Neuraminidase

[nataled]

Hi, I did find the different subtypes of Neuraminidase in PRO: - id: PRO:000011145, name: sialidase-1 - id: PRO:000011146, name: sialidase-2 - id: PRO:000011147, name: sialidase-3 - id: PRO:000011148, name: sialidase-4

Would it be possible to have a general class neuraminidase? This would be helpful as I need to define a neuraminidase assay, without specifying the subtype. Also I am interested specifically in Influenza neruaminidase (http://en.wikipedia.org/wiki/Viral\_neuraminidase, http://www.rcsb.org/pdb/static.do?p=education\_discussion/molecule\_of\_the\_month/pdb113\_1.html) which comes in subtypes N1 to N9, could the missing ones be added?

Thanks, Melanie

Reported by: mcourtot

[nataled]

A more general, though related, question: does PRO links to functions of proteins? For example, here I would like to have a has_function alpha-sialidase activity (http://www.berkeleybop.org/obo/GO:0016997).

Original comment by: mcourtot

[nataled]

• assigned_to: nobody --> arighi

Original comment by: nataled

[nataled]

This is not a trivial case. Neuraminidase is product of NA gene, disregarding of virus subtype. Therefore a term for category=gene was created (PR:000027734, translation product of the NA (neuraminidase) gene). The subtypes of neuraminidase are based on similar antigenicity (which is also a consequence of sequence/structure similarity). I added as children the 9 neuraminidase subtypes. I added these terms as organism-gene, and added a "relationship" line to Influenza A virus (not the specific strain since each subtype encloses a group of strains). I used relationship and not intersection_of because I cannot provide a unique logical definition for these. The definitions of subtypes are based on similar antigenic properties with reference to a protein for which there is some PMID or structure known. Please let me know if these definitions are OK. Also note that we previously had in the ontology the term: PR:000022008 (copied at the end) that I obsoleted it because the definition and category needed important revision. I created the new term PR:000027734.

- Cecilia Arighi

[Term] id: PR:000027734 name: viral neuraminidase def: "A protein that is a translation product of the NA gene or a 1:1 ortholog thereof. Neuraminidase is an exo-alpha-sialidase on the surface of some viruses that enables the virus to be released from the host cell." [Wikipedia:Viral_neuraminidase, PRO:CNA] comment: Category=gene. synonym: "sialidase" BROAD [] is_a: PR:000000001 ! protein

[Term] id: PR:000027735 name: neuraminidase subtype N1 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:Q9IGQ6." [Wikipedia:Viral_neuraminidase, PMID:18645233] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000027736 name: neuraminidase subtype N2 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:P06820." [Wikipedia:Viral_neuraminidase, PMID:7650674] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000027737 name: neuraminidase subtype N3 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:A9YN63." [Wikipedia:Viral_neuraminidase, PMID:20109495] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000027738 name: neuraminidase subtype N4 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:Q6XV46." [Wikipedia:Viral_neuraminidase, PMID:20109495] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000027739 name: neuraminidase subtype N5 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:P03478." [Wikipedia:Viral_neuraminidase, PMID:20109495, PMID:2922926] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000027740 name: neuraminidase subtype N6 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:Q6XV27." [Wikipedia:Viral_neuraminidase, PMID:20109495, PDB:1W1X] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000027741 name: neuraminidase subtype N7 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:P88838." [Wikipedia:Viral_neuraminidase, PMID:3221907] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000027742 name: neuraminidase subtype N8 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:Q07599." [Wikipedia:Viral_neuraminidase, PMID:9362042] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000027743 name: neuraminidase subtype N9 (Influenza A virus) def: "A viral neuraminidase that is expressed on the surface of Influenza A virus and has similar antigenic properties, i.e., it will be neutralized by a similar set of antibodies, as UniprotKB:P05803." [Wikipedia:Viral_neuraminidase, PMID:1381757] comment: Category=organism-gene. is_a: PR:000027734 ! viral neuraminidase relationship: only_in_taxon NCBITaxon:197911 ! Influenza A virus

[Term] id: PR:000022008 name: viral neuraminidase def: "A protein that is an exo-alpha-sialidase on the surface of influenza viruses that enables the virus to be released from the host cell." [Wikipedia:Viral_neuraminidase] comment: Category=family. synonym: "sialidase" BROAD [] is_a: PR:000000001 ! protein is_obsolete: true consider: PR:000027734

Original comment by: nataled

[nataled]

• status: open --> closed

Original comment by: nataled