PhiBabs935
commented
3 years ago Update: I have imported a good portion of these into my IDO Core file. More or less everything up until the section on molecules that serve as virus receptors. Will copy these terms into VIDO and IDO-COVID-19 as well.
That said, I think that the import of immune system relevant terms is going to be an ongoing project. There's tons of stuff from Cell Ontology and GO.
Update:6/19: So, looking over the Cell Ontology, we could just go through the terms that it imports from GO, including GO:immune system process and the many subclasses descending from this term, and import the ones we need. Also, there are many related terms imported in CL from GO descending from GO:localization that are relevant.
Here I will compile terms pertaining to immune response to potentially add to IDO Core:
General note: after searching, the main glossary terms from the text "Introduction to Modern Virology" scratch the surface. There are tons of related terms that could potentially be added. But I will focus on the main ones from the glossary for now.
General note: with regard to his unpublished antibody ontology, Alex has suggested using the term 'recognizes' relation from the Reagent Ontology, =def "a type of targeting relation reserved to describe the relation between an adaptive immune receptor complex and its antigenic target, as antibodies are generated with the function of targeting a specific antigen. For example, antibody x 'recognizes' antigen y if x interacts with an epitope part of y (above some threshhold affinity), and thereby realizes the binding function of the antibody." http://purl.obolibrary.org/obo/REO_0000511 It would be relevant to the stuff we are adding here. In particular, might this be relevant to 'immunological memory'? (see below)
Terms from the box 12.1 in "Introduction to Modern Virology" (I put these terms in bold) This text abbreviated IMV below
Adaptive immunity IDO Core already has the term acquired immunity to infectious agent (alternative label adaptive immunity to infectious agent) which covers this. http://purl.obolibrary.org/obo/IDO_0000621 *OWL definition refers to T cell and B cell receptor complex terms (which are imported in IDO Core)
antibody See issue #9 Lindsay says we can add GO:immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0042571 *UPDATE Alex Diehl agreed we should use this term, indeed he created it for GO!
Antigen I said in issue #9 we could use OBI:antigen, which is a material entity defined in terms of an antigen role Alternatively, we can use the CHEBI term: antigen =def Any substance that stimulates an immune response in the body, such as through antibody production or by presentation to a T-cell receptor after binding to a major histocompability complex (MHC). http://purl.obolibrary.org/obo/CHEBI_59132 will see what Alex thinks: UPDATE** Alex agrees we should use the OBI term.
"Antigen presentation: display on the cell surface of a peptide complexed with an MHC I or MHC II protein that is capable of reacting with a T cell receptor." We can use GO:antigen processing and presentation =def The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0019882
Antigen processing I guess this will also be covered by GO:antigen processing and presentation ???
Should we add subclasses for this term? Such as GO:B cell antigen processing and presentation and GO:T cell antigen processing and presentation I think perhaps we should: e.g. B cell antigen processing and presentation has axiom, part of some GO:B cell mediated immunity, the latter of which should be added along with the corresponding T cell term (see below)...although it is a process, whereas the label suggests a disposition
B effector cell: short-lived cell that makes antibody The Cell Ontology has the term Be cell which is annotated as having B effector cell as an exact synonym: =def A mature B cell that produces cytokines that can influence CD4 T cell differentiation. http://purl.obolibrary.org/obo/CL_0000968 *Though I am confused because it is asserted to be a mature cell in CL, but this textbook says these cells are short-lived?
Be cell is an indirect subclass of CL:B cell =def A lymphocyte of B lineage that is capable of B cell mediated immunity. http://purl.obolibrary.org/obo/CL_0000236 OWL definition includes the conjunct: capable of GO:B cell mediated immunity . This latter GO term should probably be imported: =def Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. http://purl.obolibrary.org/obo/GO_0019724
CL:B cell has exact synonym 'B lymphocyte', so it covers that term.
For B Cell Receptor IDO Core already imports can GO:B cell receptor complex =def An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. http://purl.obolibrary.org/obo/GO_0019815 *this is a cellular_component; has the function of antigen binding **in IDO core it is currently a subclass of GO:macromolecular complex
B and T lymphocytes For B lymphocytes see above, CL:B cell For T lymphocytes see CL:T cell below
CD4 Can use PRO:CD4 molecule =def A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. http://purl.obolibrary.org/obo/PR_000001004
Incidentally, IDO Core currently uses the CHEBI version of protein Perhaps use the PRO version, which is also used by CL and many other ontologies? Or does it matter?
CD8 PRO didn't have a general term for this. It only has more specific types of CD8 molecules, which we don't necessarily need. But, we could use OBI:CD8 receptor =def A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. http://purl.obolibrary.org/obo/OBI_1110132 *What do you think?
Cell-mediated immunity immunity mediated by various T cell responses
From GO we could import B cell mediated immunity =def Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. http://purl.obolibrary.org/obo/GO_0019724 *The only issue is that the glossary term suggests a disposition, as does the GO term, but it's a process. I think this is longstanding issue with certain GO terms. Though, the Cell Ontology already uses it, so we have good precedent.
T cell mediated immunity =def Any process involved in the carrying out of an immune response by a T cell. http://purl.obolibrary.org/obo/GO_0002456
We should also add its subclass, T cell mediated immunity (see under Cytotoxic T lymphocyte below). Also add its subclass, T cell cytokine production
Both are subclasses of GO:adaptive immune response which is already in IDO core
Chemokines: superfamily of small soluble proteins involved in variety of immune (etc) processes
I had trouble finding a general term for these in PRO; PRO of course has tons of specific terms (which we can add later, but I would rather confer with Lindsay and Alex, as going through these specific terms it's all Greek to me!!!)
(note, all reference to NCI Thesaurus terms are to the OBO edition) Maybe just use the NCI Thesaurus term? =def Chemokines constitute a superfamily of small (8-10 kDa), inducible, secreted, pro-inflammatory cytokines that are involved in a variety of immune and inflammatory responses as well as in viral infection. Chemokines act primarily as chemoattractants and activators of specific types of leukocytes. Some members of this family were initially identified on the basis of their biological activities (e.g., IL-8, GRO), others were discovered using subtractive hybridization (e.g., RANTES) or signal sequence trap (e.g., PBSF/SDF-1)11 cloning strategies. They attract and activate leukocytes and regulate diverse cellular systems and organs ranging from blood vessels to the central nervous system. http://purl.obolibrary.org/obo/NCIT_C20466
Related: PRO has the term chemokine receptor http://purl.obolibrary.org/obo/PR_000001128
Related: GO has the related process terms chemokinesis http://purl.obolibrary.org/obo/GO_0042466 and chemokine receptor activity http://purl.obolibrary.org/obo/GO_0004950 Indeed, GO has tons of immune process terms involving chemokines. Will have to think about which to add eventually. Likewise, it has tons of immune process terms relating to cytokines.
Cytokines: "superfamily of soluble protein mediators and communicators released from cells by specific stimuli"
NCIT has cytokine =def A class of soluble glycoproteins which act nonenzymatically through specific receptors to regulate immune responses. Cytokines are derived from both immune and non-immune cells and are intercellular mediators that differ from hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. http://purl.obolibrary.org/obo/NCIT_C20464
Cytotoxic T lymphocyte: activated T cells that can kill target cells by lysing them. (IMV)
CL has the following term: cytotoxic T cell =def A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive. http://purl.obolibrary.org/obo/CL_0000910 cytotoxic T lymphocyte listed as synonym has OWL definition: effector T cell and (capable of some T cell mediated cytotoxicity) *This OWL definition involves GO: T cell mediated cytotoxicity which we should add as well.
When you search Cytotoxic T lymphocyte in OntoBee you will see that PRO has various related proteins
Epitope part of a molecule that binds the paratope of a cognate T or B cell receptor
We have options here: Sequence Ontology has: epitope =def A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells. http://purl.obolibrary.org/obo/SO_0001018
Alternatively, OBI has: epitope =def A material entity bearing the epitope role http://purl.obolibrary.org/obo/OBI_1110001 While SO term more straightforwardly captures the concept, the pros of using the OBI term is that it has rich OWL axioms associated with it. Update: con: I don't see a term for epitope role in OBI.
Searching 'epitope' in OntoBee you will see that OBI also has lots of potentially relevant biological processes involving epitopes (e.g., epitope specific T cell activation, epitope specific immune intervention & its two B cell and T cell specific children, as well as epitope binding by adaptive immune receptor, etc)
Humoral immunity: antibody-mediated immunity
IDO Core already has a term pertaining to this, a resistance disposition that is a direct child of immunity to infectious agent: humoral immunity to infectious agent =def An immunity to infectious agent that inheres in an organism in virtue of components of its circulating body fluid.
John, I noticed that you don't have the IDO Core subclasses of immunity to infectious agent in the IDO Virus file you sent to me. Is that intentional?
Immunogen: a molecule that stimulates adaptive immunity to its epitopes.
CHEBI has immunogen =def An antigen capable, on its own, of inducing an immune response. http://purl.obolibrary.org/obo/CHEBI_60816
But OBI has immunogen =def A material entity bearing the immunogen role http://purl.obolibrary.org/obo/OBI_1110023 So we would import immunogen role from OBI too: =def Any entity capable of eliciting an immune response when introduced to components of the immune system
*Obviously, immunogen role requires curation, since it confuses the role with the entity bearing the role. Suggested fix, something like: Role borne by a material entity in virtue of the fact it is capable of eliciting an immune response when introduced to components of the immune system.
Immunological memory: "the ability to remember a foreign antigen experienced by the body... (etc). (IMV) **This seems like a term that where the Reagent Ontology relation 'recognizes' (mentioned above) might be relevant.
GO has a related process term, the definition of which refers to this ability: immunological memory process =def Any process of the immune system that can contribute to the formation of immunological memory or an immune response based upon activation of immunological memory. http://purl.obolibrary.org/obo/GO_0090713
But I didn't find any term in OntoBee for the ability itself. The only two terms that mention it are the above GO process and GO:immunological memory formation process
Perhaps we should submit a term request to GO? Here's a start: immunological memory: =def Disposition inhering in the immune system that is the ability of the body to remember an antigen experienced by the body at any earlier time, which leads to a more easily activated, more rapid, and greater immune response on subsequent encounters with that antigen. [citing the Introduction to Modern Virology text as a definition source]
Is there a danger of circularity if we add the axiom it is realized in some immunological memory process?
But I wouldn't be surprised if Alex was already working on something for his antibody ontology, we'll see what he says.
Innate Immunity: a defense system that is always ready to act and is unchanged by infection... (IMV)
This is probably covered already by IDO:innate immunity to infectious agent http://purl.obolibrary.org/obo/IDO_0000576
*my only question: should it be changed to 'pathogen', in case innate immunity applies to pathogens that are not infectious agents.
MHC (major histocompatibility) protein "(in man usually referred to as human leukocyte antigen (HLA)): MHC class I – integral plasma membrane protein found on nearly all" (IMV) cells of the body; MHC class II – integral plasma membrane protein that is normally restricted to cells of the immune system."
NCI Thesaurus has a term for the whole protein family: HLA =def A family of proteins that are essential for the presentation of peptide antigens on cell surfaces that modulate the host defensive activities of T-cells. This protein family includes major histocompatibility complex (MHC) class I and class II proteins. [def-source: NCI] http://purl.obolibrary.org/obo/NCIT_C121977
NCIT also has: MHC Class I Protein =def Found on virtually every cell, MHC (Major Histocompatibility, HLA) Class-I (Antigens) Proteins consist of noncovalently bound polymorphic 44-kDa MHC membrane glycoprotein and nonpolymorphic 12-kDa b2-microglobulin. The HLA antigens are encoded by closely linked multiallelic genes of the HLA (MHC) complex, a region containing several genetic loci (HLA-A, -B, -C, -DP, -DQ, -DR, -MB, -MT, and -Te). http://purl.obolibrary.org/obo/NCIT_C20706 MHC Class II Protein =def MHC Class-II Proteins are non-covalently linked polymorphic alpha/beta transmembrane glycoproteins. The immunological function of MHC Class-II proteins is to bind and present antigenic peptides on the surfaces of cells for recognition by the antigen-specific T cell receptors of lymphocytes. These proteins plays an important role in the mediation of immune response. http://purl.obolibrary.org/obo/NCIT_C20705
PRO has: MHC class I-related gene protein =def A protein that is a translation product of the human MR1 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001819
*it has a variety of subclasses with 'major histocompatibility complex' in the label, but they are all specific to particular organisms (e.g. rat, mouse, etc)
For MHC class II, the most relevant thing PRO has is: MHC class II histocompatibility antigen alpha chain =def A protein with core architecture consisting of a signal sequence, a Class II histocompatibility antigen, alpha domain (Pfam:PF00993) and an Immunoglobulin C1-set domain (Pfam:PF07654); these form the extracellular domain and are followed by a single-pass transmembrane region and a small cytoplasmic region. http://purl.obolibrary.org/obo/PR_000001820
MHC Update 6/17/20: So I just searched GO again: it has the following relevant terms:
MHC class I protein complex http://purl.obolibrary.org/obo/GO_0042612 MHC class II protein complex http://purl.obolibrary.org/obo/GO_0042613
6/21 These GO classes include MHC complexes in which the MHC protein is bound with a antigen peptide (as a result of antigen processing) so that it can be presented on the cell surface where it will be recognized by a T cell. [Though these classes also cover MHC complexes without antigen peptides]
Monoclonal antibody (MAb): "antibody of a single sequence and hence specific for a single epitope made by a clonal population of immortalized B effector cells (a hybridoma)." (IMV)
The Reagent Ontology has monoclonal antibody =def An antibody reagent produced by clonal hybridoma cells deriving from the fusion of a single activated B-cell with a neoplastic cell, such that antibodies isolated from such cells are monospecific for a single epitope. A collection of such antibodies has specificity for a single epitopes on its target antigen - versus a collection of 'polyclonal antibodies', which recognize various different epitopes. But at the structural level of the individual molecular reagent, there is of course no distinction between mono- and poly-clonal antibodies. http://purl.obolibrary.org/obo/REO_0000501
Alternatively, NCIT has: Monoclonal Antibody =def An antibody produced by a clone or genetically homogenous fast-growing cells i.e., hybridoma. Hybridoma cells are cloned to establish cell lines producing a specific antibody that is chemically and immunologically homogeneous. They are widely used in cancer detection, diagnosis, and treatment. http://purl.obolibrary.org/obo/NCIT_C20401
Non-self "any antigen that is not normally present in that individual" (IMV) Self (antigen) "any antigen normally present in that individual."
Couldn't find these terms in any ontology. GO does have the process tolerance induction to self antigen which refers to self antigens http://purl.obolibrary.org/obo/GO_0002513
**Think I will have to look into this more, and see what Alex might know. Maybe he is working on something for the antibody ontology.
Paratope: "region of a B or T cell receptor that recognizes and binds a cognate epitope." (IMV)
I found nothing with this label in OntoBee. From wikipedia: Paratopes are also called 'antigen-binding sites'--have to determined if these are better defined as sites or spatial regions. It is a part of an antibody (immunoglobulin complex) that recognizes and binds to an antigen. -contains parts of the antibody's heavy and light chains. -it is a small region of the antibody's Fab region or antigen-binding fragment.
NCIT does have a term Fab fragment =def Part of an immunoglobulin antibody that binds a specific antigen and consists of both a light chain and part of a heavy chain. By comparison, natural antibodies consist of two heavy and two light chains. An FAB (fragment antibody) offers the advantages of smaller size and lower cross-reactivity compared to the complete antibody. http://purl.obolibrary.org/obo/NCIT_C13246
I will have to double check with Alex, but not sure there is a term out there with a different label. In case there isn't, something like: =def A small region (of 5 to 10 amino acids) of an antibody's Fab region that recognizes and binds to an antigen, and contains parts of the antibody's heavy and light chains.
Based on the above, it's not clear what the essential difference is between the Fab region and the paratope region that it has as a part. Both are defined as binding to antigens, except the paratope only has part of the light and heavy chain.
T cell receptor (TCR) "integral plasma membrane protein of T cells that recognizes a T cell epitope; the epitope is a peptide complexed with an MHC I or MHC II protein on the surface of another cell of the same person; also known as antigen or epitope presentation" (IMV)
We should import GO:T cell receptor complex =def A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. http://purl.obolibrary.org/obo/GO_0042101
T effector cell: "short lived cells that directly act on other cells of the body"
I think the relevant term would be CL:effector T cell =def A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response. http://purl.obolibrary.org/obo/CL_0000911 *Some of its superclasses which descend from CL:T cell may be relevant imports as well.
Terms for components of the innate immune system (chemokines, cytokines are part of this, but already covered above)
I. Soluble components (includes chemokines, cytokines)
interferons: -protein released by animal cells, usually in response to the entry of a virus, which has the property of inhibiting virus replication. Are these specific to viral infection immune response? If so, should this go in VIDO and not IDO? Either way, whichever term we import we should assert it as a subclass of has some disposition 'virostatic disposition' -We could use NCIT:inteferon See http://purl.obolibrary.org/obo/NCIT_C20493 (the definition is quite long. Alternatively we could use OMIT:Receptors, Interferon http://purl.obolibrary.org/obo/OMIT_0017824 (though this term, like most OMIT terms, has no textual definition)
*CHEBI and OMIT also have terms for more specific types of interferons, depending on needed specificity (i.e. interferon alpha-2a, interferon beta-1b, etc)
Update Protein Ontology has the relevant classes under:
type I interferon [http://purl.obolibrary.org/obo/PR_000025848], along with subclasses interferon alpha and interferon beta type II interferon [http://purl.obolibrary.org/obo/PR_000024990], along with the subclass interferon gamma, which is particularly important to coronavirus-host interactions and pathogenesis.
There are also plenty of specific subclasses we can import for IDO-COVID-19 or other virus ontologies where appropriate
GO has the related process term, which may be relevant: GO:interferon binding http://purl.obolibrary.org/obo/GO_0019961
complement We could use the term complement from NCIT http://purl.obolibrary.org/obo/NCIT_C16459
II. Cells
macrophages mobile while blood cell that patrols tissues outside the blood stream. -use CL:macrophage http://purl.obolibrary.org/obo/CL_0000235
polymorphonuclear leukocytes, these are white blood cells that patrol the blood; abbreviated as PMNL; they are also called granulocytes so we can import:
CL:granulocyte http://purl.obolibrary.org/obo/CL_0000094]
***Issue: In IMV, both macrophages and PMNLs are classified as phagocytes and are said to be capable of phagocytosis (basically destroying antigens via ingestion), but I found that in CL, granulocyte is a subclass of myeloid leukocyte which is a leukocyte, and it is not classified as a phagocyte. Nor is it asserted to be capable of phagocytosis. In CL macrophage is a subclass of leukocyte, via ‘professional antigen presenting cell’. It is also a subclass of phagocyte, and is asserted to be capable of phagocytosis. I emailed Alex Diehl about this.
-For phagocyte we can import CL:phagocyte “Any cell capable of ingesting particulate matter via phagocytosis.” http://purl.obolibrary.org/obo/CL_0000234 -For phagocytosis we can import GO:phagocytosis: A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. http://purl.obolibrary.org/obo/GO_0006909
dendritic cells Use CL:dendritic cell "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative)." http://purl.obolibrary.org/obo/CL_0000451
Natural killer cells Use CL:natural killer cell A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. http://purl.obolibrary.org/obo/CL_0000623
Terms from IMV concerning virus attachment that are also relevant to immune response (Table 5.1 p. 63-64) Note, though these terms we discussed specifically with respect to their application to viral immunology, I think they have application generally as well, but not sure. Some scientific terms use special symbols for 'alpha' 'beta', etc, but I didn't know how to do them here.
Molecules that serve as receptors for viruses
I. Proteins
ICAM-1: Primary: receptor for most (but not all) Rhinoviruses: PRO:ICAM1 http://purl.obolibrary.org/obo/PR_000001467
CAR (Coxsackie-adenovirus receptor): Primary receptor for many adenoviruses, Coxsackie B viruses: PRO:coxsackievirus and adenovirus receptor http://purl.obolibrary.org/obo/PR_000006062
AlphavBeta6 integrin: primary receptor for foot and mouth disease virus -I believe that the term would be GO:integrin alphav-beta6 complex: “An integrin complex that comprises one alphav subunit and one beta6 subunit http://purl.obolibrary.org/obo/GO_0034685 (protein-containing complex, plasma membrane protein complex)
AlphavBetax integrin: Coreceptor for adenoviruses -couldn’t find this one in GO. Maybe send a term request. -I did find this paper referencing the AlphavBetax protein complex https://pubmed.ncbi.nlm.nih.gov/2467745/
CD4:Primary receptor for HIV-1, HIV-2, SIV: -use PRO:CD4 molecule: http://purl.obolibrary.org/obo/PR_000001004
CCR5: Coreceptor for HIV-1, HIV-2, SIV -Use PRO:C-C chemokine receptor type 5 (short label, CCR5) “A chemokine receptor that is a translation product of the human CCR5 gene or a 1:1 ortholog thereof. The preferred ligands include CCL3, CCL4, CCL5, CCL8, CCL14.” http://purl.obolibrary.org/obo/PR_000001201
CXCR4 Coreceptor for HIV-1, HIV-2, SIV -Use PRO:C-X-C chemokine receptor type 4: A chemokine receptor that is a translation product of the human CXCR4 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL12. http://purl.obolibrary.org/obo/PR_000001208
DC-SIGN: (abbreviation for Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin), also called CD209, Cluster of differentiation 209: Primary receptor for HIV-1, SIV -Use: PRO:CD209 molecule: http://purl.obolibrary.org/obo/PR_000001300
CDW150 (SLAM); Primary receptor for the measles virus. -Use: PRO:SLAM family member 1 http://purl.obolibrary.org/obo/PR_000001833
CD 155: primary receptor for poliovirus. -Use PRO:poliovirus receptor “A poliovirus receptor-related protein that is a translation product of the human PVR gene or a 1:1 ortholog thereof.” http://purl.obolibrary.org/obo/PR_000002067
MHC I; Primary receptor for human cytomegalovirus. -(maybe?) NCIT:MHC Class I Protein http://purl.obolibrary.org/obo/NCIT_C20706 -related: GO:MHC class I protein complex http://purl.obolibrary.org/obo/GO_0042612
MHC II; Primary receptor for Lactate dehydrogenase-elevating virus -use (maybe) NCIT:MHC Class II Protein http://purl.obolibrary.org/obo/NCIT_C20705 -related: GO:MHC class II protein complex http://purl.obolibrary.org/obo/GO_0042613
CR2; primary; is a receptor for complement component C3d; -receptor for Epstein-Barr virus -use PRO:completed receptor type 2 http://purl.obolibrary.org/obo/PR_000001338
IgA receptor; Primary receptor for Hepatitis B virus. -Not sure what the proper term is for IgA receptor, here are some I thought might apply: -GO:immunoglobulin complex, http://purl.obolibrary.org/obo/GO_0071745 [it has the comment, “Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available.” And has narrow synonym: IgA2 antibody. This term has the subclass: GO:IgA B cell receptor complex http://purl.obolibrary.org/obo/GO_0071747 -Related term: PRO:IgA heavy chain protein http://purl.obolibrary.org/obo/PR_000050176
Phosphate transporter; primary receptor for some retroviruses. -This is a general term. I couldn’t find a general term for such proteins in PRO, just very specific types. -***OMIT has Phosphate transport proteins http://purl.obolibrary.org/obo/OMIT_0021392, but has no textual definition. Not sure what to use here.
Virus-specific IgG bound to cells by Fc receptors; primary receptor for Dengue virus in vivo and many others in vitro. -IgG stands for ‘immunoglobulin G (gamma)’, I am not sure, would the term be the following? PRO:immunoglobulin gamma Fc receptor I -related term: PRO:IgG heavy chain protein http://purl.obolibrary.org/obo/PR_000050252
Beta-adrenergic receptor; primary receptor for reoviruses. -Not sure here: PRO has the following term: -beta-adrenergic receptor kinase 1 http://purl.obolibrary.org/obo/PR_000003791 -OMIT has Receptors, Adrenergic, beta http://purl.obolibrary.org/obo/OMIT_0012871
Acetylcholine receptor; Primary receptor for Rabies virus. -PRO has a term for one of the two major types of acetylcholine receptors: PRO:muscarinic acetylcholine receptors http://purl.obolibrary.org/obo/PR_000001488 And also one for the nicotinic subtype. Haven’t found anything more general.
II. Carbohydrates:
N-acetylneuraminic acid (only acts as receptor when terminal in the carbohydrate moiety); primary receptor for influenza virus A, B, C; paramyxoviruses, polyomavirus, encephalomyocarditis virus, reviruses -use CHEBI:N-acetylneuraminic acid http://purl.obolibrary.org/obo/CHEBI_17012
Heparan sulfate; coreceptor for HIV-I, herpes simplex virus, dengue virus, Sindbis virus, cytomegalovirus, adeno-associated virus, respiratory syncytial virus, foot-and mouth disease virus. -use CHEBI:heparan sulfate http://purl.obolibrary.org/obo/CHEBI_28815
III. Lipids
Phosphatidylserine; primary receptor for Vesicular stomatitis virus -CHEBI has a variety of specific types, but not the general class. -NCIT has the general class phosphatidylserine, defined as “A phospholipid with a polar serine found in phosphoester linkage to diacylglycerol” http://purl.obolibrary.org/obo/NCIT_C68417