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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
              • larva_appendage
              • leg
Search & control

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

Details
ID: TrOn_0000031
Name: larva_leg
Definition: "Paired locomotory organ on the ventrolateral side of the three larval thoracic segments, which is used for locomotion." [ISBN:978-3-11-014898-5, 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.

334 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_00016iB_00101iB_00116iB_00371iB_00456
iB_00659iB_00680iB_00766iB_00793iB_00860
iB_00886iB_00946iB_00955iB_00966iB_00993
iB_01057iB_01172iB_01241iB_01252iB_01266
iB_01266iB_01344iB_01359iB_01359iB_01397
iB_01464iB_01466iB_01475iB_01475iB_01526
iB_01543iB_01556iB_01687iB_01757iB_01840
iB_01936iB_01957iB_02180iB_02207iB_02212
iB_02212iB_02212iB_02213iB_02263iB_02263
iB_02265iB_02265iB_02280iB_02290iB_02375
iB_02375iB_02399iB_02468iB_02520iB_02520
iB_02543iB_02543iB_02548iB_02622iB_02643
iB_02774iB_02785iB_02858iB_02880iB_02880
iB_02888iB_02914iB_02952iB_02952iB_03102
iB_03102iB_03105iB_03110iB_03110iB_03110
iB_03233iB_03233iB_03496iB_03590iB_03591
iB_03623iB_03725iB_03762iB_03796iB_03802
iB_03803iB_03829iB_03831iB_03831iB_03859
iB_03890iB_04008iB_04015iB_04057iB_04063
iB_04090iB_04100iB_04316iB_04316iB_04360
iB_04413iB_04413iB_04421iB_04423iB_04423
iB_04549iB_04557iB_04564iB_04564iB_04570
iB_04629iB_04631iB_04659iB_04659iB_04695
iB_04695iB_04744iB_04760iB_04764iB_04772
iB_04791iB_04836iB_04850iB_04890iB_04890
iB_04905iB_04929iB_04937iB_04939iB_04944
iB_04952iB_04983iB_05042iB_05045iB_05045
iB_05064iB_05072iB_05073iB_05074iB_05117
iB_05133iB_05155iB_05191iB_05223iB_05238
iB_05245iB_05247iB_05252iB_05290iB_05291
iB_05294iB_05294iB_05513iB_05524iB_05578
iB_05579iB_05634iB_05694iB_05694iB_05759
iB_05877iB_05895iB_06051iB_06051iB_06072
iB_06181iB_06235iB_06248iB_06274iB_06274
iB_06402iB_06402iB_06545iB_06547iB_06616
iB_06651iB_06659iB_06659iB_06663iB_06663
iB_06691iB_06706iB_06709iB_06709iB_06709
iB_06764iB_06796iB_06815iB_06815iB_06815
iB_06815iB_06842iB_06892iB_06916iB_06918
iB_06941iB_06985iB_07022iB_07025iB_07025
iB_07168iB_07208iB_07208iB_07209iB_07241
iB_07297iB_07376iB_07376iB_07479iB_07852
iB_07870iB_07870iB_08012iB_08058iB_08105
iB_08131iB_08156iB_08167iB_08167iB_08169
iB_08234iB_08234iB_08265iB_08561iB_08590
iB_08640iB_08660iB_08824iB_08893iB_08910
iB_08915iB_08961iB_08965iB_09009iB_09152
iB_09153iB_09154iB_09278iB_09278iB_09278
iB_09328iB_09328iB_09377iB_09377iB_09377
iB_09395iB_09396iB_09409iB_09409iB_09424
iB_09495iB_09495iB_09522iB_09578iB_09592
iB_09719iB_09797iB_09825iB_09836iB_09836
iB_09836iB_09848iB_09961iB_09991iB_10013
iB_10021iB_10069iB_10072iB_10119iB_10132
iB_10133iB_10262iB_10316iB_10343iB_10376
iB_10411iB_10412iB_10493iB_10565iB_10566
iB_10573iB_10573iB_10575iB_10575iB_10591
iB_10591iB_10594iB_10604iB_10604iB_10614
iB_10619iB_10619iB_10630iB_10637iB_10645
iB_10645iB_10645iB_10652iB_10652iB_10653
iB_10666iB_10679iB_10694iB_10703iB_10712
iB_10718iB_10972iB_10972iB_10977iB_10978
iB_11023
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