publication . Article . Other literature type . 2016

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

Hoehndorf, Robert; Alshahrani, Mona; Gkoutos, Georgios V.; Gosline, George; Groom, Quentin; Hamann, Thomas; Kattge, Jens; de Oliveira, Sylvia Mota; Schmidt, Marco; Sierra, Soraya; ...
Open Access
  • Published: 14 Nov 2016 Journal: Journal of Biomedical Semantics, volume 7 (eissn: 2041-1480, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
Background The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, tra...
Subjects
free text keywords: Phenotype ; Flora ; Botany ; Morphological traits ; Biodiversity, Ecology, Ecosystem, Phenotype ontology, Phylogenetics, Biodiversity, Phenotype, Plant species, Biological Ontologies, Biology, Plant traits, Flora, Botany, Morphological traits, Research, ddc:580
Funded by
EC| PRO-IBIOSPHERE
Project
PRO-IBIOSPHERE
Coordination and policy development in preparation for a European Open Biodiversity Knowledge Management System, addressing Acquisition, Curation, Synthesis, Interoperability and Dissemination
  • Funder: European Commission (EC)
  • Project Code: 312848
  • Funding stream: FP7 | SP4 | INFRA
,
NSF| cROP: Common Reference Ontologies and Applications for Plant Biology
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1340112
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
,
EC| EPPN
Project
EPPN
European Plant Phenotyping Network
  • Funder: European Commission (EC)
  • Project Code: 284443
  • Funding stream: FP7 | SP4 | INFRA
52 references, page 1 of 4

Frodin, DG. Guide to Standard Floras of the World: An Annotated, Geographically Arranged Systematic Bibliography of the Principal Floras, Enumerations, Checklists and Chorological Atlases of Different Areas. 2001

2 Gruber TR. Toward principles for the design of ontologies used for knowledge sharing. Int J Human-Computer Stud. 1995; 43:5–6. doi:http://dx.doi.org/10.1006/ijhc.1995.1081.

Guarino, N, Guarino, N. Formal ontology and information systems. Proceedings of the 1st International Conference on Formal Ontologies in Information Systems. 1998

4 Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW. Ontologies as integrative tools for plant science. Am J Botany. 2012; 99(8):1263–1275. doi:http://dx.doi.org/10.3732/ajb.1200222.

5 Gkoutos GV, Green EC, Mallon AMM, Hancock JM, Davidson D. Using ontologies to describe mouse phenotypes. Genome Biol. 2005; 6(1):5. doi:http://dx.doi.org/10.1186/gb-2004-6-1-r8.

6 Hoehndorf R, Oellrich A, Rebholz-Schuhmann D. Interoperability between phenotype and anatomy ontologies. Bioinformatics; 26(24):3112–118.

Grau, B, Horrocks, I, Motik, B, Parsia, B, Patelschneider, P, Sattler, U. OWL 2: The next step for OWL. Web Semant Sci Serv Agents World Wide Web. 2008; 6 (4): 309-22 [DOI]

8 Kattge J, Diaz S, Lavorel S, Prentice C, Leadley P, Boenisch G, Garnier E, Westoby M, Reich PB, Wright IJ, Cornelissen JHC, Violle C, Harrison SP, van Bodegom PM, Reichstein M, Enquist BJ, Soudzilovskaia NA, Ackerly DD, Anand M, Atkin O, Bahn M, Baker TR, Baldocchi D, Bekker R, Blanco CC, Blonder B, Bond WJ, Bradstock R, Bunker DE, Casanoves F, Cavender-Bares J, Chambers JQ, Chapin IFS, Chave J, Coomes D, Cornwell WK, Craine JM, Dobrin BH, Duarte L, Durka W, Elser J, Esser G, Estiarte M, Fagan WF, Fang J, Fernandez-Mendez F, Fidelis A, Finegan B, Flores O, Ford H, Frank D, Freschet GT, Fyllas NM, Gallagher RV, Green WA, Gutierrez AG, Hickler T, Higgins SI, Hodgson JG, Jalili A, Jansen S, Joly CA, Kerkhoff AJ, Kirkup D, Kitajima K, Kleyer M, Klotz S, Knops JMH, Kramer K, Kuehn I, Kurokawa H, Laughlin D, Lee TD, Leishman M, Lens F, Lenz T, Lewis SL, Lloyd J, Llusia J, Louault F, Ma S, Mahecha MD, Manning P, Massad T, Medlyn BE, Messier J, Moles AT, Mueller SC, Nadrowski K, Naeem S, Niinemets U, Noellert S, Nueske A, Ogaya R, Oleksyn J, Onipchenko VG, Onoda Y, Ordonez J, Overbeck G, Ozinga WA, et al. Try - a global database of plant traits. Glob Chang Biol. 2011; 17(9):2905–935. doi:http://dx.doi.org/10.1111/j.1365-2486.2011.02451.x.

9 Parr CS, Wilson N, Leary P, Schulz K, Lans K, Walley L, Hammock J, Goddard A, Rice J, Studer M, Holmes J, Robert Corrigan J. The encyclopedia of life v2: Providing global access to knowledge about life on earth. Biodivers Data J. 2014; 2:1079. doi:http://dx.doi.org/10.3897/BDJ.2.e1079.

10 Vos R, Biserkov J, Balech B, Beard N, Blissett M, Brenninkmeijer C, van Dooren T, Eades D, Gosline G, Groom Q, Hamann T, Hettling H, Hoehndorf R, Holleman A, Hovenkamp P, Kelbert P, King D, Kirkup D, Lammers Y, DeMeulemeester T, Mietchen D, Miller J, Mounce R, Nicolson N, Page R, Pawlik A, Pereira S, Penev L, Richards K, Sautter G, Shorthouse D, Tähtinen M, Weiland C, Williams A, Sierra S. Enriched biodiversity data as a resource and service. Biodivers Data J. 2014; 2:1125. doi:http://dx.doi.org/10.3897/BDJ.2.e1125.

11 Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen Y-a, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$\check {s}$\end{document}š M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packe r NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. Biohackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semant. 2014; 5(1):1–13.

12 van Steenis CGGJ, van Steenis-Kruseman MJ. Flora Malesiana. General Editor, C.G.G.J. van Steenis. Washington: Smithsonian Institution. (1950–2011). doi:http://dx.doi.org/10.5962/bhl.title.40744.

13 Aubréville A. Flore du Gabon, Vols 1-37. Flore du Gabon. Paris: Muséum National d’Histoire Naturelle. (1961–2004).

14 Sosef MSM, Florence J, Banakd LN, Bourobou HPB. Flore du Gabon, Vols 38-45. Flore du Gabon. Weikersheim: Margraf Publishers. (2009–2013).

15 Bamps P, Robyns W, van België NP. Flore d’Afrique Centrale (Zaïre-Rwanda-Burundi). Flore d’Afrique Centrale (Zaïre-Rwanda-Burundi). Meise: Jardin Botanique National de Belgique; 1948. http://www.br.fgov.be/RESEARCH/DATABASES/FOCA/index.php. Accessed 6 Nov 2016.

52 references, page 1 of 4
Abstract
Background The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, tra...
Subjects
free text keywords: Phenotype ; Flora ; Botany ; Morphological traits ; Biodiversity, Ecology, Ecosystem, Phenotype ontology, Phylogenetics, Biodiversity, Phenotype, Plant species, Biological Ontologies, Biology, Plant traits, Flora, Botany, Morphological traits, Research, ddc:580
Funded by
EC| PRO-IBIOSPHERE
Project
PRO-IBIOSPHERE
Coordination and policy development in preparation for a European Open Biodiversity Knowledge Management System, addressing Acquisition, Curation, Synthesis, Interoperability and Dissemination
  • Funder: European Commission (EC)
  • Project Code: 312848
  • Funding stream: FP7 | SP4 | INFRA
,
NSF| cROP: Common Reference Ontologies and Applications for Plant Biology
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1340112
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
,
EC| EPPN
Project
EPPN
European Plant Phenotyping Network
  • Funder: European Commission (EC)
  • Project Code: 284443
  • Funding stream: FP7 | SP4 | INFRA
52 references, page 1 of 4

Frodin, DG. Guide to Standard Floras of the World: An Annotated, Geographically Arranged Systematic Bibliography of the Principal Floras, Enumerations, Checklists and Chorological Atlases of Different Areas. 2001

2 Gruber TR. Toward principles for the design of ontologies used for knowledge sharing. Int J Human-Computer Stud. 1995; 43:5–6. doi:http://dx.doi.org/10.1006/ijhc.1995.1081.

Guarino, N, Guarino, N. Formal ontology and information systems. Proceedings of the 1st International Conference on Formal Ontologies in Information Systems. 1998

4 Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW. Ontologies as integrative tools for plant science. Am J Botany. 2012; 99(8):1263–1275. doi:http://dx.doi.org/10.3732/ajb.1200222.

5 Gkoutos GV, Green EC, Mallon AMM, Hancock JM, Davidson D. Using ontologies to describe mouse phenotypes. Genome Biol. 2005; 6(1):5. doi:http://dx.doi.org/10.1186/gb-2004-6-1-r8.

6 Hoehndorf R, Oellrich A, Rebholz-Schuhmann D. Interoperability between phenotype and anatomy ontologies. Bioinformatics; 26(24):3112–118.

Grau, B, Horrocks, I, Motik, B, Parsia, B, Patelschneider, P, Sattler, U. OWL 2: The next step for OWL. Web Semant Sci Serv Agents World Wide Web. 2008; 6 (4): 309-22 [DOI]

8 Kattge J, Diaz S, Lavorel S, Prentice C, Leadley P, Boenisch G, Garnier E, Westoby M, Reich PB, Wright IJ, Cornelissen JHC, Violle C, Harrison SP, van Bodegom PM, Reichstein M, Enquist BJ, Soudzilovskaia NA, Ackerly DD, Anand M, Atkin O, Bahn M, Baker TR, Baldocchi D, Bekker R, Blanco CC, Blonder B, Bond WJ, Bradstock R, Bunker DE, Casanoves F, Cavender-Bares J, Chambers JQ, Chapin IFS, Chave J, Coomes D, Cornwell WK, Craine JM, Dobrin BH, Duarte L, Durka W, Elser J, Esser G, Estiarte M, Fagan WF, Fang J, Fernandez-Mendez F, Fidelis A, Finegan B, Flores O, Ford H, Frank D, Freschet GT, Fyllas NM, Gallagher RV, Green WA, Gutierrez AG, Hickler T, Higgins SI, Hodgson JG, Jalili A, Jansen S, Joly CA, Kerkhoff AJ, Kirkup D, Kitajima K, Kleyer M, Klotz S, Knops JMH, Kramer K, Kuehn I, Kurokawa H, Laughlin D, Lee TD, Leishman M, Lens F, Lenz T, Lewis SL, Lloyd J, Llusia J, Louault F, Ma S, Mahecha MD, Manning P, Massad T, Medlyn BE, Messier J, Moles AT, Mueller SC, Nadrowski K, Naeem S, Niinemets U, Noellert S, Nueske A, Ogaya R, Oleksyn J, Onipchenko VG, Onoda Y, Ordonez J, Overbeck G, Ozinga WA, et al. Try - a global database of plant traits. Glob Chang Biol. 2011; 17(9):2905–935. doi:http://dx.doi.org/10.1111/j.1365-2486.2011.02451.x.

9 Parr CS, Wilson N, Leary P, Schulz K, Lans K, Walley L, Hammock J, Goddard A, Rice J, Studer M, Holmes J, Robert Corrigan J. The encyclopedia of life v2: Providing global access to knowledge about life on earth. Biodivers Data J. 2014; 2:1079. doi:http://dx.doi.org/10.3897/BDJ.2.e1079.

10 Vos R, Biserkov J, Balech B, Beard N, Blissett M, Brenninkmeijer C, van Dooren T, Eades D, Gosline G, Groom Q, Hamann T, Hettling H, Hoehndorf R, Holleman A, Hovenkamp P, Kelbert P, King D, Kirkup D, Lammers Y, DeMeulemeester T, Mietchen D, Miller J, Mounce R, Nicolson N, Page R, Pawlik A, Pereira S, Penev L, Richards K, Sautter G, Shorthouse D, Tähtinen M, Weiland C, Williams A, Sierra S. Enriched biodiversity data as a resource and service. Biodivers Data J. 2014; 2:1125. doi:http://dx.doi.org/10.3897/BDJ.2.e1125.

11 Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen Y-a, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$\check {s}$\end{document}š M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packe r NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. Biohackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semant. 2014; 5(1):1–13.

12 van Steenis CGGJ, van Steenis-Kruseman MJ. Flora Malesiana. General Editor, C.G.G.J. van Steenis. Washington: Smithsonian Institution. (1950–2011). doi:http://dx.doi.org/10.5962/bhl.title.40744.

13 Aubréville A. Flore du Gabon, Vols 1-37. Flore du Gabon. Paris: Muséum National d’Histoire Naturelle. (1961–2004).

14 Sosef MSM, Florence J, Banakd LN, Bourobou HPB. Flore du Gabon, Vols 38-45. Flore du Gabon. Weikersheim: Margraf Publishers. (2009–2013).

15 Bamps P, Robyns W, van België NP. Flore d’Afrique Centrale (Zaïre-Rwanda-Burundi). Flore d’Afrique Centrale (Zaïre-Rwanda-Burundi). Meise: Jardin Botanique National de Belgique; 1948. http://www.br.fgov.be/RESEARCH/DATABASES/FOCA/index.php. Accessed 6 Nov 2016.

52 references, page 1 of 4
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publication . Article . Other literature type . 2016

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

Hoehndorf, Robert; Alshahrani, Mona; Gkoutos, Georgios V.; Gosline, George; Groom, Quentin; Hamann, Thomas; Kattge, Jens; de Oliveira, Sylvia Mota; Schmidt, Marco; Sierra, Soraya; ...