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glycosylation-sites-UniCarbKB.json
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{
"bco_id": "https://w3id.org/biocompute/examples/glycosylation-sites-UniCarbKB",
"checksum": "D231C92C660CD1DD818D412E10F86F07338BA730FBE6898EF8F7DF1B1ECBFD3C",
"bco_spec_version" : "https://w3id.org/biocompute/spec/1.3.0",
"provenance_domain":{
"name": "glycosylation-sites-UniCarbKB",
"version": "1.0",
"review":[
{
"status": "approved",
"reviewer_comment": "The dataset has passed the manual and automated QC steps and the readme has also been reviewed",
"reviewer":{
"name": "Rahi Navelkar",
"affiliation": "The George Washington University",
"email": "[email protected]",
"contribution":["curatedBy"]
}
}
],
"created": "2018-07-09T11:34:02-5:00",
"modified": "2018-11-22T14:44:02-5:00",
"contributors":[
{
"name": "Matthew Campbell",
"affiliation": "Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia",
"email": "[email protected]",
"contribution":["contributedBy"]
},
{
"name": "Rahi Navelkar",
"affiliation": "The George Washington University",
"email": "[email protected]",
"contribution":["curatedBy"]
},
{
"name": "Brian Fochtman",
"affiliation": "The George Washington University",
"email": "[email protected]",
"contribution":["createdBy"]
},
{
"name": "Robel Kahsay",
"affiliation": "The George Washington University",
"email": "[email protected]",
"contribution":["createdBy"]
}
],
"license": "https://creativecommons.org/licenses/by/4.0/"
},
"usability_domain":[
"List of human [taxid:9606] proteins with information on glycosylation sites from UniCarbKB database [https://academic.oup.com/nar/article/42/D1/D215/1052197, https://doi.org/10.1093/nar/gkt1128]. The file also includes GlyTouCan accessions and UniCarbKB structure ids for associated glycan structures."
],
"extension_domain":{
"license":{
"data_license": "https://creativecommons.org/licenses/by/4.0/",
"scripts_license": "https://www.gnu.org/licenses/gpl-3.0.en.html"
},
"scm_extension":{
"scm_repository": "https://github.com/GW-HIVE/glygen-backend-integration/",
"scm_type": "git",
"scm_commit": "d34b85553e775dd5452005d786fe6e47d6048ee0",
"scm_path": "/data/projects/glygen/generated/datasets/reviewed/human_proteoform_glycosylation_sites_unicarbkb_glytoucan.readme.txt"
}
},
"description_domain":{
"keywords":[
"protein",
"canonical",
"glycosylation",
"glycan"
],
"xref":[
{
"namespace": "taxonomy",
"name": "Taxonomy",
"ids": ["9606"],
"access_time": "2018-21-02T14:46:55-5:00"
}
],
"platform": ["centos7"],
"pipeline_steps":[
{
"step_number":1,
"name": "make-proteoform_glycosylation_sites_unicarbkb_glytoucan-csv-step2.py",
"description": "Python script for assigning glycosylation type (linkage type)",
"version": "",
"input_list":[
{
"uri": "/unicarbkb_human_2018_10_31_02_22_23.clean.csv"
},
{
"uri": "/human_glytoucan_140918_2018_10_31_02_17_32.txt"
}
],
"output_list":[
{
"uri": "/human_glycosylation_types.csv"
},
{
"uri": "/human_glycosylation_types.log"
}
]
},
{
"step_number":2,
"name": "make-proteoform_glycosylation_sites_unicarbkb_glytoucan-csv-step3.py",
"description": "Python scripts for mapping to canonical protein accession and process data fro quality checks. a. If the protein accession is not included in UniProt protein list [UniProt Nov-2017 Release]. b. If the amino acid position does not match to the amino acid on the associated position on fasta sequence [UniProt Nov-2017 Release]. c. If the id (UnicarbKB structure id) is not present in input file. d. If the glycosylation type (linkage type) is not retrieved through step 2. e. If a serine or threonine is reported for an N-linked glycan structure. f. If an asparagine is reported for an O-linked glycan structure. g. If the glycosylation type (linkage type) has both 'N-linked;O-linked' assignment through step 2.",
"input_list":[
{"uri": "/unicarbkb_human_2018_10_31_02_22_23.clean.csv"},
{"uri": "/human_protein_all.fasta"}
],
"output_list":[
{"uri": "/human_proteoform_glycosylation_sites_unicarbkb_glytoucan.csv"},
{"uri": "/human_proteoform_glycosylation_sites_unicarbkb_glytoucan.log"}
]
}
]
},
"execution_domain":{
"script":[
{
"uri": {
"uri": "https://github.com/glygener/glygen-backend-integration/blob/master/integration/make-proteoform_glycosylation_sites_unicarbkb_glytoucan-csv-step2.py"
}
},
{
"uri": {
"uri": "https://github.com/glygener/glygen-backend-integration/blob/master/integration/make-proteoform_glycosylation_sites_unicarbkb_glytoucan-csv-step3.py"
}
}
],
"script_driver": "manual",
"software_prerequisites":[
{
"name": "Python",
"version": "2.7.13",
"uri": {
"uri": "https://www.python.org/downloads/release/python-2713/",
"access_time": "2017-01-24T09:40:17-0500",
"sha1_chksum": "17add4bf0ad0ec2f08e0cae6d205c700"
}
}
],
"external_data_endpoints": [
{
"name": "UniCarbKB",
"url": "http://www.unicarbkb.org/"
},
{
"name": "access glygen-backend-integration",
"url": "https://github.com/glygener/glygen-backend-integration"
}
],
"environment_variables":{
}
},
"io_domain":{
"input_subdomain":[
{
"uri":{
"filename": "unicarbkb_human_2018_10_31_02_22_23.clean.csv",
"uri": "http://data.glygen.org/datasets/source/unicarbkb_human_2018_10_31_02_22_23.clean.csv",
"access_time": "2018-10-10T11:34:02-5:00"
}
},
{
"uri":{
"filename": "human_glytoucan_140918_2018_10_31_02_17_32.txt",
"uri": "http://data.glygen.org/datasets/source/human_glytoucan_140918_2018_10_31_02_17_32.txt",
"access_time": "2018-10-10T11:34:02-5:00"
}
},
{
"uri":{
"filename": "human_protein_all.fasta",
"uri": "http://data.glygen.org/GLYDS00053",
"access_time": "2018-10-10T11:34:02-5:00"
}
}
],
"output_subdomain":[
{
"mediatype": "csv/text",
"uri":{
"filename": "human_glycosylation_types.csv",
"uri": "http://data.glygen.org/datasets/source/human_glycosylation_types.csv",
"access_time": "2018-10-10T11:37:02-5:00"
}
},
{
"mediatype": "csv/text",
"uri":{
"filename": "human_glycosylation_types.log",
"uri": "http://data.glygen.org/datasets/logs/human_glycosylation_types.log",
"access_time": "2018-10-10T11:37:02-5:00"
}
},
{
"mediatype": "csv/text",
"uri":{
"filename": "human_proteoform_glycosylation_sites_unicarbkb_glytoucan.log",
"uri": "http://data.glygen.org/datasets/logs/human_proteoform_glycosylation_sites_unicarbkb_glytoucan.log",
"access_time": "2018-10-10T11:37:02-5:00"
}
},
{
"mediatype": "csv/text",
"uri":{
"filename": "human_proteoform_glycosylation_sites_unicarbkb_glytoucan.csv",
"uri": "http://data.glygen.org/GLYDS00040",
"access_time": "2018-10-10T11:37:02-5:00"
}
}
]
},
"error_domain":{
"empirical_error":{
"statistics":[
{
"comment": "Unique value statistics for the dataset"
},
{
"key": "uniprotkb_acc_canonical",
"value":58,
"description": "Accession assigned to the protein isoform chosen to be the canonical sequence in UniProtKB database"
},
{
"key": "glycosylation_site",
"value":162,
"description": "Site on the protein sequence where glycosylation is observed"
},
{
"key": "evidence",
"value":127,
"description": "NCBI PubMed Id (PMID) as evidence for the entry"
},
{
"key": "unicarbkb_id",
"value":807,
"description": "UnicarbKB data structure identifier"
},
{
"key": "glytoucan_ac",
"value":675,
"description": "Unique accession assigned to the registered glycan structure in GlyTouCan database"
},
{
"key": "amino_acid",
"value":3,
"description": "Three letter code abbreviation of the amino acid"
},
{
"key": "glycosylation_type",
"value":2,
"description": "Type of glycosylation [linkage type]"
}
]
},
"algorithmic_error":{}
}
}