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STUDY FACTORS



Study Factor Name

temperature

solvent medium

Study Factor Name Term Accession Number

PATO_0000146

NPO_1855

Study Factor Name Term Source REF

PATO

NPO

Study Factor Unit

celsius


Study Factor Unit Term Accession Number

UO_0000027


Study Factor Unit Term Source REF

UO


Study Factor Type

condition

condition

Study Factor Type Term Accession Number



Study Factor Type Term Source REF



 Fields

The field names in an investigation file are organized vertically in the first column.  These fields are divided into 11 sections as defined by ISA-TAB. These sections are:

  • ONTOLOGY SOURCE REFERENCE
  • INVESTIGATION
  • INVESTIGATION CONTACTS
  • INVESTIGATION PUBLICATION
  • STUDY
    • STUDY DESIGN DESCRIPTORS
    • STUDY CONTACTS
    • STUDY PUBLICATIONS
    • STUDY ASSAYS
    • STUDY FACTORS
    • STUDY PROTOCOLS

Ontology Source Reference

This section is used to define the vocabulary source from which a term is selected and referenced in the nano-TAB files.  TABLE 2 shows an example of the ONTOLOGY SOURCE REFERENCE section along with example data.

The ONTOLOGY SOURCE REFERENCE section uses the four concepts described below:

Term source name---The name of the source from where a term is selected and referenced in the nano-TAB files.  The source could be an ontology or a controlled vocabulary. The source name is the full name or the acronym of the ontology/controlled vocabulary. This is a required field if the term source name is referenced in any of the nano-TAB files.  This concept is taken from ISA-TAB.

Term source file--- A file name or a URI of the source named in the term source name field.  This concept is taken from ISA-TAB.

Term source version---version number of the vocabulary source file.  This is a required field if the field for term source file has a value.   This concept is taken from ISA-TAB.

Term source description---Text description to disambiguate resources when homologous acronyms are used.  This concept is taken from ISA-TAB.

Investigation

This section is used to describe an investigation. An example of the INVESTIGATION section is in the TABLE 13 along with example data.

The INVESTIGATION section uses 9 concepts.  These concepts are the nine concepts described below:

Investigation identifier--- A locally unique identifier or an accession number provided by a repository.  This concept is taken from ISA-TAB.

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Investigation public release date---The date on which the investigation is publicly released or published (format: YYYY-MM-DD).  This concept is taken from ISA-TAB.

Investigation Contacts

The INVESTIGATION CONTACTS section allows for the identification of the point(s) of contact for an investigation.  An example of the INVESTIGATION CONTACTS section of the spreadsheet is in TABLE 2 along with example data.

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