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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
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Use the context menu to expand all children of a selected class.

Details
ID: TrOn_0000964
Name: egg_chamber
Definition: "Female germline cyst that is not part of a germarium." [FBC:DOS]
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.

621 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_00006iB_00008iB_00025iB_00029iB_00032
iB_00062iB_00083iB_00088iB_00091iB_00099
iB_00119iB_00119iB_00129iB_00129iB_00166
iB_00173iB_00173iB_00189iB_00189iB_00189
iB_00218iB_00228iB_00235iB_00243iB_00243
iB_00255iB_00255iB_00257iB_00257iB_00257
iB_00259iB_00282iB_00290iB_00311iB_00321
iB_00325iB_00328iB_00331iB_00334iB_00338
iB_00356iB_00366iB_00379iB_00392iB_00392
iB_00397iB_00398iB_00457iB_00489iB_00499
iB_00507iB_00521iB_00532iB_00548iB_00548
iB_00587iB_00592iB_00603iB_00638iB_00640
iB_00647iB_00664iB_00666iB_00670iB_00677
iB_00679iB_00709iB_00733iB_00733iB_00734
iB_00734iB_00743iB_00743iB_00755iB_00803
iB_00803iB_00803iB_00826iB_00881iB_00894
iB_00959iB_01017iB_01030iB_01036iB_01036
iB_01100iB_01135iB_01136iB_01167iB_01239
iB_01256iB_01257iB_01273iB_01276iB_01308
iB_01308iB_01446iB_01450iB_01452iB_01452
iB_01470iB_01491iB_01542iB_01564iB_01564
iB_01602iB_01602iB_01669iB_01703iB_01717
iB_01743iB_01745iB_01764iB_01781iB_01803
iB_01813iB_01835iB_01846iB_01891iB_01931
iB_01950iB_01960iB_01977iB_02193iB_02201
iB_02206iB_02218iB_02227iB_02276iB_02276
iB_02278iB_02289iB_02289iB_02289iB_02295
iB_02297iB_02329iB_02335iB_02335iB_02339
iB_02343iB_02374iB_02374iB_02409iB_02411
iB_02413iB_02429iB_02448iB_02448iB_02469
iB_02484iB_02500iB_02512iB_02512iB_02516
iB_02529iB_02542iB_02563iB_02574iB_02574
iB_02591iB_02603iB_02618iB_02619iB_02619
iB_02619iB_02620iB_02653iB_02668iB_02674
iB_02681iB_02815iB_02825iB_02838iB_02855
iB_02855iB_02911iB_02913iB_02924iB_02941
iB_03051iB_03136iB_03238iB_03239iB_03239
iB_03248iB_03248iB_03256iB_03294iB_03300
iB_03300iB_03331iB_03354iB_03362iB_03480
iB_03522iB_03530iB_03555iB_03577iB_03577
iB_03577iB_03634iB_03669iB_03669iB_03709
iB_03763iB_03884iB_03896iB_03907iB_03956
iB_04029iB_04150iB_04161iB_04161iB_04211
iB_04236iB_04236iB_04300iB_04332iB_04365
iB_04454iB_04480iB_04598iB_04627iB_04702
iB_04702iB_04727iB_04727iB_04777iB_04781
iB_04931iB_05081iB_05102iB_05172iB_05184
iB_05233iB_05233iB_05235iB_05236iB_05236
iB_05236iB_05246iB_05263iB_05292iB_05295
iB_05302iB_05313iB_05313iB_05352iB_05352
iB_05387iB_05397iB_05397iB_05397iB_05438
iB_05465iB_05509iB_05522iB_05547iB_05547
iB_05547iB_05599iB_05633iB_05669iB_05686
iB_05686iB_05752iB_05770iB_05770iB_05787
iB_05813iB_05848iB_05942iB_05998iB_06025
iB_06025iB_06037iB_06062iB_06260iB_06260
iB_06282iB_06319iB_06326iB_06352iB_06352
iB_06398iB_06403iB_06419iB_06419iB_06419
iB_06444iB_06479iB_06491iB_06560iB_06560
iB_06589iB_06622iB_06623iB_06659iB_06823
iB_06846iB_07020iB_07067iB_07067iB_07146
iB_07269iB_07290iB_07324iB_07480iB_07663
iB_07799iB_07869iB_07897iB_08108iB_08303
iB_08367iB_08421iB_08431iB_08431iB_08656
iB_08816iB_08823iB_08861iB_08868iB_08921
iB_08943iB_08986iB_09065iB_09145iB_09145
iB_09162iB_09190iB_09240iB_09383iB_09383
iB_09383iB_09390iB_09437iB_09437iB_09482
iB_09500iB_09536iB_09542iB_09544iB_09544
iB_09576iB_09577iB_09693iB_09697iB_09733
iB_09739iB_09749iB_09758iB_09759iB_09768
iB_09768iB_09772iB_09783iB_09812iB_09822
iB_09921iB_09925iB_09932iB_09955iB_09958
iB_09958iB_09975iB_10062iB_10062iB_10062
iB_10069iB_10093iB_10103iB_10205iB_10232
iB_10232iB_10279iB_10279iB_10333iB_10431
iB_10530iB_10544iB_10599iB_10599iB_10599
iB_10644iB_10956iB_10968iB_10981iB_11010
iB_11026iB_11038iB_11040
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