{ "object_id": "https://biocomputeobject.org/GLY_000410/v-2.3.1", "spec_version": "1.3.0", "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": "Protein", "category_name": "molecule" }, { "category_value": "GlyGen-UniProtKB Crossreferences", "category_name": "tag" }, { "category_value": "tsv", "category_name": "file_type" }, { "category_value": "Reviewed", "category_name": "status" }, { "category_value": "internal", "category_name": "scope" }, { "category_name": "species", "category_value": "Homo sapiens" }, { "category_name": "species", "category_value": "Rattus norvegicus" }, { "category_name": "species", "category_value": "Mus musculus" }, { "category_name": "species", "category_value": "Drosophila melanogaster" }, { "category_name": "species", "category_value": "Saccharomyces cerevisiae S288C" }, { "category_name": "species", "category_value": "Hepatitis C virus (isolate Japanese)" }, { "category_name": "species", "category_value": "Severe acute respiratory syndrome coronavirus 2" }, { "category_name": "species", "category_value": "Severe acute respiratory syndrome-related coronavirus" }, { "category_name": "species", "category_value": "Hepatitis C virus (isolate H)" } ] } } ], "provenance_domain": { "license": "\"https://creativecommons.org/licenses/by/4.0/\"", "name": "GlyGen-UniProtKB Crossreferences Mapping", "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": "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" } ], "created": "2020-04-01T12:08:42.022917", "modified": "2022-09-26T09:05:56.496595", "version": "v-2.3.1" }, "description_domain": { "keywords": [ "UniProtKB", "GlyGen", "crossreferences", "human", "mouse", "rat" ], "pipeline_steps": [ { "name": "make-species-agnostic-dataset.py", "step_number": 1, "version": "", "input_list": [], "output_list": [], "prerequisite": [], "description": "The script loads the GlyGen's UniProtKB protein accessions for human, mouse and rat species and extracts it into a csv dataset file" } ] }, "execution_domain": { "external_data_endpoints": [], "environment_variables": {}, "script_driver": "manual", "software_prerequisites": [ { "version": "2.7.5", "name": "Python", "uri": { "uri": "https://www.python.org/download/releases/2.7.5/" } } ], "script": [ { "uri": { "uri": "https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-species-agnostic-dataset.py", "filename": "make-species-agnostic-dataset.py" } } ] }, "parametric_domain": [ { "step": "", "param": "", "value": "" } ], "usability_domain": [ "The GlyGen-UniProtKB Crossreferences dataset contains UniProtKB glycoprotein accessions for human [taxid:9606], mouse [taxid:10090], rat [taxid:10116], hcv1a [taxid:11108], hcv1b [taxid:11116], sarscov1 [taxid:694009] and sarscov2 [taxid:2697049] glycoproteins for the purpose of UniProtKB to GlyGen crossreferences. In the dataset, the UniProtKB glycoprotein accessions have corresponding glycosylation annotation present in the datasets. The glycosylation annotation provides information about total (N,O,S,C) glycosylation sites followed by (if available) reported N-glycans and/or reported O-glycans with the number of sites. 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