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\n\nUsability Domain\n - The Yeast O-GlcNAc Glycosylation Sites (O-GlcNAc Atlas) contains yeast (taxid:559292) O-GlcNAc modifications on Serine and Threonine extracted from the publication and mapped to the UniProtKB canonical accession and fasta sequence. The GlyTouCan ID for the O-GlcNAc is G49108TO.\n\nDescription Domain\n Keywords\n - \n - O-GlcNAc\n - Serine\n\n Pipeline Steps\n - Step-1: The script maps the UniProtKB accesions to the UniProtKB Canonical accessions and also checks the position and amino acid of O-GlcNAc modified residue against UniProtKB Canonical sequences. The script also maps the sample type to correct sample term id and sample term name. \n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-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: yeast_protein_info_uniprotkb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_info_uniprotkb.csv\n Name: yeast_protein_masterlist.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_masterlist.csv\n Name: yeast_protein_recnames.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_protein_recnames.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/misc/sample_mapping.csv\n Name: ambiguous_sites_version_2.0.csv\n URI: https:/data.glygen.org/ln2downloads/atlas_oglcnac/2022_10_20/ambiguous_sites_version_2.0.csv\n Name: unambiguous_sites_version_2.0.csv\n URI: https:/data.glygen.org/ln2downloads/atlas_oglcnac/2022_10_20/unambiguous_sites_version_2.0.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2023_07_13/cellosaurus.txt\n Output Subdomain\n Name: yeast_proteoform_glycosylation_sites_oglcnac_atlas.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_proteoform_glycosylation_sites_oglcnac_atlas.csv\n Name: yeast_proteoform_glycosylation_sites_oglcnac_atlas.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.2.1/reviewed/yeast_proteoform_glycosylation_sites_oglcnac_atlas.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"462\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"969\"\n Name: \"amino_acid\"\n Description: \"Three letter abbreviation code of the amino acid\"\n Unique Values: \"2\"\n Name: \"saccharide\"\n Description: \"Sugar\"\n Unique Values: \"1\"\n Name: \"glycosylation_type\"\n Description: \"Type of glycosylation (N/O/C/S linked glycosylation)\"\n Unique Values: \"1\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"463\"\n Name: \"src_xref_key\"\n Description: \"Source Xref key\"\n Unique Values: \"1\"\n Name: \"src_xref_id\"\n Description: \"Source X-ref ID\"\n Unique Values: \"462\"\n Name: \"sample_type\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"method\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"analytical_throughput\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"notes\"\n Description: \"Notes\"\n Unique Values: \"2\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"1\"\n Name: \"glycosylation_subtype\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"source_tissue_id\"\n Description: \"Tissue ID from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_tissue_name\"\n Description: \"Tissue NAME from GlyConnect\"\n Unique Values: \"1\"\n Name: \"source_cell_line_cellosaurus_id\"\n Description: \"cellosaurus ID of the cell line\"\n Unique Values: \"1\"\n Name: \"source_cell_line_cellosaurus_name\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"peptide\"\n Description: \"Protein peptide\"\n Unique Values: \"2854\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"969\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"969\"\n Name: \"start_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"end_aa\"\n Description: \"\"\n Unique Values: \"2\"\n Name: \"site_seq\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.2.1/reviewed/yeast_proteoform_glycosylation_sites_oglcnac_atlas.csv" }