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Define a bco specific uri object #60

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Define a bco specific uri object #60

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[WIP] Define a BCO specific `uri` object
HadleyKing Dec 6, 2018
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uri in execution-domain.md
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Update README.md
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Update and rename bco-specification.md to user_guide.md
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rename spec -> user_guide.md
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Update README.md
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update intro.md
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update user_guide.md
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links and `check`sum
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links
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provenance domain
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Update provenance-domain.md
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usability domain
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usability domain
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fhir
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71 changes: 37 additions & 34 deletions HCV1a.json
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@@ -1,14 +1,15 @@
{
"bco_id": "https://github.com/biocompute-objects/BCO_Specification/blob/master/HCV1a.json",
"digital_signature": "0B61E7C0EFF537CADADE475AA6386262FCDBC4DC",
"bco_spec_version" : "https://w3id.org/biocompute/spec/v1.2",
"bco_id": "https://w3id.org/biocompute/examples/HCV1a.json",
"checksum": "0B61E7C0EFF537CADADE475AA6386262FCDBC4DC",
"bco_spec_version" : "https://w3id.org/biocompute/spec/1.3.0",
"provenance_domain": {
"name": "HCV1a ledipasvir resistance SNP detection",
"version": "2.9",
"review": [
{
"status": "approved",
"reviewer_comment": "Approved by GW staff. Waiting for approval from FDA Reviewer",
"date": "2017-11-12T12:30:48-0400",
"reviewer": {
"name": "Charles Hadley King",
"affiliation": "George Washington University",
Expand All @@ -20,6 +21,7 @@
{
"status": "approved",
"reviewer_comment": "The revised BCO looks fine",
"date": "2017-12-12T12:30:48-0400",
"reviewer": {
"name": "Eric Donaldson",
"affiliation": "FDA",
Expand Down Expand Up @@ -140,52 +142,52 @@
{
"name": "Hepatitis C virus genotype 1",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus type 1b complete genome",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus clone J8CF, complete genome",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus S52 polyprotein gene",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
"access_time": "2017-01-24T09:40:17-0500"
}
}
],
"input_list": [
{
"address": "http://example.com/dna.cgi?cmd=objFile&ids=514683",
"uri": "http://example.com/dna.cgi?cmd=objFile&ids=514683",
"access_time": "2017-01-24T09:40:17-0500"
},
{
"address": "http://example.com/dna.cgi?cmd=objFile&ids=514682",
"uri": "http://example.com/dna.cgi?cmd=objFile&ids=514682",
"access_time": "2017-01-24T09:40:17-0500"
}
],
"output_list": [
{
"address": "http://example.com/data/514769/allCount-aligned.csv",
"uri": "http://example.com/data/514769/allCount-aligned.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
]
Expand All @@ -197,33 +199,34 @@
"version": "1.3",
"input_list": [
{
"address": "http://example.com/data/514769/dnaAccessionBased.csv",
"uri": "http://example.com/data/514769/dnaAccessionBased.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
],
"output_list": [
{
"address": "http://example.com/data/514801/SNPProfile.csv",
"uri": "http://example.com/data/514801/SNPProfile.csv",
"access_time": "2017-01-24T09:40:17-0500"
},
{
"address": "http://example.com/data/14769/allCount-aligned.csv",
"uri": "http://example.com/data/14769/allCount-aligned.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
]
}
]
},
"execution_domain": {
"script_access_type": "URI",
"script": ["https://example.com/workflows/antiviral_resistance_detection_hive.py"],
"script": {
"uri": "https://example.com/workflows/antiviral_resistance_detection_hive.py"
},
"script_driver": "shell",
"software_prerequisites": [
{
"name": "HIVE-hexagon",
"version": "babajanian.1",
"uri": {
"address": "http://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
"uri": "http://example.com/dna.cgi?cmd=dna-hexagon&cmdMode=-",
"access_time": "2017-01-24T09:40:17-0500",
"sha1_chksum": "d60f506cddac09e9e816531e7905ca1ca6641e3c"
}
Expand All @@ -232,7 +235,7 @@
"name": "HIVE-heptagon",
"version": "albinoni.2",
"uri": {
"address": "http://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-",
"uri": "http://example.com/dna.cgi?cmd=dna-heptagon&cmdMode=-",
"access_time": "2017-01-24T09:40:17-0500"
}
}
Expand Down Expand Up @@ -262,51 +265,51 @@
"io_domain": {
"input_subdomain": [
{
"name": "Hepatitis C virus genotype 1",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
"filename": "Hepatitis C virus genotype 1",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/22129792",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus type 1b complete genome",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/5420376",
"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"
}
},
{
"name": "Hepatitis C virus (isolate JFH-1) genomic RNA",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/13122261",
"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"
}
},
{
"name": "Hepatitis C virus clone J8CF, complete genome",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/386646758",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "Hepatitis C virus S52 polyprotein gene",
"uri": {
"address": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
"filename": "Hepatitis C virus S52 polyprotein gene",
"uri": "http://www.ncbi.nlm.nih.gov/nuccore/295311559",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "HCV1a_drug_resistant_sample0001-01",
"uri": {
"address": "http://example.com/nuc-read/514682",
"filename": "HCV1a_drug_resistant_sample0001-01",
"uri": "http://example.com/nuc-read/514682",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"name": "HCV1a_drug_resistant_sample0001-02",

"uri": {
"address": "http://example.com/nuc-read/514683",
"filename": "HCV1a_drug_resistant_sample0001-02",
"uri": "http://example.com/nuc-read/514683",
"access_time": "2017-01-24T09:40:17-0500"
}
}
Expand All @@ -315,14 +318,14 @@
{
"mediatype": "text/csv",
"uri": {
"address": "http://example.com/data/514769/dnaAccessionBased.csv",
"uri": "http://example.com/data/514769/dnaAccessionBased.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
},
{
"mediatype": "text/csv",
"uri": {
"address": "http://example.com/data/514801/SNPProfile*.csv",
"uri": "http://example.com/data/514801/SNPProfile*.csv",
"access_time": "2017-01-24T09:40:17-0500"
}
}
Expand Down
6 changes: 3 additions & 3 deletions README.md
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BioCompute
==========

Main website: http://biocomputeobject.org/
BioCompute Partnership: http://biocomputeobject.org

GitHub repository for BioCompute Objects:
https://github.com/biocompute-objects/
Expand All @@ -20,15 +20,15 @@ To facilitate a means for different stakeholders in the HTS communities to provi

## User Guide

The [BioCompute Objects user guide](/schema/user_guide.md) provides an introduction to implementing/writing a BCO for a pipeline and/or a workflow, and is taken from the [BioCompute Objects Specification Document](/bco-specification.md).
The [BioCompute Objects user guide](/user_guide.md) provides an introduction to implementing/writing a BCO for a pipeline and/or a workflow, and is taken from the [BioCompute Objects Specification Document](/IEEE_Docs/standard.md).

### Repository

Note that unless you are viewing a [release](https://github.com/biocompute-objects/BCO_Specification/releases) this is a draft subject to change.

Table of content:

* [BioCompute Object (BCO) specification document](bco-specification.md)
* [BioCompute Object (BCO) User Guide](user_guide.md)
* [Introduction to BioCompute Objects](introduction.md)
* [BCO domains](bco-domains.md)
* [Top level fields](top-level.md)
Expand Down
6 changes: 3 additions & 3 deletions bco-domains.md
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@@ -1,4 +1,4 @@
_This document is part of the [BioCompute Object specification](bco-specification.md)_
_This document is part of the [BioCompute Object User Guide](user_guide.md)_

# BCO domains

Expand All @@ -11,7 +11,7 @@ Condensed example:
"bco_spec_version" : "https://w3id.org/biocompute/spec/v1.2",
"bco_id": "https://example.com/bco/9487ae7e-c1aa-4a3c-b18f-3d3695b33ace",
"type": "antiviral_resistance_detection",
"digital_signature": "584C7FE128717E1712426AB19CAAEA8BC1E27365B54285BBEA1221284C7D3A48",
"checksum": "584C7FE128717E1712426AB19CAAEA8BC1E27365B54285BBEA1221284C7D3A48",
"provenance_domain": {
},
"usability_domain": [
Expand Down Expand Up @@ -66,7 +66,7 @@ Specification:

## 2.3 Extension Domain "extension_domain"

The `extension_domain` is a space for a user to add more structured information that is defined in the BCO type definition. The `extension_domain` section is not evaluated by checks for BCO validity or computational correctness and as such is the place to add *ANY* type of additional **structured** information. We provide two examples that are neither exclusive or exhaustive.
The `extension_domain` is a space for a user to add additional structured information that is not defined in the BioCompute shcema. The `extension_domain` section is not evaluated by checks for BCO validity or computational correctness and as such is the place to add *ANY* type of additional **structured** information. We provide two examples that are neither exclusive or exhaustive.

Specifications:

Expand Down
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