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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 subdivision
            • appendage
              • pupal_appendage
              • wing
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Use the context menu to expand all children of a selected class.

Details
ID: TrOn_0000846
Name: pupal_wing
Definition: "The paired (membranous) organ of a pupa on the dorsolateral margin of the meso-and/or metathorax. The pupal wing consists of the hindwing and the elytra which are both in this stage not usable for flying. The elytra protects the underlying hindwing." [ISBN:0-19-857353-7, ISBN:978-3-11-014898-6]
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.

277 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_00014iB_00022iB_00022iB_00028iB_00083
iB_00119iB_00133iB_00166iB_00168iB_00170
iB_00170iB_00213iB_00213iB_00226iB_00243
iB_00257iB_00258iB_00258iB_00289iB_00290
iB_00300iB_00338iB_00363iB_00366iB_00376
iB_00385iB_00430iB_00445iB_00455iB_00463
iB_00463iB_00468iB_00475iB_00487iB_00487
iB_00497iB_00499iB_00499iB_00514iB_00514
iB_00548iB_00549iB_00555iB_00573iB_00585
iB_00588iB_00638iB_00666iB_00666iB_00671
iB_00685iB_00696iB_00696iB_00696iB_00714
iB_00714iB_00733iB_00733iB_00784iB_00794
iB_00796iB_00796iB_00826iB_00826iB_00827
iB_00881iB_00881iB_00894iB_00961iB_01003
iB_01006iB_01006iB_01023iB_01087iB_01098
iB_01098iB_01106iB_01111iB_01135iB_01136
iB_01136iB_01167iB_01167iB_01172iB_01173
iB_01200iB_01206iB_01220iB_01221iB_01237
iB_01252iB_01328iB_01331iB_01331iB_01346
iB_01346iB_01359iB_01461iB_01505iB_01517
iB_01517iB_01524iB_01524iB_01669iB_01726
iB_01726iB_01762iB_01776iB_01777iB_01805
iB_01810iB_01810iB_01815iB_01822iB_01856
iB_01886iB_01886iB_01918iB_01973iB_01973
iB_01973iB_01973iB_02218iB_02218iB_02218
iB_02218iB_02238iB_02238iB_02240iB_02268
iB_02268iB_02275iB_02275iB_02297iB_02297
iB_02299iB_02334iB_02344iB_02344iB_02360
iB_02360iB_02370iB_02459iB_02486iB_02498
iB_02498iB_02505iB_02510iB_02512iB_02512
iB_02516iB_02542iB_02548iB_02548iB_02548
iB_02599iB_02628iB_02631iB_02631iB_02674
iB_02674iB_02681iB_02681iB_02845iB_02858
iB_02889iB_02909iB_02913iB_02924iB_02924
iB_02941iB_02941iB_03403iB_03421iB_03422
iB_03444iB_03456iB_03456iB_03484iB_03511
iB_03577iB_03591iB_03595iB_03725iB_03756
iB_03793iB_03795iB_03822iB_03851iB_04047
iB_04060iB_04211iB_04254iB_04299iB_04393
iB_04393iB_04550iB_04577iB_04596iB_04596
iB_04604iB_04760iB_04855iB_04883iB_04887
iB_04897iB_04931iB_04935iB_04964iB_04964
iB_04966iB_04966iB_04986iB_05008iB_05014
iB_05014iB_05014iB_05019iB_05019iB_05048
iB_05048iB_05053iB_05053iB_05098iB_05179
iB_05204iB_05204iB_05214iB_05214iB_05235
iB_05237iB_05246iB_05246iB_05290iB_05290
iB_05290iB_05301iB_05302iB_05302iB_05302
iB_05331iB_05331iB_05371iB_05371iB_05422
iB_05422iB_05431iB_05431iB_05436iB_05436
iB_05436iB_05471iB_05473iB_05478iB_05478
iB_05481iB_05481iB_05481iB_05522iB_05543
iB_05547iB_05547iB_05547iB_05552iB_05552
iB_05563iB_05569iB_05634iB_05671iB_05671
iB_05671iB_05673iB_05688iB_05697iB_05718
iB_05718iB_05728iB_05728iB_05958iB_05958
iB_06230
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