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add metagenomics
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‎HIVE_metagenomics.json‎

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{
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"bco_id": "https://github.com/biocompute-objects/HIVE_metagenomics/blob/master/HIVE_metagenomics.json",
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"checksum": "ECD541AE0F61AAAAA1FAC14B2B08ABE18F610E1AA4677D54E89B292550F5058A",
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"bco_spec_version" : "https://w3id.org/biocompute/spec/v1.2",
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"provenance_domain": {
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"name": "Healthy human fecal metagenomic diversity",
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"version": "1.0.0",
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"review": [
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{
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"status": "approved",
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"reviewer_comment": "Approved by GW staff.",
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"reviewer": {
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"name": "Charles Hadley King",
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"affiliation": "George Washington University",
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"email": "[email protected]",
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"contribution": ["curatedBy"],
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"orcid": "https://orcid.org/0000-0003-1409-4549"
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}
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}
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],
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"obsolete_after" : "2118-09-26T14:43:43-0400",
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"embargo" : {
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"start_time": "2000-09-26T14:43:43-0400",
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"end_time": "2000-09-26T14:43:45-0400"
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},
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"created": "2018-11-29T11:29:08-0500",
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"modified": "2018-11-30T11:29:08-0500",
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"contributors": [
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{
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"name": "Charles Hadley King",
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"affiliation": "George Washington University",
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"email": "[email protected]",
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"contribution": ["createdBy", "curatedBy", "authoredBy"],
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"orcid": "https://orcid.org/0000-0003-1409-4549"
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},
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{
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"name": "Raja Mazumder",
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"affiliation": "George Washington University",
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"email": "[email protected]",
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"contribution": ["createdBy", "curatedBy", "authoredBy"],
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"orcid": "https://orcid.org/0000-0001-88238-9945"
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}
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],
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"license": "https://spdx.org/licenses/CC-BY-4.0.html"
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},
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"usability_domain": [
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"Identify the most common organism present in a human [taxID:9606] fecal [UBERON:0001988] sample, ",
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"Identify the general community composition of organisms in a human [taxID:9606] fecal [UBERON:0001988] sample, ",
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"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."
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],
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"extension_domain":{
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"scm_extension": {
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"scm_repository": "https://github.com/biocompute-objects/HIVE_metagenomics",
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"scm_type": "git",
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"scm_commit": "e4620f642fb20557f6c679397696614305ed07b1",
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"scm_path": "biocompute-objects/HIVE_metagenomics",
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"scm_preview": "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl"
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}
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},
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"description_domain": {
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"keywords": [
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"metagenome",
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"metagenomic analysis",
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"fecal"
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],
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"xref": [
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{
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"namespace": "uberon",
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"name": "Uber Anatomy Ontology",
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"ids": ["0001988"],
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"access_time": "2016-11-30T06:46-0500"
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},
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{
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"namespace": "taxonomy",
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"name": "Taxonomy",
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"ids": ["9606"],
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"access_time": "2016-11-30T06:46-0500"
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}
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],
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"platform": ["hive"],
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"pipeline_steps": [
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{
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"step_number": 1,
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"name": "CensuScope",
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"description": "Detect taxonomic composition of a metagenomic data set.",
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"version": "1.3",
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"prerequisite": [
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{
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"name": "Filtered_NT_feb18_2016",
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"uri": {
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"uri": "https://hive.biochemistry.gwu.edu/genome/513957",
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"access_time": "2016-11-30T06:46-0500"
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}
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}
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],
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"input_list": [
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{
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"uri": "https://hive.biochemistry.gwu.edu/nuc-read/545722",
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"access_time": "2016-11-30T06:46-0500"
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},
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{
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"uri": "https://hive.biochemistry.gwu.edu/nuc-read/545721",
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"access_time": "2016-11-30T06:46-0500"
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}
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],
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"output_list": [
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{
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"uri": "https://hive.biochemistry.gwu.edu/546223/dnaAccessionBasedResult.csv",
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"access_time": "2016-11-30T06:46-0500"
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}
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]
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},
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{
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"step_number": 2,
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"name": "HIVE-hexagon",
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"description": "Alignment of reads to a set of references",
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"version": "1.3",
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"input_list": [
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{
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"uri": "http://example.com/data/546223/dnaAccessionBased.csv",
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"access_time": "2016-11-30T06:46-0500"
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},
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{
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"uri": "https://hive.biochemistry.gwu.edu/nuc-read/545722",
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"access_time": "2016-11-30T06:46-0500"
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},
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{
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"uri": "https://hive.biochemistry.gwu.edu/nuc-read/545721",
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"access_time": "2016-11-30T06:46-0500"
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}
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],
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"output_list": [
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{
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"uri": "https://hive.biochemistry.gwu.edu/546232/alCount-Unalignedo524569-alCount--1.csv",
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"access_time": "2016-11-30T06:46-0500"
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}
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]
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}
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]
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},
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"execution_domain": {
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"script": [
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{
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"uri": {
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"uri": "https://github.com/biocompute-objects/HIVE_metagenomics/blob/master/driverHIVEmetagenomic.py"
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}
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}
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],
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"script_driver": "shell",
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"software_prerequisites": [
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{
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"name": "CensuScope",
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"version": "albinoni.2",
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"uri": {
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"uri": "http://example.com/dna.cgi?cmd=dna-screening&cmdMode=-",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"name": "HIVE-hexagon",
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"version": "babajanian.1",
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"uri": {
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"uri": "http://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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}
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],
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"external_data_endpoints": [
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{
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"name": "HIVE",
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"url": "https://hive.biochemistry.gwu.edu/dna.cgi?cmd=login"
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},
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{
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"name": "access to e-utils",
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"url": "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
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}
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],
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"environment_variables": {
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"key": "HOSTTYPE",
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"value" : "x86_64-linux"
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}
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},
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"parametric_domain": [
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{"param": "seed", "value": "14", "step": "2"},
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{"param":"minimum_match_len", "value": "66", "step": "2"},
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{"param": "divergence_threshold_percent", "value": "0.30", "step": "2"},
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{"param": "minimum_coverage", "value": "15", "step": "2"},
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{"param": "freq_cutoff", "value": "0.10", "step": "2"}
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],
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"io_domain": {
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"input_subdomain": [
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{
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"uri": {
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"filename": "Hepatitis C virus genotype 1",
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"uri": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"uri": {
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"filename": "Hepatitis C virus type 1b complete genome",
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"uri": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"uri": {
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"filename": "Hepatitis C virus (isolate JFH-1) genomic RNA",
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"uri": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"uri": {
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"filename": "Hepatitis C virus clone J8CF, complete genome",
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"uri": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"uri": {
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"filename": "Hepatitis C virus S52 polyprotein gene",
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"uri": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"uri": {
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"filename": "HCV1a_drug_resistant_sample0001-01",
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"uri": "http://example.com/nuc-read/514682",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"uri": {
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"filename": "HCV1a_drug_resistant_sample0001-02",
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"uri": "http://example.com/nuc-read/514683",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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}
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],
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"output_subdomain": [
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{
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"mediatype": "text/csv",
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"uri": {
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"uri": "http://example.com/data/514769/dnaAccessionBased.csv",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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},
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{
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"mediatype": "text/csv",
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"uri": {
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"uri": "http://example.com/data/514801/SNPProfile*.csv",
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"access_time": "2017-01-24T09:40:17-0500"
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}
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}
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]
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},
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"error_domain": {
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"empirical_error": {
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"false_negative_alignment_hits": "<0.0010",
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"false_discovery": "<0.05"
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},
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"algorithmic_error": {
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"false_positive_mutation_calls_discovery": "<0.00005",
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"false_discovery": "0.005"
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}
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}
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}

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