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immunoglobulin ontology #7448

Closed gocentral closed 9 years ago

gocentral commented 14 years ago

Isotype specific Ig terms, essentially a sub-ontology of immunoglobulins. These are needed in part for cross-product development for the CL, and in part for better representation of these immunoglobulin protein complexes in the GO. The daring among you could hack the GO obo file with a text editor and directly add the terms and save a bunch of time, since they are already given as obo-1.2 compliant term stanzas. Perhaps obomerge could handle this.

Thanks,

Alex (CL)

[Term] id: GO:NewTer1 name: IgG immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG 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] comment: Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. synonym: "IgG1" NARROW [] synonym: "IgG2" NARROW [] synonym: "IgG2a" NARROW [] synonym: "IgG2b" NARROW [] synonym: "IgG2c" NARROW [] synonym: "IgG3" NARROW [] synonym: "IgG4" NARROW [] is_a: GO:0019814 ! immunoglobulin complex

[Term] id: GO:NewTer2 name: IgG immunoglobulin complex, circulating namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, 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] comment: Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. synonym: "IgG antibody" NARROW [] synonym: "IgG1 antibody" NARROW [] synonym: "IgG2 antibody" NARROW [] synonym: "IgG2a antibody" NARROW [] synonym: "IgG2b antibody" NARROW [] synonym: "IgG2c antibody" NARROW [] synonym: "IgG3 antibody" NARROW [] synonym: "IgG4 antibody" NARROW [] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:NewTer1 ! IgG immunoglobulin complex

[Term] id: GO:NewTer3 name: IgG B cell receptor complex namespace: cellular_component def: "An IgG immunoglobulin complex that is present in the plasma membrane of B cells and is composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781765196] comment: Note that an IgG immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Also, IgG isotypes vary by species. synonym: "surface IgG" NARROW [] synonym: "surface IgG1" NARROW [] synonym: "surface IgG2" NARROW [] synonym: "surface IgG2a" NARROW [] synonym: "surface IgG2b" NARROW [] synonym: "surface IgG2c" NARROW [] synonym: "surface IgG3" NARROW [] synonym: "surface IgG4" NARROW [] synonym: "membrane-bound IgG" NARROW [] synonym: "membrane-bound IgG1" NARROW [] synonym: "membrane-bound IgG2" NARROW [] synonym: "membrane-bound IgG2a" NARROW [] synonym: "membrane-bound IgG2b" NARROW [] synonym: "membrane-bound IgG2c" NARROW [] synonym: "membrane-bound IgG3" NARROW [] synonym: "membrane-bound IgG4" NARROW []is_a: GO:0019815 ! B cell receptor complex is_a: GO:NewTer1 ! IgG immunoglobulin complex

[Term] id: GO:NewTer4 name: IgD immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, 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:0019814 ! immunoglobulin complex

[Term] id: GO:NewTer5 name: IgD immunoglobulin complex, circulating namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, 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] comment: Note that an IgD immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgD antibody" EXACT [] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:NewTer4 ! IgD immunoglobulin complex

[Term] id: GO:NewTer6 name: IgD B cell receptor complex namespace: cellular_component 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 and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [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. synonym: "surface IgD" EXACT [] synonym: "membrane-bound IgD" EXACT [] is_a: GO:0019815 ! B cell receptor complex is_a: GO:NewTer4 ! IgD immunoglobulin complex

[Term] id: GO:NewTer7 name: IgD immunoglobulin complex, GPI-anchored namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and bound via a GPI-anchor to the plasma membrane of B cells." [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. synonym: "GPI-anchored IgD" EXACT [] is_a: GO:NewTer4 ! IgD immunoglobulin complex

[Term] id: GO:NewTer8 name: IgE immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE 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] comment: Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex

[Term] id: GO:NewTer9 name: IgE immunoglobulin complex, circulating namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, 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] comment: Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgE antibody" EXACT [] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:NewTer8 ! IgE immunoglobulin complex

[Term] id: GO:NewTe10 name: IgE B cell receptor complex namespace: cellular_component def: "An IgE immunoglobulin complex that is present in the plasma membrane of B cells and is composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781765196] comment: Note that an IgE immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "surface IgE" EXACT [] synonym: "membrane-bound IgE" EXACT [] is_a: GO:0019815 ! B cell receptor complex is_a: GO:NewTer8 ! IgE immunoglobulin complex

[Term] id: GO:NewTe11 name: IgA immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA 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 IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgA1 antibody" NARROW [] synonym: "IgA2 antibody" NARROW [] is_a: GO:0019814 ! immunoglobulin complex

[Term] id: GO:NewTe12 name: IgA immunoglobulin complex, circulating namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, 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: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgA antibody" EXACT [] synonym: "IgA1 antibody" NARROW [] synonym: "IgA2 antibody" NARROW [] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:NewTe11 ! IgA immunoglobulin complex

[Term] id: GO:NewTe13 name: IgA B cell receptor complex namespace: cellular_component def: "An IgA immunoglobulin complex that is present in the plasma membrane of B cells and is composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781765196, PMID:16362985] comment: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "surface IgA" NARROW [] synonym: "membrane-bound IgA" NARROW [] synonym: "surface IgA1" NARROW [] synonym: "surface IgA2" NARROW [] synonym: "membrane-bound IgA1" NARROW [] synonym: "membrane-bound IgA2" NARROW [] is_a: GO:0019815 ! B cell receptor complex is_a: GO:NewTe11 ! IgA immunoglobulin complex

[Term] id: GO:NewTe14 name: monomeric IgA immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, 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] comment: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "monomeric IgA antibody" EXACT [] synonym: "monomeric IgA1 antibody" NARROW [] synonym: "monomeric IgA2 antibody" NARROW [] is_a: GO:NewTe12 ! IgA immunoglobulin complex, circulating

[Term] id: GO:NewTe15 name: polymeric IgA immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two, three, or four monomeric IgA immunoglobulin complexes linked through both direct disulfide bonds and through disulfide binded monomers of J chain acting as a bridge. Each IgA monomer consists of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds. Dimeric IgA 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: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Dimeric IgA is by far the most common form of polymeric IgA. In human only the IgA1 isotype is capable of a polymeric forms. synonym: "polymeric IgA antibody" EXACT [] synonym: "polymeric IgA1 antibody" NARROW [] synonym: "pIgA antibody" EXACT [] synonym: "pIgA1 antibody" NARROW [] is_a: GO:NewTe12 ! IgA immunoglobulin complex, circulating

[Term] id: GO:NewTe16 name: dimeric IgA immunoglobulin complex namespace: cellular_component 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 IgA monomer consists of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds. Dimeric IgA 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: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Dimeric IgA is by far the most common form of polymeric IgA. In human only the IgA1 isotype is capable of a dimeric form. synonym: "dimeric IgA antibody" EXACT [] synonym: "dimeric IgA1 antibody" NARROW [] is_a: GO:NewTe15 ! polymeric IgA immunoglobulin complex

[Term] id: GO:NewTe17 name: secretory IgA immunoglobulin complex namespace: cellular_component def: "A polymeric IgA immunoglobulin complex that is complexed with one chain of secretory component (SC). Polymeric IgA 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: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. In human only the IgA1 isotype in the polymeric form is capable of becoming secretory IgA. synonym: "secretory IgA antibody" EXACT [] synonym: "sIgA antibody" EXACT [] synonym: "sIgA1 antibody" NARROW [] is_a: GO:NewTe15 ! polymeric IgA immunoglobulin complex

[Term] id: GO:NewTe18 name: secretory dimeric IgA immunoglobulin complex namespace: cellular_component def: "A dimeric form of secretory IgA immunoglobulin complex." [GOC:add, ISBN:0781765196, PMID:16362985] comment: Note that an IgA immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Dimeric IgA 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" EXACT [] synonym: "secretory dimeric IgA1 antibody" NARROW [] is_a: GO:NewTe16 ! dimeric IgA immunoglobulin complex is_a: GO:NewTe17 ! secretory IgA immunoglobulin complex

[Term] id: GO:NewTe19 name: IgM immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM 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:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. is_a: GO:0019814 ! immunoglobulin complex

[Term] id: GO:NewTe20 name: IgM immunoglobulin complex, circulating namespace: cellular_component def: "A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "IgM antibody" EXACT [] is_a: GO:0042571 ! immunoglobulin complex, circulating is_a: GO:NewTe19 ! IgM immunoglobulin complex

[Term] id: GO:NewTe21 name: IgM B cell receptor complex namespace: cellular_component def: "An IgM immunoglobulin complex that is present in the plasma membrane of B cells and is composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "surface IgM" NARROW [] synonym: "membrane-bound IgM" NARROW [] is_a: GO:0019815 ! B cell receptor complex is_a: GO:NewTe19 ! IgM immunoglobulin complex

[Term] id: GO:NewTe22 name: pentameric IgM immunoglobulin complex namespace: cellular_component def: "A circulating form of IgM consisting of a pentamer of IgM core units with a single J chain polypeptide." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "pentameric IgM antibody" EXACT [] is_a: GO:NewTe20 ! IgM immunoglobulin complex, circulating

[Term] id: GO:NewTe23 name: hexameric IgM immunoglobulin complex namespace: cellular_component def: "A circulating form of IgM consisting of a hexamer of IgM core units with a single J chain polypeptide." [GOC:add, ISBN:0781765196, PMID:20176268] comment: Note that an IgM immunoglobulin complex has the function of antigen binding if a suitable antigen is available. synonym: "hexameric IgM antibody" EXACT [] is_a: GO:NewTe20 ! IgM immunoglobulin complex, circulating

[Term] id: GO:NewTe24 name: IgW immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgW isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgW 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] comment: Note that an IgW immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Note that IgW is found in fish. is_a: GO:0019814 ! immunoglobulin complex

[Term] id: GO:NewTe25 name: IgX immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgX isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgX 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] comment: Note that an IgX immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Note that IgX is found in amphibians. is_a: GO:0019814 ! immunoglobulin complex

[Term] id: GO:NewTe26 name: IgY immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgY isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgY 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] comment: Note that an IgY immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Note that IgY is found in amphibians, reptiles, and birds. is_a: GO:0019814 ! immunoglobulin complex

[Term] id: GO:NewTe27 name: IgZ immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgZ isotype and two identical immunoglobulin light chains, held together by disulfide bonds. The IgZ isotype is also known as the IgT isotype in certain species of fish." [GOC:add, ISBN:0781765196] comment: Note that an IgZ immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Note that IgZ is found in bony fish, and called IgT in certain species, such as trout. synonym: "IgZ antibody" NARROW [] synonym: "IgT immunoglobulin complex" EXACT [ISBN:0781765196] synonym: "IgT antibody" NARROW [] is_a: GO:0019814 ! immunoglobulin complex

[Term] id: GO:NewTe28 name: heavy chain immunoglobulin complex namespace: cellular_component def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgNAR isotype held together by disulfide bonds and lacking immunoglobulin ligt chains." [GOC:add, ISBN:0781765196, PMID:12543123, PMID:16051357] comment: Note that a heavy chain immunoglobulin complex has the function of antigen binding if a suitable antigen is available. Note that IgNAR is found in serum of cartilaginous fish as a heavy chain dimer without immunoglobulin light chains. Note that HCab is found in camels as a heavy chain dimer without immunoglobulin light chains. synonym: "Ig NAR immunoglobulin complex" NARROW [] synonym: "IgNAR immunoglobulin complex" NARROW [] synonym: "IgNAR antibody" NARROW [] synonym: "HCab" NARROW [] is_a: GO:0019814 ! immunoglobulin complex

Reported by: addiehl

Original Ticket: geneontology/ontology-requests/7229

gocentral commented 14 years ago

Original comment by: mah11

gocentral commented 14 years ago

added terms IgG immunoglobulin complex GO:0071735 IgG immunoglobulin complex, circulating GO:0071736 IgG B cell receptor complex GO:0071737 IgD immunoglobulin complex GO:0071738 IgD immunoglobulin complex, circulating GO:0071739 IgD B cell receptor complex GO:0071740 IgD immunoglobulin complex, GPI-anchored GO:0071741 IgE immunoglobulin complex GO:0071742 IgE immunoglobulin complex, circulating GO:0071743 IgE B cell receptor complex GO:0071744 IgA immunoglobulin complex GO:0071745 IgA immunoglobulin complex, circulating GO:0071746 IgA B cell receptor complex GO:0071747 monomeric IgA immunoglobulin complex GO:0071748 polymeric IgA immunoglobulin complex GO:0071749 dimeric IgA immunoglobulin complex GO:0071750 secretory IgA immunoglobulin complex GO:0071751 secretory dimeric IgA immunoglobulin complex GO:0071752 IgM immunoglobulin complex GO:0071753 IgM immunoglobulin complex, circulating GO:0071754 IgM B cell receptor complex GO:0071755 pentameric IgM immunoglobulin complex GO:0071756 hexameric IgM immunoglobulin complex GO:0071757 IgW immunoglobulin complex GO:0071758 IgX immunoglobulin complex GO:0071759 IgY immunoglobulin complex GO:0071760 IgZ immunoglobulin complex GO:0071761 heavy chain immunoglobulin complex GO:0071762

Original comment by: mah11

gocentral commented 14 years ago

Original comment by: mah11

gocentral commented 14 years ago

Thanks Midori,

Alex

Original comment by: addiehl