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Any GlycoProtDB ID which was mapped to a protein outside GlyGen protein master list was excluded from the output 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-protein-dataset.py","filename":"make-protein-dataset.py"}}]},"error_domain":{"empirical_error":{},"algorithmic_error":{}},"parametric_domain":[{"step":"","param":"","value":""}],"usability_domain":["The Mouse (TaxID:10090) Xref GlycoProtDB  contains x-refs to IDs present in the GlycoProtDB database (https://acgg.asia/gpdb2/index). If you use this dataset please provide proper attribution to GlycoProtDB and GlyGen. 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The dataset also contains other information such as O-GlcNAc score, the count and the techniques used to determine the O-GlcNAc modification and the peptide sequence from the -5 to +5 postion of the modified residue. The dataset also containes disclaimer and notes where the position of sites in publication and in the fasta sequence varies.","The dataset is contributed from The O-GlcNAc Database maintained by Stephanie Olivier's lab ","Wulff-Fuentes E, Berendt RR, Massman L, Danner L, Malard F, Vora J, Kahsay R, and Olivier-Van Stichelen S, The Fruitfly O-GlcNAcome Database and Meta-Analysis. Scientific Data 8, 25 (2021) ","QC check -  The python script is used to process each protein entry of the database table and perform quality control (QC). In the QC checks, the reported UniProtKB accessions in the database are matched with the GlyGen’s fruitfly protein masterlist of UniProtKB canonical accessions to ensure all of the proteins belong to fruitfly species. Next, the O-GlcNAc site data that contained the amino acid residue and its position are mapped to the GlyGen’s fasta sequence for the corresponding fruitfly UniProtKB canonical proteins. The amino acid residues and positions that don't match with the fasta sequence of the canonical protein were flagged and excluded from the table. Similarly, the protein entries that don't have any site information are also excluded. The entries that passed all the quality control steps are exported as a final csv dataset file whereas the excluded entries are exported in a log file with the reasons for exclusion for further manual verification.","DISCLAIMER - For each entry, an O-GlcNAc score was attributed to each O-GlcNAcylated protein, reflecting the confidence in the protein’s O-GlcNAcylation identification. The score combined the number of articles and techniques used and the availability of some O-GlcNAcylation sites. 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The amino acid residues and positions that don't match with the fasta sequence of the canonical protein were flagged and excluded from the table. Similarly, the protein entries that don't have any site information are also excluded. The entries that passed all the quality control steps are exported as a final csv dataset file whereas the excluded entries are exported in a log file with the reasons for exclusion for further manual verification.","DISCLAIMER - For each entry, an O-GlcNAc score was attributed to each O-GlcNAcylated protein, reflecting the confidence in the protein’s O-GlcNAcylation identification. The score combined the number of articles and techniques used and the availability of some O-GlcNAcylation sites. Interestingly, a O-GlcNAc score of 3 or under, means that (1) no sites were identified, (2) only one technique was used, and (3) 1-2 articles were associated with the entry. Often identified from large-scale proteomics studies, at least an extra-validation step would be highly recommended to confirm their O-GlcNAcylation."],"extension_domain":[{"extension_schema":"http://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":"Mus musculus","category_name":"species"},{"category_value":"Proteoform","category_name":"molecule"},{"category_value":"O-GlcNAc Glycosylation Sites (MCW)","category_name":"tags"},{"category_value":"csv","category_name":"file_type"},{"category_value":"Reviewed","category_name":"status"},{"category_value":"internal","category_name":"scope"}]}}],"description_domain":{"keywords":["O-GlcNAc"],"pipeline_steps":[{"step_number":1,"name":"make-proteoform-dataset.py","description":"The script maps the UniProtKB accesions to the UniProtKB Canonical accessions and also checks the position and amino acid of O-GlcNAc modified residue against UniProtKB Canonical sequences. 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The dataset also containes disclaimer and notes where the position of sites in publication and in the fasta sequence varies.","The dataset is contributed from The O-GlcNAc Database maintained by Stephanie Olivier's lab ","Wulff-Fuentes E, Berendt RR, Massman L, Danner L, Malard F, Vora J, Kahsay R, and Olivier-Van Stichelen S, The Mouse O-GlcNAcome Database and Meta-Analysis. Scientific Data 8, 25 (2021) ","QC check -  The python script is used to process each protein entry of the database table and perform quality control (QC). In the QC checks, the reported UniProtKB accessions in the database are matched with the GlyGen’s rat protein masterlist of UniProtKB canonical accessions to ensure all of the proteins belong to rat species. Next, the O-GlcNAc site data that contained the amino acid residue and its position are mapped to the GlyGen’s fasta sequence for the corresponding rat UniProtKB canonical proteins. The amino acid residues and positions that don't match with the fasta sequence of the canonical protein were flagged and excluded from the table. Similarly, the protein entries that don't have any site information are also excluded. The entries that passed all the quality control steps are exported as a final csv dataset file whereas the excluded entries are exported in a log file with the reasons for exclusion for further manual verification.","DISCLAIMER - For each entry, an O-GlcNAc score was attributed to each O-GlcNAcylated protein, reflecting the confidence in the protein’s O-GlcNAcylation identification. The score combined the number of articles and techniques used and the availability of some O-GlcNAcylation sites. Interestingly, a O-GlcNAc score of 3 or under, means that (1) no sites were identified, (2) only one technique was used, and (3) 1-2 articles were associated with the entry. 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