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TrOn: Tribolium Ontology

One part of the iBeetle project is the creation of an anatomical ontology for Tribolium. The annotation of the ontology is an ongoing process. The current version can be browsed and downloaded below.

Ontology tree

The tree below displays the class hierarchy of the ontology. Next to the tree additional information for the selected term is displayed.

Tribolium Ontology
  • anatomical_entity
    • material_anatomical_entity
      • anatomical structure
        • multicellular_structure
          • organism
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Details
ID: TrOn_0000027
Name: pupa
Definition: "The pupa is the name given to the organism at the period of the life cycle that begins once larval/pupal apolysis is complete, as indicated by the expulsion of the larval armature. \nDuring the pupal stage the attachment of muscles is modified, and the adult structures are formed." [FlyBase:FBrf0036849, FlyBase:FBrf0048355, ISBN:0-19-857353-7]
Parent(s):
Relations:
    Links to iB details pages

    Links to iB detail views

    Number of links of the selected node and all descending ones

    The printed number is the amount of iBeetle data sets, which are linked to the current node and the downstream ones. For the downstream search the class hierarchy as well as the part_of relation ship is used. The later one is not displayed in the tree on the left, so that not all involved nodes can be seen directly in the ontology tree. For the caluclation of the number the same nodes are taken into account as in the algorithm for the "Search for morphological defects" (without developmental stage or any other selections made)
    For example the descending nodes for adult_leg are:

    • adult_coxa
    • adult_cuticle_of_mesothoracic_leg
    • adult_femur
    • adult_leg
    • adult_mesothoracic_coxa
    • adult_mesothoracic_femur
    • adult_mesothoracic_tarsomere
    • adult_mesothoracic_tarsus
    • adult_metathoracic_femur
    • adult_metathoracic_leg
    • adult_metathoracic_pretarsus
    • adult_metathoracic_tarsus
    • adult_metathoracic_tibia
    • adult_pretarsus
    • adult_prothoracic_leg
    • adult_prothoracic_tarsomere
    • adult_prothoracic_tarsus
    • adult_tarsomere
    • adult_tarsus
    • adult_tibia

    The list of hyperlinks belong all to the selected node.

    897 detail pages are linked to the selected node and descending ones. (following the is_a and part_of relations).

    List of datasets linked directly to the selected ontology class:
    iB_00002iB_00004iB_00007iB_00008iB_00010
    iB_00014iB_00015iB_00018iB_00022iB_00023
    iB_00024iB_00025iB_00032iB_00035iB_00037
    iB_00041iB_00044iB_00066iB_00072iB_00074
    iB_00075iB_00078iB_00088iB_00090iB_00094
    iB_00100iB_00101iB_00101iB_00102iB_00103
    iB_00104iB_00107iB_00110iB_00113iB_00114
    iB_00115iB_00116iB_00117iB_00119iB_00120
    iB_00121iB_00123iB_00124iB_00125iB_00126
    iB_00128iB_00129iB_00130iB_00131iB_00132
    iB_00133iB_00133iB_00137iB_00138iB_00139
    iB_00140iB_00141iB_00142iB_00143iB_00144
    iB_00145iB_00146iB_00147iB_00148iB_00151
    iB_00152iB_00153iB_00155iB_00156iB_00158
    iB_00159iB_00163iB_00165iB_00166iB_00167
    iB_00168iB_00169iB_00171iB_00173iB_00179
    iB_00180iB_00182iB_00185iB_00186iB_00187
    iB_00189iB_00193iB_00194iB_00198iB_00203
    iB_00206iB_00210iB_00215iB_00225iB_00226
    iB_00227iB_00232iB_00234iB_00236iB_00238
    iB_00242iB_00251iB_00255iB_00257iB_00260
    iB_00261iB_00263iB_00264iB_00265iB_00275
    iB_00276iB_00280iB_00284iB_00285iB_00286
    iB_00291iB_00295iB_00298iB_00318iB_00319
    iB_00325iB_00334iB_00342iB_00363iB_00363
    iB_00368iB_00376iB_00377iB_00404iB_00415
    iB_00438iB_00449iB_00461iB_00463iB_00464
    iB_00485iB_00486iB_00487iB_00488iB_00491
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    iB_00504iB_00510iB_00512iB_00573iB_00580
    iB_00584iB_00585iB_00592iB_00593iB_00604
    iB_00613iB_00621iB_00650iB_00681iB_00706
    iB_00708iB_00709iB_00712iB_00739iB_00757
    iB_00762iB_00766iB_00770iB_00776iB_00778
    iB_00786iB_00791iB_00803iB_00809iB_00823
    iB_00841iB_00861iB_00863iB_00910iB_00924
    iB_00930iB_00931iB_00936iB_00951iB_00952
    iB_00958iB_00964iB_00969iB_00972iB_00980
    iB_00984iB_00985iB_01007iB_01014iB_01015
    iB_01017iB_01025iB_01031iB_01033iB_01036
    iB_01062iB_01066iB_01072iB_01074iB_01078
    iB_01088iB_01097iB_01099iB_01111iB_01113
    iB_01123iB_01133iB_01136iB_01163iB_01185
    iB_01194iB_01197iB_01200iB_01201iB_01212
    iB_01220iB_01230iB_01242iB_01243iB_01253
    iB_01318iB_01357iB_01380iB_01446iB_01460
    iB_01484iB_01517iB_01518iB_01529iB_01536
    iB_01540iB_01549iB_01552iB_01617iB_01671
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    iB_01763iB_01805iB_01808iB_01812iB_01813
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    iB_01849iB_01871iB_01895iB_01896iB_01906
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    iB_02389iB_02395iB_02402iB_02414iB_02423
    iB_02424iB_02429iB_02438iB_02439iB_02448
    iB_02451iB_02452iB_02454iB_02464iB_02476
    iB_02499iB_02503iB_02512iB_02536iB_02540
    iB_02561iB_02571iB_02577iB_02618iB_02631
    iB_02665iB_03516iB_03520iB_03525iB_03553
    iB_03585iB_03683iB_03749iB_03757iB_03766
    iB_03806iB_03813iB_04877iB_05098iB_05139
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    iB_05259iB_05260iB_05261iB_05262iB_05263
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    iB_05376iB_05377iB_05380iB_05381iB_05382
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    iB_05391iB_05392iB_05394iB_05400iB_05401
    iB_05403iB_05407iB_05408iB_05409iB_05410
    iB_05411iB_05412iB_05413iB_05414iB_05418
    iB_05422iB_05424iB_05425iB_05428iB_05433
    iB_05434iB_05435iB_05436iB_05440iB_05443
    iB_05445iB_05446iB_05447iB_05451iB_05452
    iB_05454iB_05457iB_05458iB_05459iB_05460
    iB_05463iB_05464iB_05468iB_05472iB_05474
    iB_05475iB_05476iB_05477iB_05480iB_05486
    iB_05487iB_05488iB_05489iB_05492iB_05493
    iB_05494iB_05496iB_05497iB_05502iB_05508
    iB_05509iB_05511iB_05514iB_05515iB_05518
    iB_05519iB_05519iB_05521iB_05522iB_05523
    iB_05530iB_05531iB_05542iB_05545iB_05549
    iB_05550iB_05551iB_05558iB_05561iB_05568
    iB_05575iB_05583iB_05587iB_05592iB_05595
    iB_05598iB_05600iB_05603iB_05604iB_05606
    iB_05613iB_05616iB_05618iB_05619iB_05697
    iB_05748iB_05751iB_05757iB_05758iB_05767
    iB_05774iB_05781iB_05791iB_05799iB_05800
    iB_05803iB_05806iB_05808iB_05815iB_05817
    iB_05823iB_05825iB_05827iB_05831iB_05833
    iB_05834iB_05842iB_05980iB_05981iB_05989
    iB_05992iB_05993iB_06000iB_06006iB_06008
    iB_06009iB_06011iB_06017iB_06023iB_06029
    iB_06032iB_06035iB_06038iB_06042iB_06043
    iB_06046iB_06051iB_06060iB_06061iB_06069
    iB_06070iB_06074iB_06081
    Publication
    The Tribolium Ontology is published in:

    Dönitz, J., Großmann, D., Schild, I., Schmitt-Engel, C., Bradler, S., Prpic, N.-M. and Bucher, G. (2013):
    TrOn: An anatomical ontology for the beetle Tribolium castaneum
    PLoS ONE 8(7): e70695. doi:10.1371/journal.pone.0070695.

    OntoScope

    OntoScope is a graphical ontology viewer developed at the Dept. of Bioinformatics of the University Medical Center Göttingen (UMG). The link below will start OntoScope as Java Web Start application, with the ontologies of Tribolium and Drosophila loaded.

    OntoScope is still in the beta phase, more information is available at the homepage of the project.

    Launch OntoScope
    OBA server
    Within the iBeetle project the OBA service is used to access the ontology. The oba service with the Tribolium ontology can also be integrate the ontology in other projects. The address of a public oba server providing the Tribolium ontology is: http://oba.sybig.de
    Download
    The Tribolium ontology can also be downloaded in the OBO format: tribolium.obo