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Term issue: New terms for human IgA and IgD protein complexes #147

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addiehl opened this issue May 24, 2019 · 20 comments

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@addiehl
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commented May 24, 2019

Here are a set of new terms in OBO format for human IgA and IgD immunoglobulin protein complexes, 17 terms in all. The terms are linked to and modeled on the GO protein complexes for these immunoglobulin isotypes.

This work is prepared as part of HIPC data standards working group and Cell Ontology projects.

Feel free to change as needed to conform to PRO guidelines.

Thanks,
Alex

[Term]
id: PR:NewTerm01
name: IgA1 immunoglobulin complex (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda) held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA1 immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
comment: Note that an IgA1 immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
synonym: "IgA1 antibody" NARROW [GOC:add]
synonym: "IgA antibody" BROAD [GOC:add]
is_a: GO:0071745 ! IgA immunoglobulin complex

[Term]
id: PR:NewTerm02
name: IgA2 immunoglobulin complex (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA2 isotype and two identical immunoglobulin light chains (kappa or lambda) held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA2 immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
comment: Note that an IgA2 immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
synonym: "IgA2 antibody" NARROW [GOC:add]
synonym: "IgA antibody" BROAD [GOC:add]
is_a: GO:0071745 ! IgA immunoglobulin complex

[Term]
id: PR:NewTerm03
name: IgA1 immunoglobulin complex, circulating (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
synonym: "IgA antibody" BROAD [GOC:add]
synonym: "IgA1 antibody" EXACT [GOC:add]
is_a: GO:0071746 ! IgA immunoglobulin complex, circulating
is_a: PR:NewTerm01 ! IgA1 immunoglobulin complex (human)

[Term]
id: PR:NewTerm04
name: IgA2 immunoglobulin complex, circulating (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA2 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
synonym: "IgA antibody" BROAD [GOC:add]
synonym: "IgA2 antibody" EXACT [GOC:add]
is_a: GO:0071746 ! IgA immunoglobulin complex, circulating
is_a: PR:NewTerm02 ! IgA2 immunoglobulin complex (human)

[Term]
id: PR:NewTerm05
name: IgA1 B cell receptor complex (human)
def: "An IgA1 immunoglobulin complex that is present in the plasma membrane of B cells and is composed of two identical immunoglobulin heavy chains of the IgA1 isotype, two identical immunoglobulin light chains (kappa or lambda), and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781765196, PMID:16362985]
synonym: "membrane-bound IgA" BROAD [GOC:add]
synonym: "membrane-bound IgA1" EXACT [GOC:add]
synonym: "surface IgA" BROAD [GOC:add]
synonym: "surface IgA1" EXACT [GOC:add]
is_a: GO:0071747 ! IgA B cell receptor complex
is_a: PR:NewTerm01 ! IgA1 immunoglobulin complex (human)
relationship: has_part PR:P11912 ! B-cell antigen receptor complex-associated protein alpha chain (human)
relationship: has_part PR:P40259 ! B-cell antigen receptor complex-associated protein beta chain (human)

[Term]
id: PR:NewTerm06
name: IgA2 B cell receptor complex (human)
def: "An IgA2 immunoglobulin complex that is present in the plasma membrane of B cells and is composed of two identical immunoglobulin heavy chains of the IgA2 isotype, two identical immunoglobulin light chains (kappa or lambda), and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781765196, PMID:16362985]
synonym: "membrane-bound IgA" BROAD [GOC:add]
synonym: "membrane-bound IgA2" EXACT [GOC:add]
synonym: "surface IgA" BROAD [GOC:add]
synonym: "surface IgA2" EXACT [GOC:add]
is_a: GO:0071747 ! IgA B cell receptor complex
is_a: PR:NewTerm02 ! IgA2 immunoglobulin complex (human)
relationship: has_part PR:P11912 ! B-cell antigen receptor complex-associated protein alpha chain (human)
relationship: has_part PR:P40259 ! B-cell antigen receptor complex-associated protein beta chain (human)

[Term]
id: PR:NewTerm07
name: monomeric IgA1 immunoglobulin complex (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
synonym: "monomeric IgA antibody" BROAD [GOC:add]
synonym: "monomeric IgA1 antibody" EXACT [GOC:add]
is_a: PR:NewTerm03 ! IgA1 immunoglobulin complex, circulating (human)

[Term]
id: PR:NewTerm08
name: monomeric IgA2 immunoglobulin complex (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA2 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
synonym: "monomeric IgA antibody" BROAD [GOC:add]
synonym: "monomeric IgA2 antibody" EXACT [GOC:add]
is_a: PR:NewTerm04 ! IgA2 immunoglobulin complex, circulating (human)

[Term]
id: PR:NewTerm09
name: polymeric IgA1 immunoglobulin complex (human)
def: "A protein complex composed of two, three, or four monomeric IgA1 immunoglobulin complexes linked through both direct disulfide bonds and through disulfide binded monomers of J chain acting as a bridge. Each IgA1 monomer consists of two identical immunoglobulin heavy chains of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds. Dimeric IgA1 is sometimes complexed additionally with secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
comment: Dimeric IgA1 is by far the most common form of polymeric IgA1. In human only the IgA1 isotype is capable of a polymeric forms.
synonym: "pIgA antibody" BROAD [GOC:add]
synonym: "pIgA1 antibody" EXACT [GOC:add]
synonym: "polymeric IgA antibody" BROAD [GOC:add]
synonym: "polymeric IgA1 antibody" EXACT [GOC:add]
is_a: PR:NewTerm03 ! IgA1 immunoglobulin complex, circulating (human)
relationship: has_part PR:P01591 ! immunoglobulin J chain (human)

[Term]
id: PR:NewTerm10
name: dimeric IgA1 immunoglobulin complex
def: "A protein complex composed of two monomeric IgA immunoglobulin complexes linked through both direct disulfide bonds and through a disulfide binded monomer of J chain acting as a bridge. Each IgA1 monomer consists of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds. Dimeric IgA1 is sometimes complexed additionally with secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
comment: Dimeric IgA1 is by far the most common form of polymeric IgA1. In human only the IgA1 isotype is capable of a dimeric form.
synonym: "dimeric IgA antibody" BROAD [GOC:add]
synonym: "dimeric IgA1 antibody" EXACT [GOC:add]
is_a: PR:NewTerm09 ! polymeric IgA1 immunoglobulin complex (human)
relationship: has_part PR:P01591 ! immunoglobulin J chain (human)

[Term]
id: PR:NewTerm11
name: secretory IgA1 immunoglobulin complex
def: "A polymeric IgA1 immunoglobulin complex that is complexed with one chain of secretory component (SC). Polymeric IgA1 is present in mucosal areas, having been transported via a transcytosis mechanism in mucosal epithelial cells relying on the polymeric Ig receptor, a portion of which then remains bound to the polymeric IgA as secretory component." [GOC:add, ISBN:0781765196, PMID:16362985]
comment: In human only the IgA1 isotype in the polymeric form is capable of becoming secretory IgA.
synonym: "secretory IgA antibody" BROAD [GOC:add]
synonym: "secretory IgA1 antibody" EXACT [GOC:add]
synonym: "sIgA antibody" BROAD [GOC:add]
synonym: "sIgA1 antibody" EXACT [GOC:add]
is_a: PR:NewTerm09 ! polymeric IgA1 immunoglobulin complex (human)
relationship: has_part PR:P01591 ! immunoglobulin J chain (human)
relationship: has_part PR:NewTerm13 ! secretory component (human)

[Term]
id: PR:NewTerm12
name: secretory dimeric IgA1 immunoglobulin complex
def: "A dimeric form of secretory IgA1 immunoglobulin complex." [GOC:add, ISBN:0781765196, PMID:16362985]
comment: Note that an IgA1 immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Dimeric IgA1 is by far the most common form of polymeric IgA. In human only the IgA1 isotype is capable of a dimeric form.
synonym: "secretory dimeric IgA antibody" BROAD [GOC:add]
synonym: "secretory dimeric IgA1 antibody" EXACT [GOC:add]
is_a: PR:NewTerm10 ! dimeric IgA1 immunoglobulin complex (human)
is_a: PR:NewTerm11 ! secretory IgA1 immunoglobulin complex (human)
relationship: has_part PR:P01591 ! immunoglobulin J chain (human)
relationship: has_part PR:NewTerm13 ! secretory component (human)

[Term]
id: PR:NewTerm13
name: secretory component (human)
def: A fragment of the human polymeric immunoglobulin receptor, residues 19-603 of the full-length sequence of the protein encoded by the human PIGR gene. [UniProtKB:P01833, GOC:add, ISBN:0781765196, PMID:16362985]
synonym: "SC" EXACT [GOC:add]
is_a: PR:000018263 ! amino acid chain
relationship: derives_from PR:P01833 ! polymeric immunoglobulin receptor (human)

[Term]
id: PR:NewTerm14
name: IgD immunoglobulin complex (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:11282392]
comment: Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available.
is_a: GO:0071738 ! IgD immunoglobulin complex

[Term]
id: PR:NewTerm15
name: IgD immunoglobulin complex, circulating (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:11282392]
synonym: "IgD antibody" BROAD [GOC:add]
is_a: GO:0071739 ! IgD immunoglobulin complex, circulating
is_a: PR:NewTerm14 ! IgD immunoglobulin complex (human)

[Term]
id: PR:NewTerm16
name: IgD B cell receptor complex (human)
def: "An IgD immunoglobulin complex that is present in the plasma membrane of B cells and is composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains (kappa or lambda) and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781765196, PMID:11282392]
synonym: "membrane-bound IgD" BROAD [GOC:add]
synonym: "surface IgD" BROAD [GOC:add]
is_a: GO:0071740 ! IgD B cell receptor complex
is_a: PR:NewTerm14 ! IgD immunoglobulin complex (human)

[Term]
id: PR:NewTerm17
name: IgD immunoglobulin complex, GPI-anchored (human)
def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, and bound via a GPI-anchor to the plasma membrane of B cells." [GOC:add, ISBN:0781765196, PMID:11282392, PMID:20727035]
synonym: "GPI-anchored IgD" BROAD [GOC:add]
is_a: GO:0071741 ! IgD immunoglobulin complex, GPI-anchored
is_a: PR:NewTerm14 ! IgD immunoglobulin complex (human)

@addiehl

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commented May 24, 2019

This includes a term for human secretory component as discussed with Darren via email.

Also note that human IgA2 only occurs in monomeric forms.

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commented May 28, 2019

Hi Alex,

There are three terms (10, 11, 12) that by name are not specific to humans, yet by subunits are. All the rest are specific to humans both by name and by subunits. Would it be correct to presume that these three are indeed intended to be human specific?

Thanks,
Darren

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commented May 28, 2019

yes, I forgot to append the (human) to the names. I knew I would make some such mistake, glad you saw it.

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commented May 28, 2019

In working through the request, I'm finding the need (or desire, really) to make new terms for the components. These will prove useful for logical definitions in GO as well. To start, I made these two terms. Children will include the specific chains (like IgA1, etc). Can you review these and suggest changes, if necessary?

[Term]
id: PR:000050174
name: immunoglobulin heavy chain protein
def: "A protein that is a translation product of some mRNA produced by the following steps using genes found specifically within the immunoglobulin heavy chain locus: (1) the allelic output of V-D-J recombination juxtaposed with the gene segments from the constant region; (2) alternative splicing to remove specific constant region gene segments." [PRO:DAN]
comment: Category=family. Note: In human, the IgH locus is described by https://www.genenames.org/data/genegroup/#!/group/349. In mouse, the locus is described by MGI:96442.
synonym: "IgH" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000000001 ! protein

[Term]
id: PR:000050175
name: immunoglobulin light chain protein
def: "A protein that is a translation product of some mRNA produced by the following steps using genes found specifically within the immunoglobulin light chain kappa, lambda , or sigma loci: (1) the allelic output of V-J recombination juxtaposed with the gene segments from the constant region; (2) alternative splicing to remove specific constant region gene segments." [PRO:DAN]
comment: Category=family. Note: In human, the kappa light chain locus is described by https://www.genenames.org/data/genegroup/#!/group/351, and the lambda light chain locus is described by https://www.genenames.org/data/genegroup/#!/group/353. In mouse, the kappa locus is described by MGI:96494, and the lambda locus is described by MGI:96526.
synonym: "IgL" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000000001 ! protein

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commented May 28, 2019

At least for the heavy chain, choice of constant region (isotope switching) is typically fixed by somatic recombination, but alternative splicing can also be used, particularly for switching between IgM and IgD. I can't remember all the details. Your definition suggests both of these mechanisms, but is a bit too succinct to be clear. Kappa vs lambda usage is a different mechanism entirely, with separate kappa and lambda gene loci and single constant regions for each (so def ought to be rewritten). Sigma light gene loci don't occur in mammals, birds, or reptiles, but I assume it works the same way.

I could help you a bit with these definitions by have no more free time today.

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commented May 29, 2019

Would it be better to define these based on function or structure instead?

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commented May 29, 2019

Define which terms?

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commented May 29, 2019

The heavy and light chains. I'm thinking the details of how they are made aren't really necessary to define them. The main requirement for each subtype, definition-wise, is that the specific constant region is indicated, and that can be done referencing the appropriate gene segment.

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commented May 29, 2019

As simple as this?

[Term]
id: PR:000050174
name: immunoglobulin heavy chain protein
def: "A protein that is a translation product of some mRNA produced by a somatically recombined immunoglobulin heavy chain locus." [PRO:DAN]
comment: Category=family. Note: In human, the IgH locus is described by https://www.genenames.org/data/genegroup/#!/group/349. In mouse, the locus is described by MGI:96442.
synonym: "IgH" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000000001 ! protein

[Term]
id: PR:000050175
name: immunoglobulin light chain protein
def: "A protein that is a translation product of some mRNA produced by a somatically recombined immunoglobulin heavy chain locus." [PRO:DAN]
comment: Category=family. Note: In human, the kappa light chain locus is described by https://www.genenames.org/data/genegroup/#!/group/351, and the lambda light chain locus is described by https://www.genenames.org/data/genegroup/#!/group/353. In mouse, the kappa locus is described by MGI:96494, and the lambda locus is described by MGI:96526.
synonym: "IgL" EXACT PRO-short-label [PRO:DAN]
is_a: PR:000000001 ! protein

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commented May 29, 2019

I was thinking along the lines of defining based on participation in the antibody structure, but there are cases where such will fail. Your definitions are better. Thanks!

Also, I noticed that you made terms for dimeric, etc forms if IgA1 but not IgA2. Was that intentional? If not, I'll make them using the IgA1 forms as templates.

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commented May 29, 2019

Disregard that last statement. Just noticed the comments.

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commented May 30, 2019

I've completed the terms, and quite a few more. This is so we could use reasoning to achieve the multiple inheritance hierarchy you indicated. The mapping between your requests and the final PRO identifier is given below. I've also attached two files that I'd like you to review. The first is an OBO format file (I had to add a .txt extension so that github will accept it). Please review this for accuracy of names and definitions. I did simplify a few things (and definitely ignore everything below the [Typedef] stanza). The second is an OWL file, which I provide for your review of the hierarchy. The OBO format will actually not show the proper hierarchy because OBO doesn't allow certain statements that are needed to get the reasoning to work the way it needs to. Thus, the OWL logical definitions have been minimally tweaked. While these won't show in the integrated PRO file, these will give an idea of how it will work in the future. Let me know once you review the files, and if everything is okay, I'll put the terms into PRO.

id: PR:NewTerm01 -> PR:000050157
id: PR:NewTerm02 -> PR:000050158
id: PR:NewTerm03 -> PR:000050159
id: PR:NewTerm04 -> PR:000050160
id: PR:NewTerm05 -> PR:000050161
id: PR:NewTerm06 -> PR:000050162
id: PR:NewTerm07 -> PR:000050163
id: PR:NewTerm08 -> PR:000050164
id: PR:NewTerm09 -> PR:000050165
id: PR:NewTerm10 -> PR:000050166
id: PR:NewTerm11 -> PR:000050167
id: PR:NewTerm12 -> PR:000050168
id: PR:NewTerm13 -> PR:000050169
id: PR:NewTerm14 -> PR:000050170
id: PR:NewTerm15 -> PR:000050171
id: PR:NewTerm16 -> PR:000050172
id: PR:NewTerm17 -> PR:000050173

imm.obo.txt
imm.owl.txt

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commented May 31, 2019

Hi Darren,

In reviewing the structure I realize that because monomeric IgA2 is the only circulating form of human IgA2, PR:000050160 and PR:000050164 are redundant and we should only have one term with additional synonyms and changed logical axioms:

[Term]
id: PR:000050160
name: IgA2 immunoglobulin complex, circulating (human)
def: "A protein complex that in monomeric form is composed of two identical immunoglobulin heavy chains of the IgA2 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:16362985]
comment: Category=organism-complex. Requested by=HIPC. Requested by=CL. Human circulating IgA2 is only found as a monomeric form.
synonym: "hIgA2/circulating" EXACT PRO-short-label [PRO:DAN]
synonym: "IgA antibody (human)" BROAD [GOC:add]
synonym: "IgA2 antibody (human)" EXACT [GOC:add]
synonym: "h(IgA2)monomeric" EXACT [PRO:DAN]
synonym: "monomeric IgA antibody (human)" BROAD [GOC:add]
synonym: "monomeric IgA2 antibody (human)" EXACT [GOC:add]
is_a: GO:0071746 ! IgA immunoglobulin complex, circulating
relationship: has_component PR:000050180 {cardinality="2"} ! IgA2 heavy chain protein (human)
relationship: has_component PR:000050183 {cardinality="2"} ! immunoglobulin light chain protein (human)
relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens

and you should skip instantiating this term:
[Term]
id: PR:000050164
name: monomeric IgA2 immunoglobulin complex (human)

I'm still checking other stuff.

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commented May 31, 2019

Probably "monomeric IgA2 immunoglobulin complex (human)" should also be an exact synonym of the combined term. Thanks

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commented Jun 3, 2019

We should probably make a generic version of this 'secretory component' term since SC is important for IgA in mouse and most other mammalian species:
[Term]
id: PR:000050169
name: polymeric immunoglobulin receptor secretory component (human)
def: A polymeric immunoglobulin receptor, signal peptide removed form in human that has been processed by proteolytic cleavage to separate the extracellular domain (represented here) from the transmembrane domain. UniProtKB:P01833, 19-603. [UniProtKB:P01833, GOC:add, ISBN:0781765196, PMID:16362985]
comment: Category=organism-modification. Requested by=HIPC. Requested by=CL.
synonym: "hPIGR/SC" EXACT PRO-short-label [PRO:DAN]
synonym: "PRO_0000014901" EXACT PRO-proteoform-ftid [PRO:DNx]
synonym: "UniProtKB:P01833, 19-603" EXACT PRO-proteoform-std [PRO:DNx]
synonym: "SC (human)" EXACT [GOC:add]
synonym: "secretory component (human)" EXACT [GOC:add]
is_a: PR:000000001
relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens

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commented Jun 3, 2019

I wonder if PR:000050167 'secretory IgA1 immunoglobulin complex (human)' ought to be named 'secretory polymeric IgA1 immunoglobulin complex (human)' in parallel with PR:000050168 'secretory dimeric IgA1 immunoglobulin complex (human)', as I found the name a bit confusing, when considering its parent and child terms' names.

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commented Jun 3, 2019

Apart from these changes, the rest looks good.

Thanks!

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commented Jun 4, 2019

Great, thanks! I've incorporated your latest suggestions and uploaded the new 'working version' (the between-release version). This means you can download the terms, and see them online, but they won't appear in the hierarchy or in the main PRO files until the next release.

http://purl.obolibrary.org/obo/pr/pr-dev.obo

@nataled nataled closed this Jun 4, 2019

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commented Jun 4, 2019

Excellent, look great, thank you very much

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commented Aug 15, 2019

Hi Alex,
I wanted to double check something. We have PR:000050163 (monomeric IgA1 immunoglobulin complex) and PR:000050165 (polymeric IgA1 immunoglobulin complex) as children of PR:000050159 (IgA1 immunoglobulin complex, circulating). But, based on the definitions, it seems that the polymeric should not be, since it states "sometimes" complexed with secretory component. Can you verify?

[Term]
id: PR:000050163
name: monomeric IgA1 immunoglobulin complex (human)
def: "An IgA1 immunoglobulin complex, circulating (human) that is composed of two identical immunoglobulin heavy chains of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [PRO:ADD, ISBN:0781765196, PMID:16362985]
comment: Category=organism-complex. Requested by=HIPC. Requested by=CL.
synonym: "h(IgA1)monomeric" EXACT PRO-short-label [PRO:DAN]
synonym: "monomeric IgA antibody (human)" BROAD [PRO:ADD]
synonym: "monomeric IgA1 antibody (human)" EXACT [PRO:ADD]
is_a: PR:000050159 ! IgA1 immunoglobulin complex, circulating (human)
relationship: has_component PR:000050179 {cardinality="2"} ! IgA1 heavy chain protein (human)
relationship: has_component PR:000050183 {cardinality="2"} ! immunoglobulin light chain protein (human)
relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens

[Term]
id: PR:000050165
name: polymeric IgA1 immunoglobulin complex (human)
def: "A protein complex composed of two, three, or four monomeric IgA1 immunoglobulin complexes linked through both direct disulfide bonds and through disulfide binded monomers of J chain acting as a bridge. Each IgA1 monomer consists of two identical immunoglobulin heavy chains of the IgA1 isotype and two identical immunoglobulin light chains (kappa or lambda), held together by disulfide bonds. Dimeric IgA1 is sometimes complexed additionally with secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [PRO:ADD, ISBN:0781765196, PMID:16362985]
comment: Category=organism-complex. Requested by=HIPC. Requested by=CL. Dimeric IgA1 is by far the most common form of polymeric IgA1. In human only the IgA1 isotype is capable of a polymeric forms.
synonym: "h(IgA1)polymeric" EXACT PRO-short-label [PRO:DAN]
synonym: "pIgA antibody (human)" BROAD [PRO:ADD]
synonym: "pIgA1 antibody (human)" EXACT [PRO:ADD]
synonym: "polymeric IgA antibody (human)" BROAD [PRO:ADD]
synonym: "polymeric IgA1 antibody (human)" EXACT [PRO:ADD]
intersection_of: PR:000050159 ! IgA1 immunoglobulin complex, circulating (human)
intersection_of: has_component PR:000050163 {minCardinality=2} ! monomeric IgA1 immunoglobulin complex (human)
intersection_of: has_component PR:000050163 {maxCardinality=4} ! monomeric IgA1 immunoglobulin complex (human)
intersection_of: has_component PR:P01591 {cardinality=1} ! immunoglobulin J chain (human)
relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens

@nataled nataled reopened this Aug 15, 2019

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