{ "object_id": "https://biocomputeobject.org/GLY_000042/v-2.8.1", "spec_version": "1.3.0", "etag": "cfed2867f81c00c812bce1c04c485a8c", "provenance_domain": { "name": "Human Glycosylation Sites (RCSB PDB)", "version": "v-2.8.1", "license": "https://creativecommons.org/licenses/by/4.0/", "created": "2019-01-23T17:21:05.909814", "modified": "2024-12-10T16:57:20.331Z", "contributors": [ { "name": "Jeet Vora", "affiliation": "The George Washington University", "email": "jeetvora@gwu.edu", "contribution": [ "createdBy" ] }, { "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "name": "Robel Kahsay", "email": "rykahsay@gwu.edu" }, { "affiliation": "RCSB PDB", "contribution": [ "contributedBy" ], "name": "Jasmine Young", "email": "jasmine@rcsb.rutgers.edu" }, { "affiliation": "RCSB PDB", "contribution": [ "contributedBy" ], "name": "Chenghua Shao", "email": "chenghua@rcsb.rutgers.edu" }, { "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "name": "Karina Martinez", "email": "karinamartinez@gwu.edu" }, { "name": "Luke Johnson", "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "email": "luke.johnson@email.gwu.edu" }, { "name": "Urnisha Bhuiyan", "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "email": "sbhuiyan28@email.gwu.edu" }, { "name": "Cyrus Au-Yeung", "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "email": "cyruschauyeung@gwu.edu" }, { "name": "Kate Warner", "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "email": "k.warner1@gwu.edu" } ] }, "usability_domain": [ "The Human Glycosylation Sites (RCSB PDB) dataset contains Homo sapiens [taxid:9606] 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/)]." ], "description_domain": { "pipeline_steps": [ { "name": "make-proteoform-dataset.py", "step_number": 1, "input_list": [], "description": "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.", "prerequisite": [], "output_list": [] }, { "input_list": [], "prerequisite": [], "output_list": [] } ], "keywords": [ "PDB", "glycosylation sites", "amino acid", "amino acid chain" ] }, "parametric_domain": [ { "value": "" } ], "io_domain": { "output_subdomain": [ { "mediatype": "csv", "uri": { "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/human_proteoform_glycosylation_sites_pdb.csv", "filename": "human_proteoform_glycosylation_sites_pdb.csv" } }, { "mediatype": "csv", "uri": { "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/human_proteoform_glycosylation_sites_pdb.stat.csv", "filename": "human_proteoform_glycosylation_sites_pdb.stat.csv" } } ], "input_subdomain": [ { "uri": { "filename": "n_sequon_info.csv", "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/misc/n_sequon_info.csv" } }, { "uri": { "filename": "sample_mapping.csv", "uri": "https:/data.glygen.org/ln2releases/data/v-2.8.1/misc/sample_mapping.csv" } }, { "uri": { "filename": "cellosaurus.txt", "uri": "https:/data.glygen.org/ln2downloads/cellosaurus/2025_01_13/cellosaurus.txt" } }, { "uri": { "filename": "N-linked-ARG-details", "uri": "https:/data.glygen.org/ln2downloads/pdb/07-15-2024/N-linked-ARG-details" } }, { "uri": { "filename": "N-linked-ASN-details", "uri": "https:/data.glygen.org/ln2downloads/pdb/07-15-2024/N-linked-ASN-details" } }, { "uri": { "filename": "O-linked-ASP-details", "uri": "https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-ASP-details" } }, { "uri": { "filename": "O-linked-GLU-details", "uri": "https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-GLU-details" } }, { "uri": { "filename": "O-linked-SER-details", "uri": "https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-SER-details" } }, { "uri": { "filename": "O-linked-THR-details", "uri": "https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-THR-details" } }, { "uri": { "filename": "O-linked-TYR-details", "uri": "https:/data.glygen.org/ln2downloads/pdb/07-15-2024/O-linked-TYR-details" } }, { "uri": { "filename": "pdb_chain_uniprot.csv", "uri": "https:/data.glygen.org/ln2downloads/pdb/07-15-2024/pdb_chain_uniprot.csv" } } ] }, "execution_domain": { "script": [ { "uri": { "uri": "https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-proteoform-dataset.py", "filename": "make-proteoform-dataset.py" } } ], "script_driver": "manual", "software_prerequisites": [ { "version": "2.7.5", "name": "Python", "uri": { "uri": "https://www.python.org/download/releases/2.7.5/" } } ], "external_data_endpoints": [], "environment_variables": {} }, "extension_domain": [ { "extension_schema": "https://www.w3id.org/biocompute/extension_domain/1.2.0/dataset/dataset_extension.json", "dataset_extension": { "additional_license": { "data_license": "https://creativecommons.org/licenses/by/4.0/", "script_license": "https://www.gnu.org/licenses/gpl-3.0.en.html" }, "dataset_categories": [ { "category_value": "Homo sapiens", "category_name": "species" }, { "category_value": "Proteoform", "category_name": "molecule" }, { "category_value": "Glycosylation Sites", "category_name": "tag" }, { "category_value": "csv", "category_name": "file_type" }, { "category_value": "Reviewed", "category_name": "status" }, { "category_value": "internal", "category_name": "scope" } ] } } ], "error_domain": {} }