BACKGROUND: Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are interoperable across the biomedical research continuum. There is also an increasing need for methods to interrelate phenotypic data easily and accurately from experiments in animal models with human development and disease. RESULTS: Here we present the Xenopus phenotype ontology (XPO) to annotate phenotypic data from experiments in Xenopus, one of the major vertebrate model organisms used to study gene function in development and disease. The XPO implements design patterns from the Unified Phenotype Ontology (uPheno), and the principles outlined by the Open Biological and Biomedical Ontologies (OBO Foundry) to maximize interoperability with other species and facilitate ongoing ontology management. Constructed in Web Ontology Language (OWL) the XPO combines the existing uPheno library of ontology design patterns with additional terms from the Xenopus Anatomy Ontology (XAO), the Phenotype and Trait Ontology (PATO) and the Gene Ontology (GO). The integration of these different ontologies into the XPO enables rich phenotypic curation, whilst the uPheno bridging axioms allows phenotypic data from Xenopus experiments to be related to phenotype data from other model organisms and human disease. Moreover, the simple post-composed uPheno design patterns facilitate ongoing XPO development as the generation of new terms and classes of terms can be substantially automated. CONCLUSIONS: The XPO serves as an example of current best practices to help overcome many of the inherent challenges in harmonizing phenotype data between different species. The XPO currently consists of approximately 22,000 terms and is being used to curate phenotypes by Xenbase, the Xenopus Model Organism Knowledgebase, forming a standardized corpus of genotype-phenotype data that can be directly related to other uPheno compliant resources.

One of the practical challenges facing the creation of self-assembling systems is being able to exploit a limited set of fixed components and their bonding mechanisms. The method of staging divides the self-assembly process into time intervals, during which components can be added to, or removed from, an environment at each interval. Staging addresses the challenge of using components that lack plasticity by encoding the construction of a target structure in the staging algorithm itself and not exclusively in the design of the components. Previous staging strategies do not consider the interplay between component physical features (morphological information). In this work we use morphological information to stage the self-assembly process, during which components can only be added to their environment at each time interval, to demonstrate our concept. Four experiments are presented, which use heterogeneous, passive, mechanical components that are fabricated using 3D printing. Two orbital shaking environments are used to provide energy to the components and to investigate the role of morphological information with component movement in either two or three spatial dimensions. The benefit of our staging strategy is shown by reducing assembly errors and exploiting bonding mechanisms with rotational properties. As well, a doglike target structure is used to demonstrate in theory how component information used at an earlier time interval can be reused at a later time interval, inspired by the use of a body plan in biological development. We propose that a staged body plan is one method toward scaling self-assembling systems with many interacting components. The experiments and body plan example demonstrate, as proof of concept, that staging enables the self-assembly of more complex morphologies not otherwise possible.

Abstract Summary: The Gene Expression Viewer is a web-launched three-dimensional visualization tool, tailored to compare surface reconstructions of multi-channel image volumes generated by confocal microscopy or micro-CT. Availability: Software is available on request from the authors and is free to academics. Contact: [email protected] Supplementary information: Revisions and additional documentation to the Gene Expression Viewer are maintained at http://www.cbrbio.ucalgary.ca/3DModels and http://www.xenbase.org/3DModels. The idx3dIII Advanced Programming Interface is freely available for non-commercial use at http://www.idx3d.ch/