Transforming the study of organisms: Phenomic data models and knowledge bases.

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science, [2005]-

Databases, Genetic* ; Knowledge Bases* ; Phenomics*; Animals ; Classification ; Computational Biology ; Ecosystem ; Gene-Environment Interaction ; Humans ; Models, Biological ; Models, Genetic ; Models, Statistical ; Phenotype ; Semantics

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.
Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: Jessica Singer and Robert Warren are employed by Annex Agriculture. They have no consultancies, patents, products in development, or marketed products that form a competing interest. This does not alter our adherence to all PLOS Computational Biology policies on sharing data and materials.

Methods Mol Biol. 2018;1757:251-305. (PMID: 29761462)
Nucleic Acids Res. 2018 Jan 4;46(D1):D1181-D1189. (PMID: 29165610)
Database (Oxford). 2015 May 13;2015:bav040. (PMID: 25972520)
PLoS One. 2010 May 20;5(5):e10708. (PMID: 20505755)
Plant Methods. 2015 Feb 25;11:10. (PMID: 25774204)
J Biomed Semantics. 2019 Jun 20;10(1):12. (PMID: 31221226)
Plant Physiol. 2005 Oct;139(2):643-51. (PMID: 16219925)
J Biomed Semantics. 2019 Jan 28;10(1):4. (PMID: 30691505)
Nucleic Acids Res. 2020 Jan 8;48(D1):D704-D715. (PMID: 31701156)
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8271-6. (PMID: 12060770)
Nucleic Acids Res. 1998 Jan 1;26(1):73-9. (PMID: 9399804)
Nucleic Acids Res. 2019 Jan 8;47(D1):D801-D806. (PMID: 30407599)
Genetics. 2016 Aug;203(4):1491-5. (PMID: 27516611)
Cell. 2012 Jul 20;150(2):389-401. (PMID: 22817898)
Annu Rev Biomed Data Sci. 2020 Jul;3:23-41. (PMID: 33954284)
Sci Transl Med. 2014 Sep 3;6(252):252ra123. (PMID: 25186178)
IET Syst Biol. 2008 Sep;2(5):369-82. (PMID: 19045832)
Cladistics. 2010 Jun;26(3):301-325. (PMID: 34875783)
Nucleic Acids Res. 2015 Jan;43(Database issue):D707-13. (PMID: 25510499)
PeerJ. 2015 Dec 14;3:e1470. (PMID: 26713234)
PLoS Biol. 2009 Nov;7(11):e1000247. (PMID: 19956802)
Trends Ecol Evol. 2012 Feb;27(2):78-84. (PMID: 22189359)
Curr Biol. 2009 Mar 10;19(5):R192-3. (PMID: 19278628)
Genome Biol. 2008;9(6):R102. (PMID: 18570664)
Nat Biotechnol. 2007 Nov;25(11):1251-5. (PMID: 17989687)
PLoS Curr. 2013 Jun 26;5:. (PMID: 23827969)
J Biomed Semantics. 2019 Jul 15;10(1):13. (PMID: 31307550)
PLoS One. 2014 Mar 03;9(3):e89606. (PMID: 24595056)
Bioinformatics. 1999 Jan;15(1):72-84. (PMID: 10068694)
Comp Funct Genomics. 2004;5(6-7):545-51. (PMID: 18629136)
Appl Plant Sci. 2019 Mar 07;7(3):e01231. (PMID: 30937223)
Nucleic Acids Res. 2020 Jan 8;48(D1):D927-D932. (PMID: 31566222)
Plant Physiol. 2005 Jul;138(3):1310-7. (PMID: 16010005)
Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6681-6. (PMID: 15090651)
J Biomed Semantics. 2014 Feb 25;5(1):12. (PMID: 24568621)
BMC Bioinformatics. 2016 Dec 13;17(1):528. (PMID: 27955641)
J Am Med Inform Assoc. 2020 Mar 1;27(3):457-470. (PMID: 31794016)
BMC Bioinformatics. 2014;15 Suppl 14:S4. (PMID: 25472428)
Biodivers Data J. 2014 Jan 17;(2):e1024. (PMID: 24855436)
PLoS One. 2010 May 05;5(5):e10500. (PMID: 20463926)
Nature. 2013 Mar 21;495(7441):305-7. (PMID: 23518546)
Database (Oxford). 2011 Nov 26;2011:bar051. (PMID: 22120662)
J Biomed Inform. 2018 Nov;87:12-20. (PMID: 30217670)
G3 (Bethesda). 2018 Dec 10;8(12):3813-3828. (PMID: 30291107)
Science. 2011 Feb 11;331(6018):703-5. (PMID: 21311007)
PLoS One. 2018 Nov 30;13(11):e0198270. (PMID: 30500839)
Trends Ecol Evol. 2007 Jul;22(7):345-50. (PMID: 17416439)
Trends Plant Sci. 2017 Nov;22(11):961-975. (PMID: 28965742)
Nucleic Acids Res. 2019 Jan 8;47(D1):D1146-D1154. (PMID: 30407532)
Nucleic Acids Res. 2017 Jan 4;45(D1):D865-D876. (PMID: 27899602)
J Biomed Semantics. 2013 Oct 18;4(1):30. (PMID: 24138933)
Comp Funct Genomics. 2002;3(2):137-42. (PMID: 18628842)
Am J Bot. 2017 Apr;104(4):505-508. (PMID: 28400413)
J Biomed Semantics. 2018 Jan 18;9(1):6. (PMID: 29347969)
Genome Biol. 2012 Jan 31;13(1):R5. (PMID: 22293552)
Nat Rev Microbiol. 2012 Feb 27;10(4):291-305. (PMID: 22367118)
PLoS Comput Biol. 2009 Mar;5(3):e1000312. (PMID: 19282977)
G3 (Bethesda). 2016 Sep 08;6(9):2725-44. (PMID: 27342738)
Nucleic Acids Res. 2018 Jan 4;46(D1):D1168-D1180. (PMID: 29186578)
Nucleic Acids Res. 2015 Jan;43(Database issue):D743-50. (PMID: 25355511)
Syst Biol. 2007 Dec;56(6):879-86. (PMID: 18027281)
Cladistics. 2017 Oct;33(5):513-539. (PMID: 34724752)
Nucleic Acids Res. 2016 Jan 4;44(D1):D834-9. (PMID: 26481361)
Front Plant Sci. 2018 May 01;9:517. (PMID: 29765382)
BMC Bioinformatics. 2009 May 06;10 Suppl 5:S2. (PMID: 19426459)
Nucleic Acids Res. 2003 Jan 1;31(1):224-8. (PMID: 12519987)
Mamm Genome. 2015 Oct;26(9-10):548-55. (PMID: 26092691)
Nat Ecol Evol. 2020 Mar;4(3):294-303. (PMID: 32066887)
Trends Plant Sci. 2011 Dec;16(12):635-44. (PMID: 22074787)
Nucleic Acids Res. 2011 Oct;39(18):e119. (PMID: 21737429)
Nucleic Acids Res. 2017 Jan 4;45(D1):D347-D352. (PMID: 27733503)
Mol Biol Evol. 2016 Jan;33(1):13-24. (PMID: 26500251)
J Biomed Semantics. 2017 Jun 5;8(1):18. (PMID: 28583177)
Biotechnol Bioeng. 1984 Sep;26(9):1140. (PMID: 18553544)
Nucleic Acids Res. 2018 Jan 4;46(D1):D869-D874. (PMID: 29069413)
Harmful Algae. 2015 Nov 1;49:68-93. (PMID: 27011761)
Nat Biotechnol. 2010 Mar;28(3):245-8. (PMID: 20212490)
PLoS One. 2012;7(1):e30004. (PMID: 22253856)
PLoS One. 2010 Dec 29;5(12):e15991. (PMID: 21209921)
Bioinformatics. 2007 Jul 1;23(13):i337-46. (PMID: 17646315)
PeerJ Prepr. 2018;4:e147. (PMID: 32704456)
PLoS Biol. 2015 Jan 06;13(1):e1002033. (PMID: 25562316)
Genome Biol. 2010 Jan 08;11(1):R2. (PMID: 20064205)
PLoS One. 2012;7(1):e29715. (PMID: 22238640)
Science. 2002 Mar 1;295(5560):1669-78. (PMID: 11872831)
Nucleic Acids Res. 2010 Jan;38(Database issue):D843-6. (PMID: 20008513)
PLoS One. 2019 Mar 27;14(3):e0213090. (PMID: 30917137)
J Forensic Sci. 2010 Mar 1;55(2):315-22. (PMID: 20158590)
Adv Bioinformatics. 2012;2012:391574. (PMID: 22685456)
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W170-3. (PMID: 19483092)
F1000Res. 2013 Feb 01;2:30. (PMID: 24358873)
Am J Hum Genet. 2015 Jul 2;97(1):111-24. (PMID: 26119816)

R24 OD011883 United States OD NIH HHS; RM1 HG010860 United States HG NHGRI NIH HHS; U13 CA221044 United States CA NCI NIH HHS; U2C ES026555 United States ES NIEHS NIH HHS

Date Created: 20201124 Date Completed: 20210128 Latest Revision: 20231104

20250114

PMC7685442

10.1371/journal.pcbi.1008376

33232313