View source for Other Organisms and Viruses (2005-2013)

=Multi-Organism Process=

Multi-organism process and its children were created in Jan 2005 in collaboration with the Plant-Associated Microbe GO interest group (PAMGO) to describe interactions that occur between organisms of different species, and to subsume the existing terms that described interactions between organisms, e.g. pathogenesis and host-pathogen interaction. These terms were felt to be too 'host-centric', due to their reference to the disease process and their non-systematic placement in the ontologies. Further terms were added after the November 2005 content meeting to flesh out the node further.

Complementary terms exist for annotating cellular locations such as host cell nucleus; see the cellular component guidelines for more details. The GO annotation conventions have a guide to annotating with these terms and how to represent the other organism in the interaction.

=Terms and structure=

Multi-organism processes are categorized according to the nature of the interaction (behavioral or physiological), and by whether they are inter- or intra-species. Interspecies interactions of an intimate or co-dependent nature fall under the term symbiosis, encompassing mutualism through parasitism, which covers all types of symbiosis between species, including mutualism (where the association is advantageous to one, or usually both, organisms) and parasitism (where the association is advantageous to one organism but detrimental to the other). All new terms that describe interactions between organisms should be placed in the interaction between organisms node under the appropriate parent(s).

The node is structured broadly like this (not all terms shown):

    multi-organism process
    [i] interspecies interaction between organisms
    ---[i] symbiosis, encompassing mutualism through parasitism
    [i] intraspecies interaction between organisms

Symbiotic relationships may be between two organisms of similar sizes or of differing sizes, and most of the processes under symbiosis, encompassing mutualism through parasitism have child terms to specify the sizes of the organisms involved. These terms use the nomenclature host for the larger organism and symbiont for the smaller organism. For interactions where there is no clear host or symbiont, the wording other organism is used, and terms are appended with during symbiotic interaction to make it clear that they represent processes occurring during symbiosis.

    symbiosis, encompassing mutualism through parasitism
    [i] acquisition of nutrients from other organism during symbiotic interaction
    ---[i] acquisition of nutrients from host
    ---[i] acquisition of nutrients from symbiont
    [i] interaction with host
    ---[i] acquisition of nutrients from host
    [i] interaction with symbiont
    ---[i] acquisition of nutrients from symbiont

Some processes may occur as part of symbiosis or outside it; the structure to represent such a process is illustrated below. Note that terms representing non-symbiotic interactions between organisms should use the wording another organism to refer to the second organism.

    interaction between organisms
    [i] physiological interaction between organisms
    ---[i] killing of cells of another organism
    ------[i] killing of cells of other organism during symbiotic interaction
    ---------[i] killing of host cells
    ---------[i] killing of symbiont cells
    [i] interspecies interaction between organisms
    ---[i] symbiosis, encompassing mutualism through parasitism
    ------[i] killing of cells of other organism during symbiotic interaction
    ---------[i] killing of host cells
    ---------[i] killing of symbiont cells

==More reading material==
[https://docs.google.com/document/d/196nLKiQ2Go4toilCq226w7u0p52odvCkq-bU5qgtzu0/edit?usp=sharing host_symbiont_annotation doc from Chris]

=Standard Definitions=

*'''[process involving] other organism during symbiotic interaction''':  [definition of process], where the two organisms are in a symbiotic relationship. 

*'''[process involving] host''': [definition of process]. The host is defined as the larger of the organisms involved in a symbiotic interaction. 

*'''[process involving] symbiont''': [definition of process]. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction. 

Taking the process acquisition of nutrients as an example, the terms and definitions would be as follows:

*'''acquisition of nutrients from other organism during symbiotic interaction''':  The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from a second organism, where the two organisms are in a symbiotic relationship. 
*'''acquisition of nutrients from host''':  The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its host. The host is defined as the larger of the organisms involved in a symbiotic interaction. 
*'''acquisition of nutrients from symbiont''':  The production of structures and/or molecules in an organism that are required for the acquisition and/or utilization of nutrients obtained from its symbiont. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction. 

=Hosts, Symbionts and Viruses=

The cellular component ontology provides terms to complement those in the biological process ontology representing multi-organism processes. There are two main locations for these terms: the first set, for the representation of the larger organism in the interaction, can be found under host in extraorganismal space; the second set are to capture virus components, and are under the term virion.

    cellular_component
    [i] extracellular region
    ---[p] extracellular region part
    ------[i] extraorganismal space
    ---------[i] host
    ...
    [i] virion

Viruses should be annotated like any other organism involved in a multi-organism process, using cellular component terms such as host cell cytoplasm or host cell nucleus. Locations in the virus itself are found under the term virion.



The GO annotation conventions have a guide to annotating with these terms and how to represent the other organism in the interaction. '''DOES THAT STILL EXIST ?'''

==2013 Virus cross-products==
* [[Virus_call_2013-11-27]]
** Jane, Becky, Chris, David OS 
** better way to represent viral modulation of cell activity
** terms that reference a specific host protein, where the virus modulates one or more functions of that protein
** Processes where the differentia is that it involves a virus

==2009-2012 Virus work==
Jane Lomax, Rebecca Foulger, Brenley McIntosh - July 2012
    Michelle Gwinn Giglio, Candace Collmer, Ariane Toussaint, Alexander Diehl, Fiona McCarthy, Marcus Chibucos

* '''Summary''': [[Virus_terms_(Completed_2012)]]
* [[Virus_ontology_devt_July_2012]]
* [[Spanins_and_Holins]] 14 August 2012‎ 
* [[Brenley's_Suggested_Terms]] 16 August 2012‎

==Phage calls 2012==
* [[Phage_jamboree-_I_July_31st_2012]]
* [[Phage_jamboree-_II_August_2nd_2012]]
* [[Phage_call_August_9th_2012]]
* [[Phage_call_August_21st-23rd_2012]]
* [[Phage_call_August_30th_2012]]
* [[Phage_call_September_6th_2012]]


==Virus discussions 2009==
* Michelle, Candace, Marcus, Fiona, Jane, Alex, Ariane, Brenley, Fiona 
* [[First_email_for_virus-term_overhaul,_march_09]]
** The terms themselves are a real jumble with no overall structure, and the annotations we have a mainly to a small number of these terms (e.g. GO:0019059 : initiation of viral infection, GO:0019047 : provirus integration, GO:0019061 : uncoating of virus)
* [[Viral_term_WebEx_meeting_june_3_2009]]
** lysis/lysogeny split
**  discussion of top-level term names and whether 'viral reproduction encompassed all viral processes. Perhaps use 'viral-host interaction' instead?
** discussion of the annotation of 'abnormal' processes
** necessity to have a specific 'viral' term - for example 'viral transcription' (or not)
* [[Viral term WebEx meeting august 21 2009]]
** Creating separate viral v/s host terms.
** Reproduction v/s growth v/s development
** Symbiont granularity (unicellular vs multicellular)
* [[Candace's_email_21_July_2009]]
** GO:0009626 : plant-type hypersensitive response
** GO:0034053 : modulation by symbiont of host defense-related programmed cell death


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