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

Details
ID: TrOn_0000951
Name: female_reproductive_system
Definition: "The reproductive system of the female consists of the sex glands, or gonads (female ovaries), the ducts through which the sexual products are carried to the exterior, and the accessory glands.\nEach of the two ovaries consists of a number of ovarioles. The ovarioles converge upon the two oviducts, and the oviducts unite to form a common oviduct down which the ripe eggs are discharged. Each ovariole consists of a germarium and a tropharium. The germarium is a mass of undifferentiated cells that form oocytes, nurse cells, and follicular cells. The nurse cells provide nourishment for the oocytes during the early stages of their growth; follicular cells, which invest the enlarging oocyte as a continuous epithelium, provide the materials for yolk formation and, in the final stages, lay down the eggshell or chorion. The ovarial follicles increase progressively in size as the oocytes grow to form ripe eggs." [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.

1127 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:
No records found.
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