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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
          • germline_cyst
            • female_germline_cyst
              • egg_chamber
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Use the context menu to expand all children of a selected class.

Details
ID: TrOn_0000967
Name: vitellogenic_egg_chamber
Definition: "to do" [XX:<new dbxref>]
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.

    322 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_00010iB_00028iB_00028iB_00099iB_00100
    iB_00105iB_00129iB_00144iB_00165iB_00170
    iB_00181iB_00189iB_00196iB_00228iB_00228
    iB_00235iB_00236iB_00236iB_00243iB_00248
    iB_00291iB_00291iB_00292iB_00292iB_00292
    iB_00311iB_00363iB_00366iB_00372iB_00372
    iB_00419iB_00441iB_00460iB_00460iB_00463
    iB_00487iB_00521iB_00552iB_00555iB_00589
    iB_00592iB_00595iB_00598iB_00613iB_00619
    iB_00684iB_00752iB_00771iB_00846iB_00874
    iB_00874iB_00913iB_00914iB_00927iB_00943
    iB_00953iB_00953iB_00977iB_00994iB_00999
    iB_01003iB_01010iB_01010iB_01020iB_01027
    iB_01060iB_01067iB_01067iB_01106iB_01136
    iB_01144iB_01146iB_01151iB_01188iB_01193
    iB_01193iB_01193iB_01194iB_01225iB_01250
    iB_01256iB_01302iB_01346iB_01349iB_01359
    iB_01379iB_01461iB_01470iB_01477iB_01505
    iB_01518iB_01539iB_01542iB_01544iB_01556
    iB_01614iB_01665iB_01717iB_01733iB_01743
    iB_01776iB_01781iB_01834iB_01834iB_01859
    iB_01861iB_01861iB_01875iB_01875iB_01903
    iB_01931iB_01937iB_01943iB_01943iB_01943
    iB_01945iB_01945iB_01945iB_01960iB_01979
    iB_01979iB_02017iB_02083iB_02083iB_02185
    iB_02195iB_02195iB_02197iB_02201iB_02201
    iB_02201iB_02209iB_02209iB_02209iB_02218
    iB_02220iB_02227iB_02238iB_02261iB_02269
    iB_02275iB_02282iB_02287iB_02288iB_02289
    iB_02292iB_02297iB_02344iB_02354iB_02393
    iB_02402iB_02402iB_02413iB_02417iB_02417
    iB_02417iB_02420iB_02429iB_02429iB_02429
    iB_02484iB_02484iB_02500iB_02517iB_02517
    iB_02529iB_02536iB_02541iB_02541iB_02541
    iB_02563iB_02588iB_02588iB_02618iB_02619
    iB_02619iB_02619iB_02639iB_02639iB_02655
    iB_02655iB_02657iB_02664iB_02664iB_02666
    iB_02674iB_02681iB_02815iB_02838iB_02838
    iB_02855iB_02913iB_02913iB_02913iB_02918
    iB_02918iB_02930iB_02946iB_02946iB_02998
    iB_02998iB_03089iB_03109iB_03177iB_03177
    iB_03177iB_03239iB_03245iB_03256iB_03294
    iB_03294iB_03331iB_03331iB_03334iB_03334
    iB_03354iB_03362iB_03362iB_03444iB_03502
    iB_03506iB_03577iB_03595iB_03669iB_03669
    iB_03702iB_03702iB_03907iB_03956iB_04092
    iB_04161iB_04236iB_04336iB_04336iB_04357
    iB_04499iB_04997iB_05012iB_05031iB_05102
    iB_05103iB_05184iB_05206iB_05209iB_05214
    iB_05214iB_05214iB_05236iB_05237iB_05237
    iB_05271iB_05271iB_05271iB_05272iB_05290
    iB_05302iB_05515iB_05520iB_05520iB_05547
    iB_05549iB_05586iB_05586iB_05624iB_05626
    iB_05626iB_05686iB_05686iB_05686iB_05709
    iB_05787iB_05794iB_05813iB_05813iB_05848
    iB_05848iB_05998iB_05998iB_06001iB_06025
    iB_06025iB_06033iB_06037iB_06047iB_06047
    iB_06077iB_06077iB_06081iB_06081iB_06264
    iB_06284iB_06297iB_06480iB_06480iB_06608
    iB_06623iB_06671iB_06688iB_06688iB_06823
    iB_06823iB_06867iB_06962iB_06966iB_07020
    iB_07231iB_07237iB_07269iB_07290iB_07324
    iB_07324iB_07326iB_07326iB_07373iB_07414
    iB_07414iB_07510iB_07512iB_07512iB_07542
    iB_07594iB_07594iB_07619iB_07748iB_07862
    iB_07869iB_07869iB_07875iB_07893iB_08191
    iB_08260iB_08367iB_08468iB_08518iB_08579
    iB_08610iB_08610iB_08710iB_08749iB_08760
    iB_08764iB_08916iB_08921iB_08931iB_08943
    iB_08947iB_08969iB_08969iB_08986iB_08991
    iB_08991iB_09010iB_09010iB_09013iB_09013
    iB_09059iB_09065iB_09122iB_09122iB_09125
    iB_09144iB_09152iB_09168iB_09168iB_09190
    iB_09190iB_09206iB_09206iB_09206iB_09206
    iB_09238iB_09238iB_09256iB_09256iB_09256
    iB_09306iB_09378iB_09378iB_09389iB_09389
    iB_09390iB_09428iB_09437iB_09452iB_09464
    iB_09464iB_09464iB_09605iB_09628iB_09638
    iB_09644iB_09693iB_09697iB_09758iB_09762
    iB_09780iB_09780iB_09793iB_09812iB_09839
    iB_09858iB_09862iB_09921iB_09992iB_09992
    iB_10029iB_10039iB_10043iB_10043iB_10062
    iB_10119iB_10119iB_10153iB_10160iB_10196
    iB_10205iB_10333iB_10333iB_10376iB_10376
    iB_10435iB_10435iB_10485iB_10501iB_10530
    iB_10544iB_10599iB_10707iB_10956iB_11010
    iB_11048
    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