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Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex

James P Balhoff, Wasila M Dahdul, T Dececchi, Hilmar Lapp, Paula M Mabee, Todd J Vision
2014 Journal of Biomedical Semantics  
Results: We decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex.  ...  Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues.  ...  Acknowledgments Early design work on the Phenex ORB was undertaken by Mtakai Ngara. This work has been supported by NSF collaborative grants DBI-1062404 and DBI-1062542. Author details  ... 
doi:10.1186/2041-1480-5-45 pmid:25411634 pmcid:PMC4236444 fatcat:jm73jdhqxzbz7m73txajmnyrgy

Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy

Wasila Dahdul, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Paula Mabee
2015 Database: The Journal of Biological Databases and Curation  
The workflow consists of: (i) data preparation, (ii) phenotype annotation, (iii) ontology development and (iv) curation team discussions and software development feedback.  ...  Abstract The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form.  ...  Acknowledgements We thank Phenoscape collaborators for comments and advice that improved this work.  ... 
doi:10.1093/database/bav040 pmid:25972520 pmcid:PMC4429748 fatcat:2hzs6htrlfhqrdxiiywenhrxmq

Enabling Machine-Actionable Semantics For Comparative Analyses Of Trait Evolution

Wasila Dahdul, James Balhoff, Hilmar Lapp, Josef Uyeda, Todd Vision
2017 Zenodo  
To accomplish this, the project will adapt key products and know-how developed by the Phenoscape project, including an integrative knowledgebase of ontology-linked phenotype data, metrics for quantifying  ...  the semantic similarity of phenotype descriptions, and algorithms for synthesizing morphological data from [...]  ...  OWL ontologies, ontology-annotated (using Phenex [40, 41] ) character matrix files, and gene phenotype annotations from model organism databases into a unified data model expressed in OWL (Web Ontology  ... 
doi:10.5281/zenodo.885538 fatcat:se2izcnlizdjrmqohjbrkd5qne