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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
          • stink_gland
            • abdominal_stink_gland
            • adult_stink_gland
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Details
ID: TrOn_0000990
Name: adult_abdominal_stink_gland
Definition: "A gland that functions in secretion of defensive compounds located in the posterior end of the adult abdomen." [ISBN:0-19-857353-7, ISBN:978-3-11-014898-5]
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.

    177 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_00081iB_00081iB_00105iB_00105iB_00110
    iB_00185iB_00185iB_00185iB_00304iB_00304
    iB_00489iB_00701iB_00754iB_01013iB_01013
    iB_01044iB_01169iB_01169iB_01169iB_01236
    iB_01236iB_01236iB_01315iB_01372iB_01440
    iB_01440iB_01499iB_01499iB_01499iB_01499
    iB_01516iB_01644iB_01798iB_01814iB_01874
    iB_01910iB_01975iB_02297iB_02301iB_02367
    iB_02401iB_02411iB_02416iB_02428iB_02428
    iB_02428iB_02428iB_02459iB_02471iB_02471
    iB_02516iB_02517iB_02517iB_02542iB_02542
    iB_02563iB_02563iB_02584iB_02625iB_02625
    iB_02625iB_02627iB_02633iB_02633iB_02673
    iB_02673iB_02673iB_02673iB_02692iB_02692
    iB_02716iB_02716iB_02743iB_02774iB_02774
    iB_02774iB_02931iB_03294iB_03401iB_03552
    iB_03552iB_03637iB_03693iB_03693iB_03695
    iB_03780iB_03913iB_03963iB_04066iB_04066
    iB_04066iB_04137iB_04205iB_04420iB_04717
    iB_04717iB_04797iB_04797iB_04839iB_04839
    iB_04839iB_04850iB_04893iB_04893iB_05042
    iB_05119iB_05264iB_05278iB_05284iB_05329
    iB_05331iB_05331iB_05342iB_05442iB_05449
    iB_05518iB_05584iB_05712iB_05712iB_05719
    iB_05719iB_05942iB_05942iB_06333iB_06359
    iB_06359iB_06684iB_06684iB_06684iB_06778
    iB_06806iB_06806iB_06868iB_07188iB_07188
    iB_07469iB_07717iB_07717iB_07747iB_07747
    iB_07759iB_07759iB_07759iB_07760iB_07764
    iB_07764iB_07772iB_07782iB_07782iB_07783
    iB_07830iB_07830iB_07871iB_07900iB_07902
    iB_07902iB_07915iB_07915iB_07917iB_07917
    iB_07918iB_07918iB_07925iB_07925iB_07925
    iB_07925iB_07926iB_07926iB_07926iB_07938
    iB_08140iB_08143iB_08179iB_08179iB_08184
    iB_08202iB_08303iB_08303iB_08398iB_08398
    iB_08398iB_08468iB_08506iB_08506iB_08506
    iB_08561iB_08561iB_08587iB_08587iB_08587
    iB_08587iB_08625iB_08625iB_08634iB_08634
    iB_08660iB_08666iB_08666iB_08760iB_08861
    iB_08919iB_08933iB_08952iB_08956iB_08962
    iB_08962iB_08983iB_09010iB_09043iB_09043
    iB_09043iB_09050iB_09050iB_09103iB_09239
    iB_09239iB_09272iB_09272iB_09272iB_09272
    iB_09308iB_09308iB_09308iB_09308iB_09311
    iB_09311iB_09326iB_09326iB_09326iB_09329
    iB_09329iB_09329iB_09337iB_09337iB_09337
    iB_09337iB_09340iB_09340iB_09340iB_09355
    iB_09355iB_09403iB_09403iB_09430iB_09661
    iB_09736iB_09869iB_09896iB_09910iB_09924
    iB_09988iB_09988iB_09991iB_10004iB_10007
    iB_10104iB_10104iB_10104iB_10133iB_10133
    iB_10156iB_10156iB_10159iB_10159iB_10181
    iB_10181iB_10205iB_10206iB_10206iB_10206
    iB_10466iB_10488iB_10488iB_10488iB_10520
    iB_10520iB_10520iB_10547iB_10547iB_10547
    iB_10560iB_10561iB_10611iB_10611iB_10674
    iB_10701iB_10701iB_10718iB_10718iB_10741
    iB_10748iB_10954iB_10978iB_10981iB_10981
    iB_10984iB_11050iB_11050
    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