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New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models

P. N. Schofield, J. P. Sundberg, R. Hoehndorf, G. V. Gkoutos
2011 Briefings in Functional Genomics  
across species and into an improved understanding of human disease.  ...  His expertise is in mammalian genetics and bioinformatics. He works on the control of mammalian pre-natal growth and the development of biomedical ontologies to relate human disease to mouse models.  ...  [53] who annotated the phenotypes of 11 gene-linked human diseases from OMIM and computationally compared these with other ontology-based phenotype descriptions from model organisms.  ... 
doi:10.1093/bfgp/elr031 pmid:21987712 pmcid:PMC3189694 fatcat:xgppdrqndvba5ppmijvqhkuraa

Semantic Social Networks for Integrated Healthcare [chapter]

Eleni Kaldoudi, Nikolas Dovrolis
2013 IFIP Advances in Information and Communication Technology  
The paper discusses a blending of notions of social networks and semantic technologies in order to develop comprehensive personalized and dynamic models of the chronic comorbid patient, their environment  ...  and healthcare related issues, procedures, etc., so as to be able to support meaningful patient empowerment and decision support services.  ...  This work has been funded in part by the Project HELCOHOP: Development of Electronic Clinical Protocols, 2012-2015, MIS 375876, co-funded by European and National funds.  ... 
doi:10.1007/978-3-642-40543-3_76 fatcat:se6lq22txrfu7ermyxou25rgei

The Chinchilla Research Resource Database: resource for an otolaryngology disease model

Mary Shimoyama, Jennifer R. Smith, Jeff De Pons, Marek Tutaj, Pawjai Khampang, Wenzhou Hong, Christy B. Erbe, Garth D. Ehrlich, Lauren O. Bakaletz, Joseph E. Kerschner
2016 Database: The Journal of Biological Databases and Curation  
and Pathway assigned to chinchilla genes based on annotations from the corresponding human orthologs.  ...  The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others.  ...  Its middle ear and Eustachian tube structures are also similar to that of humans and unlike other rodent models it is not susceptible to innate middle ear infections, making it an ideal model organism  ... 
doi:10.1093/database/baw073 pmid:27173523 pmcid:PMC4865329 fatcat:fqvpe2zq2vc4lbnieakuwphquy

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J.P. Gourdine (+14 others)
2016 Nucleic Acids Research  
Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human  ...  or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations.  ...  ACKNOWLEDGEMENTS We thank members of the Undiagnosed Disease Program, the International Mouse Phenotyping Consortium, the NCI Semantic Infrastructure team, and NIF/SciCrunch for their contributions.  ... 
doi:10.1093/nar/gkw1128 pmid:27899636 pmcid:PMC5210586 fatcat:tbsgmbgu4vfmpiwwsenemxj2cm

An integrative, translational approach to understanding rare and orphan genetically based diseases

R. Hoehndorf, P. N. Schofield, G. V. Gkoutos
2013 Interface Focus  
Subject Areas: systems biology, computational biology, bioinformatics PhenomeNet is an approach for integrating phenotypes across species and identifying candidate genes for genetic diseases based on the  ...  Our results demonstrate that integration and computational analysis of human disease and animal model phenotypes using PhenomeNet has the potential to reveal novel insights into the pathobiology underlying  ...  In order to study these parameters, researchers use a variety of organisms and approaches, such as forward and reverse genetics, in an attempt to link the phenotypic manifestations observed in an organism  ... 
doi:10.1098/rsfs.2012.0055 pmid:23853703 pmcid:PMC3638468 fatcat:3dswicpurnd3zpzagfo5q7x2jy

Role of the Ontologies in the Context of Grid Computing and Application for the Human Disease Studies [chapter]

Maja Hadzic, Elizabeth Chang
2004 Lecture Notes in Computer Science  
The Generic Human Disease ontology stands here central as a link between multiple heterogeneous information resources on one side and the users on the other side.  ...  Computer based ontologies may be seen as shared formal conceptualizations of domain knowledge and therefore constitute an essential resource for enabling interoperation in an open environment such as the  ... 
doi:10.1007/978-3-540-30145-5_22 fatcat:ab6c7llrn5aw5oa5asklljkh4e

Disease Compass– a navigation system for disease knowledge based on ontology and linked data techniques

Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
2017 Journal of Biomedical Semantics  
It is developed as linked data so that information scientists can access it using SPARQL queries through an Resource Description Framework (RDF) model for causal chain of diseases.  ...  Results: We designed the RDF model as an implementation of the RFM for the fact repository based on the ontological definitions of the RFM. 1554 diseases and 7080 abnormal states in six major clinical  ...  Natsuko Ohtomo, Aki Hayashi, Takayoshi Matsumura, Ryota Sakurai, Satomi Terada, Kayo Waki, and others at the University of Tokyo Hospital for describing the disease ontology and providing us with their  ... 
doi:10.1186/s13326-017-0132-2 pmid:28629436 pmcid:PMC5477351 fatcat:ze3zjddhkfdjddvh25rgmdijbe

An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence

Satya S. Sahoo, Olivier Bodenreider, Joni L. Rutter, Karen J. Skinner, Amit P. Sheth
2008 Journal of Biomedical Informatics  
Methods: We use an ontology-driven approach to integrate two gene resources (Entrez Gene and Homol-oGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans.  ...  We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources.  ...  The authors want to thank Lee Peters who created the RDF store in Oracle and helped craft and run the SPARQL queries and Jonathan Pollock for valuable input on model organism databases.  ... 
doi:10.1016/j.jbi.2008.02.006 pmid:18395495 pmcid:PMC2766186 fatcat:2pyc76cacvfl5npklwhksksb7a

Gene2Function: An Integrated Online Resource For Gene Function Discovery [article]

Yanhui Hu, Aram Comjean, Stephanie Mohr, Norbert Perrimon
2017 bioRxiv   pre-print
Model organism databases (MODs) and other resources are rich with functional information but difficult to mine.  ...  One of the most powerful ways to develop hypotheses regarding biological functions of conserved genes in a given species, such as in humans, is to first look at what is known about function in another  ...  To address the broad need for an integrated resource, we developed (G2F), an online resource that maps orthologs among human genes and common genetic model species supported by MODs  ... 
doi:10.1101/133975 fatcat:k5767u2mhnawpmsmsiewuxrcju

The Rat Genome Database, update 2007--Easing the path from disease to data and back again

S. N. Twigger, M. Shimoyama, S. Bromberg, A. E. Kwitek, H. J. Jacob
2007 Nucleic Acids Research  
The Rat Genome Database (RGD, http://rgd.mcw. edu) is one of the core resources for rat genomics and recent developments have focused on providing support for disease-based research using the rat model  ...  This work has centered on rat but also includes data for mouse and human to create 'disease portals' that provide a unified view of the genes, QTL and strain models for these diseases across the three  ...  ACKNOWLEDGEMENTS In addition to the listed authors RGD is built and maintained by the following group of dedicated people: Jiali Chen, Weihong Jin, Nataliya Nenasheva, Rajni Nigam, Andrew Patzer, Victoria  ... 
doi:10.1093/nar/gkl988 pmid:17151068 pmcid:PMC1761441 fatcat:2zdfnka2dfh7fgggb5ulwxznti

Knowledge Representation and Management, It's Time to Integrate!

F. Dhombres, J. Charlet
2017 IMIA Yearbook of Medical Informatics  
The third paper is dedicated to model the association between multiple phenotypic traits described within the Human Phenotype Ontology (HPO) and the corresponding genotype in the specific context of rare  ...  Conclusion: Ontologies have started to show their efficiency to integrate medical data for various tasks in medical informatics: electronic health records data management, clinical research, and knowledge-based  ...  Acknowledgements We would like to thank Adrien Hugon and Martina Hutter for her support, the external reviewers for their participation in the selection process of the IMIA Yearbook, and Paul Landais who  ... 
doi:10.15265/iy-2017-030 pmid:29063556 pmcid:PMC6239236 fatcat:bwdoq7p4w5al5afjyq4ngmwi6q

Of mice and men: aligning mouse and human anatomies

Olivier Bodenreider, Terry F Hayamizu, Martin Ringwald, Sherri De Coronado, Songmao Zhang
2005 AMIA Annual Symposium Proceedings  
This study compares two approaches to aligning ontologies. One is fully automatic, based on a combination of lexical and structural similarity; the other is manual.  ...  This paper reports on the alignment between mouse and human anatomies, a critical resource for comparative science as diseases in mice are used as mod-els of human disease.  ...  Acknowledgements The research was supported in part by an appointment to the National Library of Medicine Research Participation Program administrated by the Oak Ridge Institute of Science and Education  ... 
pmid:16779002 pmcid:PMC1560846 fatcat:ewahm43vnza3hg77e3qwltj7em

Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research

Teri A. Manolio, Douglas M. Fowler, Lea M. Starita, Melissa A. Haendel, Daniel G. MacArthur, Leslie G. Biesecker, Elizabeth Worthey, Rex L. Chisholm, Eric D. Green, Howard J. Jacob, Howard L. McLeod, Dan Roden (+19 others)
2017 Cell  
Close collaborations between basic scientists and clinical genomicists are now needed to link genetic variants with disease causation.  ...  , and promoting data sharing.  ...  Current efforts to align phenotypic profiles in model organisms with human diseases via an ontology-based approach include the Monarch Initiative (https://, which uses expertly  ... 
doi:10.1016/j.cell.2017.03.005 pmid:28340351 pmcid:PMC5511379 fatcat:gg4f555uo5edbaibtz6y5mjvme

Learning to Recognize Phenotype Candidates in the Auto-Immune Literature Using SVM Re-Ranking

Nigel Collier, Mai-vu Tran, Hoang-quynh Le, Quang-Thuy Ha, Anika Oellrich, Dietrich Rebholz-Schuhmann, Luis M. Rocha
2013 PLoS ONE  
We observed the advantage of using SVM-based learn-to-rank for sequence label combination over maximum entropy and a priority list approach.  ...  Any progress will support knowledge discovery and linkage to other resources.  ...  model organism and human as the most important species.  ... 
doi:10.1371/journal.pone.0072965 pmid:24155869 pmcid:PMC3796529 fatcat:jcy2fr7yrjgwngtfqvr4vhczdq

The Monarch Initiative: Insights across species reveal human disease mechanisms [article]

Christopher Mungall, Julie McMurry, Sebastian Koehler, James Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, TOM CONLIN, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine (+14 others)
2016 bioRxiv   pre-print
We can exploit this common ancestry at the level of sequences, but also in terms of observable outcomes (phenotypes), to learn more about health and disease for humans and all other species.  ...  Applying the range of available knowledge to solve challenging disease problems requires unified data relating genomics, phenotypes, and disease; it also requires computational tools that leverage these  ...  Acknowledgments We thank members of the Undiagnosed Disease Program, the International Mouse Phenotyping Consortium, the NCI Semantic Infrastructure team, and NIF/SciCrunch for their contributions.  ... 
doi:10.1101/055756 fatcat:26ov5gydkvgmxekc5z7yvcqzly
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