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TABLE1 Example Subset of the Investigation File Format
A | B | C | |
|---|---|---|---|
STUDY FACTORS | n/a |
| n/a |
Study Factor Name | temperature | solvent | |
Study Factor Type | temperature | solvent medium | |
Study Factor Name Type Term Accession Number | PATO_0000146 | NPO_1855 | |
Study Factor Name Type Term Source REF | PATO | NPO | |
Study Factor Type | condition | condition | |
Study Factor Type Term Accession Number | none | none | |
Study Factor Type Term Source REF | none | none |
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 PUBLICATIONS
- INVESTIGATION CONTACTSINVESTIGATION PUBLICATION
- MATERIAL
- STUDY
- STUDY DESIGN DESCRIPTORS
- STUDY CONTACTSPUBLICATIONS
- STUDY PUBLICATIONSFACTORS
- STUDY ASSAYS
- STUDY FACTORSPROTOCOLS
- STUDY PROTOCOLSCONTACTS
ISA-TAB-Nano Extensions--- ISA-TAB-Nano 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.
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This section is used to define the vocabulary source from which a term is selected and referenced in the ISA-TAB-Nano files. TABLE 3 shows an example of the ONTOLOGY SOURCE REFERENCE section along with example data. This section uses four ISA-TAB concepts:
Term source nameSource Name---The name of the source from where a term is selected and referenced in the ISA-TAB-Nano 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 ISA-TAB-Nano files.
Term source fileSource File--- A file name or a URI of the source named in the term source name field.
Term source versionSource Version---Version number of the vocabulary source file. This is a required field if the field for term source file has a value.
Term source descriptionSource Description---Text description to disambiguate resources when homologous acronyms are used.
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This section is used to describe an investigation. An example of the INVESTIGATION section is in TABLE 4 along with example data. The INVESTIGATION section uses nine concepts and the source is indicated in the definition belowincludes concepts from ISA-TAB and extensions made in support of ISA-TAB-Nano:
Investigation identifierIdentifier--- A locally unique identifier or an accession number provided by a repository. This concept is taken from ISA-TAB.
Investigation titleTitle---A concise phrase used as a title for the investigation. This concept is adapted from ISA-TAB.
Investigation descriptionDescription---A textual description of the investigation. This concept is taken from ISA-TAB.
Investigation Dubmission Date---The date on which the investigation was reported to a repository (format: YYYY-MM-DD).
Investigation Public Release Date---The date on which the investigation is publicly released or published (format: YYYY-MM-DD).
Investigation DiseaseInvestigation disease---Disease(s) that are the subject of an investigation, if applicable. This concept is introduced in ISA-TAB-Nano to identify the disease(s) related to the subject of the investigation.
Investigation disease term accession numberDisease 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 ISA-TAB-Nano.
Investigation Disease Term Source 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 ISA-TAB-Nano.
Investigation outcomeOutcome---A textual description of the outcome(s) of an investigation. This concept is introduced in ISA-TAB-Nano to provide a brief summary or conclusion of description summarizing the conclusion of an investigation.
Investigation
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Publications
The INVESTIGATION PUBLICATIONS
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 pointarticles (s) of contact for an investigation. An published) associated with the investigation. TABLE 6 shows an example of the INVESTIGATION CONTACTS section of the spreadsheet is in TABLE 5 PUBLICATIONS section along with example data. There are 11 seven ISA-TAB concepts used as field namesin this section:
Investigation person last namePubmed ID---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 PubMed identifier of the publication associated with the investigation.
Investigation person mid initialsPublication DOI---The middle initial(sA Digital Object Identifier (DOI) of a person who is the point of contact for the publication associated with the investigation.
Investigation person emailPublication Author List----The email address of a person who is the point of contact for the 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 person phonePublication Status---The telephone number A term describing the status of a person who is the point of contact for the investigation.Investigation person faxpublication (that is, submitted, in preparation, published).
Investigation Publication Status Term Accession Number---The fax identification 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.
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.
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 5 along with example data. There are 11 ISA-TAB concepts used as field names:
Investigation Person Last Name---The last name of a Investigation person roles--- The term which classifies the role(s) performed by person who is the point of contact for the investigation.
Investigation person roles term accession numberPerson First Name--- 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 roles 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 6 shows an example of the INVESTIGATION PUBLICATIONS section along with example data. There are seven ISA-TAB concepts used in this section:
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 (that is, submitted, in preparation, published).
The first name of a person who is the point of contact for the investigation.
Investigation Person Mid 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 Roles--- The term which classifies the role(s) performed by person who is the point of contact for the investigation.
Investigation Person Roles Term Accession Number--- Identification 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 statusperson role.
Investigation publication status term source Person Roles 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 fieldName of the ontology or controlled vocabulary from which a term is selected and entered as a value for investigation person role.
Study
The STUDY section allows for the description of one or more studies conducted as part of an investigation. TABLE 7 shows an example of the STUDY section along with example data. There are 11 concepts used in the STUDY section, seven of which are taken from ISA-TAB and four are introduced in ISA-TAB-Nano and are indicated as such in the definition. These concepts are described below:
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