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

Details
ID: TrOn_0001017
Name: larva_head_appendage
Definition: "Jointed, sensory, feeding and no walking appendage attached to the anterior of the head capsule of the larva. Some of the appendage are paired and segmented and some not." [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.

572 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_00065iB_00089iB_00101iB_00244iB_00244
iB_00304iB_00561iB_00579iB_00579iB_00597
iB_00659iB_00709iB_00709iB_00754iB_00793
iB_00793iB_00838iB_00896iB_00946iB_00955
iB_00955iB_00966iB_00983iB_01008iB_01055
iB_01055iB_01055iB_01160iB_01160iB_01283
iB_01326iB_01326iB_01397iB_01397iB_01397
iB_01421iB_01421iB_01464iB_01464iB_01475
iB_01513iB_01513iB_01551iB_01551iB_01556
iB_01653iB_01653iB_01653iB_01707iB_01719
iB_01726iB_01729iB_01729iB_01791iB_01794
iB_01795iB_01886iB_01888iB_01936iB_01936
iB_01944iB_01944iB_01983iB_02260iB_02356
iB_02389iB_02437iB_02441iB_02476iB_02513
iB_02587iB_02587iB_02643iB_02661iB_02697
iB_02712iB_02736iB_02744iB_02759iB_02803
iB_02902iB_02926iB_03053iB_03084iB_03093
iB_03150iB_03150iB_03158iB_03158iB_03163
iB_03163iB_03184iB_03184iB_03193iB_03233
iB_03233iB_03234iB_03234iB_03280iB_03292
iB_03296iB_03303iB_03303iB_03309iB_03318
iB_03388iB_03397iB_03526iB_03591iB_03623
iB_03725iB_03725iB_03725iB_03764iB_03772
iB_03795iB_03835iB_03859iB_03859iB_03861
iB_03882iB_03886iB_03889iB_03898iB_03909
iB_03926iB_03927iB_03932iB_03946iB_03946
iB_03951iB_03959iB_03959iB_03966iB_03966
iB_03976iB_03978iB_03978iB_03978iB_03992
iB_03996iB_03996iB_04000iB_04008iB_04013
iB_04013iB_04014iB_04014iB_04023iB_04029
iB_04041iB_04146iB_04152iB_04190iB_04190
iB_04190iB_04198iB_04198iB_04198iB_04199
iB_04203iB_04203iB_04218iB_04218iB_04222
iB_04222iB_04224iB_04224iB_04227iB_04227
iB_04247iB_04252iB_04252iB_04252iB_04294
iB_04294iB_04294iB_04399iB_04407iB_04407
iB_04407iB_04409iB_04423iB_04433iB_04433
iB_04437iB_04473iB_04474iB_04482iB_04484
iB_04484iB_04487iB_04500iB_04500iB_04544
iB_04549iB_04564iB_04630iB_04636iB_04639
iB_04639iB_04643iB_04656iB_04656iB_04656
iB_04659iB_04695iB_04730iB_04744iB_04760
iB_04760iB_04772iB_04772iB_04776iB_04776
iB_04800iB_04821iB_04829iB_04841iB_04841
iB_04850iB_04850iB_04890iB_04890iB_04929
iB_04929iB_04937iB_04944iB_05045iB_05045
iB_05072iB_05073iB_05073iB_05074iB_05096
iB_05117iB_05160iB_05160iB_05299iB_05299
iB_05393iB_05456iB_05498iB_05654iB_05694
iB_05698iB_05728iB_05758iB_05805iB_05807
iB_05877iB_05934iB_05943iB_06248iB_06248
iB_06268iB_06289iB_06390iB_06519iB_06519
iB_06527iB_06554iB_06616iB_06616iB_06654
iB_06663iB_06699iB_06699iB_06709iB_06738
iB_06740iB_06796iB_06796iB_06815iB_06854
iB_06868iB_06868iB_06887iB_06892iB_06915
iB_06916iB_06916iB_06978iB_07007iB_07022
iB_07025iB_07025iB_07051iB_07057iB_07076
iB_07096iB_07145iB_07178iB_07209iB_07239
iB_07239iB_07304iB_07355iB_07355iB_07357
iB_07443iB_07490iB_07531iB_07553iB_07553
iB_07555iB_07598iB_07627iB_07665iB_07682
iB_07682iB_07852iB_07862iB_07900iB_07911
iB_08065iB_08123iB_08123iB_08131iB_08131
iB_08148iB_08148iB_08167iB_08172iB_08234
iB_08237iB_08241iB_08265iB_08265iB_08354
iB_08461iB_08501iB_08590iB_08611iB_08616
iB_08625iB_08646iB_08691iB_08719iB_08719
iB_08736iB_08737iB_08779iB_08814iB_08819
iB_08824iB_08894iB_08895iB_08907iB_08910
iB_08915iB_08933iB_08961iB_08965iB_09011
iB_09013iB_09103iB_09103iB_09149iB_09154
iB_09159iB_09278iB_09302iB_09309iB_09328
iB_09374iB_09374iB_09396iB_09396iB_09402
iB_09409iB_09443iB_09443iB_09469iB_09471
iB_09491iB_09517iB_09518iB_09522iB_09533
iB_09578iB_09587iB_09592iB_09609iB_09649
iB_09709iB_09719iB_09742iB_09753iB_09776
iB_09797iB_09836iB_09848iB_09848iB_09876
iB_09876iB_09881iB_09881iB_09888iB_09888
iB_09897iB_09947iB_09947iB_09961iB_09961
iB_09977iB_09978iB_09978iB_09980iB_09987
iB_09991iB_09991iB_10013iB_10029iB_10132
iB_10223iB_10262iB_10316iB_10332iB_10343
iB_10376iB_10489iB_10489iB_10493iB_10516
iB_10542iB_10565iB_10566iB_10573iB_10577
iB_10589iB_10589iB_10594iB_10594iB_10604
iB_10604iB_10619iB_10652iB_10679iB_10694
iB_10703iB_10703iB_10711iB_10712iB_10712
iB_10718iB_10720iB_10739iB_10739iB_10752
iB_10752iB_10961iB_10972iB_10972iB_10972
iB_10977iB_10977iB_10978iB_10978iB_10979
iB_10988iB_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