Pooling samples in ISAjson
rafael buono
Can someone direct me to an ISA-JSON example where pooling of Samples is done?
In the documentation (copied and pasted below), there is an example of how to deal with this in ISA-Tab. But I couldn't find a similar example for ISA-JSON.
Example copied below from https://isa-specs.readthedocs.io/en/latest/isamodel.html#study :
"In a pooling example, multiple sources may be used to create a single sample:
(source material 1)->(sample collection)->(sample material 1)
Philippe
Hi Rafael,
Hope all is well in Ghent.
Here is a code snippet and the corresponding serialization to ISA-JSON:
(I have also documented that in an jupyter-notebook, which will be posted on the ISA-API documentation with the coming release).
-------
from isatools.model
import *
from isatools.create.model import *
import datetime
# creating an
ISA.Investigation object
investigation = Investigation()
# creating an ISA.Study object
study = Study(filename="s_study.txt")
study.identifier = "S1"
study.title = "ISA Study example: creating sample pools"
# creating the necessary ISA.Protocol objects
study.protocols = [Protocol(name="sample
collection",protocol_type="pooling"),
Protocol(name="intracellular fraction
extraction",
protocol_type=OntologyAnnotation(term="extraction"),
parameters=[ProtocolParameter(parameter_name=OntologyAnnotation(term="concentration")),
ProtocolParameter(parameter_name=OntologyAnnotation(term="sample
QC"))]),
Protocol(name="data collection",
protocol_type=OntologyAnnotation(term="data acquisition")),
Protocol(name="data transformation",
protocol_type=OntologyAnnotation(term="data normalization"))
]
# creating 4
ISA.Source objects
study.sources =
[Source(name="source1"),Source(name="source2"),Source(name="source3"),Source(name="source4")]
# creating 2 ISA.Sample objects
study.samples = [Sample(name="sample1"),Sample(name="sample2")]
# creating an ISA.ProtocolApplication pooling Source1 and
Source2 into Sample1
study.process_sequence =
[Process(executes_protocol=study.protocols[0],
inputs=[study.sources[0],study.sources[1]],
outputs=[study.samples[0]])]
# doing the same again for pooling Source3 and Source4 into
Sample2
study.process_sequence.append(Process(executes_protocol=study.protocols[0],
inputs=[study.sources[2],study.sources[3]],
outputs=[study.samples[1]]))
investigation.studies = [study]
# let's check how
this looks in ISA-Tab
from isatools.isatab import dumps
print(dumps(investigation))
# let's check how this looks in ISA-JSON
import json
from isatools.isajson import ISAJSONEncoder
print(json.dumps(investigation, cls=ISAJSONEncoder,
sort_keys=True, indent=4, separators=(',', ': ')))
--------
the JSON looks like this:
{
"comments": [],
"description": "",
"identifier": "",
"ontologySourceReferences": [],
"people": [],
"publicReleaseDate": "",
"publications": [],
"studies": [
{
"assays": [],
"characteristicCategories": [],
"comments": [],
"description": "a jupytern notebook showing how to create pooled samples (a node merging event with material nodes)",
"factors": [],
"filename": "s_study.txt",
"identifier": "S1",
"materials": {
"otherMaterials": [],
"samples": [
{
"@id": "#sample/5116543904",
"characteristics": [],
"factorValues": [],
"name": "sample1"
},
{
"@id": "#sample/5116545584",
"characteristics": [],
"factorValues": [],
"name": "sample2"
}
],
"sources": [
{
"@id": "#source/5116545344",
"characteristics": [],
"name": "source1"
},
{
"@id": "#source/5116545824",
"characteristics": [],
"name": "source2"
},
{
"@id": "#source/5119072912",
"characteristics": [],
"name": "source3"
},
{
"@id": "#source/5119071040",
"characteristics": [],
"name": "source4"
}
]
},
"people": [],
"processSequence": [
{
"@id": "#process/5119073488",
"comments": [],
"date": "",
"executesProtocol": {
"@id": "#5109903952"
},
"inputs": [
{
"@id": "#source/5116545344"
},
{
"@id": "#source/5116545824"
}
],
"name": "",
"outputs": [
{
"@id": "#sample/5116543904"
}
],
"parameterValues": [],
"performer": ""
},
{
"@id": "#process/5119071088",
"comments": [],
"date": "",
"executesProtocol": {
"@id": "#5109903952"
},
"inputs": [
{
"@id": "#source/5119072912"
},
{
"@id": "#source/5119071040"
}
],
"name": "",
"outputs": [
{
"@id": "#sample/5116545584"
}
],
"parameterValues": [],
"performer": ""
}
],
"protocols": [
{
"@id": "#5109903952",
"comments": [],
"components": [],
"description": "",
"name": "sample collection",
"parameters": [],
"protocolType": {
"@id": "#87632ca1-1109-4f42-bdc9-fd56c30cead8",
"annotationValue": "pooling",
"comments": [],
"termAccession": "",
"termSource": ""
},
"uri": "",
"version": ""
},
{
"@id": "#5118472000",
"comments": [],
"components": [],
"description": "",
"name": "intracellular fraction extraction",
"parameters": [
{
"@id": "#5119051952",
"parameterName": {
"@id": "#590aaeb5-2e11-4aff-a2c9-9b34bf676249",
"annotationValue": "concentration",
"comments": [],
"termAccession": "",
"termSource": ""
}
},
{
"@id": "#5119050704",
"parameterName": {
"@id": "#33dfce38-e133-4bc0-9666-9a81bfb39362",
"annotationValue": "sample QC",
"comments": [],
"termAccession": "",
"termSource": ""
}
}
],
"protocolType": {
"@id": "#9a41779d-eb92-467d-88ac-d1595fe189de",
"annotationValue": "extraction",
"comments": [],
"termAccession": "",
"termSource": ""
},
"uri": "",
"version": ""
},
{
"@id": "#5118472096",
"comments": [],
"components": [],
"description": "",
"name": "data collection",
"parameters": [],
"protocolType": {
"@id": "#26e7d865-e6be-454b-bd91-a8ee33a3cbcd",
"annotationValue": "data acquisition",
"comments": [],
"termAccession": "",
"termSource": ""
},
"uri": "",
"version": ""
},
{
"@id": "#5116464528",
"comments": [],
"components": [],
"description": "",
"name": "data transformation",
"parameters": [],
"protocolType": {
"@id": "#e3ed694a-215c-45f5-bb09-cf4c2a6154e7",
"annotationValue": "data normalization",
"comments": [],
"termAccession": "",
"termSource": ""
},
"uri": "",
"version": ""
}
],
"publicReleaseDate": "",
"publications": [],
"studyDesignDescriptors": [],
"submissionDate": "",
"title": "ISA Study example: creating sample pools",
"unitCategories": []
}
],
"submissionDate": "",
"title": ""
}--
--
--
You received this message because you are subscribed to the Google
Groups "ISAforum" group.
To post to this group, send email to isaf...@googlegroups.com
To unsubscribe from this group, send email to
isaforum+u...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/isaforum?hl=en-GB
Visit the ISA tools website at http://isa-tools.org and http://isacommons.org
---
You received this message because you are subscribed to the Google Groups "ISAforum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to isaforum+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/isaforum/be058b4f-9e94-4cbe-9699-8d49f6b8f2a2n%40googlegroups.com.
rafael buono
To make sure I am following, in summary I would have the following.