Importing data into ISA formats¶

We have provided a number of modules that allow you to import data into ISA formats from well-known databases or services. Imports from these services is supported by modules found in the isatools.net package:

Obtaining Functional Genomics Data¶

Importing from the European Nucleotide Archive to ISA-Tab¶

Notice: this method depends on SAXON XSLT Processor

To import an SRA study from the European Nucleotide Archive (ENA) as ISA-Tab files, provide an ENA accession number and your path to the SAXON JAR file:

from isatools.net import sra2isatab

sra2isatab.sra_to_isatab_batch_convert('BN000001', 'your/path/to/saxon9.jar')

This method returns the ISA-Tab files as a byte stream (io.BytesIO).

Importing MAGE-TAB to ISA¶

To import metadata from MAGE-TAB files (e.g. from EBI ArrayExpress database), you can do the following to import a MAGE-TAB to ISA-Tab:

from isatools.convert import magetab2isatab
with open('your/path/to/magetab.idf.txt', 'r') as input_magetab:
    magetab2isatab.convert(input_sampletab, 'tmp/')

To import a MAGE-TAB to ISA JSON, you can do:

from isatools.convert import sampletab2json
with open('your/path/to/magetab.idf.txt', 'r') as input_sampletab:
    with open('your/path/to/myjson.json', 'w') as output_json:
        magetab2json.convert(input_magetab, output_json)

Obtaining Metabolomics Data¶

Importing from EMBL-EBI MetaboLights to ISA¶

To import an MetaboLights study from the MetaboLights as ISA-Tab files, provide an MetaboLights accession number:

from isatools.net import mtbls as MTBLS

tmp_dir = MTBLS.get('MTBLS1')

This method downloads the ISA-Tab files for a study, and returns a string path to a temporary directory containing the ISA-Tab files.

To import an MetaboLights study from the MetaboLights as ISA JSON files, provide an MetaboLights accession number:

from isatools.net import mtbls as MTBLS

isa_json = MTBLS.getj('MTBLS1')

This method gets the study and returns the ISA content as ISA JSON.

You can also do simple queries on MetaboLights studies to retrieve samples and related data files, based on factor selection:

from isatools.net import mtbls as MTBLS

MTBLS.get_factor_names('MTBLS1')
# response:
# {'Gender', 'Age'}
MTBLS.get_factor_values('MTBLS1', 'Gender')
# response:
# {'Male', 'Female'}
query = {
      "Gender": "Male"
   }
samples_and_files = MTBLS.get_data_files('MTBLS1', factor_query=query)
# response:
#  [
#     {
#        'sample': 'ADG10003u_007'},
#        'data_files': ['ADG10003u_007.zip'],
#        'query_used': {'Gender': 'Male'}
#     }, ...
#  ]

Importing from MetabolomicsWorkbench, to ISA-Tab¶

To import a study from the Metabolomics Workbench as ISA-Tab files, provide an accession number and your local path to write your files to:

from isatools.net.mw2isa import mw2isa_convert

success, study_id, validate = mw2isa_convert(studyid="ST000367", outputdir='tmp/', dl_option="no", validate_option="yes")
#  If success == True, download and conversion ran OK. If validate == True, the ISA-Tabs generated passed validation

See isa-api/isatools/convert/mw2isa.py

Importing from Biocrates, to ISA-Tab¶

Notice: this method depends on SAXON XSLT Processor

See isa-api/isatools/net/biocrates2isatab.py

Importing from third-party formats is supported with our conversion modules found in the isatools.convert package:

Importing mzML to ISA-Tab¶

To import metadata from mzML mass spectrometry files, the ISA API integrates with the mzml2isa tool from https://github.com/ISA-tools/mzml2isa and can be run as follows:

from isatools.convert import mzml2isa
mzml2isa.convert('your/path/to/mzml/files/', 'tmp/', "My Study ID")

Importing SampleTab to ISA¶

Warning

As of July 2020, EBI Biosample has decommissioned SampleTab format and now only accepts submission via a REST API. Future releases of the ISA-API will support this mode of data deposition.

To import metadata from SampleTab files (e.g. from EBI BioSamples database), you can do the following to import a SampleTab to ISA-Tab:

from isatools.convert import sampletab2isatab
with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
    sampletab2isatab.convert(input_sampletab, 'tmp/')

To import a SampleTab to ISA JSON, you can do:

from isatools.convert import sampletab2json
with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
    with open('your/path/to/myjson.json', 'w') as output_json:
        sampletab2json.convert(input_sampletab, output_json)

You can also load SampleTab content directly into ISA Python objects:

from isatools import sampletab
with open('your/path/to/sampletab.txt', 'r') as input_sampletab:
    ISA = sampletab.load(input_sampletab)

The ISA cookbook