CaltechAUTHORS
  A Caltech Library Service

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

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. (2016) Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PLoS ONE, 11 (2). Art. No. e0149102. ISSN 1932-6203. PMCID PMC4752357. https://resolver.caltech.edu/CaltechAUTHORS:20160222-104844651

[img] PDF - Published Version
Creative Commons Attribution.

1166Kb
[img] Image (PNG) (S1 Fig. Screenshot of Textpresso for FEED category menus) - Supplemental Material
Creative Commons Attribution.

314Kb
[img] Image (PNG) (S2 Fig. Screenshot of search for recordings from the lateral pterygoid muscle in FEED) - Supplemental Material
Creative Commons Attribution.

324Kb
[img] Image (PNG) (S3 Fig. Screenshot of a search for lateral pterygoid in Google Scholar) - Supplemental Material
Creative Commons Attribution.

281Kb
[img] Image (PNG) (S4 Fig. Screenshot of a search for external pterygoid in Google Scholar) - Supplemental Material
Creative Commons Attribution.

280Kb
[img] Image (PNG) (S5 Fig. Screenshot of a search in PubMed for muscles attached to the mandible) - Supplemental Material
Creative Commons Attribution.

261Kb
[img] Image (PNG) (S6 Fig. Screenshot of a DL Query in Protégé for muscles innervated by the trigeminal nerve that are attached to the mandible) - Supplemental Material
Creative Commons Attribution.

109Kb
[img] Image (PNG) (S7 Fig. Screenshot of the results from a query in Textpresso for FEED) - Supplemental Material
Creative Commons Attribution.

204Kb

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20160222-104844651

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 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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.pone.0149102DOIArticle
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149102PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752357/PubMed CentralArticle
ORCID:
AuthorORCID
Sternberg, Paul W.0000-0002-7699-0173
Van Auken, Kimberly0000-0002-1706-4196
Additional Information:© 2016 The Authors. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Received: August 14, 2015. Accepted: January 27, 2016. Published: February 12, 2016. Editor: Sharon Swartz, Brown University. This work received support from the following sources: National Science Foundation (nsf.gov) to RED DBI-1062350; to SHW DBI-1062327; to CEW DBI-1062333; to RZG DBI-1343588; to CJV DBI-1062332; to PMM DBI-1062542 and DEB-0956049; National Evolutionary Synthesis Center (https://www.nescent.org/; NESCent; NSF EF-0905606). NESCent hosted FEED Workshops in May, 2012, and May, 2014. CJM was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 (http://energy.gov/eere/vehicles/downloads/office-science-basic-energy-sciences). PMM acknowledges funding from the National Science Foundation (DBI-1062542) and the Phenotype Ontology Research Coordination Network (DEB-0956049). Phenotype RCN (www.phenotypercn.org/) also provided support for RED and CJM. National Institutes of Health (www.nih.gov/; U41-HG002223) to PWS. PWS is also an investigator of the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Gowri Ramachandran and Matt O'Neill provided support to help organize and enter data on muscle anatomy and terminology. Kun Peng and Elizabeth Ro performed data entry for the Textpresso for FEED project. Work on the MFMO is supported by the National Science Foundation (DBI-1062350 to Robert Druzinsky). We thank Wasila Dahdul for all of her advice and support. We would like to thank Kathleen Smith, Allen Rodrigo, Susan Alberts, and the National Evolutionary Synthesis Center (NESCent; NSF EF-0905606). NESCent hosted FEED Workshops in May, 2012, and May, 2014. Chris Mungall was supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Paula Mabee and Wasila Dahdul acknowledge funding from the National Science Foundation (DBI-1062542) and the Phenotype Ontology Research Coordination Network (DEB-0956049). The Phenotype RCN (NSF DEB-0956049) also provided support for Robert Druzinsky and Chris Mungall. Paul Sternberg is an investigator of the Howard Hughes Medical Institute. Author Contributions: Conceived and designed the experiments: RED MAH HL PMM CJM CEW. Performed the experiments: RED. Analyzed the data: RED HL PMM CEW. Contributed reagents/materials/analysis tools: RED JPB AWC JD RZG MAH AH SWH HL PMM HMM CJM PWS KVA CJV SHW CEW. Wrote the paper: RED JPB MAH AH SWH HL PMM HMM CJM PWS KVA CJV SHW CEW. All relevant data are within the paper and its Supporting Information files or can be found via the URLs in the paper.
Funders:
Funding AgencyGrant Number
NSFDBI-1062350
NSFDBI-1062327
NSFDBI-1062333
NSFDBI-1343588
NSFDBI-1062332
NSFDBI-1062542
NSFDEB-0956049
National Evolutionary Synthesis Center (NESCent)UNSPECIFIED
NSFEF-0905606
Department of Energy (DOE)DE-AC02-05CH11231
NIHU41-HG002223
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Issue or Number:2
PubMed Central ID:PMC4752357
Record Number:CaltechAUTHORS:20160222-104844651
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160222-104844651
Official Citation:Druzinsky RE, Balhoff JP, Crompton AW, Done J, German RZ, Haendel MA, et al. (2016) Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PLoS ONE 11(2): e0149102. doi:10.1371/journal.pone.0149102
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:64632
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:23 Feb 2016 00:28
Last Modified:03 Oct 2019 09:39

Repository Staff Only: item control page