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The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain

Tudor Groza, Jane Hunter, Andreas Zankl
2012 BMC Bioinformatics  
We also describe the different components of the ontology, including a comprehensive and formal representation of the skeletal dysplasia domain as well as the related genotypes and phenotypes.  ...  SKELETOME enables domain experts to use, refine and extend and apply the ontology without any prior ontology engineering experience-to advance the body of knowledge in the skeletal dysplasia field.  ...  We wish to thank Yuan-Fang Li, Hasti Ziamatin and Razan Paul for their input in designing the ontology.  ... 
doi:10.1186/1471-2105-13-50 pmid:22449239 pmcid:PMC3338382 fatcat:flu5hsohtvahhmd5kwfec4es6u

The Human Phenotype Ontology

PN Robinson, S Mundlos
2010 Clinical Genetics  
algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition  ...  Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described.  ...  The views expressed in this publication are those of the authors and not necessarily those of the funding agencies involved.  ... 
doi:10.1111/j.1399-0004.2010.01436.x pmid:20412080 fatcat:ltjtumlbpnfqdkp6vjahbzu35u

The Human Phenotype Ontology in 2017

Sebastian Köhler, Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M. Bello, Cornelius F. Boerkoel, Kym M. Boycott, Michael Brudno, Orion J. Buske (+47 others)
2016 Nucleic Acids Research  
algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition  ...  Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described.  ...  The views expressed in this publication are those of the authors and not necessarily those of the funding agencies involved.  ... 
doi:10.1093/nar/gkw1039 pmid:27899602 pmcid:PMC5210535 fatcat:55iggw3tzvei7ispy3gu6rwqum

Using Semantic Web Technologies to Build a Community-Driven Knowledge Curation Platform for the Skeletal Dysplasia Domain [chapter]

Tudor Groza, Andreas Zankl, Yuan-Fang Li, Jane Hunter
2011 Lecture Notes in Computer Science  
In this paper we report on our on-going efforts in building SKELETOME -a community-driven knowledge curation platform for the skeletal dysplasia domain.  ...  SKELETOME introduces an ontologydriven knowledge engineering cycle that supports the continuous evolution of the domain knowledge.  ...  Acknowledgments The work presented in this paper is supported by the Australian Research Council (ARC) under the Linkage grant SKELETOME -LP100100156.  ... 
doi:10.1007/978-3-642-25093-4_6 fatcat:2ei5szrkjbdjllx76mdb4yygy4

Capturing domain knowledge from multiple sources: the rare bone disorders use case

Tudor Groza, Tania Tudorache, Peter N Robinson, Andreas Zankl
2015 Journal of Biomedical Semantics  
We exemplify the approach in the rare bone disorders domain by proposing the Rare Bone Disorders Ontology (RBDO).  ...  Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information.  ...  Acknowledgements This research is funded by the Australian Research Council (ARC) under the Discovery Early Career Researcher Award (DECRA) -DE120100508. Author details  ... 
doi:10.1186/s13326-015-0008-2 pmid:25926964 pmcid:PMC4414390 fatcat:pkfol7iopjbqfiydyb7kikrdqa

Semantic Similarity-Driven Decision Support in the Skeletal Dysplasia Domain [chapter]

Razan Paul, Tudor Groza, Andreas Zankl, Jane Hunter
2012 Lecture Notes in Computer Science  
The outcome of this research enables us to understand the feasibility of developing decision support methods based on ontology-driven semantic similarity in the skeletal dysplasia domain.  ...  In this paper, we focus on using such similarity measures to predict disorders on undiagnosed patient cases in the bone dysplasia domain.  ...  Acknowledgments The work presented in this paper is supported by the Australian Research Council (ARC) under the Discovery Early Career Researcher Award (DECRA) -DE120100508 and the Linkage grant SKELETOME  ... 
doi:10.1007/978-3-642-35173-0_11 fatcat:ge427radlrezzf6q2khpdak7c4

Semantic interestingness measures for discovering association rules in the skeletal dysplasia domain

Razan Paul, Tudor Groza, Jane Hunter, Andreas Zankl
2014 Journal of Biomedical Semantics  
We apply the method in our domain of interest -bone dysplasias -using the core ontologies characterising it and an annotated dataset of patient clinical summaries, with the goal of discovering implicit  ...  Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information.  ...  Acknowledgements We gratefully acknowledge the editor and anonymous reviewers whose comments and advices have helped us improve our manuscript.  ... 
doi:10.1186/2041-1480-5-8 pmid:24499729 pmcid:PMC3936824 fatcat:grysne55e5dnvl6nmhwnu2aryy

The radiologic diagnosis of skeletal dysplasias: past, present and future

Amaka C. Offiah, Christine M. Hall
2020 Pediatric Radiology  
dysplasias, and by the recent explosion in identified genes.  ...  This article provides a historical overview of aids to the radiologic diagnosis of skeletal dysplasias.  ...  The Bone Dysplasia Ontology aims to integrate genotypic and phenotypic findings in skeletal dysplasias [35] , while the dynamic Radiological Electronic Atlas of Malformation Syndromes (dREAMS) [36] provides  ... 
doi:10.1007/s00247-019-04533-y pmid:33135135 fatcat:uuokcii7arfxffvtsgfwqw4cw4

Whole Exome Sequencing with Comprehensive Gene Set Analysis Identified a Biparental-Origin Homozygous c.509G>A Mutation in PPIB Gene Clustered in Two Taiwanese Families Exhibiting Fetal Skeletal Dysplasia during Prenatal Ultrasound

Ting-Yu Chang, I-Fang Chung, Wan-Ju Wu, Shun-Ping Chang, Wen-Hsiang Lin, Norman A. Ginsberg, Gwo-Chin Ma, Ming Chen
2020 Diagnostics  
Skeletal dysplasia (SD) is a complex group of bone and cartilage disorders often detectable by fetal ultrasound, but the definitive diagnosis remains challenging because the phenotypes are highly variable  ...  Hundreds of genes are involved in the pathogenesis of SD, but most of them are yet to be elucidated, rendering genotyping almost infeasible except those most common such as fibroblast growth factor receptor  ...  Conflicts of Interest: The authors declare no conflicts of interest.  ... 
doi:10.3390/diagnostics10050286 pmid:32392875 fatcat:aywcopah3banrnhwtjat4rlcme

Improving Disease Gene Prioritization by Comparing the Semantic Similarity of Phenotypes in Mice with Those of Human Diseases

Anika Oellrich, Robert Hoehndorf, Georgios V. Gkoutos, Dietrich Rebholz-Schuhmann, Markus Schuelke
2012 PLoS ONE  
(using the Human Phenotype Ontology).  ...  Furthermore, our method has been integrated in PhenomeNET and the results can be explored using the PhenomeBrowser at http://phenomebrowser.net.  ...  The second report contains the information about genotypes and their observed phenotypes. The phenotypes are represented using the MP.  ... 
doi:10.1371/journal.pone.0038937 pmid:22719993 pmcid:PMC3375301 fatcat:ajsbuifb4bgxjkgqy3cgvotvnu

Insights in the etiopathology of galactosyltransferase II (GalT-II) deficiency from transcriptome-wide expression profiling of skin fibroblasts of two sisters with compound heterozygosity for two novel B3GALT6 mutations

Marco Ritelli, Nicola Chiarelli, Nicoletta Zoppi, Chiara Dordoni, Stefano Quinzani, Michele Traversa, Marina Venturini, Piergiacomo Calzavara-Pinton, Marina Colombi
2015 Molecular Genetics and Metabolism Reports  
factors of the HOX and LIM families implicated in skeletal and limb development.  ...  and homeostasis of various connective tissues, including skin, bone, cartilage, tendons, and ligaments, and generates the wide phenotypic spectrum of GalT-II-deficient patients.  ...  Acknowledgments The authors thank the patients and their family for their kind availability for this study.  ... 
doi:10.1016/j.ymgmr.2014.11.005 pmid:28649518 pmcid:PMC5471164 fatcat:djnk6c7msfdphatnfusxf4dsbi

Compound heterozygous variants in NBAS as a cause of atypical osteogenesis imperfecta

M. Balasubramanian, J. Hurst, S. Brown, N.J. Bishop, P. Arundel, C. DeVile, R.C. Pollitt, L. Crooks, D. Longman, J.F. Caceres, F. Shackley, S. Connolly (+6 others)
2017 Bone  
We explore the mechanism underlying NBAS and the striking skeletal phenotype in our patients.  ...  Conclusions: Here we report on variants in NBAS, as a cause of bone fragility in humans, and expand the phenotypic spectrum associated with NBAS.  ...  A dysplasia skeletal survey showed multiple Wormian bones, slender tubular bones and osteopenia (Figure 2a-d) .  ... 
doi:10.1016/j.bone.2016.10.023 pmid:27789416 pmcid:PMC6067660 fatcat:psjmnryuabgchimyoue746f334

Ciliary Signalling and Mechanotransduction in the Pathophysiology of Craniosynostosis

Federica Tiberio, Ornella Parolini, Wanda Lattanzi
2021 Genes  
In this review, we aimed to highlight the implication of the primary cilium components and active signalling in CS pathophysiology, dissecting their biological functions in craniofacial development and  ...  Interestingly, a prevalent implication of midline sutures is observed in CS ciliopathies, possibly explained by the specific neural crest origin of the frontal bone.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes12071073 pmid:34356089 pmcid:PMC8306115 fatcat:5ikp6p3krfh2xefd6wwwnrqjly

Guidelines for managing data and processes in bone and cartilage tissue engineering

Federica Viti, Silvia Scaglione, Alessandro Orro, Luciano Milanesi
2014 BMC Bioinformatics  
the domain knowledge and can provide a suitable means to integrate data across the field.  ...  In this context, integration and meta-analysis approaches are gaining importance for analyses and reuse of data as, for example, those concerning the bone and cartilage biomarkers, the biomolecular factors  ...  Acknowledgements This work has been supported by the Italian Ministry of Education and Research (MIUR) through Flagship "InterOmics" (PB05) and HIRMA (RBAP11YS7K) projects, and by the European  ... 
doi:10.1186/1471-2105-15-s1-s14 pmid:24564199 pmcid:PMC4015954 fatcat:pwnpjouzknbypcewtivy6uebhm

Regenerating zebrafish scales express a subset of evolutionary conserved genes involved in human skeletal disease

Dylan J. M. Bergen, Qiao Tong, Ankit Shukla, Elis Newham, Jan Zethof, Mischa Lundberg, Rebecca Ryan, Scott E. Youlten, Monika Frysz, Peter I. Croucher, Gert Flik, Rebecca J. Richardson (+3 others)
2022 BMC Biology  
Hypergeometric tests involving monogenetic skeletal disorders showed that DEGs were strongly enriched for human orthologues that are mutated in low bone mass and abnormal bone mineralisation diseases (  ...  The DEGs were also enriched for human orthologues associated with polygenetic skeletal traits, including height (P< 6× 10−4), and estimated bone mineral density (eBMD, P< 2× 10−5).  ...  We would like to thank Mathew Green and Pablo Peon Garcia for fish care at UoB, and Tom Spanings and Antoon van der Horst for fish care at RU.  ... 
doi:10.1186/s12915-021-01209-8 pmid:35057801 pmcid:PMC8780716 fatcat:ox2o35jvxvhdfoyqcr6fvzehle
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