Genes Phenotypes Help, News, Blog

Help & Documentation

Help

I see some phenotypic terms that are associated to more than one biological system; why does this happen?

This is dictated by the ontology.

Some associations are quite obvious:

  • For example, the phenotype term “short tibia” is a “limbs/digits/tail” as well as a “skeleton” phenotype (e.g., Aak1)
Section of the Significant Phenotypes table in the Aak1 gene page, showing the significant phenotype “short tibia” and its main features.

There are other associations that might be less obvious:

  • The phenotype term “abnormal optic disk morphology” is a “nervous system” and a “vision/eye” phenotype (e.g., Cant1)
  • The phenotype term “abnormal retinal vasculature morphology” is a “cardiovascular system” and a “vision/eye” phenotype (e.g., Cant1)
Section of the Significant Phenotypes table in the Cant1 gene page, showing four significant phenotypes and their main features.

For this reason, when you select a biological system to use as a filter in the All Data table, you may find procedures that, at first glance, may not seem to be associated with the biological system you are filtering for. For example, if you are interested in behaviour phenotypes, you need to filter for “behaviour/neurological or nervous system” phenotypes, which will include startle reflex and limb grasping phenotypes, but also other less obvious phenotypes, such as vision/eye phenotypes, among others.

A section of the All Data table in the Cib2 gene page, with filter “behaviour/neurological or nervous system” selected.

See the EMBL-EBI Ontology Lookup Service:

Tree view of “abnormal optic disk morphology” phenotype, showing it is both a nervous system and a vision/eye phenotype
Tree view of “impaired pupillary reflex” phenotype, showing it is both a behaviour/neurological and a vision/eye phenotype