{ "io_domain": { "input_subdomain": [ { "uri": { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/merge_human_rat_mouse_gps_06022020_130220.csv", "filename": "merge_human_rat_mouse_gps_06022020_130220.csv" } }, { "uri": { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_idmapping.csv", "filename": "rat_protein_idmapping.csv" } }, { "uri": { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/classification.tsv", "filename": "classification.tsv" } }, { "uri": { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/glycan_properties.tsv", "filename": "glycan_properties.tsv" } }, { "uri": { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_allsequences.fasta", "filename": "rat_protein_allsequences.fasta" } }, { "uri": { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/aadict.csv", "filename": "aadict.csv" } }, { "uri": { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/glycan_xref_unicarbkb.csv", "filename": "glycan_xref_unicarbkb.csv" } } ], "output_subdomain": [ { "mediatype": "csv", "uri": { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.csv" } }, { "mediatype": "csv", "uri": { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.1.log" } }, { "mediatype": "csv", "uri": { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.2.log" } }, { "mediatype": "csv", "uri": { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.stats.csv" } }, { "mediatype": "csv", "uri": { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.stat.csv", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.stat.csv" } } ] }, "spec_version": "1.3.0", "object_id": "https://biocomputeobject.org/GLY_000221/v-1.8.24", "extension_domain": [ { "extension_schema": "http://www.w3id.org/biocompute/extension_domain/1.1.0/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": "Reviewed", "category_name": "status" }, { "category_value": "Proteoform", "category_name": "molecule" }, { "category_value": "Rattus norvegicus", "category_name": "species" }, { "category_value": "UniCarbKB glycosylation sites", "category_name": "tags" }, { "category_value": "csv", "category_name": "file_type" }, { "category_value": "internal", "category_name": "scope" } ] } } ], "provenance_domain": { "license": "https://creativecommons.org/licenses/by/4.0/", "name": "Glycosylation sites - UniCarbKB [Rat proteins]", "contributors": [ { "affiliation": "George Washington University", "contribution": [ "createdBy" ], "name": "Rahi Navelkar", "email": "rsn13@gwu.edu" }, { "affiliation": "George Washington University", "contribution": [ "createdBy" ], "name": "Jeet Vora", "email": "jeetvora@gwu.edu" }, { "affiliation": "UniCarbKB", "contribution": [ "authoredBy" ], "name": "Matthew Campbell ", "email": "m.campbell2@griffith.edu.au" }, { "affiliation": "George Washington University", "contribution": [ "contributedBy" ], "name": "Robel Kahsay", "email": "rykahsay@email.gwu.edu" }, { "affiliation": "Georgetown University", "contribution": [ "contributedBy" ], "name": "Nathan Edwards", "email": "Georgetown University" } ], "created": "2019-09-05T14:34:59.005886", "modified": "2020-05-01T15:21:53.655183", "version": "v-1.8.24" }, "description_domain": { "keywords": [ "proteins", "canonical", "glycosylation sites", "glycan", "UniCarbKB", "GlyTouCan" ], "pipeline_steps": [ { "name": "make-proteoform-dataset.py", "step_number": 0, "version": "", "input_list": [ { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/merge_human_rat_mouse_gps_06022020_130220.csv", "filename": "merge_human_rat_mouse_gps_06022020_130220.csv" }, { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_masterlist.csv", "filename": "rat_protein_masterlist.csv" }, { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/classification.tsv", "filename": "classification.tsv" }, { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/glycan_properties.tsv", "filename": "glycan_properties.tsv" }, { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_protein_allsequences.fasta", "filename": "rat_protein_allsequences.fasta" }, { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/source/aadict.csv", "filename": "aadict.csv" }, { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/glycan_xref_unicarbkb.csv", "filename": "glycan_xref_unicarbkb.csv" } ], "output_list": [ { "uri": "http://data.glygen.org/ln2data/releases/data/v-1.8.24/reviewed/rat_proteoform_glycosylation_sites_unicarbkb.csv", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.csv" }, { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/logs/rat_proteoform_glycosylation_sites_unicarbkb.1.log", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.1.log" }, { "uri": "https://data.glygen.org/ln2data/releases/data/v-1.8.24/logs/rat_proteoform_glycosylation_sites_unicarbkb.2.log", "filename": "rat_proteoform_glycosylation_sites_unicarbkb.2.log" } ], "prerequisite": [], "description": "The input file was received directly from the author (Matthew Campbell). A python script along with additional inputs was used to process data and generate a final dataset object. The script checks the GlyTouCan accessions against the existing accessions from GlyTouCan. (Input file 3). The missing accessions are added in log 2 file (human_proteoform_glycosylation_sites_unicarbkb.2.log) for validation purposes but are not eliminated during the processing. The unicarbkb id's which are glycan compostion strings, are mapped to GlyTouCan accession using input file 7, generated by Nathan Edwards. The script additionally implements 10 QC checks. Any row that fails for one or more checks is eliminated. All eliminated rows can be accessed from the log 1 (human_proteoform_glycosylation_sites_unicarbkb.1.log) file along the QC tags. QC tags and description: 1) no_canon: The given protein accession cannot be mapped to a canonical accession. (input file 2) 2) bad_pos: The given amino-acid position is invalid or exceeds the length of the protein sequence. 3) aa_mismatch: Bad amino acid reported (input file 6) 4) invalid_aa: The given amino acid is invalid. 5) glycan_without_glytype: glycan is not in the glycan classification file (Glycan classification file is generated by Author Nathan Edwards; input file 3). 6) bad_glytype: A bad glycan type is detected 7) n_glycan_aa_mismatch: An N glycan is associated with a ser/thr residue 8) o_glycan_aa_mismatch: An O glycan is associated with a Asn residue. 9) no_pmid: The PubMed ID value is zero or blank. 10) no_glycan_invalid_aa: row has no glycan and amino acid is invalid. " } ] }, "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/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-proteoform-dataset.py", "filename": "make-proteoform-dataset.py" } } ] }, "error_domain": { "empirical_error": {}, "algorithmic_error": {}, "emperical_error": {} }, "parametric_domain": [ { "step": "", "value": "", "param": "" } ], "usability_domain": [ "List of rat [taxid:10116] proteins with information on glycosylation sites and associated glycans (if available) from UniCarbKB database [https://academic.oup.com/nar/article/42/D1/D215/1052197 ,https://doi.org/10.1093/nar/gkt1128]. The listed protein (UniProtKB) accessions are part of the GlyGen UniProtKB canonical list (https://data.glygen.org/GLYDS000244)." ], "etag": "991ab7dae241b906fc07aff5ff530ea2", "_id": { "$oid": "5d715553f5c47b18c064d651" } }