{ "object_id": "https://biocomputeobject.org/GLY_000805/v-2.3.1", "etag": "195bd9a6309403e41bdf1bec05cf3b79", "spec_version": "1.3.0", "provenance_domain": { "name": "Yeast Glycosylation Sites (GlyConnect) ", "version": "v-2.3.1", "created": "2022-08-16T12:24:13.810189", "modified": "2023-09-11T20:42:55", "contributors": [ { "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "name": "Jeet Vora", "email": "jeetvora@gwu.edu" }, { "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "name": "Robel Kahsay", "email": "rykahsay@gwu.edu" }, { "affiliation": "GlyConnect", "contribution": [ "contributedBy" ], "name": "Frederique Lisacek", "email": "frederique.lisacek@sib.swiss" }, { "affiliation": "GlyConnect", "contribution": [ "contributedBy" ], "name": "Julien Mariethoz", "email": "julien.mariethoz@sib.swiss" }, { "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "name": "Karina Martinez", "email": "karinamartinez@gwu.edu" }, { "name": "Jingyue Wu", "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "email": "jingyue.wu@email.gwu.edu" }, { "name": "Jingyue Wu", "affiliation": "The George Washington University", "contribution": [ "createdBy" ], "email": "jingyue.wu@email.gwu.edu" } ], "license": "https://creativecommons.org/licenses/by/4.0/" }, "usability_domain": [ "The Yeast Glycosylation Sites (GlyConnect) dataset contains yeast [taxid:559292] UniProtKB canonical accessions with information on reported glycans in GlyConnect database (https://glyconnect.expasy.org/; PMID: 30574787).A json file was derived through GlyConnect API (https://glyconnect.expasy.org/api/docs/index.html?url=/api/assets/swagger.json#/Glycosylation/listGlycosylationsAsJson) (Query: taxonomy:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)). If you use this dataset please provide proper attribution to GlyConnect and GlyGen. Please note that this dataset does not contain protein or sites information just the glycans" ], "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": "Saccharomyces cerevisiae S288C", "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" } ] } } ], "description_domain": { "keywords": [ "glycosylation", "reported glycosylation" ], "pipeline_steps": [ { "step_number": 1, "name": "make-proteoform-dataset.py", "description": "The script loads the glycosylation information from the input JSON file and extracts the data. The QC checks filter out: 1) any rows where the UniProtKB accession is not included in the GlyGen protein list (https://data.glygen.org/GLYDS000001) and/or 2) if the given glycosylation position and amino acid does not match to the amino acid on the .fasta sequence provided in the latest UniProtKB release for that protein (However it does pass if the amino acid +glyco-site is empty (as these records correspond to the \"not reported\" glyco-sites and/or 3) If the glycosylation type does not associate to the glycostlation based on amino acid (i.e if a N-linked is associated with Ser/Thr residue, etc). 4) If the glyco-site is not reported and the glycosylation type is ambigious (c-Linked/o-linked) and/or 5) if the saccharide (GlyTouCan) is not present in the GlyGen glycan masterlist. All the flagged entries are added in the log file (yeast_proteoform_glycosylation_sites_glyconnect.1.log) In this dataset the script only extracts the glycan information. CURRENTLY - THE ABOVE QC STEP IS NOT DONE AS THE DATA DOES NOT HAVE PROTEIN AND SITES.", "version": "", "prerequisite": [], "input_list": [], "output_list": [] } ] }, "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": {} }, "parametric_domain": [ { "param": "", "value": "", "step": "" } ], "io_domain": { "input_subdomain": [ { "uri": { "filename": "n_sequon_info.csv", "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/misc/n_sequon_info.csv" } }, { "uri": { "filename": "sample_mapping.csv", "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/misc/sample_mapping.csv" } }, { "uri": { "filename": "cellosaurus.txt", "uri": "https:/data.glygen.org/ln2downloads/cellosaurus/2023_10_11/cellosaurus.txt" } }, { "uri": { "filename": "glyconnect_yeast.json", "uri": "https:/data.glygen.org/ln2downloads/glyconnect/2023_12_05/glyconnect_yeast.json" } } ], "output_subdomain": [ { "mediatype": "csv", "uri": { "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_glycosylation_sites_glyconnect.csv", "filename": "yeast_proteoform_glycosylation_sites_glyconnect.csv" } }, { "mediatype": "csv", "uri": { "uri": "https:/data.glygen.org/ln2releases/data/v-2.3.1/reviewed/yeast_proteoform_glycosylation_sites_glyconnect.stat.csv", "filename": "yeast_proteoform_glycosylation_sites_glyconnect.stat.csv" } } ] }, "error_domain": { "empirical_error": {}, "algorithmic_error": {} } }