Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

Functional Anatomy of Incisal Biting in Aplodontia rufa and Sciuromorph Rodents – Part 2: Sciuromorphy Is Efficacious for Production of Force at the Incisors

The protrogomorph condition of the rodent masticatory apparatus is thought to be present in only one living species, the mountain beaver Aplodontia rufa. The major anatomical difference between protrogomorphs and sciuromorphs is that the relative size of one part of the masseter muscle, the anterior lateral masseter, is much greater in sciuromorphs than in protrogomorphs. The mechanics of force production at the incisors were compared in A. rufa and six sciuromorph rodents. Is the sciuroid masticatory apparatus more effective for production of forces at the incisors during biting than the primitive, protrogomorph condition? To answer this question, three measures of mechanical ability were employed and three hypotheses were tested: (1) the mechanical advantage of the adductor musculature is greater in sciuromorphs than in A. rufa; (2) the relative force produced at the incisors is greater in sciuromorphs than in A. rufa, and (3) the relative amount of force produced that can be used to drive the incisors into an object, is greater in sciuromorphs than in A. rufa. The results demonstrated that the protrogomorph, A. rufa, is not as efficient at generating bite forces at the incisors as the sciuromorphs

Incisal biting in Aplodontia rufa and Marmota monax.

Incisal biting in Aplodontia rufa and Marmota monax

Mammalian masticatory muscles : homology, nomenclature, and diversification

There is a deep and rich literature of comparative studies of jaw muscles in mammals but no recent analyses employ modern phylogenetic techniques to better understand evolutionary changes that have occurred in these muscles. In order to fully develop and utilize the Feeding Experiments End-user Database (FEED), we are constructing a comprehensive ontology of mammalian jaw muscles. This process has led to a careful consideration of nomenclature and homologies of the muscles and their constituent parts. Precise determinations of muscle attachments have shown that muscles with similar names are not necessarily homologous. Using new anatomical descriptions derived from the literature, we defined character states for the jaw muscles in diverse mammalian species. We then mapped those characters onto a recent phylogeny of mammals with the aid of the Mesquite software package. Our data further elucidate how muscle groups associated with the feeding apparatus differ and have become highly specialized in certain mammalian orders, such as Rodentia, while remaining conserved in other orders. We believe that careful naming of muscles and statistical analyses of their distributions among mammals, in association with the FEED database, will lead to new, significant insights into the functional, structural, and evolutionary morphology of the jaw muscles

What is an anatomy ontology?

What is an anatomy ontology

Classes returned from a DL Query for muscles innervated by the trigeminal nerve that are attached to the mandible.

<p>Classes returned from a DL Query for muscles innervated by the trigeminal nerve that are attached to the mandible.</p

Classes returned by the MFMO from a DL Query in Protégé for muscles attached to the mandible.

<p>Classes returned by the MFMO from a DL Query in Protégé for muscles attached to the mandible.</p