Reading ISA-Tab from files and Validating ISA-Tab files¶

Abstract:¶

The aim of this notebook is to:

show essential function to read and load an ISA-tab file in memory.
navigate key objects and pull key attributes.
learn how to invoke the ISA-tab validation function.
interpret the output of the validation report.

1. Getting the tools¶

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# If executing the notebooks on `Google Colab`,uncomment the following command 
# and run it to install the required python libraries. Also, make the test datasets available.

# !pip install -r requirements.txt

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import isatools
import os
import sys
from isatools import isatab

2. Reading and loading an ISA Investigation in memory from an ISA-Tab instance¶

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with open(os.path.join('./BII-S-3', 'i_gilbert.txt')) as fp:
            ISA = isatab.load(fp)

Let's check the description of the first study object present in an ISA Investigation object¶

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ISA.studies[0].description

Let's check the protocols declared in ISA the study (using a python list comprehension):¶

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[protocol.description for protocol in ISA.studies[0].protocols]

Let's now checks the ISA Assay Measurement and Technology Types are used in this ISA Study object¶

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[f'{assay.measurement_type.term} using {assay.technology_type.term}' for assay in ISA.studies[0].assays]

Let's now check the `ISA Study Source` Material:¶

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[source.name for source in ISA.studies[0].sources]

Let's check what is the first `ISA Study Source property`:¶

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# here, we get all the characteristics of the first Source object
first_source_characteristics = ISA.studies[0].sources[0].characteristics

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first_source_characteristics[0].category.term

Let's now check what is the `value` associated with that first `ISA Study Source property`:¶

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first_source_characteristics[0].value.term

Let's now check what are all the properties associated with this first `ISA Study Source`¶

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[char.category.term for char in first_source_characteristics]

And the corresponding values are:¶

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[char.value for char in first_source_characteristics]

3. Invoking the python ISA-Tab Validator¶

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my_json_report_bii_i_1 = isatab.validate(open(os.path.join('./BII-I-1/', 'i_investigation.txt')))

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my_json_report_bii_s_3 = isatab.validate(open(os.path.join('./BII-S-3/', 'i_gilbert.txt')))

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my_json_report_bii_s_4 = isatab.validate(open(os.path.join('./BII-S-4/', 'i_investigation.txt')))

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my_json_report_bii_s_7 = isatab.validate(open(os.path.join('./BII-S-7/', 'i_matteo.txt')))

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my_json_report_bii_s_7

This Validation Report shows that No Error has been logged
The rest of the report consists in warnings meant to draw the attention of the curator to elements which may be provided but which do not break the ISA syntax.
Notice the study group information reported on both study and assay files. If ISA Factor Value[] fields are found present in the ISA Study or ISA Assay tables, the validator will try to identify the set of unique Factor Value combination defining a Study Group.
- When no Factor Value are found in a ISA Study or Assay table, the value is left to its default value: -1, which means that No Study Group have been found.
- ISA strongly encourages to declare Study Group using ISA Factor Value to unambiguously identify the Independent Variables of an experiment.

4. How does a validation failure looks like ?¶

BII-S-5 contains an error located in the `i_investigation.txt` file of the submission¶

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my_json_report_bii_s_5 = isatab.validate(open(os.path.join('./BII-S-5/', 'i_investigation.txt')))

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my_json_report_bii_s_5["errors"]

The Validator report the Error Array is not empty and shows the root cause of the syntactic validator error.
There is a typo in the Investigation file which affects 2 positions on the file for both Investigation and Study Object:

Publication list. vs Publication List

About this notebook¶

authors: philippe.rocca-serra@oerc.ox.ac.uk, massimiliano.izzo@oerc.ox.ac.uk
license: CC-BY 4.0
support: isatools@googlegroups.com
issue tracker: https://github.com/ISA-tools/isa-api/issues

Reading ISA-Tab from files and Validating ISA-Tab files¶

Abstract:¶

1. Getting the tools¶

2. Reading and loading an ISA Investigation in memory from an ISA-Tab instance¶

Let's check the description of the first study object present in an ISA Investigation object¶

Let's check the protocols declared in ISA the study (using a python list comprehension):¶

Let's now checks the ISA Assay Measurement and Technology Types are used in this ISA Study object¶

Let's now check the ISA Study Source Material:¶

Let's check what is the first ISA Study Source property:¶

Let's now check what is the value associated with that first ISA Study Source property:¶

Let's now check what are all the properties associated with this first ISA Study Source¶

And the corresponding values are:¶

3. Invoking the python ISA-Tab Validator¶

4. How does a validation failure looks like ?¶

BII-S-5 contains an error located in the i_investigation.txt file of the submission¶

About this notebook¶

Let's now check the `ISA Study Source` Material:¶

Let's check what is the first `ISA Study Source property`:¶

Let's now check what is the `value` associated with that first `ISA Study Source property`:¶

Let's now check what are all the properties associated with this first `ISA Study Source`¶

BII-S-5 contains an error located in the `i_investigation.txt` file of the submission¶