Species-Specific Terms

Handling Species Specificity

One of the biggest problems for a controlled vocabulary is choosing term names and definitions that will unambiguously identify a component, function or process. If a word or phrase refers to different entities or processes depending upon the organism, subclasses are created based on differentiating characteristics, such structure, physical composition or order of subprocesses, rather than by identifying the taxonomic group in which the component or process occurs.

Sensory Perception

Terms and Structure

Sensory perception occurs in organisms capable of performing neurophysiological processing of the stimuli in their environment, and covers the processes commonly called "the senses": hearing, vision, taste, smell and so on. Sensory perception involves detection of the stimulus and subsequent recognition and characterization of it. There are five different stimulus types involved in sensory processing - chemical, mechanical, electrical, light and temperature.

  • neurophysiological process
    • [i] sensory perception

    Detection and Response To Stimulus

    Terms and Structure

    The response of a cell or an organism to a stimulus is all the processes that occur as a result of the stimulus occurring within or outside the cell or organism. Detection of the stimulus, the process in which a stimulus is received by a cell and converted into a molecular signal, is thus a class of stimulus response. The general structure of this node is as follows:

    • response to stimulus
      • [i] detection of stimulus
        • [i] detection of [stimulus type] stimulus



    Biological regulation is defined as any process that modulates the frequency, rate or extent of any biological process, quality or function.

    The regulates relation

    Protein Complexes

    Definition of a Protein Complex

    A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains.

    Membrane Proteins

    As GO cellular component terms describe locations where a gene product may act, rather than physical features of proteins or RNAs, the terms integral membrane protein and peripheral membrane protein are present only as non-exact synonyms. GO distinguishes classes of membrane-related location:

    extrinsic component of membrane ; GO:0019898 refers to gene products that are associated with membranes, but are neither directly embedded in the membrane nor anchored by covalent bonds to any moiety embedded in the membrane.


    The set of standard terms below can be applied to each developing structure in each species covered in the ontology. However it is generally not practical to implement every term for every structure, since this would lead to a massive proliferation of terms. Where one term e.g. x development, is present, the rest of the terms for the development of x are considered to be implied, without having actually been implemented. Further terms are generally only implemented when they are required for annotation.