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Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

Sirarat Sarntivijai, Drashtti Vasant, Simon Jupp, Gary Saunders, A. Patrícia Bento, Daniel Gonzalez, Joanna Betts, Samiul Hasan, Gautier Koscielny, Ian Dunham, Helen Parkinson, James Malone
2016 Journal of Biomedical Semantics  
Twenty common diseases are linked to 85 rare diseases by shared phenotypes. A generalizable OBAN model for association representation is presented in this study.  ...  The indirect disease-to-disease associations are exposed through shared phenotypes. This was applied to the use case of linking rare to common diseases at the CTTV.  ...  and Mei-Lun Wang for their expert input.  ... 
doi:10.1186/s13326-016-0051-7 pmid:27011785 pmcid:PMC4804633 fatcat:t3qvy6gshbg4hafeytmtokimha

Disease insights through cross-species phenotype comparisons

Melissa A. Haendel, Nicole Vasilevsky, Matthew Brush, Harry S. Hochheiser, Julius Jacobsen, Anika Oellrich, Christopher J. Mungall, Nicole Washington, Sebastian Köhler, Suzanna E. Lewis, Peter N. Robinson, Damian Smedley
2015 Mammalian Genome  
New sequencing technologies have ushered in a new era for diagnosis and discovery of new causative mutations for rare diseases.  ...  We are grateful to Cynthia Smith of MGI for her help in developing logical definitions for MP.  ...  Acknowledgments This work was supported by core infrastructure funding from the Wellcome Trust and National Institutes of Health (NIH) Grant [1 U54 HG006370-01] and NIH Office of the Director Grant #5R24OD011883  ... 
doi:10.1007/s00335-015-9577-8 pmid:26092691 pmcid:PMC4602072 fatcat:kcvbrpu2zbfgjpyooivbj2rwjq

Drug repositioning for orphan diseases

D. Sardana, C. Zhu, M. Zhang, R. C. Gudivada, L. Yang, A. G. Jegga
2011 Briefings in Bioinformatics  
The need and opportunity to discover therapeutics for rare or orphan diseases are enormous.  ...  An alternative and efficient strategy to boost the discovery of orphan disease therapeutics is to find connections between an existing drug product and orphan disease.  ...  Knowledge-based approaches can be used not only to identify new therapeutic agents, but also to validate new therapeutic targets.  ... 
doi:10.1093/bib/bbr021 pmid:21504985 fatcat:urmedevsi5fcti6wem3izr7glq

Disease Ontology: improving and unifying disease annotations across species

Susan M. Bello, Mary Shimoyama, Elvira Mitraka, Stanley J. F. Laulederkind, Cynthia L. Smith, Janan T. Eppig, Lynn M. Schriml
2018 Disease Models & Mechanisms  
Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools.  ...  A unified disease ontology is required that connects data annotated using diverse disease terminologies, and in which the terminology relationships are continuously maintained.  ...  Acknowledgements The Disease Ontology project would like to acknowledge the efforts of DO's engineering team members, Michael Schor and Victor Felix.  ... 
doi:10.1242/dmm.032839 pmid:29590633 pmcid:PMC5897730 fatcat:55yukkyp5ja7re36ejopkqyism

International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases

Kym M. Boycott, Ana Rath, Jessica X. Chong, Taila Hartley, Fowzan S. Alkuraya, Gareth Baynam, Anthony J. Brookes, Michael Brudno, Angel Carracedo, Johan T. den Dunnen, Stephanie O.M. Dyke, Xavier Estivill (+28 others)
2017 American Journal of Human Genetics  
, working groups, and task forces.  ...  Acknowledgments We thank the present and former staff of the IRDiRC Scientific Secretariat, Ségolène Aymé, Lilian Lau, Anneliene Jonker, Antonia Mills, Barbara Cagniard, and members of the scientific committees  ...  genes and in discovering and validating new drug targets, candidate drugs, and other therapeutic strategies.  ... 
doi:10.1016/j.ajhg.2017.04.003 pmid:28475856 pmcid:PMC5420351 fatcat:q4rcjzhz6ff4hmbc66u4u62s3y

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

Sebastian Köhler, Sandra C. Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, Isabelle Bailleul-Forestier, Graeme C. M. Black, Danielle L. Brown, Michael Brudno, Jennifer Campbell, David R. FitzPatrick, Janan T. Eppig (+35 others)
2013 Nucleic Acids Research  
We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple  ...  The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and welldefined set of 10,088 classes (terms) describing human phenotypic  ...  consent, share this information with the wider clinical research community to find clusters of rare cases having phenotype and structural rearrangement in common (18) .  ... 
doi:10.1093/nar/gkt1026 pmid:24217912 pmcid:PMC3965098 fatcat:p2ubynvoprbopaeyoboloexzcq

Disease networks and their contribution to disease understanding and drug repurposing. A survey of the state of the art [article]

Eduardo Garcia del Valle, Gerardo Lagunes Garcia, Lucia Prieto Santamaria, Massimiliano Zanin, Ernestina Menasalvas Ruiz, Alejandro Rodriguez Gonzalez
2018 bioRxiv   pre-print
The importance of drug repurposing lies in the high costs and the prolonged time from target selection to regulatory approval of traditional drug development.  ...  In this document we analyze the evolution of disease network concept during the last decade and apply a data science pipeline approach to evaluate their functional units.  ...  and phenotypic comorbidity links, will have to be integrated in a context-dependent manner.  ... 
doi:10.1101/415257 fatcat:rahsf6ugdfcytnatt6i7jqjxaq

Discovering disease-disease associations by fusing systems-level molecular data

Marinka Žitnik, Vuk Janjić, Chris Larminie, Blaž Zupan, Nataša Pržulj
2013 Scientific Reports  
In it, we find 14 disease-disease associations currently not present in Disease Ontology and provide evidence for their relationships through comorbidity data and literature curation.  ...  Here, we aim to find relationships between diseases based on evidence from fusing all available molecular interaction and ontology data.  ...  For instance, genes are one data type which can be linked to other data types such as Gene Ontology (GO) terms or diseases through two distinct data sources, namely GO annotations and disease-gene mapping  ... 
doi:10.1038/srep03202 pmid:24232732 pmcid:PMC3828568 fatcat:sdf4hbxjtvbynp5zpjc5ensp3q

Modules, networks and systems medicine for understanding disease and aiding diagnosis

Mika Gustafsson, Colm E Nestor, Huan Zhang, Albert-László Barabási, Sergio Baranzini, Sören Brunak, Kian Fan Chung, Howard J Federoff, Anne-Claude Gavin, Richard R Meehan, Paola Picotti, Miguel Ángel Pujana (+5 others)
2014 Genome Medicine  
For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine.  ...  In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as  ...  Acknowledgements We thank Robert Liljenström, Jan Ernerudh, Antonella Muraro and Stefan Thor for valuable comments and discussion.  ... 
doi:10.1186/s13073-014-0082-6 pmid:25473422 pmcid:PMC4254417 fatcat:bvxoyd3tfvbi3hnzri4tvk3q2q

Rare inherited kidney diseases: challenges, opportunities, and perspectives

Olivier Devuyst, Nine V A M Knoers, Giuseppe Remuzzi, Franz Schaefer
2014 The Lancet  
In this review, we discuss the nature of rare inherited kidney diseases, the challenges they pose, and opportunities from technological advances, which are well suited to target the kidney.  ...  Mechanistic insights into rare disorders are relevant for common conditions such as hypertension, kidney stones, cardiovascular disease, and progression of chronic kidney disease in general.  ...  Torra for fruitful discussions and help in selecting milestones in inherited kidney diseases.  ... 
doi:10.1016/s0140-6736(14)60659-0 pmid:24856029 pmcid:PMC4135047 fatcat:meccz7hejve3xlj4jlntnkrbaa

Pathway Maps of Orphan and Complex Diseases Using an Integrative Computational Approach

Kais Ghedira, Soumaya Kouidhi, Yosr Hamdi, Houcemeddine Othman, Sonia Kechaou, Sadri Znaidi, Sghaier Haïtham, Imen Rabhi, Aparup Das
2020 BioMed Research International  
and CDs through binary associations based on common associated genes, and (3) linking ODs and CDs to common enriched pathways.  ...  The principal fundamental aspects related to these diseases include insufficient knowledge of mechanisms involved in the physiopathology necessary to access correct diagnosis and to develop appropriate  ...  Previously, the Centre for Therapeutic Target Validation was able to develop an experimental factor ontology (EFO) by integrating rare and complex disease-related phenotype and genotype ontologies and  ... 
doi:10.1155/2020/4280467 pmid:33376724 pmcid:PMC7744584 fatcat:7orxwlwmabc65diwkdvnn2w6sq

MalaCards: an integrated compendium for diseases and their annotation

Noa Rappaport, Noam Nativ, Gil Stelzer, Michal Twik, Yaron Guan-Golan, Tsippi Iny Stein, Iris Bahir, Frida Belinky, C. Paul Morrey, Marilyn Safran, Doron Lancet
2013 Database: The Journal of Biological Databases and Curation  
MalaCards: an integrated compendium for diseases and their annotation.  ...  Warshawsky and A.  ...  Rinon for helpful discussions and ideas. .............................................................................................................................................................  ... 
doi:10.1093/database/bat018 pmid:23584832 pmcid:PMC3625956 fatcat:ju462m3cezgqtkai2jjrdvatuq

Human Disease Ontology 2018 update: classification, content and workflow expansion

Lynn M Schriml, Elvira Mitraka, James Munro, Becky Tauber, Mike Schor, Lance Nickle, Victor Felix, Linda Jeng, Cynthia Bearer, Richard Lichenstein, Katharine Bisordi, Nicole Campion (+8 others)
2018 Nucleic Acids Research  
The Human Disease Ontology (DO) (http://www. disease-ontology.org), database has undergone significant expansion in the past three years.  ...  The DO disease classification includes specific formal semantic rules to express meaningful disease models and has expanded from a single asserted classification to include multiple-inferred mechanistic  ...  In particular, we thank James Overton for ROBOT and your willingness to share ROBOT with the DO project, the generous and ongoing collaborations with MGI and RGD (Sue Bello, Cynthia Smith, Stan Laulederkind  ... 
doi:10.1093/nar/gky1032 pmid:30407550 fatcat:q3u7vqejlbechc25orcqbgawzi

Biological Network Approaches and Applications in Rare Disease Studies

Peng Zhang, Yuval Itan
2019 Genes  
Biological networks have recently been shown to be very useful for studies that decipher biological mechanisms and disease etiologies and for studies that predict therapeutic responses, at both the molecular  ...  We also introduce several recent biological network applications and methods for the studies of rare diseases.  ...  Abel for valuable advice, and Y. Nemirovskaya, D. Papandrea and M. Woollett for administrative support. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes10100797 pmid:31614842 pmcid:PMC6827097 fatcat:c2q3csd4fnevxfxwx3jgitznge

Molecular disease presentation in diabetic nephropathy

Andreas Heinzel, Irmgard Mühlberger, Gil Stelzer, Doron Lancet, Rainer Oberbauer, Maria Martin, Paul Perco
2015 Nephrology, Dialysis and Transplantation  
uncovering diagnostic and prognostic as well as therapeutic leads to tackle this highly prevalent clinical problem.  ...  Kidney disease is a common problem in patients with diabetes. Depending on the degree of GFR impairment and/or albuminuria, roughly 30% of subjects are affected.  ...  uncovering diagnostic and prognostic as well as therapeutic leads to tackle this highly prevalent clinical problem.  ... 
doi:10.1093/ndt/gfv267 pmid:26209734 fatcat:umjf3m74wjfg3o4wwbawoyjoge
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