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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

Investigation

An example of the INVESTIGATION section is in the TABLE 1. The INVESTIGATION section uses 9 concepts.  These concepts are described below:

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

Investigation title---A concise phrase used as a title for the investigation.  This concept is adapted from ISA-TAB.

Investigation description---A textual description of the investigation.  This concept is taken from ISA-TAB.

Investigation disease---Disease(s) that are the subject of an investigation, if applicable.  This concept is introduced in nano-TAB to identify the disease(s) related to the subject of the investigation

Investigation disease term accession number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation disease. This concept is introduced in nano-TAB.

Investigation disease term source REF--- The name which identifies the source from where the term for investigation disease is selected. This name should match one of the names entered in the term source name field.  This concept is introduced in nano-TAB.

Investigation outcome---A textual description of the outcome(s) of an investigation.  This concept is introduced in nano-TAB to provide a brief summary or conclusion of an investigation

Investigation submission date---The date on which the investigation was reported to a repository (format: YYYY-MM-DD).  This concept is taken from ISA-TAB.

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.

There are 11 concepts used as field names in the INVESTIGATION CONTACTS section.  These concepts are taken from ISA-TAB and are described below:

Investigation person last name---The last name of a person who is the point of contact for the investigation. 

Investigation person first name---The first name of a person who is the point of contact for the investigation. 

Investigation person middle initials---The middle initial(s) of a person who is the point of contact for the investigation.

Investigation person email---The email address of a person who is the point of contact for the investigation. 

Investigation person phone---The telephone number of a person who is the point of contact for the investigation.

Investigation person fax---The fax number of a person who is the point of contact for the investigation. 

Investigation person address---The mailing address of a person who is the point of contact for the investigation. 

Investigation person affiliation--- The name of the organization to which the point of contact belongs. 

Investigation person role--- The term which classifies the role(s) performed by person who is the point of contact for the investigation.

Investigation person role term accession number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation person role. 

Investigation person role term source REF--- Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for investigation person role.

investigation Publications

The INVESTIGATION PUBLICATIONS section allows for the identification of articles (published) associated with the investigation. TABLE 3 shows an example of the INVESTIGATION PUBLICATIONS section along with example data.

There are 7 concepts used in the INVESTIGATION PUBLICATIONS section.  These concepts are taken from ISA-TAB and are described below:

Investigation pubmed ID---PubMed identifier of the publication associated with the investigation.

Investigation publication DOI---A Digital Object Identifier (DOI) of the publication associated with the investigation.

Investigation publication author list---A semicolon-delimited (";") list of authors of a publication associated with the investigation.

Investigation publication title---A concise phrase used as a title for the publication associated with the investigation.

Investigation publication status---A term describing the status of a publication (i.e., submitted, in preparation, published).

Investigation publication status term accession number---The identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation publication status.

Investigation publication status term source REF---The name which identifies the source from where the term for investigation publication status is selected.  This name should match one of the names entered in the term source name field.

Nano-TAB Extensions--- Nano-TAB extends the ISA-TAB Investigation File specification by introducing new fields, which are listed in TABLE 2.

TABLE  TABLE 2 Extensions and Constraints Applied to the ISA-TAB Investigation File in Support of Nano-TAB

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