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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
          • organ_system_subdivision
            • region_of_integument
              • head_capsule
Search & control

Search

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

Details
ID: TrOn_0000715
Name: larva_head_capsule
Definition: "The fused compact cephalic plates that comprise the head of the larva, excluding the eyes, antennae and mouthparts." [http://api.hymao.org/api/ref/67841, 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.

312 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_00052iB_00065iB_00089iB_00092iB_00092
iB_00101iB_00561iB_00705iB_00782iB_00783
iB_00793iB_00797iB_00838iB_00884iB_00951
iB_00981iB_00983iB_01055iB_01146iB_01160
iB_01178iB_01178iB_01303iB_01303iB_01326
iB_01389iB_01392iB_01551iB_01601iB_01653
iB_01653iB_01680iB_01687iB_01707iB_01710
iB_01725iB_01726iB_01766iB_01794iB_01795
iB_01843iB_01944iB_01957iB_02350iB_02482
iB_02555iB_02556iB_02556iB_02604iB_02759
iB_02803iB_02818iB_02844iB_02902iB_02954
iB_03008iB_03036iB_03036iB_03053iB_03064
iB_03084iB_03093iB_03158iB_03163iB_03184
iB_03196iB_03234iB_03292iB_03309iB_03352
iB_03397iB_03419iB_03432iB_03557iB_03591
iB_03669iB_03725iB_03772iB_03778iB_03779
iB_03795iB_03796iB_03802iB_03831iB_03859
iB_03861iB_03889iB_03898iB_03926iB_03927
iB_03932iB_03946iB_03966iB_03978iB_03992
iB_03996iB_04000iB_04008iB_04018iB_04023
iB_04029iB_04032iB_04041iB_04087iB_04103
iB_04146iB_04190iB_04199iB_04218iB_04227
iB_04247iB_04252iB_04294iB_04399iB_04407
iB_04409iB_04426iB_04429iB_04437iB_04471
iB_04473iB_04474iB_04475iB_04484iB_04544
iB_04564iB_04630iB_04791iB_04821iB_04825
iB_04825iB_04841iB_05074iB_05133iB_05159
iB_05393iB_05493iB_05654iB_05694iB_05742
iB_05834iB_06248iB_06364iB_06461iB_06554
iB_06600iB_06616iB_06659iB_06691iB_06709
iB_06721iB_06738iB_06815iB_06815iB_06816
iB_06818iB_06887iB_06887iB_06892iB_06916
iB_06916iB_06939iB_06978iB_06985iB_07007
iB_07014iB_07019iB_07051iB_07057iB_07076
iB_07092iB_07096iB_07096iB_07106iB_07267
iB_07267iB_07278iB_07295iB_07304iB_07355
iB_07357iB_07357iB_07357iB_07443iB_07555
iB_07647iB_07682iB_07852iB_07862iB_07900
iB_07911iB_08058iB_08086iB_08123iB_08123
iB_08131iB_08148iB_08205iB_08461iB_08501
iB_08542iB_08561iB_08590iB_08611iB_08625
iB_08640iB_08646iB_08718iB_08736iB_08748
iB_08819iB_08894iB_08895iB_08904iB_08908
iB_08910iB_08915iB_08933iB_08961iB_09009
iB_09106iB_09112iB_09149iB_09159iB_09278
iB_09309iB_09320iB_09346iB_09374iB_09377
iB_09395iB_09396iB_09396iB_09409iB_09424
iB_09432iB_09443iB_09443iB_09448iB_09495
iB_09509iB_09522iB_09530iB_09534iB_09540
iB_09578iB_09586iB_09609iB_09649iB_09716
iB_09742iB_09876iB_09897iB_09947iB_09978
iB_10013iB_10021iB_10029iB_10069iB_10173
iB_10223iB_10316iB_10332iB_10376iB_10565
iB_10567iB_10573iB_10575iB_10575iB_10577
iB_10577iB_10594iB_10619iB_10645iB_10654
iB_10657iB_10694iB_10703iB_10712iB_10718
iB_10752iB_10977iB_10988iB_11023iB_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