat:4vpyqngr2vgzla73mxgqghzmoi

Ontologies in radiation oncology

Mark H. Phillips, Lucas M. Serra, Andre Dekker, Preetam Ghosh, Samuel M.H. Luk, Alan Kalet, Charles Mayo
2020 Physica medica (Testo stampato)  
At the 2019 International Conference on the Use of Computers in Radiation Therapy, there was a session devoted to ontologies in radiation therapy.  ...  Ontologies are a formal, computer-compatible method for representing scientific knowledge about a given domain. They provide a standardized vocabulary, taxonomy and set of relations between concepts.  ...  The resultant OBO foundry persists to this day and consists of over 128 ontologies including two of the most widely-used ontologies, the Gene Ontology and the Ontology for Chemical Entities of Biological  ... 
doi:10.1016/j.ejmp.2020.03.017 pmid:32247963 fatcat:lpnubg3ir5errfuujntqwagp24

A toxicology ontology roadmap
EN

Barry Hardy
2012 ALTEX: Alternatives to Animal Experimentation  
which are composed of financial contribution from the European Union̓s Seventh Framework Programme (FP7/2007(FP7/ -2013 and eFPIA companies' in kind contribution.  ...  An Open Source Predictive toxicology Framework, www.opentox.org, was funded under the eU Seventh Framework Program: HeAltH-2007-1.3-3 Promotion, development, validation, acceptance and implementation of  ...  , and laboratory tests in rodents or cell culture models.  ... 
doi:10.14573/altex.2012.2.129 pmid:22562486 fatcat:fhz6mn32zbcsfoz2vqv4uc6d4q

Challenges for Ontology Repositories and Applications to Biomedicine & Agronomy

Clément Jonquet
2017 Symposium on Information Management and Big Data  
The explosion of the number of ontologies and vocabularies available in the Semantic Web makes ontology libraries and repositories mandatory to find and use them.  ...  In this position paper, we describe six high level challenges for ontology repositories: metadata & selection, multilingualism, alignment, new generic ontology-based services, annotations & linked data  ...  I also acknowledge the National Center for Biomedical Ontologies for their insights and thanks all my collaborators in Montpellier or Stanford interested like me on ontology repositories.  ... 
dblp:conf/simbig/Jonquet17 fatcat:v7xrirond5dkzjqy7u4nyra3yu

IMIA LaMB WG related event: Proceedings of 3rd International Conference on Biomedical Ontology, 2012, Graz

Ronald Cornet, Robert Stevens, Melanie Courtot, Trish Whetzel, Janna Hastings, Stefan Schulz, Ludger Jansen
2019 Zenodo  
It brings together representatives of all major communities involved in the development and application of ontologies in biomedical research ...  ...  This conference carried on the tradition of discussing medical ontologies, increasingly used in biology and medicine, and their use in annotation of both clinical and experimental data is now a common  ...  Though the use of multiple ontologies, MGI is able to robustly represent many components of knowledge about the mouse model system.  ... 
doi:10.5281/zenodo.3381830 fatcat:pnndilxgzzbujnoqz7pytggtdi

Cells in experimental life sciences - challenges and solution to the rapid evolution of knowledge

Sirarat Sarntivijai, Alexander D. Diehl, Yongqun He
2017 BMC Bioinformatics  
The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO framework.  ...  Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortalised cell lineages.  ...  Even though all the activities at the OBO Foundry have always been open, most OBO Foundry outreach and maintenance efforts are based on voluntary effort.  ... 
doi:10.1186/s12859-017-1976-2 pmid:29322916 pmcid:PMC5763506 fatcat:r7y4wcuw6jezvbxfy2ovo6jfh4

Empowering industrial research with shared biomedical vocabularies

Lee Harland, Christopher Larminie, Susanna-Assunta Sansone, Sorana Popa, M. Scott Marshall, Michael Braxenthaler, Michael Cantor, Wendy Filsell, Mark J. Forster, Enoch Huang, Andreas Matern, Mark Musen (+6 others)
2011 Drug Discovery Today  
The life science industries (including pharmaceuticals, agrochemicals and consumer goods) are exploring new business models for research and development that focus on external partnerships.  ...  In this article we highlight the risks to future productivity that are associated with incomplete biological and chemical vocabularies and suggest a new model to address this long-standing issue.  ...  We thank the following participants for valuable contributions which provided the substrate for this perspective: Michael Ashburner, Susanna Lewis, Alan Ruttenberg, Barry Smith (OBO Foundry); Johanna McEntyre  ... 
doi:10.1016/j.drudis.2011.09.013 pmid:21963522 pmcid:PMC7098809 fatcat:rs35p6w34bgifaz7gcdta36mka

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J.S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran (+190 others)
2021 Cell Genomics  
We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders.  ...  We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and  ...  DUO can be browsed online via the Ontology Lookup Service or Ontobee. It has been registered with the OBO Foundry (http://obofoundry.org/ontology/duo.html).  ... 
doi:10.1016/j.xgen.2021.100029 pmid:35072136 pmcid:PMC8774288 fatcat:ho5hntolr5gdrlrfcgfzgah6s4

Interoperability Standards - Digital Objects in Their Own Right [article]

Susanna-Assunta Sansone, Philippe Rocca-Serra
2020 figshare.com  
of stakeholders and initiatives.  ...  research and data management enterprise of the future.  ...  The OBO Foundry 67 is an example of an umbrella organization for ontologies; it brings together groups who are committed to adhering to common development principles that ensure ontologies are orthogonal  ... 
doi:10.6084/m9.figshare.13193783.v1 fatcat:2lfpapewpzcfzjdfpfijgcn3yy

Review%3A Interoperability standards

Susanna-Assunta Sansone, Philippe Rocca-Serra
2016 Figshare  
The OBO Foundry 67 is an example of an umbrella organization for ontologies; it brings together groups who are committed to adhering to common development principles that ensure ontologies are orthogonal  ...  explosion of cross-referencing required to align the (same) entity across each data source.  ... 
doi:10.6084/m9.figshare.4055496.v1 fatcat:ixmy3rpkvvahzc5pfwtr5ztgi4

Surgical Data Science: A Consensus Perspective [article]

Lena Maier-Hein, Matthias Eisenmann, Carolin Feldmann, Hubertus Feussner, Germain Forestier, Stamatia Giannarou, Bernard Gibaud, Gregory D. Hager, Makoto Hashizume, Darko Katic, Hannes Kenngott, Ron Kikinis (+14 others)
2018 arXiv   pre-print
Surgical data science is a scientific discipline with the objective of improving the quality of interventional healthcare and its value through capturing, organization, analysis, and modeling of data.  ...  This document summarizes the key findings.  ...  All ontologies from the OBO-Foundry share the Basic Formal Ontology (BFO) [111] as a common top-level ontology and common design principles to ensure interoperability.  ... 
arXiv:1806.03184v1 fatcat:omofwzmhznfexdbad3kocb3nge

Calling International Rescue: knowledge lost in literature and data landslide!

Teresa K. Attwood, Douglas B. Kell, Philip McDermott, James Marsh, Steve R. Pettifer, David Thorne
2009 Biochemical Journal  
We also thank Pauline Starley and the editorial team for their hard work in marking up the current issue of BJ.  ...  , biomedical, disease and anatomy ontologies are already in place and accessible via the OBO Foundry.  ...  To bring order to these proliferating initiatives, and better support biomedical data annotation and integration, the Open Biomedical Ontologies (OBO) Foundry was set up to unify these diverse resources  ... 
doi:10.1042/bj20091474 pmid:19929850 pmcid:PMC2805925 fatcat:7it5axfto5dbnlisys73ejhixy

Eu Us Roadmap Nanoinformatics 2030 [article]

Haase, Klaessig
2018 Zenodo  
Instead, interested readers will find plenty of additional references mentioned in each of the chapters that will provide more detailed insights.  ...  of the Army, the U.S.  ...  OBO Foundry http://obofoundry.org/ Community project to develop and maintain ontologies in biology. Ontology Lookup Service https://www.ebi.ac.uk/ols/ Searchable registry of ontologies.  ... 
doi:10.5281/zenodo.1486012 fatcat:yll2tsodjbgmlmyoyjfkcptxja

Semantics for interoperability of distributed data and models: Foundations for better-connected information

Ferdinando Villa, Stefano Balbi, Ioannis N. Athanasiadis, Caterina Caracciolo
2017 F1000Research  
We discuss the first outcomes of an investigation in the conceptual and methodological aspects of semantic annotation of data and models, aimed to enable a high standard of interoperability of information  ...  semantic specifications that can integrate semantics across diverse domains and disciplines.  ...  A fitting ontology available in the OBO foundry 29 that provides concepts adequate for this task is the Plant Trait Ontology (PTO, 37 ), which draws on the work of many experts and enjoys good community  ... 
doi:10.12688/f1000research.11638.1 fatcat:qtvfe5hao5do3aphmtanlnh5uq

DEVELOPMENT AND IMPLEMENTATION OF ONTOLOGY-BASED SYSTEMS FOR MAMMALIAN GENE EXPRESSION PROFILING

Adéle Kruger
2009 unpublished
in the mapping of gene expression events provides an effective and comparable method to determine the expression profile of an entire genome across a large collection of experiments derived from different  ...  Model organisms represent an important resource for understanding the fundamental aspects of mammalian biology.  ...  The authors declare no conflict of interest.  ... 
fatcat:fdco5mpqwjhcnh5i7moyv2d4ue
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