title: Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.
abstract: 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.
  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.
  
  
  CONCLUSIONS
  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.
authors: Department of Oral Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America.
authors: Robert E
authors: RE
authors: Druzinsky
authors: RTI International, Research Triangle Park, North Carolina, United States of America.
authors: James P
authors: JP
authors: Balhoff
authors: Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
authors: Alfred W
authors: AW
authors: Crompton
authors: Division of Biology and Biological Engineering, M/C 156-29, California Institute of Technology, Pasadena, California, United States of America.
authors: James
authors: J
authors: Done
authors: Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, United States of America.
authors: Rebecca Z
authors: RZ
authors: German
authors: Oregon Health and Science University, Portland, Oregon, United States of America.
authors: Melissa A
authors: MA
authors: Haendel
authors: Département d'Ecologie et de Gestion de la Biodiversité, Museum National d'Histoire Naturelle, Paris, France.
authors: Anthony
authors: A
authors: Herrel
authors: University of Washington, Department of Orthodontics, Seattle, Washington, United States of America.
authors: Susan W
authors: SW
authors: Herring
authors: National Evolutionary Synthesis Center, Durham, North Carolina, United States of America.|Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America.
authors: Hilmar
authors: H
authors: Lapp
authors: Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.
authors: Paula M
authors: PM
authors: Mabee
authors: Division of Biology and Biological Engineering, M/C 156-29, California Institute of Technology, Pasadena, California, United States of America.
authors: Hans-Michael
authors: HM
authors: Muller
authors: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
authors: Christopher J
authors: CJ
authors: Mungall
authors: Division of Biology and Biological Engineering, M/C 156-29, California Institute of Technology, Pasadena, California, United States of America.|Howard Hughes Medical Institute, M/C 156-29, California Institute of Technology, Pasadena, California, United States of America.
authors: Paul W
authors: PW
authors: Sternberg
authors: Division of Biology and Biological Engineering, M/C 156-29, California Institute of Technology, Pasadena, California, United States of America.
authors: Kimberly
authors: K
authors: Van Auken
authors: Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio, United States of America.
authors: Christopher J
authors: CJ
authors: Vinyard
authors: Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Athens, Ohio, United States of America.
authors: Susan H
authors: SH
authors: Williams
authors: Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America.
authors: Christine E
authors: CE
authors: Wall
mesh_terms: D000818:Animals; D019992:Databases as Topic; D006801:Humans; D009960:Oropharynx / Q000033:anatomy & histology; D010609:Pharyngeal Muscles / Q000033:anatomy & histology*; D057386:Search Engine