메뉴 건너뛰기




Volumn 1374, Issue , 2016, Pages 89-114

The plant ontology: A tool for plant genomics

(2)  Cooper, Laurel a   Jaiswal, Pankaj a  

a NONE

Author keywords

Bioinformatics; Comparative genomic s; Genome annotation; Ontology; Phenomics; Plant anatomy; Plant development; Semantic web; Transcriptomics

Indexed keywords

ANGIOSPERM; ARABIDOPSIS; BIOINFORMATICS; DEVELOPMENTAL STAGE; GENE ONTOLOGY; GENETIC DATABASE; GREEN ALGA; MAIZE; NONHUMAN; PLANT DEVELOPMENT; PLANT GENETICS; PLANT GROWTH; PLANT STRUCTURES; RICE; TRANSCRIPTOMICS; VIRIDIPLANTAE; ANATOMY AND HISTOLOGY; BIOLOGICAL ONTOLOGY; BIOLOGY; GENOMICS; PLANT; PLANT PHYSIOLOGY; PROCEDURES; WEB BROWSER;

EID: 84946038084     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3167-5_5     Document Type: Chapter
Times cited : (43)

References (56)
  • 1
    • 84883757684 scopus 로고    scopus 로고
    • The first 50 plant genomes
    • Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome 6:1–7. doi: 10.3835/plantgenome2013.03.0001in
    • (2013) Plant Genome , vol.6 , pp. 1-7
    • Michael, T.P.1    Jackson, S.2
  • 2
    • 84901250709 scopus 로고    scopus 로고
    • De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum
    • Fox SE, Geniza M, Hanumappa M et al (2014) De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS One 9:e96855. doi: 10.1371/journal.pone.0096855
    • (2014) Plos One , vol.9
    • Fox, S.E.1    Geniza, M.2    Hanumappa, M.3
  • 3
    • 84946091030 scopus 로고    scopus 로고
    • Fox SE, Preece J, Kimbrel JA et al (2013) Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). Appl Plant Sci 1:1200011. doi: 10.3732/apps.1200011
    • Fox, S.E.1    Preece, J.2    Kimbrel, J.A.3
  • 4
    • 84897946907 scopus 로고    scopus 로고
    • Transcriptome sequencing and profiling of expressed genes in cambial zone and differentiating xylem of Japanese cedar (Cryptomeria japonica)
    • Mishima K, Fujiwara T, Iki T et al (2014) Transcriptome sequencing and profiling of expressed genes in cambial zone and differentiating xylem of Japanese cedar (Cryptomeria japonica). BMC Genomics 15:219
    • (2014) BMC Genomics , vol.15 , pp. 219
    • Mishima, K.1    Fujiwara, T.2    Iki, T.3
  • 6
    • 84905481571 scopus 로고    scopus 로고
    • De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism
    • Ranjan A, Ichihashi Y, Farhi M et al (2014) De novo assembly and characterization of the transcriptome of the parasitic weed Cuscuta pentagona identifies genes associated with plant parasitism. Plant Physiol 166:1186. doi: 10.1104/pp. 113.234864
    • (2014) Plant Physiol , vol.166 , pp. 1186
    • Ranjan, A.1    Ichihashi, Y.2    Farhi, M.3
  • 7
    • 84897428547 scopus 로고    scopus 로고
    • An integrative analysis of the transcriptome and proteome of the pulp of a spontaneous late-ripening sweet orange mutant and its wild type improves our understanding of fruit ripening in citrus
    • Wu J, Xu Z, Zhang Y et al (2014) An integrative analysis of the transcriptome and proteome of the pulp of a spontaneous late-ripening sweet orange mutant and its wild type improves our understanding of fruit ripening in citrus. J Exp Bot 65:1651–1671. doi: 10.1093/jxb/eru044
    • (2014) J Exp Bot , vol.65 , pp. 1651-1671
    • Wu, J.1    Xu, Z.2    Zhang, Y.3
  • 8
    • 0034649566 scopus 로고    scopus 로고
    • Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
    • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815. doi: 10.1038/35048692
    • (2000) Nature , vol.408 , pp. 796-815
  • 9
    • 84903203459 scopus 로고    scopus 로고
    • The genome of Eucalyptus grandis
    • Myburg AA, Grattapaglia D, Tuskan GA et al (2014) The genome of Eucalyptus grandis. Nature 510:356. doi: 10.1038/nature13308
    • (2014) Nature , vol.510 , pp. 356
    • Myburg, A.A.1    Grattapaglia, D.2    Tuskan, G.A.3
  • 10
    • 84878420758 scopus 로고    scopus 로고
    • The Norway spruce genome sequence and conifer genome evolution
    • Nystedt B, Street NR, Wetterbom A et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497: 579–584
    • (2013) Nature , vol.497 , pp. 579-584
    • Nystedt, B.1    Street, N.R.2    Wetterbom, A.3
  • 11
    • 84903517143 scopus 로고    scopus 로고
    • A reference genome for common bean and genome-wide analysis of dual domestications
    • Schmutz J, McClean PE, Mamidi S et al (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 46:707
    • (2014) Nat Genet , vol.46 , pp. 707
    • Schmutz, J.1    McClean, P.E.2    Mamidi, S.3
  • 12
    • 84863393183 scopus 로고    scopus 로고
    • Toward interoperable bioscience data
    • Sansone S-A, Rocca-Serra P, Field D et al (2012) Toward interoperable bioscience data. Nat Genet 44:121–126. doi: 10.1038/ng.1054
    • (2012) Nat Genet , vol.44 , pp. 121-126
    • Sansone, S.-A.1    Rocca-Serra, P.2    Field, D.3
  • 13
    • 84893152857 scopus 로고    scopus 로고
    • Toward more transparent and reproducible omics studies through a common metadata checklist and data publications
    • Kolker E, Özdemir V, Martens L et al (2014) Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS J Integr Biol 18:10–14. doi: 10.1089/omi.2013.0149
    • (2014) OMICS J Integr Biol , vol.18 , pp. 10-14
    • Kolker, E.1    Özdemir, V.2    Martens, L.3
  • 14
    • 84893011962 scopus 로고    scopus 로고
    • Data management strategies for multinational large-scale systems biology projects
    • Wruck W, Peuker M, Regenbrecht CRA (2014) Data management strategies for multinational large-scale systems biology projects. Brief Bioinform 15:65–78. doi: 10.1093/bib/bbs064
    • (2014) Brief Bioinform , vol.15 , pp. 65-78
    • Wruck, W.1    Peuker, M.2    Regenbrecht, C.3
  • 15
    • 45749118607 scopus 로고    scopus 로고
    • Promoting coherent minimum reporting guidelines for biological and biomedical investigations: The MIBBI project
    • Taylor CF, Field D, Sansone S-A et al (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 26:889–896. doi: 10.1038/nbt0808-889
    • (2008) Nat Biotechnol , vol.26 , pp. 889-896
    • Taylor, C.F.1    Field, D.2    Sansone, S.-A.3
  • 16
    • 77956548952 scopus 로고    scopus 로고
    • ISA software suite: Supporting standards- compliant experimental annotation and enabling curation at the community level
    • Rocca-Serra P, Brandizi M, Maguire E et al (2010) ISA software suite: supporting standards- compliant experimental annotation and enabling curation at the community level. Bioinformatics 26:2354–2356. doi: 10.1093/bioinformatics/btq415
    • (2010) Bioinformatics , vol.26 , pp. 2354-2356
    • Rocca-Serra, P.1    Brandizi, M.2    Maguire, E.3
  • 17
    • 84895852223 scopus 로고    scopus 로고
    • Advances in genome studies in plants and animals - Springer
    • Appels R, Nystrom-Persson J, Keeble-Gagnere G (2014) Advances in genome studies in plants and animals - Springer. Funct Integr Genomics 14:1–9. doi: 10.1007/s10142-014-0364-5
    • (2014) Funct Integr Genomics , vol.14 , pp. 1-9
    • Appels, R.1    Nystrom-Persson, J.2    Keeble-Gagnere, G.3
  • 18
    • 84864996772 scopus 로고    scopus 로고
    • What is an ontology? Ontogenesis 19. Walls RL, Athreya B, Cooper L et al (2012) Ontologies as integrative tools for plant science
    • Stevens R, Rector A, Hull D (2010) What is an ontology? Ontogenesis 19. Walls RL, Athreya B, Cooper L et al (2012) Ontologies as integrative tools for plant science. Am J Bot 99:1263–1275. doi: 10.3732/ajb.1200222
    • (2010) Am J Bot , vol.99 , pp. 1263-1275
    • Stevens, R.1    Rector, A.2    Hull, D.3
  • 19
    • 84874265271 scopus 로고    scopus 로고
    • The Plant Ontology as a tool for comparative plant anatomy and genomic analyses
    • Cooper L, Walls RL, Elser J et al (2013) The Plant Ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol 54:e1. doi: 10.1093/pcp/pcs163
    • (2013) Plant Cell Physiol , pp. 54
    • Cooper, L.1    Walls, R.L.2    Elser, J.3
  • 20
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29. doi: 10.1038/75556
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 21
    • 84874253819 scopus 로고    scopus 로고
    • Gene ontology annotations and resources
    • The Gene Ontology Consortium (2013) Gene ontology annotations and resources. Nucleic Acids Res 41:D530–D535. doi: 10.1093/nar/gks1050
    • (2013) Nucleic Acids Res , vol.41 , pp. D530-D535
  • 23
    • 84862234802 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools
    • Lamesch P, Berardini TZ, Li D et al (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:1202–1210. doi: 10.1093/nar/gkr1090
    • (2012) Nucleic Acids Res , vol.40 , pp. 1202-1210
    • Lamesch, P.1    Berardini, T.Z.2    Li, D.3
  • 24
    • 84891793130 scopus 로고    scopus 로고
    • Gramene 2013: Comparative plant genomics resources
    • Monaco MK, Stein J, Naithani S et al (2014) Gramene 2013: comparative plant genomics resources. Nucleic Acids Res 42:1193–1199. doi: 10.1093/nar/gkt1110
    • (2014) Nucleic Acids Res , vol.42 , pp. 1193-1199
    • Monaco, M.K.1    Stein, J.2    Naithani, S.3
  • 25
    • 84891822189 scopus 로고    scopus 로고
    • Ensembl Genomes 2013: Scaling up access to genome-wide data
    • Kersey PJ, Allen JE, Christensen M et al (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res 42:546–552. doi: 10.1093/nar/gkt979
    • (2014) Nucleic Acids Res , vol.42 , pp. 546-552
    • Kersey, P.J.1    Allen, J.E.2    Christensen, M.3
  • 26
    • 84899103272 scopus 로고    scopus 로고
    • Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
    • R59
    • Neale DB, Wegrzyn JL, Stevens KA et al (2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 15:R59. doi: 10.1186/gb-2014-15-3-r59
    • (2014) Genome Biol , vol.15
    • Neale, D.B.1    Wegrzyn, J.L.2    Stevens, K.A.3
  • 27
    • 79251636555 scopus 로고    scopus 로고
    • The genome of woodland strawberry (Fragaria vesca)
    • Shulaev V, Sargent DJ, Crowhurst RN et al (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–116. doi: 10.1038/ng.740
    • (2011) Nat Genet , vol.43 , pp. 109-116
    • Shulaev, V.1    Sargent, D.J.2    Crowhurst, R.N.3
  • 28
    • 84898058782 scopus 로고    scopus 로고
    • Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
    • Varshney RK, Mir RR, Bhatia S et al (2014) Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Funct Integr Genomics 14:59–73. doi: 10.1007/s10142-014-0363-6
    • (2014) Funct Integr Genomics , vol.14 , pp. 59-73
    • Varshney, R.K.1    Mir, R.R.2    Bhatia, S.3
  • 29
    • 84873454463 scopus 로고    scopus 로고
    • Assembly and characterization of the European Hazelnut “Jefferson” transcriptome
    • Rowley ER, Fox SE, Bryant DW et al (2012) Assembly and characterization of the European Hazelnut “Jefferson” transcriptome. Crop Sci 52:2679. doi: 10.2135/cropsci2012.02.0065
    • (2012) Crop Sci , vol.52 , pp. 2679
    • Rowley, E.R.1    Fox, S.E.2    Bryant, D.W.3
  • 31
    • 84867036879 scopus 로고    scopus 로고
    • Transcriptome sequencing and de novo analysis for ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform
    • Liu M, Qiao G, Jiang J et al (2012) Transcriptome sequencing and de novo analysis for ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform. PLoS One 7:e46766. doi: 10.1371/journal.pone.0046766
    • (2012) Plos One , vol.7
    • Liu, M.1    Qiao, G.2    Jiang, J.3
  • 32
    • 19044393068 scopus 로고    scopus 로고
    • TAIR: A resource for integrated Arabidopsis data
    • Garcia-Hernandez M, Berardini TZ, Chen G et al (2002) TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics 2:239–253. doi: 10.1007/s10142-002-0077-z
    • (2002) Funct Integr Genomics , vol.2 , pp. 239-253
    • Garcia-Hernandez, M.1    Berardini, T.Z.2    Chen, G.3
  • 33
    • 0345358538 scopus 로고    scopus 로고
    • Polacco ML (2003) Zea mays ontology - a database of international terms
    • Vincent L, Coe EH, Polacco ML (2003) Zea mays ontology - a database of international terms. Trends Plant Sci 8:517–520. doi: 10.1016/j.tplants.2003.09.014
    • Trends Plant Sci , vol.8 , pp. 517-520
    • Vincent, L.1    Coe, E.H.2
  • 34
    • 0036092171 scopus 로고    scopus 로고
    • Gramene: Development and integration of trait and gene ontologies for rice
    • Jaiswal P, Ware D, Ni J et al (2002) Gramene: development and integration of trait and gene ontologies for rice. Comp Funct Genom 3:132–136
    • (2002) Comp Funct Genom , vol.3 , pp. 132-136
    • Jaiswal, P.1    Ware, D.2    Ni, J.3
  • 35
    • 33644751190 scopus 로고    scopus 로고
    • Plant Ontology (PO): A controlled vocabulary of plant structures and growth stages
    • Jaiswal P, Avraham S, Ilic K et al (2005) Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp Funct Genom 6:388–397
    • (2005) Comp Funct Genom , vol.6 , pp. 388-397
    • Jaiswal, P.1    Avraham, S.2    Ilic, K.3
  • 36
    • 34247192074 scopus 로고    scopus 로고
    • The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
    • Ilic K, Kellogg EA, Jaiswal P et al (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol 143:587–599. doi: 10.1104/pp. 106.092825
    • (2007) Plant Physiol , vol.143 , pp. 587-599
    • Ilic, K.1    Kellogg, E.A.2    Jaiswal, P.3
  • 37
    • 33750079855 scopus 로고    scopus 로고
    • Whole-plant growth stage ontology for Angiosperms and its application in plant biology
    • Pujar A, Jaiswal P, Kellogg EA et al (2006) Whole-plant growth stage ontology for Angiosperms and its application in plant biology. Plant Physiol 142:414–428. doi: 10.1104/pp. 106.085720
    • (2006) Plant Physiol , vol.142 , pp. 414-428
    • Pujar, A.1    Jaiswal, P.2    Kellogg, E.A.3
  • 38
    • 63349106239 scopus 로고    scopus 로고
    • The foundational model of anatomy ontology
    • In: Burger A, Davidson D, Baldock R, Springer, New York, NY
    • Rosse C, Mejino JLV (2007) The foundational model of anatomy ontology. In: Burger A, Davidson D, Baldock R (eds) Anatomy ontologies for bioinformatics: principles and practice. Springer, New York, NY, pp 59–117
    • (2007) Anatomy Ontologies for Bioinformatics: Principles and Practice , pp. 59-117
    • Rosse, C.1    Mejino, J.2
  • 40
    • 84883257856 scopus 로고    scopus 로고
    • Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens
    • O’Donoghue M-T, Chater C, Wallace S et al (2013) Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens. J Exp Bot 64:3567–3581. doi: 10.1093/jxb/ert190
    • (2013) J Exp Bot , vol.64 , pp. 3567-3581
    • O’Donoghue, M.-T.1    Chater, C.2    Wallace, S.3
  • 41
  • 42
    • 35948989284 scopus 로고    scopus 로고
    • The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration
    • Smith B, Ashburner M, Rosse C et al (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25:1251–1255. doi: 10.1038/nbt1346
    • (2007) Nat Biotechnol , vol.25 , pp. 1251-1255
    • Smith, B.1    Ashburner, M.2    Rosse, C.3
  • 43
    • 0842283371 scopus 로고    scopus 로고
    • A reference ontology for biomedical informatics: The foundational model of anatomy
    • Rosse C, Mejino JLV Jr (2003) A reference ontology for biomedical informatics: the foundational model of anatomy. J Biomed Inform 36:478–500. doi: 10.1016/j.jbi.2003.11.007
    • (2003) J Biomed Inform , vol.36 , pp. 478-500
    • Rosse, C.1    Mejino, J.2
  • 44
    • 78650789238 scopus 로고    scopus 로고
    • Logical development of the cell ontology
    • Meehan T, Masci A, Abdulla A et al (2011) Logical development of the cell ontology. BMC Bioinform 12:6
    • (2011) BMC Bioinform , vol.12 , pp. 6
    • Meehan, T.1    Masci, A.2    Abdulla, A.3
  • 45
    • 79952016835 scopus 로고    scopus 로고
    • Cross-product extensions of the gene ontology
    • Mungall CJ, Bada M, Berardini TZ et al (2011) Cross-product extensions of the gene ontology. J Biomed Inform 44:80–86. doi: 10.1016/j.jbi.2010.02.002
    • (2011) J Biomed Inform , vol.44 , pp. 80-86
    • Mungall, C.J.1    Bada, M.2    Berardini, T.Z.3
  • 46
    • 84889036107 scopus 로고    scopus 로고
    • Comparison of reasoners for large ontologies in the OWL 2 EL profile
    • Dentler K, Cornet R, ten Teije A, de Keizer N (2011) Comparison of reasoners for large ontologies in the OWL 2 EL profile. Semant Web 2:71–87. doi: 10.3233/SW-2011-0034
    • (2011) Semant Web , vol.2 , pp. 71-87
    • Dentler, K.1    Cornet, R.2    Ten Teije, A.3    De Keizer, N.4
  • 48
    • 34548595489 scopus 로고    scopus 로고
    • OBO-Edit an ontology editor for biologists
    • Day-Richter J, Harris MA, Haendel M et al (2007) OBO-Edit an ontology editor for biologists. Bioinformatics 23:2198–2200. doi: 10.1093/bioinformatics/btm112
    • (2007) Bioinformatics , vol.23 , pp. 2198-2200
    • Day-Richter, J.1    Harris, M.A.2    Haendel, M.3
  • 49
    • 84908330794 scopus 로고    scopus 로고
    • Mapping between the OBO and OWL ontology languages
    • Tirmizi S, Aitken S, Moreira D et al (2011) Mapping between the OBO and OWL ontology languages. J Biomed Semant 2:S3
    • (2011) J Biomed Semant , vol.2 , pp. 3
    • Tirmizi, S.1    Aitken, S.2    Moreira, D.3
  • 51
    • 84858339176 scopus 로고    scopus 로고
    • The OWL API: A Java API for OWL ontologies
    • Horridge M, Bechhofer S (2011) The OWL API: a Java API for OWL ontologies. Semant Web 2:11–21. doi: 10.3233/SW-2011-0025
    • (2011) Semant Web , vol.2 , pp. 11-21
    • Horridge, M.1    Bechhofer, S.2
  • 52
    • 84906213269 scopus 로고    scopus 로고
    • WebProtégé: A collaborative web based platform for editing biomedical ontologies
    • Horridge M, Tudorache T, Nuylas C et al (2014) WebProtégé: a collaborative web based platform for editing biomedical ontologies. Bioinformatics 30:2384. doi: 10.1093/bioinformatics/btu256
    • (2014) Bioinformatics , vol.30 , pp. 2384
    • Horridge, M.1    Tudorache, T.2    Nuylas, C.3
  • 53
    • 58349111875 scopus 로고    scopus 로고
    • AmiGO: Online access to ontology and annotation data
    • Carbon S, Ireland A, Mungall CJ et al (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289. doi: 10.1093/bioinformatics/btn615
    • (2009) Bioinformatics , vol.25 , pp. 288-289
    • Carbon, S.1    Ireland, A.2    Mungall, C.J.3
  • 55
    • 20844433631 scopus 로고    scopus 로고
    • Using ontologies to describe mouse phenotypes
    • Gkoutos G, Green E, Mallon A-M et al (2004) Using ontologies to describe mouse phenotypes. Genome Biol 6:8
    • (2004) Genome Biol , vol.6 , pp. 8
    • Gkoutos, G.1    Green, E.2    Mallon, A.-M.3
  • 56
    • 84978127960 scopus 로고    scopus 로고
    • The environment ontology: Contextualizing biological and biomedical entities
    • Buttigieg PL, Morrison N, Smith B et al (2013) The environment ontology: contextualizing biological and biomedical entities. J Biomed Semant 4:43
    • (2013) J Biomed Semant , vol.4 , pp. 43
    • Buttigieg, P.L.1    Morrison, N.2    Smith, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.