Creating objects

The API provides a set of Python objects that you can create ISA content with.

The three main objects that you need to create ISA content are:

• Investigation
• Study
• Assay

...of course!

For example, to create an empty ISA structure consisting of an investigation with one study, you might do something like this:

from isatools.model.v1 import *
investigation = Investigation()
investigation.studies.append(Study())  # add a new Study object to the Investigation

The constructor of each of these objects creates empty content for each of these. If you try and serialize these out to ISA tab format, we should see some output into an i_investigation.txt file. We can do this using the isatab package.

from isatools import isatab
isatab.dump(investigation, 'tmp/')  # dumps out ISA tab format of the investigation we made earlier

If all went as expected, you should find an i_investigation.txt file with the following content in the directory you specified in the isatab.dump() function:

ONTOLOGY SOURCE REFERENCE
Term Source Name
Term Source File
Term Source Version
Term Source Description
INVESTIGATION
Investigation Identifier	
Investigation Title	
Investigation Description	
Investigation Submission Date	2016-02-25
Investigation Public Release Date	2016-02-25
INVESTIGATION PUBLICATIONS
Investigation PubMed ID
Investigation Publication DOI
Investigation Publication Author List
Investigation Publication Title
Investigation Publication Status
Investigation Publication Status Term Accession Number
Investigation Publication Status Term Source REF
INVESTIGATION CONTACTS
Investigation Person Last Name
Investigation Person First Name
Investigation Person Mid Initials
Investigation Person Email
Investigation Person Phone
Investigation Person Fax
Investigation Person Address
Investigation Person Affiliation
Investigation Person Roles
Investigation Person Roles Term Accession Number
Investigation Person Roles Term Source REF
STUDY
Study Identifier	
Study Title	
Study Description	
Study Submission Date	2016-02-25
Study Public Release Date	2016-02-25
Study File Name	
STUDY PUBLICATIONS
Study PubMed ID
Study Publication DOI
Study Publication Author List
Study Publication Title
Study Publication Status
Study Publication Status Term Accession Number
Study Publication Status Term Source REF
STUDY FACTORS
Study Factor Name
Study Factor Type
Study Factor Type Term Accession Number
Study Factor Type Term Source REF

Obviously this isn't enough to create a fully populated ISA investigation, but we would recommend that you have a look at the full worked example for reproducing an ISA representation of our BII-S-3 example of Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities by Jack A. Gilbert et al, 2008, and in the isatools.model.v1 package to inspect all the docstring documentation that is included with each of the ISA model classes.