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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_0000966
Name: previtellogenic_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.

    240 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_00028iB_00100iB_00143iB_00165iB_00235
    iB_00248iB_00292iB_00292iB_00311iB_00323
    iB_00419iB_00419iB_00419iB_00441iB_00460
    iB_00463iB_00463iB_00487iB_00487iB_00552
    iB_00552iB_00555iB_00572iB_00592iB_00598
    iB_00602iB_00619iB_00709iB_00752iB_00771
    iB_00803iB_00806iB_00846iB_00874iB_00913
    iB_00914iB_00927iB_00940iB_00943iB_00969
    iB_00977iB_00994iB_00999iB_00999iB_01010
    iB_01146iB_01151iB_01188iB_01193iB_01193
    iB_01302iB_01303iB_01346iB_01379iB_01461
    iB_01477iB_01505iB_01539iB_01542iB_01544
    iB_01556iB_01614iB_01665iB_01717iB_01733
    iB_01776iB_01776iB_01834iB_01834iB_01859
    iB_01861iB_01903iB_01943iB_01943iB_01945
    iB_01950iB_01950iB_01960iB_01979iB_02083
    iB_02184iB_02195iB_02201iB_02206iB_02269
    iB_02287iB_02288iB_02344iB_02420iB_02500
    iB_02503iB_02536iB_02619iB_02657iB_02666
    iB_03256iB_03353iB_03444iB_03506iB_03506
    iB_03577iB_03595iB_03669iB_03702iB_03703
    iB_03703iB_03703iB_03814iB_03905iB_03907
    iB_04132iB_04150iB_04236iB_04297iB_04297
    iB_04300iB_04313iB_04313iB_04336iB_04348
    iB_04454iB_04499iB_04703iB_04840iB_04873
    iB_04938iB_04997iB_05012iB_05031iB_05056
    iB_05126iB_05171iB_05209iB_05236iB_05297
    iB_05439iB_05495iB_05495iB_05515iB_05520
    iB_05626iB_05745iB_05998iB_06001iB_06033
    iB_06081iB_06284iB_06297iB_06297iB_06398
    iB_06398iB_06491iB_06671iB_06671iB_06688
    iB_06810iB_06823iB_06867iB_06867iB_06888
    iB_06888iB_06888iB_06952iB_06952iB_06982
    iB_06982iB_07215iB_07231iB_07237iB_07269
    iB_07290iB_07304iB_07324iB_07326iB_07373
    iB_07388iB_07480iB_07480iB_07480iB_07510
    iB_07594iB_07621iB_07815iB_07815iB_07862
    iB_07871iB_07875iB_07975iB_07975iB_07997
    iB_07997iB_08138iB_08150iB_08150iB_08164
    iB_08164iB_08215iB_08215iB_08260iB_08265
    iB_08327iB_08421iB_08468iB_08518iB_08524
    iB_08579iB_08579iB_08588iB_08610iB_08710
    iB_08710iB_08910iB_08910iB_08931iB_08947
    iB_08957iB_08957iB_08963iB_08969iB_08986
    iB_08986iB_09048iB_09048iB_09059iB_09066
    iB_09066iB_09076iB_09078iB_09111iB_09125
    iB_09125iB_09125iB_09144iB_09145iB_09168
    iB_09206iB_09238iB_09256iB_09273iB_09273
    iB_09306iB_09379iB_09390iB_09426iB_09426
    iB_09452iB_09485iB_09605iB_09642iB_09642
    iB_09642iB_09780iB_09793iB_09812iB_09839
    iB_09839iB_09858iB_09862iB_09998iB_09998
    iB_10000iB_10039iB_10069iB_10069iB_10093
    iB_10105iB_10153iB_10160iB_10196iB_10205
    iB_10279iB_10333iB_10376iB_10435iB_10445
    iB_10485iB_10501iB_10501iB_10530iB_10544
    iB_10599iB_10615iB_10615iB_10640iB_10641
    iB_10707iB_10956iB_10968iB_11010iB_11012
    iB_11040iB_11048iB_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