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Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation
2016
Journal of Biomedical Semantics
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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
2015
Mammalian Genome
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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
2011
Briefings in Bioinformatics
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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
2018
Disease Models & Mechanisms
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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
2017
American Journal of Human Genetics
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, 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
2013
Nucleic Acids Research
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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]
2018
bioRxiv
pre-print
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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
2013
Scientific Reports
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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
2014
Genome Medicine
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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
2014
The Lancet
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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
2020
BioMed Research International
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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
2013
Database: The Journal of Biological Databases and Curation
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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
2018
Nucleic Acids Research
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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
2019
Genes
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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
2015
Nephrology, Dialysis and Transplantation
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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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