دورية أكاديمية
أعرض في EDS

Emerging semantics to link phenotype and environment.

التفاصيل البيبلوغرافية
العنوان: Emerging semantics to link phenotype and environment.
المؤلفون: Thessen AE; Ronin Institute for Independent Scholarship , Monclair, NJ , United States ; The Data Detektiv , Waltham, MA , United States., Bunker DE; Department of Biological Sciences, New Jersey Institute of Technology , Newark, NJ , United States., Buttigieg PL; HGF-MPG Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar-und Meeresforschung , Bremerhaven , Germany., Cooper LD; Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , United States., Dahdul WM; Department of Biology, University of South Dakota , Vermillion, SD , United States., Domisch S; Department of Ecology and Evolutionary Biology, Yale University , New Haven, CT , United States., Franz NM; School of Life Sciences, Arizona State University , Tempe, AZ , United States., Jaiswal P; Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , United States., Lawrence-Dill CJ; Departments of Genetics, Development and Cell Biology and Agronomy, Iowa State University , Ames, IA , United States., Midford PE; Richmond, VA , United States., Mungall CJ; Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, CA , United States., Ramírez MJ; Division of Arachnology, Museo Argentino de Ciencias Naturales-CONICET , Buenos Aires , Argentina., Specht CD; Departments of Plant and Microbial Biology & Integrative Biology, University of California , Berkeley, CA , United States., Vogt L; Institut für Evolutionsbiologie und Ökologie, Universität Bonn , Bonn , Germany., Vos RA; Naturalis Biodiversity Center , Leiden , The Netherlands., Walls RL; iPlant Collaborative, University of Arizona , Tucson, AZ , United States., White JW; US Arid Land Agricultural Research Center, United States Department of Agriculture-ARS , Maricopa, AZ , United States., Zhang G; School of Life Sciences, Arizona State University , Tempe, AZ , United States., Deans AR; Department of Entomology, Pennsylvania State University , University Park, PA , United States., Huala E; Phoenix Bioinformatics , Redwood City, CA , United States., Lewis SE; Genomics Division, Lawrence Berkeley National Laboratory , Berkeley, CA , United States., Mabee PM; Department of Biology, University of South Dakota , Vermillion, SD , United States.
المصدر: PeerJ [PeerJ] 2015 Dec 14; Vol. 3, pp. e1470. Date of Electronic Publication: 2015 Dec 14 (Print Publication: 2015).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: PeerJ Inc Country of Publication: United States NLM ID: 101603425 Publication Model: eCollection Cited Medium: Print ISSN: 2167-8359 (Print) Linking ISSN: 21678359 NLM ISO Abbreviation: PeerJ Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: Corte Madera, CA : PeerJ Inc.
مستخلص: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.
References: Genome Biol. 2005;6(1):R8. (PMID: 15642100)
Comp Funct Genomics. 2002;3(2):132-6. (PMID: 18628886)
Proc Biol Sci. 2006 Apr 22;273(1589):895-9. (PMID: 16627273)
Zookeys. 2015 Oct 20;(528):1-133. (PMID: 26692791)
PLoS One. 2014 May 02;9(5):e94056. (PMID: 24787704)
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. (PMID: 16199517)
Database (Oxford). 2015 May 13;2015:bav040. (PMID: 25972520)
PLoS One. 2010 May 20;5(5):e10708. (PMID: 20505755)
AoB Plants. 2010;2010:plq008. (PMID: 22476066)
Biodivers Data J. 2014 Jun 16;(2):e1125. (PMID: 25057255)
Pac Symp Biocomput. 2007;:367-78. (PMID: 17992749)
Cladistics. 2014 Dec;30(6):635-649. (PMID: 34772272)
Nucleic Acids Res. 2014 Jan;42(Database issue):D966-74. (PMID: 24217912)
Sci Data. 2015 Dec 08;2:150073. (PMID: 26647296)
PLoS Biol. 2011 Jun;9(6):e1001088. (PMID: 21713030)
Trends Ecol Evol. 2012 Feb;27(2):78-84. (PMID: 22189359)
Nat Biotechnol. 2007 Nov;25(11):1251-5. (PMID: 17989687)
Zookeys. 2012;(209):255-67. (PMID: 22859892)
BMC Bioinformatics. 2015 Feb 15;16:47. (PMID: 25887779)
Stud Health Technol Inform. 2012;180:68-72. (PMID: 22874154)
J Biomed Semantics. 2013 Dec 11;4(1):43. (PMID: 24330602)
PLoS One. 2014 Mar 03;9(3):e89606. (PMID: 24595056)
JAMA. 1980 Feb 22-29;243(8):756-62. (PMID: 6986000)
Genome Biol. 2005;6(5):R44. (PMID: 15892872)
PLoS Comput Biol. 2009 Jul;5(7):e1000443. (PMID: 19649320)
Nat Biotechnol. 2011 May;29(5):415-20. (PMID: 21552244)
Brief Bioinform. 2008 Sep;9(5):345-54. (PMID: 18445641)
J Biomed Semantics. 2014 Sep 08;5(1):39. (PMID: 25276334)
Nucleic Acids Res. 2013 Jan;41(Database issue):D456-63. (PMID: 23180789)
Nat Genet. 2000 May;25(1):25-9. (PMID: 10802651)
J Econ Entomol. 2006 Apr;99(2):432-6. (PMID: 16686143)
Trends Ecol Evol. 2007 Jul;22(7):345-50. (PMID: 17416439)
PLoS One. 2015 Feb 20;10(2):e0118247. (PMID: 25700173)
J Biomed Semantics. 2014 May 19;5:21. (PMID: 25009735)
Zookeys. 2012;(223):1-38. (PMID: 23166458)
Cancer Epidemiol Biomarkers Prev. 2005 Aug;14(8):1847-50. (PMID: 16103423)
Soc Stud Sci. 2011 Oct;41(5):667-90. (PMID: 22164720)
Genome Biol. 2012 Jan 31;13(1):R5. (PMID: 22293552)
J Biomed Semantics. 2014 Aug 11;5:34. (PMID: 25140222)
Genome Biol. 2004;5(10):R80. (PMID: 15461798)
Trends Ecol Evol. 2008 Mar;23(3):159-68. (PMID: 18289717)
Trends Ecol Evol. 2012 Mar;27(3):151-9. (PMID: 22019413)
PeerJ. 2014 Dec 16;2:e703. (PMID: 25548736)
Bioinformatics. 2015 Jun 1;31(11):1872-4. (PMID: 25619994)
Phytochemistry. 2000 Jul;54(6):577-84. (PMID: 10963450)
Syst Biol. 2015 Nov;64(6):936-52. (PMID: 26018570)
Bioinformatics. 2010 Apr 15;26(8):1112-8. (PMID: 20200009)
PLoS One. 2013;8(2):e55674. (PMID: 23441153)
Bioinformatics. 2012 Apr 1;28(7):1017-20. (PMID: 22285560)
Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):390-399. (PMID: 20052305)
Syst Biol. 2013 Sep;62(5):639-59. (PMID: 23652347)
BMC Bioinformatics. 2011 Jan 24;12:32. (PMID: 21261995)
PLoS One. 2012;7(12):e51070. (PMID: 23251424)
Proc AMIA Annu Fall Symp. 1997;:640-4. (PMID: 9357704)
PLoS One. 2010 Dec 29;5(12):e15991. (PMID: 21209921)
Plant Cell Physiol. 2013 Feb;54(2):e1. (PMID: 23220694)
Nat Biotechnol. 2008 Aug;26(8):889-96. (PMID: 18688244)
PLoS Biol. 2015 Jan 06;13(1):e1002033. (PMID: 25562316)
J Biomed Inform. 2015 Aug;56:127-44. (PMID: 26048076)
Bioinformatics. 2013 Jul 01;29(13):1671-8. (PMID: 23658422)
Plant Methods. 2015 Feb 25;11:10. (PMID: 25774204)
J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7. (PMID: 20626927)
معلومات مُعتمدة: R24 OD011883 United States OD NIH HHS
فهرسة مساهمة: Keywords: Biodiversity; Data integration; Environment; Ontology; Phenotype; Semantic web
تواريخ الأحداث: Date Created: 20151230 Date Completed: 20151229 Latest Revision: 20240324
رمز التحديث: 20240324
مُعرف محوري في PubMed: PMC4690371
DOI: 10.7717/peerj.1470
PMID: 26713234
قاعدة البيانات: MEDLINE
الوصف
تدمد:2167-8359
DOI:10.7717/peerj.1470