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Page History
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A | B | C |
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 |
FieldsFields
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
Nano-TAB Extensions--- Nano-TAB extends the ISA-TAB Investigation File specification by introducing new fields, which are listed in TABLE 2 on the Investigation File Example Page. All fields are defined below.
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. This 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.
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This section is used to describe an investigation. An example of the INVESTIGATION section is in TABLE 3 along with example data. The INVESTIGATION section uses 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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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 4 along with example data. There are 11 ISA-TAB concepts used as field names which are described below:
Investigation person last name---The last name of a person who is the point of contact for the investigation.
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The INVESTIGATION PUBLICATIONS section allows for the identification of articles (published) associated with the investigation. TABLE 5 shows an example of the INVESTIGATION PUBLICATIONS section along with example data. There are seven ISA-TAB concepts used in this section and which are described below:
Investigation pubmed ID---PubMed identifier of the publication associated with the investigation.
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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 2 Extensions and Constraints Applied to the ISA-TAB Investigation File in Support of Nano-TAB
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Section
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Field
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Change
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Field Status (if applicable)
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INVESTIGATION
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Investigation disease
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Addition
...
Required
...
INVESTIGATION
...
Investigation disease term accession number
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Addition
...
Required
...
INVESTIGATION
...
Investigation disease term source REF
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Addition
...
Required
...
INVESTIGATION
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Investigation outcome
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Addition
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Optional
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STUDY
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Study disease
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Addition
...
Required
...
STUDY
...
Study disease term accession number
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Addition
...
Required
...
STUDY
...
Study disease term source REF
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Addition
...
Required
...
STUDY
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Study outcome
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Addition
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Optional
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STUDY ASSAYS
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Study assay measurement name
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Addition
...
Required
...
STUDY ASSAYS
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Study assay measurement name term accession number
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Addition
...
Required
...
STUDY ASSAYS
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Study assay measurement name term source REF
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Addition
...
Required
...
STUDY ASSAYS
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Study assay measurement unit
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Addition
...
Required
...
STUDY ASSAYS
...
Study assay measurement unit term accession number
...
Addition
...
Required
...
STUDY ASSAYS
...
Study assay measurement unit term source REF
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Addition
...
Required
...
STUDY ASSAYS
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Study assay measurement statistic
...
Addition
...
Required
...
STUDY ASSAYS
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Study assay measurement statistic term accession number
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Addition
...
Required
...
STUDY ASSAYS
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Study assay measurement statistic term source REF
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Addition
...
Required
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STUDY FACTORS
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Study factor unit
...
Addition
...
Required
...
STUDY FACTORS
...
Study factor unit term accession number
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Addition
...
Required
...
STUDY FACTORS
...
.
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Addition
...
Required
...
STUDY PROTOCOLS
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Study protocol parameter unit
...
Addition
...
Required
...
STUDY PROTOCOLS
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Study protocol parameter unit term accession number
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Addition
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Required
...
STUDY PROTOCOLS
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Study protocol parameter unit term source REF
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Addition
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