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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
Search & control

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

Details
ID: TrOn_0000957
Name: tropharium
Definition: "In each ovariole the nurse cells of all cysts are kept in at the terminal region (Tropharium) and the oocytes will be nourished by elongating nutritive cords connecting the growing oocytes with the Tropharium." [http:entwbio.nat.uni-erlangen.de/English/research/schoppmeier.shtml (Michael Schoppmeier)]
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.

193 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_00077iB_00083iB_00083
iB_00091iB_00110iB_00110iB_00129iB_00143
iB_00144iB_00173iB_00187iB_00236iB_00236
iB_00248iB_00311iB_00311iB_00419iB_00419
iB_00449iB_00449iB_00457iB_00499iB_00507
iB_00532iB_00555iB_00587iB_00587iB_00589
iB_00603iB_00619iB_00619iB_00640iB_00647
iB_00647iB_00664iB_00664iB_00677iB_00679
iB_00709iB_00752iB_00752iB_00752iB_00754
iB_00826iB_00940iB_00977iB_01030iB_01036
iB_01146iB_01156iB_01193iB_01193iB_01250
iB_01250iB_01273iB_01276iB_01276iB_01313
iB_01315iB_01325iB_01379iB_01542iB_01556
iB_01614iB_01665iB_01703iB_01703iB_01764
iB_01803iB_01835iB_01835iB_01835iB_01859
iB_01861iB_01875iB_01931iB_01945iB_01960
iB_02017iB_02184iB_02184iB_02184iB_02184
iB_02185iB_02195iB_02201iB_02206iB_02269
iB_02276iB_02276iB_02292iB_02295iB_02297
iB_02329iB_02344iB_02409iB_02411iB_02469
iB_02469iB_02484iB_02500iB_02563iB_02563
iB_02574iB_02619iB_02653iB_02664iB_02668
iB_02847iB_02862iB_02918iB_02918iB_02918
iB_02946iB_03480iB_03480iB_03522iB_03530
iB_03555iB_03555iB_03555iB_03577iB_03577
iB_03577iB_03577iB_03669iB_03763iB_03763
iB_03840iB_03884iB_03907iB_04029iB_04161
iB_04211iB_04297iB_04297iB_04365iB_04365
iB_04480iB_04615iB_04615iB_04702iB_04727
iB_04777iB_04781iB_04840iB_04840iB_04873
iB_04997iB_05010iB_05010iB_05012iB_05012
iB_05083iB_05184iB_05184iB_05184iB_05214
iB_05214iB_05214iB_05235iB_05236iB_05236
iB_05236iB_05263iB_05295iB_05295iB_05302
iB_05352iB_05387iB_05397iB_05438iB_05439
iB_05547iB_05547iB_05599iB_05624iB_05633
iB_05669iB_05686iB_05686iB_05686iB_05745
iB_05770iB_05942iB_05942iB_05998iB_06025
iB_06033iB_06062iB_06077iB_06297iB_06352
iB_06589iB_06659iB_06688iB_06688iB_06823
iB_06846iB_06867iB_06888iB_06985iB_07067
iB_07373iB_07388iB_07480iB_07510iB_07510
iB_07799iB_07862iB_07870iB_07875iB_07897
iB_08108iB_08209iB_08518iB_08518iB_08518
iB_08588iB_08823iB_08943iB_08986iB_09010
iB_09125iB_09168iB_09379iB_09383iB_09383
iB_09390iB_09390iB_09426iB_09437iB_09472
iB_09472iB_09576iB_09684iB_09772iB_09822
iB_09839iB_09932iB_09932iB_09955iB_09958
iB_10039iB_10069iB_10232iB_10376iB_10707
iB_10981
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