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Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology

Robert Hoehndorf, Midori A. Harris, Heinrich Herre, Gabriella Rustici, Georgios V. Gkoutos
2012 Computer applications in the biosciences : CABIOS  
The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes.  ...  Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes.  ...  ACKNOWLEDGEMENT We thank Michel Dumontier for valuable discussions about the formal representation of the axioms and the different possible interpretations of the regulates relation.  ... 
doi:10.1093/bioinformatics/bts250 pmid:22539675 pmcid:PMC3381966 fatcat:j5rixqrb4nas7hqmnp7mbkqyva

Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes

Georgios V Gkoutos, Robert Hoehndorf
2012 Journal of Biomedical Semantics  
We have applied this methodology to the Ascomycete Phenotype Ontology (APO), enabling the reuse of various orthogonal ontologies and we have converted the phenotype associated data found in the SGD following  ...  We have integrated the resulting data in the cross-species phenotype network PhenomeNET, and we make both the cross-species integration of yeast phenotypes and a similarity-based comparison of yeast phenotypes  ...  This article has been published as part of Journal of Biomedical Semantics Volume 3 Supplement 2, 2012: Proceedings of Ontologies in Biomedicine and Life Sciences (OBML 2011).  ... 
doi:10.1186/2041-1480-3-s2-s6 pmid:23046642 pmcid:PMC3448529 fatcat:hxbigyhhwbdardsq2mulpgphaq

The anatomy of phenotype ontologies: principles, properties and applications

Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
2017 Briefings in Bioinformatics  
The Phenotype And Trait Ontology framework provides a method for formal definitions of phenotypes and associated data sets and has proved to be key to our ability to develop methods for the integration  ...  Here, we describe the development and products of the ontological approach to phenotype capture, the formal content of phenotype ontologies and how their content can be used computationally.  ...  Funding The National Science Foundation (IOS:1340112 to G.V.G.), the European Commission H2020 (grant agreement number 731075) to G.V.G. and the King Abdullah University of Science and Technology (to R.H  ... 
doi:10.1093/bib/bbx035 pmid:28387809 fatcat:eouajqukvncvfjlazgmsnmyxbe

Interoperability between phenotype and anatomy ontologies

R. Hoehndorf, A. Oellrich, D. Rebholz-Schuhmann
2010 Bioinformatics  
Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology.  ...  The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and  ...  Funding: This research was funded by the European Bioinformatics Institute. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq578 pmid:20971987 pmcid:PMC2995119 fatcat:pgkfs2pofjh6bg74d5addo2mhm

Linking gene expression to phenotypes via pathway information

Irene Papatheodorou, Anika Oellrich, Damian Smedley
2015 Journal of Biomedical Semantics  
Here we discuss these efforts and identify areas of future work that could lead to a better integration of genes, pathways and phenotypes to provide insights into the mechanisms under which gene mutations  ...  In recent years there have been many efforts to develop the computational means to traverse from genes to gene expression, model pathways and classify phenotypes.  ...  In order to facilitate reasoning over the different levels of complexity needed to describe an individual with ontologies, the ontologies have to be aligned and mapped to one another.  ... 
doi:10.1186/s13326-015-0013-5 pmid:25901272 pmcid:PMC4404592 fatcat:amhyu67d4jdxviz52xyraw6uky

Multiscale information modelling for heart morphogenesis

T Abdulla, R Imms, J M Schleich, R Summers
2010 Journal of Physics, Conference Series  
This is a return to physiological medicine with a computational emphasis, exemplified by the worldwide Physiome initiative, and the European Union funded Network of Excellence in the Virtual Physiological  ...  Such an effort enables the integration of multiscale metrology. 13th IMEKO TC1-TC7 Joint Symposium  ...  At the bottom of figure 1, we illustrate the reference ontologies applicable to different levels of scale.  ... 
doi:10.1088/1742-6596/238/1/012062 fatcat:wn763cj77nhz3j4jrde5gd7gau

Modeling quantitative traits for COVID-19 case reports [article]

Nuria Queralt-Rosinach, Susan Bello, Robert Hoehndorf, Claus Weiland, Philippe Rocca-Serra, Paul N Schofield
2020 medRxiv   pre-print
entities and phenotypes annotated with the Uber-anatomy ontology (Uberon), Chemical Entities of Biological Interest (ChEBI) and the Phenotype and Trait Ontology (PATO) biomedical ontologies.  ...  The measurement of vital signs and molecular parameters in the clinics gives a complementary description of abnormal phenotypes associated with the progression of a disease.  ...  traits, and finally on integration within PhenoPackets, an exchange standard for the transmission of patient phenotype data, to showcase its applicability.  ... 
doi:10.1101/2020.06.18.20135103 fatcat:3g4zjuogmnfhlffvbvs4jkvjy4

Progress with a Multiscale Systems Engineering Approach to Cardiac Development

Ronald Summers, Tariq Abdulla, Lucile Houyel, Jean Marc Schleich
2011 Automatika  
The application of the multiscale framework gives added value by unlocking the relationships between genetic-based information at one level of analysis and the phenotype it encodes for at the cell and  ...  The discipline draws upon information engineering to provide ontological representations that are derived from digital libraries of terms, themselves found at distributed locations around the world.  ...  The Mammalian Phenotype (MP) ontology provides a robust phenotype terminology, which covers spatial scales from cellular to organism phenotypes.  ... 
doi:10.1080/00051144.2011.11828403 fatcat:whn5j6cr5jb2xgm7gntk5nezgi

Multiscale Modeling and Data Integration in the Virtual Physiological Rat Project

Daniel A. Beard, Maxwell L. Neal, Nazanin Tabesh-Saleki, Christopher T. Thompson, James B. Bassingtwaighte, Mary Shimoyama, Brian E. Carlson
2012 Annals of Biomedical Engineering  
A perspective of the current state of the art in model integration and sharing along with archiving of experimental data will be presented here in the context of multiscale physiological models.  ...  To do this with computational models often requires the integration of several models that have overlapping scales (genes to molecules, molecules to cells, cells to tissues).  ...  ACKNOWLEDGMENTS The authors would like to thank Scott Bugenhagen for the development of the baroreceptor model and discussions concerning the annotation of this model along with the cardiovascular dynamics  ... 
doi:10.1007/s10439-012-0611-7 pmid:22805979 pmcid:PMC3463790 fatcat:3w65r5ktsfbwljlatauqks2dzq

OBML – Ontologies in Biomedicine and Life Sciences

Heinrich Herre, Robert Hoehndorf, Janet Kelso, Frank Loebe, Stefan Schulz
2011 Journal of Biomedical Semantics  
In the future, OBML will continue as an annual meeting that aims to bridge the gap between theory and application of ontologies in the life sciences.  ...  Research topics of OBML 2010 included medical informatics, Semantic Web applications, formal ontology, bio-ontologies, knowledge representation as well as the wide range of applications of biomedical ontologies  ...  This article has been published as part of Journal of Biomedical Semantics Volume 2 Supplement 4, 2011: Proceedings of Ontologies in Biomedicine and Life Sciences (OBML 2010).  ... 
doi:10.1186/2041-1480-2-s4-i1 pmid:21996496 pmcid:PMC3194167 fatcat:xre5td2qxfbizku3mvna7w2xsy

PIDO: the primary immunodeficiency disease ontology

N. Adams, R. Hoehndorf, G. V. Gkoutos, G. Hansen, C. Hennig
2011 Bioinformatics  
We provide mappings to biomedical reference ontologies to ensure interoperability with ontologies in other domains.  ...  The development of an ontology of PIDs is therefore a central step toward developing informatics tools, which can support the clinician in the diagnosis and treatment of these diseases.  ...  ACKNOWLEDGEMENT We thank Dr Ulrich Baumann (Hannover Medical School) for the helpful discussions and support. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btr531 pmid:21949270 fatcat:qm2ehula2naj7ii7twueauwsie

Using ontologies to study cell transitions

Georg Fuellen, Ludger Jansen, Ulf Leser, Andreas Kurtz
2013 Journal of Biomedical Semantics  
Further, our design principles lead to ontologies that allow the meaningful application of similarity searches in the spaces of cell phenotypes and of mechanisms, and, especially, of changes of mechanisms  ...  Results: We describe the outline of two ontologies for cell phenotypes and for cellular mechanisms which together enable the representation of data curated from the literature or obtained by bioinformatics  ...  Acknowledgements DFG support to AK and UL (AK 851/3-1, LE 1428/4-1), GF (FU 583/2-1, FU 583/2-2) and LJ (JA 1904/2-1) is gratefully acknowledged.  ... 
doi:10.1186/2041-1480-4-25 pmid:24103098 pmcid:PMC4128511 fatcat:rz2wt7jdqvfd7pxi24p3xy7syq

Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases

Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos
2015 Scientific Reports  
Phenotypes are the observable characteristics of an organism arising from its response to the environment.  ...  We apply a semantic text- mining approach to identify the phenotypes (signs and symptoms) associated with over 8,000 diseases.  ...  The disease network was visualized using the Gephi graph visualization tool 47 , and the disease network browser was generated with Gephi's Sigma-js export plugin (http://blogs.oii.ox.ac.uk/vis/).  ... 
doi:10.1038/srep10888 pmid:26051359 pmcid:PMC4458913 fatcat:7to4snmfk5b7hee3gyfmg6t63i

Roles and Applications of Biomedical Ontologies in Experimental Animal Science

Hiroshi Masuya
2012 Experimental animals  
In recent years, information technologies related to "ontologies" have played more significant roles in the standardization, integration, and knowledge representation of biomedical information.  ...  This review paper outlines the history of data integration in biomedical science and its recent trends in relation to the field of experimental animal science.  ...  Phenotypic Quality Ontology The Phenotypic Quality Ontology (PATO) provides a basis for vocabularies and semantics for the description of phenotype information across species [11] .  ... 
doi:10.1538/expanim.61.365 pmid:22850636 fatcat:maswarecovdhzduhht5e2ytoxu

Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes inPython bivittatus(Burmese Python)

Kristopher J. L. Irizarry, Josep Rutllant
2016 Genetics Research International  
We employed a comparative genomics approach to produce the functional annotation ofPython bivittatusgenes encoding proteins associated with sperm phenotypes.  ...  Results obtained through our systematic analysis identified subsets of python genes exhibiting associations with gene ontology annotation terms.  ...  The authors would also like to acknowledge the success of this project in spite of the obstacles. Most importantly, the authors wish to acknowledge  ... 
doi:10.1155/2016/7505268 pmid:27200191 pmcid:PMC4855019 fatcat:j5s2glsqxbardkbxvmx24dyzgu
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