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.
I will update this periodically, cataloguing assay terms related to virology that can potentially be imported from elsewhere.
UPDATE The term 'antibody titer' should be imported from somewhere, as this is relevant to viral assays. IDOFLU created its own term for this (defined as "A antibody titer is output of a measurement that describes the measure of antibodies in a biomaterial'), but the term is clearly more general than influenza.
-I check OBI, but they do not have the term 'antibody titer' nor 'titer'
-I found the following term from the Clinical Measurement Ontology (an OBO library ontology):
antibody titer; see definition here [http://purl.obolibrary.org/obo/CMO_0001862]. It is a subclass of 'antibody measure' and it has various children.
IDOFLU also has the term hemagglutinin titer. That may also warrant moving up to VIDO.
-The following IDOFLU term certainly should be reassigned/curated as a VIDO term:
viral replication titer =def A scalar measurement datum that denotes the virus replication level
Related, IDOFLU has the titer related term which should be moved up:
tissue culture infectious dose 50 = def 'The quantity of virus in a specified suspension volume (e.g., 0.1 ml) that will infect 50% of a number (n) of cell culture microplate wells, or tubes.'
This is called TCID50 in the literature
viral hemagglutination inhibition assay =def An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the evaluant. [http://purl.obolibrary.org/obo/OBI_0000875]
serum neutralization of viral infectivity assay =def An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect. The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. [http://purl.obolibrary.org/obo/OBI_0000872]
...which has the child...
96-well neutralization assay =def A serum neutralization of viral infectivity assay which is performed in a 96-well plate. [http://purl.obolibrary.org/obo/OBI_0000865]
pseudovirus entry assay =def An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. [http://purl.obolibrary.org/obo/OBI_0002680]
...incidentally, this is a subclass of:
infectious agent detection assay =def An assay that measures the presence or amount of an infectious agent in an evaluant [http://purl.obolibrary.org/obo/OBI_0001187]
...which seems to warrant inclusion in IDO Core.
Not an assay term, but relevant:
viral RNA extraction =def The extraction of RNA from an input material that specifically isolates viral RNA [http://purl.obolibrary.org/obo/OBI_0000407]
...descends from OBI:material processing Should add this OBI term, and its hierarchy as we will need it for terms for virus related material processing (I know IDO FLU has many such terms--will discuss in another issue)
From IDO FLU (terms to be potentially moved up and in some cases curated)
hemagglutinin typing =def An assay which aims at determining the hemagglutinin subtype of an influenza virus.
...Update. hemagglutinin is not specific to influenza viruses. But from the literature it appears that this type of assay is used specifically for influenza viruses. Also, it appears that neuraminidase typing, for which IDOFLU created a term, is specific to influenza. Although, other viruses have neuraminidase activity, such as mumps. Of interest, it seems like the term 'viral neuraminidase' is only used for the neuraminidase in influenza]
Incidentally, the IDOFLU term hemagglutinin should be reassigned to VIDO perhaps as it is more general than influenza.
The definition needs minor curation though: "Hemagglutinin is a substance that causes red blood cells to agglutinate (has disposition hemagglutination)": UPDATE: see discussion of this in issue #2
From Eagle-i Resource Ontology (ERO)
virus plaque assay =def An organismal assay that is used to determine viral titers. [http://purl.obolibrary.org/obo/ERO_0000337]
*How detailed though should the definition be? OBI definitions for assays usually go into more detail.
Serology/Antibody testing
**Note, there are many terms for serology (antibody testing) in different ontologies if you search 'serology' or 'serological test' in OntoBee
serology assay =def A tissue/organ assay that is performed to analyze blood serum and other bodily fluids, to identify antibodies in the serum. [http://purl.obolibrary.org/obo/ERO_0000671]
*As defined in ERO, this seems like the output of serology testing is the identification of antibodies. This suggests that the detection of the corresponding infectious agent is a separate process (an inference based on antibody knowledge). Should this instead be included as part of the assay?
-I should look through the literature. Maybe I am drawing an ontological distinction that is here not reflected in the scientific use of the term antibody test.
Alternatively, there is this from the Medical Action Ontology (MAXO):
Serology test =def Testing blood serum for the presence of specific antibody or antibodies to a specific antigen. Often used when an infection is suspected. [http://purl.obolibrary.org/obo/MAXO_0000609]
*By saying that the assay tests for a specific antibody to a specific antigen, this seems to imply that the assay involves the leveraging of prior knowledge to infer the corresponding antigen.
Whichever term we select for antibody testing, the idea was to use it define a VIDO term along the lines of:
viral serology assay =def Serology assay used to identify the presence of viruses.
I will update this periodically, cataloguing assay terms related to virology that can potentially be imported from elsewhere.
UPDATE The term 'antibody titer' should be imported from somewhere, as this is relevant to viral assays. IDOFLU created its own term for this (defined as "A antibody titer is output of a measurement that describes the measure of antibodies in a biomaterial'), but the term is clearly more general than influenza. -I check OBI, but they do not have the term 'antibody titer' nor 'titer' -I found the following term from the Clinical Measurement Ontology (an OBO library ontology): antibody titer; see definition here [http://purl.obolibrary.org/obo/CMO_0001862]. It is a subclass of 'antibody measure' and it has various children. IDOFLU also has the term hemagglutinin titer. That may also warrant moving up to VIDO. -The following IDOFLU term certainly should be reassigned/curated as a VIDO term:
viral replication titer =def A scalar measurement datum that denotes the virus replication level
Related, IDOFLU has the titer related term which should be moved up: tissue culture infectious dose 50 = def 'The quantity of virus in a specified suspension volume (e.g., 0.1 ml) that will infect 50% of a number (n) of cell culture microplate wells, or tubes.' This is called TCID50 in the literature
[Note, IDOFLU uses IAO measurement terms]
From OBI:
viral hemagglutination assay =def An assay that quantifies viruses by their hemagglutination activity [http://purl.obolibrary.org/obo/OBI_0000871]
viral hemagglutination inhibition assay =def An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates hemagglutination inhibition by the evaluant. [http://purl.obolibrary.org/obo/OBI_0000875]
serum neutralization of viral infectivity assay =def An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect. The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. [http://purl.obolibrary.org/obo/OBI_0000872] ...which has the child... 96-well neutralization assay =def A serum neutralization of viral infectivity assay which is performed in a 96-well plate. [http://purl.obolibrary.org/obo/OBI_0000865]
pseudovirus entry assay =def An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. [http://purl.obolibrary.org/obo/OBI_0002680] ...incidentally, this is a subclass of: infectious agent detection assay =def An assay that measures the presence or amount of an infectious agent in an evaluant [http://purl.obolibrary.org/obo/OBI_0001187] ...which seems to warrant inclusion in IDO Core.
Not an assay term, but relevant: viral RNA extraction =def The extraction of RNA from an input material that specifically isolates viral RNA [http://purl.obolibrary.org/obo/OBI_0000407] ...descends from OBI:material processing Should add this OBI term, and its hierarchy as we will need it for terms for virus related material processing (I know IDO FLU has many such terms--will discuss in another issue)
From IDO FLU (terms to be potentially moved up and in some cases curated)
hemagglutinin typing =def An assay which aims at determining the hemagglutinin subtype of an influenza virus. ...Update. hemagglutinin is not specific to influenza viruses. But from the literature it appears that this type of assay is used specifically for influenza viruses. Also, it appears that neuraminidase typing, for which IDOFLU created a term, is specific to influenza. Although, other viruses have neuraminidase activity, such as mumps. Of interest, it seems like the term 'viral neuraminidase' is only used for the neuraminidase in influenza]
Incidentally, the IDOFLU term hemagglutinin should be reassigned to VIDO perhaps as it is more general than influenza. The definition needs minor curation though: "Hemagglutinin is a substance that causes red blood cells to agglutinate (has disposition hemagglutination)": UPDATE: see discussion of this in issue #2
From Eagle-i Resource Ontology (ERO)
virus plaque assay =def An organismal assay that is used to determine viral titers. [http://purl.obolibrary.org/obo/ERO_0000337] *How detailed though should the definition be? OBI definitions for assays usually go into more detail.
Serology/Antibody testing **Note, there are many terms for serology (antibody testing) in different ontologies if you search 'serology' or 'serological test' in OntoBee
serology assay =def A tissue/organ assay that is performed to analyze blood serum and other bodily fluids, to identify antibodies in the serum. [http://purl.obolibrary.org/obo/ERO_0000671]
*As defined in ERO, this seems like the output of serology testing is the identification of antibodies. This suggests that the detection of the corresponding infectious agent is a separate process (an inference based on antibody knowledge). Should this instead be included as part of the assay? -I should look through the literature. Maybe I am drawing an ontological distinction that is here not reflected in the scientific use of the term antibody test.
Alternatively, there is this from the Medical Action Ontology (MAXO): Serology test =def Testing blood serum for the presence of specific antibody or antibodies to a specific antigen. Often used when an infection is suspected. [http://purl.obolibrary.org/obo/MAXO_0000609]
*By saying that the assay tests for a specific antibody to a specific antigen, this seems to imply that the assay involves the leveraging of prior knowledge to infer the corresponding antigen.
Whichever term we select for antibody testing, the idea was to use it define a VIDO term along the lines of: viral serology assay =def Serology assay used to identify the presence of viruses.