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infectious-disease-ontology-extensions / VIDO

The Virus Infectious Disease Ontology (IDO Virus) is an extension of the Infectious Disease Ontology (IDO). IDO Virus follows OBO Foundry guidelines, employs the Basic Formal Ontology as its starting point, and covers epidemiology, classification, pathogenesis, and treatment of terms used by Virologists, i.e. virus, prion, satellite, viroid, etc.
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Terms to move to VIDO from FLU (revised) #6

Open PhiBabs935 opened 3 years ago

PhiBabs935 commented 3 years ago

Whether all of these should be moved to VIDO is up for discussion. I am mulling whether some would be more in OBI's province.

[Edit: 11/12/2020: I added all of these to VIDO, with VIDO URIs, except for 'antiviral treatment date' and 'virus isolation protocol'. The latter seems better for OBI.

If we proceed with adding all (or some) of these, I would be happy to do the task of directly copy them to John's VIDO OWL file from my IDOFLU file. This will take a little work, as many of these have as superclasses various OBI terms not currently in VIDO.

In order to add the first 4 terms will we need to add to VIDO IAO's 'measurement datum' and the subclasses 'scalar measurement datum' and 'time measurement datum'

  1. antiviral treatment date =def Time measurement datum that specifies the date when the antiviral treatment was administered. OWL: SubClass of: 'is about' some 'antiviral treatment' [Note, I imported Apollo-SV's 'antiviral treatment' to replace the equivalently labeled FLU term. Would need to import the former to VIDO, which requires importing its superclasses OGMS:'treatment' and Apollo-SV:'drug treatment']

  2. virus passage date =def Time measurement datum specifying the date that the virus passage(s) took place.

OWL:SubClass of: 'is about' some 'virus passage'

  1. viral titer measurement datum =def Scalar measurement datum that is the measure of some viral load.

OWL definition: 'scalar measurement datum' and ('is about' some 'viral load')

  1. virus pathogenicity after passage =def A scalar measurement datum denoting the pathogenicity of a virus after several passages in cell culture.

OWL:SubClass of: 'scalar measurement datum' and ('is about' some 'pathogenic disposition') OWL:SubClass of: is_specified_output_of some 'virus passage'

  1. virus passage history record =def Passage history record that details the number of times a virus has been passaged in cell culture. [Adding this will require importing the OBI term 'passage history record' as its parent]

  2. virus isolation protocol =def Extraction protocol that specifies the procedure for isolating a virus.

[Adding this would require importing 'extraction protocol' from EFO. But also OBI's 'protocol' and IAO's 'plan specification']

  1. viral isolate =def Virus that has been extracted from a host organism.

OWL definition: virus and (is_specified_output_of some 'virus isolation')

  1. amplified virus preparation =def Virus aggregate, consisting of a large number of copies of one or more viruses, that is the specified output of some virus amplification.

OWL definition: 'virus aggregate' and (is_specified_output_of some 'virus amplification') and ('has role' some 'specimen role') ['specimen role' is from OBI]

  1. virus isolation =def Material separation to recover the virus fraction of an input material.

    has_specified_output some 'viral isolate'

  2. virus passage =def Passage process that involves the incubation of a virus in a tissue culture, a developing egg, or a living organism to increase the number of the virus or to alter its characteristics.

['passage process' is from OBI]

  1. virus amplification =def Material processing with the objective of increasing the number of viruses in a specimen.

has_specified input some specimen

  1. (newly created term) viral titer measurement datum =def Scalar measurement datum that is the measure of some viral load.

OWL definition: 'scalar measurement datum' and ('is about' some 'viral load')

PhiBabs935 commented 3 years ago

Also moved 'hospitalized host' from IDOFLU to IDO