{ "bcoid": "GLY_000536", "title": "Protein Resource Ontology [Mouse]", "description": "This dataset provides the Protein Resource Ontology (PRO) identifiers associated with the proteoforms ...", "filename_list": "mouse_protein_pro_annotation.csv", "filename": "mouse_protein_pro_annotation.csv", "filetype": "csv", "categories": { "species": [ "Mus musculus" ], "molecule": [ "Proteoform" ], "tag": [ "PRO ontology" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "O09164-1...", "PR:000058420..." ], [ "O09164-1...", "PR:000058421..." ] ], "headers": [ "uniprotkb_ca...", "pro_id..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "pro_id" }, { "type": "string", "label": "pro_protein_name" }, { "type": "string", "label": "pro_protein_definition" }, { "type": "string", "label": "pro_comment" }, { "type": "string", "label": "pro_synonym" }, { "type": "string", "label": "pro_relationship" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" } ], [ "O09164-1", "PR:000058420", "extracellular superoxide dismutase [Cu-Zn] N-glycosylated 1 (mouse)", "An extracellular superoxide dismutase [Cu-Zn] (mouse) that has been N-glycosylated at the residue equivalent to Asn-121 of the amino acid sequence represented by UniProtKB:O09164-1, in which the glycan structure is represented by GlyTouCan:G12398HZ. Example: UniProtKB:O09164-1, Asn-121, MOD:00160~GNO:G12398HZ. [PRO:DNx, PMID:21573946]", "Category=organism-modification. Requested by=GlyGen.", "mSOD3/NGlyco:1 EXACT PRO-short-label [PRO:DNx]; UniProtKB:O09164-1, Asn-121, MOD:00160~GNO:G12398HZ NARROW PRO-proteoform-std [PRO:DNx]; UniProtKB:O09164-1, Asn-121, MOD:00160~UniCarbKB:7843 NARROW [PRO:DNx]", "has_part MOD:00160 ! N4-glycosyl-L-asparagine; has_part GNO:G12398HZ ! G12398HZ; only_in_taxon NCBITaxon:10090 ! Mus musculus", "protein_xref_pro_proteoform", "PR:000058420" ], [ "O09164-1", "PR:000058421", "extracellular superoxide dismutase [Cu-Zn] N-glycosylated 2 (mouse)", "An extracellular superoxide dismutase [Cu-Zn] (mouse) that has been N-glycosylated at the residue equivalent to Asn-121 of the amino acid sequence represented by UniProtKB:O09164-1, in which the glycan structure is represented by GlyTouCan:G24498DI. Example: UniProtKB:O09164-1, Asn-121, MOD:00160~GNO:G24498DI. [PRO:DNx, PMID:21573946]", "Category=organism-modification. Requested by=GlyGen.", "mSOD3/NGlyco:2 EXACT PRO-short-label [PRO:DNx]; UniProtKB:O09164-1, Asn-121, MOD:00160~GNO:G24498DI NARROW PRO-proteoform-std [PRO:DNx]; UniProtKB:O09164-1, Asn-121, MOD:00160~UniCarbKB:7758 NARROW [PRO:DNx]", "has_part MOD:00160 ! N4-glycosyl-L-asparagine; has_part GNO:G24498DI ! G24498DI; only_in_taxon NCBITaxon:10090 ! Mus musculus", "protein_xref_pro_proteoform", "PR:000058421" ] ] }, "readme": "Name\n - Protein Resource Ontology [Mouse]\n\nVersion\n - v-2.8.1\n\nCreated on\n - 2021-01-04T11:37:44.928218\n\nModified on\n - 2024-05-21T15:27:27.205Z\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Kate Warner [k.warner1@gwu.edu]\n\nAuthors\n - Darren Natale [dan5@georgetown.edu], Matthew Campbell [m.campbell2@griffith.edu.au]\n\nChecksum\n - \n\nUsability Domain\n - This dataset provides the Protein Resource Ontology (PRO) identifiers associated with the proteoforms generated based on the protein, site, glycan information retrieved from the UniCarbKB database for mouse [taxid:10090] proteins (https://data.glygen.org/GLY_000041: v-1.4.5 09/13/2019)Source- PRO: https://proconsortium.org/pro.shtml, UniCarbKB: https://academic.oup.com/nar/article/42/D1/D215/1052197 ,https://doi.org/10.1093/nar/gkt1128. Please note that this dataset refers to the previous version of the UniCarbKB mouse glycoprotein dataset (https://data.glygen.org/GLY_000041: v-1.4.5 09/13/2019)\n\nDescription Domain\n Keywords\n - Proteoforms\n - PRO\n - UniCarbKB\n\n Pipeline Steps\n - Step-1: The source file was downloaded from the contributors (Darren Natale) and a python script was used to convert the source file into a csv format.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: GlyGen_table_to_PRO.obo\n URI: https:/data.glygen.org/ln2downloads/pro/pro_08_28_2020/GlyGen_table_to_PRO.obo\n Output Subdomain\n Name: mouse_protein_pro_annotation.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/mouse_protein_pro_annotation.csv\n Name: mouse_protein_pro_annotation.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/mouse_protein_pro_annotation.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"6\"\n Name: \"pro_id\"\n Description: \"ID associated to a proteoform from PRO database\"\n Unique Values: \"119\"\n Name: \"pro_protein_name\"\n Description: \"Protein name from PRO database\"\n Unique Values: \"119\"\n Name: \"pro_protein_definition\"\n Description: \"Protein/Proteoform defination from PRO database\"\n Unique Values: \"119\"\n Name: \"pro_comment\"\n Description: \"Comment from PRO\"\n Unique Values: \"2\"\n Name: \"pro_synonym\"\n Description: \"Synonym from PRO\"\n Unique Values: \"119\"\n Name: \"pro_relationship\"\n Description: \"Relation defination from PRO database\"\n Unique Values: \"74\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"119\"", "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/mouse_protein_pro_annotation.csv" }