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HIVE_metagenomics.json
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HIVE_metagenomics.json
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{
"bco_id": "https://w3id.org/biocompute/1.3.0/examples/HIVE_metagenomics.json",
"checksum": "ECD541AE0F61AAAAA1FAC14B2B08ABE18F610E1AA4677D54E89B292550F5058A",
"bco_spec_version" : "https://w3id.org/biocompute/1.3.0/",
"provenance_domain": {
"name": "Healthy human fecal metagenomic diversity",
"version": "1.0.0",
"review": [
{
"status": "approved",
"reviewer_comment": "Approved by GW staff.",
"reviewer": {
"name": "Charles Hadley King",
"affiliation": "George Washington University",
"email": "hadley_king@gwu.edu",
"contribution": ["curatedBy"],
"orcid": "https://orcid.org/0000-0003-1409-4549"
}
}
],
"obsolete_after" : "2118-09-26T14:43:43-0400",
"embargo" : {
"start_time": "2000-09-26T14:43:43-0400",
"end_time": "2000-09-26T14:43:45-0400"
},
"created": "2018-11-29T11:29:08-0500",
"modified": "2018-11-30T11:29:08-0500",
"contributors": [
{
"name": "Charles Hadley King",
"affiliation": "George Washington University",
"email": "hadley_king@gwu.edu",
"contribution": ["createdBy", "curatedBy", "authoredBy"],
"orcid": "https://orcid.org/0000-0003-1409-4549"
},
{
"name": "Raja Mazumder",
"affiliation": "George Washington University",
"email": "mazumder@gwu.edu",
"contribution": ["createdBy", "curatedBy", "authoredBy"],
"orcid": "https://orcid.org/0000-0001-88238-9945"
}
],
"license": "https://spdx.org/licenses/CC-BY-4.0.html"
},
"usability_domain": [
"Identify the most common organism present in a human [taxID:9606] fecal [UBERON:0001988] sample, ",
"Identify the general community composition of organisms in a human [taxID:9606] fecal [UBERON:0001988] sample, ",
"CensuScope is used to do a census of the composition of the read files. Based on a user-defined threshold, organisms identified are used for alignment in the Hexagon alignment."
],
"extension_domain":{
"scm_extension": {
"scm_repository": "https://github.com/biocompute-objects/HIVE_metagenomics",
"scm_type": "git",
"scm_commit": "e4620f642fb20557f6c679397696614305ed07b1",
"scm_path": "biocompute-objects/HIVE_metagenomics",
"scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl"
}
},
"description_domain": {
"keywords": [
"metagenome",
"metagenomic analysis",
"fecal"
],
"xref": [
{
"namespace": "uberon",
"name": "Uber Anatomy Ontology",
"ids": ["0001988"],
"access_time": "2016-11-30T06:46-0500"
},
{
"namespace": "taxonomy",
"name": "Taxonomy",
"ids": ["9606"],
"access_time": "2016-11-30T06:46-0500"
}
],
"platform": ["hive"],
"pipeline_steps": [
{
"step_number": 1,
"name": "CensuScope",
"description": "Detect taxonomic composition of a metagenomic data set.",
"version": "1.3",
"prerequisite": [
{
"name": "Filtered_NT_feb18_2016",
"uri": {
"uri": "https://hive.biochemistry.gwu.edu/genome/513957",
"access_time": "2016-11-30T06:46-0500"
}
}
],
"input_list": [
{
"uri": "https://hive.biochemistry.gwu.edu/nuc-read/545722",
"access_time": "2016-11-30T06:46-0500"
},
{
"uri": "https://hive.biochemistry.gwu.edu/nuc-read/545721",
"access_time": "2016-11-30T06:46-0500"
}
],
"output_list": [
{
"uri": "https://hive.biochemistry.gwu.edu/546223/dnaAccessionBasedResult.csv",
"access_time": "2016-11-30T06:46-0500"
}
]
},
{
"step_number": 2,
"name": "HIVE-hexagon",
"description": "Alignment of reads to a set of references",
"version": "1.3",
"input_list": [
{
"uri": "http://example.com/data/546223/dnaAccessionBased.csv",
"access_time": "2016-11-30T06:46-0500"
},
{
"uri": "https://hive.biochemistry.gwu.edu/nuc-read/545722",
"access_time": "2016-11-30T06:46-0500"
},
{
"uri": "https://hive.biochemistry.gwu.edu/nuc-read/545721",
"access_time": "2016-11-30T06:46-0500"
}
],
"output_list": [
{
"uri": "https://hive.biochemistry.gwu.edu/546232/alCount-Unalignedo524569-alCount--1.csv",
"access_time": "2016-11-30T06:46-0500"
}
]
}
]
},
"execution_domain": {
"script": [
{
"uri": {
"uri": "https://github.com/biocompute-objects/HIVE_metagenomics/blob/master/driverHIVEmetagenomic.py"
}
}
],
"script_driver": "shell",
"software_prerequisites": [
{
"name": "CensuScope",
"version": "albinoni.2",
"uri": {
"uri": "http://example.com/dna.cgi?cmd=dna-screening&cmdMode=-",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "HIVE-hexagon",
"version": "babajanian.1",
"uri": {
"uri": "http://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
"access_time": "2017-01-24T09:40:17-0500"
}
}
],
"external_data_endpoints": [
{
"name": "HIVE",
"url": "https://hive.biochemistry.gwu.edu/dna.cgi?cmd=login"
},
{
"name": "access to e-utils",
"url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
}
],
"environment_variables": {
"key": "HOSTTYPE",
"value" : "x86_64-linux"
}
},
"parametric_domain": [
{"param": "seed", "value": "14", "step": "2"},
{"param":"minimum_match_len", "value": "66", "step": "2"},
{"param": "divergence_threshold_percent", "value": "0.30", "step": "2"},
{"param": "minimum_coverage", "value": "15", "step": "2"},
{"param": "freq_cutoff", "value": "0.10", "step": "2"}
],
"io_domain": {
"input_subdomain": [
{
"uri": {
"filename": "Hepatitis C virus genotype 1",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "Hepatitis C virus type 1b complete genome",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "Hepatitis C virus (isolate JFH-1) genomic RNA",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "Hepatitis C virus clone J8CF, complete genome",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "Hepatitis C virus S52 polyprotein gene",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "HCV1a_drug_resistant_sample0001-01",
"uri": "http://example.com/nuc-read/514682",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"uri": {
"filename": "HCV1a_drug_resistant_sample0001-02",
"uri": "http://example.com/nuc-read/514683",
"access_time": "2017-01-24T09:40:17-0500"
}
}
],
"output_subdomain": [
{
"mediatype": "text/csv",
"uri": {
"uri": "http://example.com/data/514769/dnaAccessionBased.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"mediatype": "text/csv",
"uri": {
"uri": "http://example.com/data/514801/SNPProfile*.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
}
]
},
"error_domain": {
"empirical_error": {
"false_negative_alignment_hits": "<0.0010",
"false_discovery": "<0.05"
},
"algorithmic_error": {
"false_positive_mutation_calls_discovery": "<0.00005",
"false_discovery": "0.005"
}
}
}