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Inferring characteristic phenotypes via class association rule mining in the bone dysplasia domain

Razan Paul, Tudor Groza, Jane Hunter, Andreas Zankl
2014 Journal of Biomedical Informatics  
We propose a clear definition for characteristic phenotypes, we experiment with a novel, class association rule mining algorithm and we discuss our lessons learned from both an automatic and human-based  ...  In this paper we aim to deal with each of these problems in the context provided by the skeletal dysplasia domain.  ...  Acknowledgments This research is funded by the Australian Research Council (ARC) under the Linkage grant SKELETOME -LP100100156 and the Discovery Early Career Researcher Award (DECRA) -DE120100508.  ... 
doi:10.1016/j.jbi.2013.12.001 pmid:24333481 fatcat:sdw4cb7tvrantged2ja2vkhq74

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

Tudor Groza, Jane Hunter, Andreas Zankl
2012 BMC Bioinformatics  
Conclusions: The Bone Dysplasia Ontology represents the most comprehensive structured knowledge source for the skeletal dysplasias domain.  ...  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.  ...  Especial thanks also to Tania Tudorache, Timothy Redmond and Matthew Horridge for the extremely useful feed-back on the logical correctness of the class axioms and of the grounding in BFO.  ... 
doi:10.1186/1471-2105-13-50 pmid:22449239 pmcid:PMC3338382 fatcat:flu5hsohtvahhmd5kwfec4es6u

Decision Support Methods for Finding Phenotype — Disorder Associations in the Bone Dysplasia Domain

Razan Paul, Tudor Groza, Jane Hunter, Andreas Zankl, Andrey Rzhetsky
2012 PLoS ONE  
We propose a solution that combines association rule mining with the Dempster-Shafer theory (DST) to compute probabilistic associations between sets of clinical features and disorders, which can then serve  ...  A lack of mature domain knowledge and well established guidelines makes the medical diagnosis of skeletal dysplasias (a group of rare genetic disorders) a very complex process.  ...  The authors would also like to express their gratitude for receiving access to the ESDN data by thanking the ESDN Clinical and Radiographic Management Group (ESDN-CRMG, http://www.esdn.org/).  ... 
doi:10.1371/journal.pone.0050614 pmid:23226331 pmcid:PMC3511538 fatcat:7ci5ixiehrh5lc4qy6eg6jw2ty

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  
measures in the process of association rule mining.  ...  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  ...  This research is funded by the Australian Research Council (ARC) under the Linkage grant SKELETOME -LP100100156 and the Discovery Early Career Researcher Award (DECRA) -DE120100508. Author details  ... 
doi:10.1186/2041-1480-5-8 pmid:24499729 pmcid:PMC3936824 fatcat:grysne55e5dnvl6nmhwnu2aryy

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).  ...  The community-driven ontology curation process, however, ignores the possibility of multiple communities building, in parallel, conceptualisations of the same domain, and thus providing slightly different  ...  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

Artificial Intelligence (AI) in Rare Diseases: Is the Future Brighter?

Brasil, Pascoal, Francisco, dos Reis Ferreira, Videira, Valadão
2019 Genes  
The amount of data collected and managed in (bio)medicine is ever-increasing. Thus, there is a need to rapidly and efficiently collect, analyze, and characterize all this information.  ...  Of the more than 7000 RDs described worldwide, only 5% have a treatment.  ...  The characteristic feature mining algorithm (CFML) has uncovered the key features of 15 bone dysplasia disorders resorting to the European skeletal dysplasia network.  ... 
doi:10.3390/genes10120978 pmid:31783696 pmcid:PMC6947640 fatcat:wzghxueer5cahkjyxdwq2g24du

'There and Back Again'—Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension

Emilia M. Swietlik, Matina Prapa, Jennifer M. Martin, Divya Pandya, Kathryn Auckland, Nicholas W. Morrell, Stefan Gräf
2020 Genes  
In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes,  ...  causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH.  ...  Conversely, in the composite class model, a variant in one gene is sufficient to produce the phenotype, but an additional variant in a second gene impacts the disease phenotype or alters the age of onset  ... 
doi:10.3390/genes11121408 pmid:33256119 fatcat:cdi2k24anfd6tjsulnslgqwg5i

Matrix Biology Europe - July 2018 Meeting Celebrating 50 years of Federation of European Connective Tissue Societies Meetings(organised by the British Society for Matrix Biology and the University of Manchester Wellcome Trust Centre for Cell-Matrix Resear

2018 International journal of experimental pathology (Print)  
This study highlights the potential for targeting CSCs via mechanical property of tumour microenvironment as promising therapeutic strategy that inhibit tumour progression.  ...  PDAC encapsulated in stiffer hydrogel showed the high chemotherapy resistance.  ...  Further database mining identified several cancer-associated point mutations in the basigin membrane proximal region.  ... 
doi:10.1111/iep.12294 fatcat:tawvze6nore3vm4mwvo54y2nx4

A case-based assistant for diagnosis and analysis of dysmorphic syndromes

CD. Evans
1995 Medical Informatics  
There are no firm rules to deter mine how a concept or category inform ation is constructed.  ...  any object class and a t t r i b u t e is any of the slots associated with th a t class.  ...  A case presented later in the order which evcduates positively against the node may also have common features with one or more of the cases stored at that group (which were not included on the node description  ... 
doi:10.3109/14639239509025350 pmid:8569305 fatcat:yw6qpzunjrecxfsrrhabvtdoti

ICL670A [chapter]

2017 Encyclopedia of Cancer  
and mutation patterns and to make inferences about possible causes of cancer; and molecular genetics, to study genotype/phenotype associations.  ...  The phenotypes associated with the complete loss of TOR function are remarkably similar to phenotypes associated with mutations in the insulin-like receptor (Inr) pathway.  ...  Characteristics History Initial interest in isoflavones is based on the history of their discovery in the 1940s. Animals grazing on clover-rich pastures became infertile.  ... 
doi:10.1007/978-3-662-46875-3_101180 fatcat:66hbagjkhzalvc3i2pzbhoe7aa

Abstracts from the 51st European Society of Human Genetics Conference: Oral Presentations

2019 European Journal of Human Genetics  
Few of the 140 loci displayed nominally significant associations with their target biomarker in the Greek and Ugandan samples. The polygenic scores were associated I. D'Atri 1 , L. Li 2 , X.  ...  We identified a homozygous missense alteration (c.75C>A, p.D25E) in the CLCC1 gene, which encodes a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal  ...  In summary, we described the first MAU2 mutation in a patient with characteristic CdLS phenotype.  ... 
doi:10.1038/s41431-019-0407-4 fatcat:3d23n3msz5fulchpvpfipze6pq

Melanoma-Associated Retinopathy [chapter]

Claudia Pföhler
2011 Encyclopedia of Cancer  
Acknowledgments We are grateful to the Medical Research Council, UK (MCL and RVT) and the Portuguese Foundation for Science and Technology (BD/12415/2003) (MCL) for support, and to Mrs.  ...  Acknowledgment This work was supported by a grant from the Canadian Institutes of Health Research.  ...  Merlin binds directly to the actin cytoskeleton via two actin-binding sites located in its N-terminal domain.  ... 
doi:10.1007/978-3-642-16483-5_3612 fatcat:o4qtgpwxtna5haqsa57taks5j4

Mitotic Arrest-Deficient Protein 1 [chapter]

Ya-Hui Chi, Kuan-Teh Jeang
2011 Encyclopedia of Cancer  
Acknowledgments We are grateful to the Medical Research Council, UK (MCL and RVT) and the Portuguese Foundation for Science and Technology (BD/12415/2003) (MCL) for support, and to Mrs.  ...  Acknowledgment This work was supported by a grant from the Canadian Institutes of Health Research.  ...  Merlin binds directly to the actin cytoskeleton via two actin-binding sites located in its N-terminal domain.  ... 
doi:10.1007/978-3-642-16483-5_3778 fatcat:tin4mbocj5h2tn5bngkz7zp27a

Major Vault Protein [chapter]

Takeo Minaguchi, Kristin A. Waite
2011 Encyclopedia of Cancer  
Acknowledgments We are grateful to the Medical Research Council, UK (MCL and RVT) and the Portuguese Foundation for Science and Technology (BD/12415/2003) (MCL) for support, and to Mrs.  ...  Acknowledgment This work was supported by a grant from the Canadian Institutes of Health Research.  ...  Merlin binds directly to the actin cytoskeleton via two actin-binding sites located in its N-terminal domain.  ... 
doi:10.1007/978-3-642-16483-5_3504 fatcat:gitkzcftfvhlbda3ptisojtily
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