{ "bcoid": "GLY_001102", "title": "Arabidopsis Glycosylation Sites (RCSB PDB)", "description": "The Arabidopsis Glycosylation Sites (RCSB PDB) dataset contains arabidopsis [taxid:3702] proteins glycosites ...", "filename_list": "arabidopsis_proteoform_glycosylation_sites_pdb.csv", "filename": "arabidopsis_proteoform_glycosylation_sites_pdb.csv", "filetype": "csv", "categories": { "species": [ "Arabidopsis thaliana" ], "molecule": [ "Proteoform" ], "tag": [ "Glycosylation Sites" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "O22822-1...", "177..." ], [ "O22822-1...", "177..." ] ], "headers": [ "uniprotkb_ca...", "glycosylatio..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "glycosylation_site_uniprotkb" }, { "type": "string", "label": "amino_acid" }, { "type": "string", "label": "saccharide" }, { "type": "string", "label": "glycosylation_type" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" }, { "type": "string", "label": "pdb_id" }, { "type": "string", "label": "amino_acid_chain" }, { "type": "string", "label": "glycosylation_site_pdb" }, { "type": "string", "label": "carb_name" }, { "type": "string", "label": "n_sequon" }, { "type": "string", "label": "n_sequon_type" }, { "type": "string", "label": "start_pos" }, { "type": "string", "label": "end_pos" }, { "type": "string", "label": "start_aa" }, { "type": "string", "label": "end_aa" }, { "type": "string", "label": "site_seq" } ], [ "O22822-1", "177", "Tyr", "", "O-linked", "protein_xref_pdb4glycosylation", "5U6M", "protein_xref_pdb4glycosylation", "5U6M", "5U6M", "A", "177", "BGC", "", "", "177", "177", "Tyr", "Tyr", "Y" ], [ "O22822-1", "177", "Tyr", "", "O-linked", "protein_xref_pdb4glycosylation", "5U6M", "protein_xref_pdb4glycosylation", "5U6M", "5U6M", "B", "177", "BGC", "", "", "177", "177", "Tyr", "Tyr", "Y" ] ] }, "readme": "Name\n - Arabidopsis Glycosylation Sites (RCSB PDB)\n\nVersion\n - v-2.7.1\n\nCreated on\n - 2019-01-23T17:21:05.909814\n\nModified on\n - 2024-05-17T11:23:50.225Z\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 - Jasmine Young [jasmine@rcsb.rutgers.edu], Chenghua Shao [chenghua@rcsb.rutgers.edu]\n\nChecksum\n - \n\nUsability Domain\n - The Arabidopsis Glycosylation Sites (RCSB PDB) dataset contains arabidopsis [taxid:3702] proteins glycosites mapped from the associated RCSB PDB Id's using SIFTS database (https://www.ebi.ac.uk/pdbe/docs/sifts/). The glycosylation data (PDB ID, GlycoSite, Chain ID, Sugar (first link)) was retrieved from RCSB group. [www.rcsb.org, Nucleic Acids Research, 28: 235-242.(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472/)].\n\nDescription Domain\n Keywords\n - PDB\n - glycosylation sites\n - amino acid\n - amino acid chain\n\n Pipeline Steps\n - Step-1: The script extracts the PDB IDs and PDB glycosite from the input .tsv files and maps it to the corresponding UniProtKB accessions and position using the coordinate file downloaded from the SIFTS database using the formula:(SP_BEG-RES_BEG)+ PDB-Position)]. The script also validates the UniProtKB glycosite (amino acid + position) with the corresponding fasta sequences downloaded from UniProtKB.\n - Step-0: \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: n_sequon_info.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/misc/n_sequon_info.csv\n Name: sample_mapping.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/misc/sample_mapping.csv\n Name: cellosaurus.txt\n URI: https:/data.glygen.org/ln2downloads/cellosaurus/2024_09_05/cellosaurus.txt\n Name: N-linked-ARG-details\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/N-linked-ARG-details\n Name: N-linked-ASN-details\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/N-linked-ASN-details\n Name: O-linked-ASP-details\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-ASP-details\n Name: O-linked-GLU-details\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-GLU-details\n Name: O-linked-SER-details\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-SER-details\n Name: O-linked-THR-details\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-THR-details\n Name: O-linked-TYR-details\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-TYR-details\n Name: pdb_chain_uniprot.csv\n URI: https:/data.glygen.org/ln2downloads/pdb/07-15-2024/pdb_chain_uniprot.csv\n Output Subdomain\n Name: arabidopsis_proteoform_glycosylation_sites_pdb.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/arabidopsis_proteoform_glycosylation_sites_pdb.csv\n Name: arabidopsis_proteoform_glycosylation_sites_pdb.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.7.1/reviewed/arabidopsis_proteoform_glycosylation_sites_pdb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"17\"\n Name: \"glycosylation_site_uniprotkb\"\n Description: \"Site on the protein sequence of the UniProtKB entry where glycosylation is observed\"\n Unique Values: \"43\"\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: \"2\"\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: \"33\"\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: \"33\"\n Name: \"pdb_id\"\n Description: \"PDB ID associated with the UniProtKB accession.\"\n Unique Values: \"33\"\n Name: \"amino_acid_chain\"\n Description: \"Amino acid chain in pdb\"\n Unique Values: \"4\"\n Name: \"glycosylation_site_pdb\"\n Description: \"Site on the protein sequence of the PDB entry where glycosylation is observed\"\n Unique Values: \"39\"\n Name: \"carb_name\"\n Description: \"carbohydrate name\"\n Unique Values: \"3\"\n Name: \"n_sequon\"\n Description: \"\"\n Unique Values: \"28\"\n Name: \"n_sequon_type\"\n Description: \"\"\n Unique Values: \"5\"\n Name: \"start_pos\"\n Description: \"Start position of the gene on the chromosome\"\n Unique Values: \"43\"\n Name: \"end_pos\"\n Description: \"End position of the gene on the chromosome\"\n Unique Values: \"43\"\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-2.7.1/reviewed/arabidopsis_proteoform_glycosylation_sites_pdb.csv" }