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Experiences with Modeling Composite Phenotypes in the SKELETOME Project [chapter]

Tudor Groza, Andreas Zankl, Jane Hunter
2012 Lecture Notes in Computer Science  
Furthermore, we describe and evaluate an algorithm capable of mapping concepts of this ontology to exact or broader terms in the main phenotype ontology used in the bone dysplasia domain.  ...  In this paper we propose an ontology aimed at representing the intrinsic structure of such radiographic findings in a standard manner, in order to bridge the different lexical variations of the actual  ...  The work presented in this paper is supported by the Aus-  ... 
doi:10.1007/978-3-642-35173-0_6 fatcat:kfkxbxoypfbplpftqlrhzycmqu

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

Tudor Groza, Jane Hunter, Andreas Zankl
2012 BMC Bioinformatics  
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 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.  ...  Acknowledgements This research is funded by the Australian Research Council (ARC) under the Linkage grant SKELETOME-LP100100156.  ... 
doi:10.1186/1471-2105-13-50 pmid:22449239 pmcid:PMC3338382 fatcat:flu5hsohtvahhmd5kwfec4es6u

Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods

Tudor Groza, Jane Hunter, Andreas Zankl
2012 BMC Bioinformatics  
The first step in this process is the segmentation of the phenotype descriptions into their atomic elements.  ...  The approach is tested on a corpus comprised of skeletal phenotype descriptions emerged from the Human Phenotype Ontology.  ...  NeCTAR is an Australian Government project conducted as part of the Super Science initiative and financed by the Education Investment Fund. Author details  ... 
doi:10.1186/1471-2105-13-265 pmid:23061930 pmcid:PMC3495645 fatcat:hvpmzhouvbhkpn2ebrswcu4hnq

Decomposing Phenotype Descriptions for the Human Skeletal Phenome

Tudor Groza, Jane Hunter, Andreas Zankl
2013 Biomedical Informatics Insights  
We use this approach to showcase the usefulness of the generic concept of phenotype decomposition by performing an experimental study on all skeletal phenotype concepts defined in the Human Phenotype Ontology  ...  We present a meta-model (the Phenotype Fragment Ontology) and a processing pipeline that enable together the automatic decomposition and conceptualization of phenotype descriptions for the human skeletal  ...  Our focus on the HPO skeletal phenotypes has been strictly motivated by the needs emerging from the SKELETOME project, as already mentioned in Introduction.  ... 
doi:10.4137/bii.s10729 pmid:23440304 pmcid:PMC3572876 fatcat:hunhhvsisnfinkbvsedfnwif4m

Mining Skeletal Phenotype Descriptions from Scientific Literature

Tudor Groza, Jane Hunter, Andreas Zankl, Zhuang Zuo
2013 PLoS ONE  
Our hybrid approach uses an ensemble of four classifiers and experiments with several aggregation techniques.  ...  Finally, we discuss the influence of the features chosen for the model on the overall performance of the method.  ...  In the first experiment we've trained MALLET with each individual feature from the overall best model (in addition to a couple more that were part of the models of the other classifiers), while in the  ... 
doi:10.1371/journal.pone.0055656 pmid:23409017 pmcid:PMC3568099 fatcat:lw5xpqm2njf47jkw5fyq55tgsu

State of the art and open challenges in community-driven knowledge curation

Tudor Groza, Tania Tudorache, Michel Dumontier
2013 Journal of Biomedical Informatics  
However, these, in addition to OMIM which is available in a machine-understandable format in the context of the Human Phenotype Ontology (HPO) project [15] , represent pioneering examples and, as such  ...  This model is already familiar to most experts (e.g., Web 2.0) and has already proved successful in large community projects in other domains (e.g., the Open Source movement).  ... 
doi:10.1016/j.jbi.2012.11.007 pmid:23219718 fatcat:odppdhmlkrgqfk67zhphysoa5m

Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora

T. Groza, S. Kohler, S. Doelken, N. Collier, A. Oellrich, D. Smedley, F. M. Couto, G. Baynam, A. Zankl, P. N. Robinson
2015 Database: The Journal of Biological Databases and Curation  
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora.  ...  Here, we present a unique corpus, capturing text spans from 228 abstracts manually annotated with Human Phenotype Ontology (HPO) concepts and harmonized by three curators, which can be used as a reference  ...  The Bio-LarK concept recognizer has been developed as part of the SKELETOME project (28) , with an initial goal of performing automatic annotation of skeletal phenotypes in patient clinical summaries.  ... 
doi:10.1093/database/bav005 pmid:25725061 pmcid:PMC4343077 fatcat:6bc3qcxskfbybaevdtjc3u5nra