{ "bcoid": "GLY_000498", "title": "Protein Resource Ontology [Human]", "description": "This dataset provides the Protein Resource Ontology (PRO) identifiers associated with the proteoforms ...", "filename_list": "human_protein_pro_annotation.csv", "filename": "human_protein_pro_annotation.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "PRO ontology" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "A1L4H1-1...", "PR:000050601..." ], [ "A1L4H1-1...", "PR:000050602..." ] ], "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" } ], [ "A1L4H1-1", "PR:000050601", "soluble scavenger receptor cysteine-rich domain-containing protein SSC5D O-glycosylated 1 (human)", "A soluble scavenger receptor cysteine-rich domain-containing protein SSC5D (human) that has been O-glycosylated at the residue equivalent to Ser-1466 of the amino acid sequence represented by UniProtKB:A1L4H1-1, in which the glycan composition is represented by GlyTouCan:G43417UB. Example: UniProtKB:A1L4H1-1, Ser-1466, MOD:00002~GNO:G43417UB. [PRO:DNx, PMID:30459171]", "Category=organism-modification. Requested by=GlyGen.", "hSSC5D/OGlyco:1 EXACT PRO-short-label [PRO:DNx]; UniProtKB:A1L4H1-1, Ser-1466, MOD:00002~GNO:G43417UB NARROW PRO-proteoform-std [PRO:DNx]", "has_part MOD:00002 ! O-glycosyl-L-serine; has_part GNO:G43417UB ! G43417UB; only_in_taxon NCBITaxon:9606 ! Homo sapiens", "protein_xref_pro_proteoform", "PR:000050601" ], [ "A1L4H1-1", "PR:000050602", "soluble scavenger receptor cysteine-rich domain-containing protein SSC5D O-glycosylated 2 (human)", "A soluble scavenger receptor cysteine-rich domain-containing protein SSC5D (human) that has been O-glycosylated at the residue equivalent to Ser-581 of the amino acid sequence represented by UniProtKB:A1L4H1-1, in which the glycan composition is represented by GlyTouCan:G43417UB. Example: UniProtKB:A1L4H1-1, Ser-581, MOD:00002~GNO:G43417UB. [PRO:DNx, PMID:30459171]", "Category=organism-modification. Requested by=GlyGen.", "hSSC5D/OGlyco:2 EXACT PRO-short-label [PRO:DNx]; UniProtKB:A1L4H1-1, Ser-581, MOD:00002~GNO:G43417UB NARROW PRO-proteoform-std [PRO:DNx]", "has_part MOD:00002 ! O-glycosyl-L-serine; has_part GNO:G43417UB ! G43417UB; only_in_taxon NCBITaxon:9606 ! Homo sapiens", "protein_xref_pro_proteoform", "PR:000050602" ] ] }, "readme": "Name\n - Protein Resource Ontology [Human]\n\nVersion\n - v-2.7.1\n\nCreated on\n - 2020-05-13T10:38:59.901723\n\nModified on\n - 2024-05-21T15:26:55.850Z\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 human [taxid:9606] proteins (https://data.glygen.org/GLY_000040: 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 human glycoprotein dataset (https://data.glygen.org/GLY_000040: 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: human_protein_pro_annotation.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_protein_pro_annotation.csv\n Name: human_protein_pro_annotation.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/human_protein_pro_annotation.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"958\"\n Name: \"pro_id\"\n Description: \"ID associated to a proteoform from PRO database\"\n Unique Values: \"7820\"\n Name: \"pro_protein_name\"\n Description: \"Protein name from PRO database\"\n Unique Values: \"7820\"\n Name: \"pro_protein_definition\"\n Description: \"Protein/Proteoform defination from PRO database\"\n Unique Values: \"7820\"\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: \"7820\"\n Name: \"pro_relationship\"\n Description: \"Relation defination from PRO database\"\n Unique Values: \"860\"\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: \"7820\"", "downloadurl": "/ln2data/releases/data/v-2.7.1/reviewed/human_protein_pro_annotation.csv" }