Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals

Background: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. Development and Testing of the Ontology Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. Results and Significance Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities

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

Superficial Temporalis Muscle of a baboon

<p>Superficial view of the temporalis muscle in a baboon (Papio anubis).  Contributed by Chris Wall, Duke University, for the FEED Database - see http://feedexp.org</p

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

Textpresso for oro-pharyngeal anatomy: a system for searching the full text of anatomy literatures

Biological databases are a useful resource for parlaying existing data into new experimental hypotheses. Populating such databases with information from the published literature, however, can be labor intensive and thus is aided greatly by text mining tools capable of retrieving key facts from full text. The Textpresso information retrieval system (http://www.textpresso.org) is used by several Model Organism Database (MOD) communities to assist in curation [Müller HM, Kenny EE, Sternberg PW. 2004. PLoS Biol. Nov;2(11):e309; Van Auken KM, Fey P, Berardini TZ, et al. 2012. Database (Oxford). Nov 17;2012:bas040.] Textpresso searches the full text of literature using keywords and/or categories, groups of semantically related words, to identify sentences within a paper that describe specific aspects of biology. Using the anatomy ontology of oro-pharyngeal structures developed in the FEED project [Druzinsky R, et al., in prep ], we are constructing a Textpresso site to aid in curation of the oro-pharyngeal muscle literature. At this time, we have amassed a database of over 2000 searchable references. We will present a demonstration of Textpresso for Oro-Pharyngeal Anatomy and show how it can be used to construct meaningful queries on the full text of the literature