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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. 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 powerfulmore » 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.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [4];  [11];  [12];  [4];  [5];  [13];  [14]
+ Show Author Affiliations
  1. Univ. of Illinois, Chicago, IL (United States)
  2. RTI International, Research Triangle Park, NC (United States)
  3. Harvard Univ., Cambridge, MA (United States)
  4. California Inst. of Technology (CalTech), Pasadena, CA (United States)
  5. Northeast Ohio Medical Univ., Rootstown, OH (United States)
  6. Oregon Health and Science Univ., Portland, OR (United States)
  7. National Museum of Natural History, Paris (France)
  8. Univ. of Washington, Seattle, WA (United States)
  9. National Evolutionary Synthesis Center, Durham, NC (United States); Duke Univ., Durham, NC (United States)
  10. Univ. of South Dakota, Vermillion, SD (United States)
  11. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  12. California Inst. of Technology (CalTech), Pasadena, CA (United States); California Inst. of Technology (CalTech), Pasadena, CA (United States). Howard Hughes Medical Institute
  13. Ohio University Heritage College of Osteopathic Medicine, Athens, OH (United States)
  14. Duke Univ., Durham, NC (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1256957
Alternate Identifier(s):
OSTI ID: 1379069
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 2; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Druzinsky, Robert E., Balhoff, James P., Crompton, Alfred W., Done, James, German, Rebecca Z., Haendel, Melissa A., Herrel, Anthony, Herring, Susan W., Lapp, Hilmar, Mabee, Paula M., Muller, Hans-Michael, Mungall, Christopher J., Sternberg, Paul W., Van Auken, Kimberly, Vinyard, Christopher J., Williams, Susan H., and Wall, Christine E. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0149102.
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Druzinsky, Robert E., Balhoff, James P., Crompton, Alfred W., Done, James, German, Rebecca Z., Haendel, Melissa A., Herrel, Anthony, Herring, Susan W., Lapp, Hilmar, Mabee, Paula M., Muller, Hans-Michael, Mungall, Christopher J., Sternberg, Paul W., Van Auken, Kimberly, Vinyard, Christopher J., Williams, Susan H., & Wall, Christine E. Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. United States. https://doi.org/10.1371/journal.pone.0149102
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Druzinsky, Robert E., Balhoff, James P., Crompton, Alfred W., Done, James, German, Rebecca Z., Haendel, Melissa A., Herrel, Anthony, Herring, Susan W., Lapp, Hilmar, Mabee, Paula M., Muller, Hans-Michael, Mungall, Christopher J., Sternberg, Paul W., Van Auken, Kimberly, Vinyard, Christopher J., Williams, Susan H., and Wall, Christine E. Fri . "Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals". United States. https://doi.org/10.1371/journal.pone.0149102. https://www.osti.gov/servlets/purl/1256957.
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@article{osti_1256957,
title = {Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals},
author = {Druzinsky, Robert E. and Balhoff, James P. and Crompton, Alfred W. and Done, James and German, Rebecca Z. and Haendel, Melissa A. and Herrel, Anthony and Herring, Susan W. and Lapp, Hilmar and Mabee, Paula M. and Muller, Hans-Michael and Mungall, Christopher J. and Sternberg, Paul W. and Van Auken, Kimberly and Vinyard, Christopher J. and Williams, Susan H. and Wall, Christine E.},
abstractNote = {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.},
doi = {10.1371/journal.pone.0149102},
journal = {PLoS ONE},
number = 2,
volume = 11,
place = {United States},
year = {Fri Feb 12 00:00:00 EST 2016},
month = {Fri Feb 12 00:00:00 EST 2016}
}
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https://doi.org/10.1371/journal.pone.0149102
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    SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data
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