Page Tab Elements

Page tab has several elements that allow to represent a submission:

• Attribute
• Submission
• Section
• Subsection
• Sections Table
• Files
• Files Table
• File List
• Links
• Links Table

Attribute

An attribute is the most basic element in page tab because any element defined in a submission, may have attributes. An attribute has the following characteristics:

• It’s defined by a name / value combination
• It may be used as a reference to another attribute
• Its name may have additional details. These are called Name Attributes
• Its value may have additional details. These are called Value Attributes
• The break line character is allowed and will be parsed as a multiline attribute if the given value is surrounded by double quotes

Syntax

Name	The Name
Value	The Value
(Name Attribute)	The name attribute value
[Value Attribute]	The value attribute value

Examples

• Simple Attribute

  TSV

  Study Type	RNA-seq of non coding RNA
  

  JSON

  {
    "attributes": [{
      "name": "Study Type",
      "value": "RNA-seq of non coding RNA"
    }]
  }
  

• Detailed Attribute

  TSV

  Study Type	RNA-seq of non coding RNA
  [Ontology]	EFO
  (Seq Type)	RNA
  

  JSON

  {
    "attributes": [{
      "name": "Study Type",
      "value": "RNA-seq of non coding RNA",
      "nmqual": [{
        "name": "Seq Type",
        "value": "RNA"
      }],
      "valqual": [{
        "name": "Ontlogy",
        "value": "EFO"
      }]
    }]
  }
  

• Reference Attribute

  For this example, let’s assume there’s already an attribute with value “Org1”

  TSV

  <affiliation>	Org1
  

  JSON

  {
    "attributes": [{
      "name": "affiliation",
      "value": "Org1",
      "isReference": "true"
    }]
  }
  

• Special Attributes

  There are some attributes that are used as keywords.

  Submission Level

  • Title: The submission title.
  • ReleaseDate: The date when the submission should be public. The expected format is YYYY-MM-DD.
  • AttachTo: Indicates the project which submission is belongs to.
  • RootPath: A folder in the user directory that is used as a base to allocate all the submission files. Example: If the attribute RootPath has the value BaseFolder, a folder with the same name should exist in the user directory, and it should contain all the files referenced in the submission.

  Please check the All In One Example for more information.

• Section Level

  • File List: A file that can be used as an index to reference and include submission files. Please check the File List section for more information.

Submission

Root element of the submission. A submission element is created by using the reserved word Submission. It’s mandatory to have this element in the submission definition.

Syntax

Submission	AccNo
<Attributes>

Examples

TSV

Submission	E-MTAB-2950
Title	The first wave of the zygotic transcription is highly promiscuous
ReleaseDate	2018-09-28
RootPath	E-MTAB/E-MTAB-2950

JSON

{
  "accno": "E-MTAB-2950",
  "attributes": [{
    "name": "Title",
    "value": "The first wave of the zygotic transcription is highly promiscuous"
  }, {
    "name": "ReleaseDate",
    "value": "2018-09-28"
  }, {
    "name": "RootPath",
    "value": "E-MTAB/E-MTAB-2950"
  }],
  "type": "submission"
}

Section

A section is a part of the submission used to group other elements like files, links or even other sections. There’re some rules related to sections:

1. Sections can be of any type so, there’s no reserved word for them
2. The first section of a submission definition will be the Root Section
3. Every submission should have at least a root section

Syntax

Type	AccNo
<Attributes>

Examples

TSV

Study	s-E-MTAB-2950
Title	The first wave of the zygotic transcription is highly promiscuous
Description	Initiation of zygotic transcription in mammals is poorly understood

JSON

{
  "section": {
    "accno": "s-E-MTAB-2950",
    "attributes": [{
      "name": "Title",
      "value": "The first wave of the zygotic transcription is highly promiscuous"
    }, {
      "name": "Description",
      "value": "Initiation of zygotic transcription in mammals is poorly understood"
    }],
    "type": "Study"
  }
}

Subsection

A subsection is a section contained inside another section. Any section may have several subsections.

Syntax

Type	AccNo	ParentAccNo
<Attributes>

Examples

TSV

Data	DT-1	s-E-MTAB-2950
Title	Transcription Data
Description	The data for zygotic transcription in mammals

JSON

{
  "section": {
    "accno": "s-E-MTAB-2950",
    "subsections": [{
      "accno": "DT-1",
      "attributes": [{
        "name": "Title",
        "value": "Transcription Data"
      }, {
        "name": "Description",
        "value": "The data for zygotic transcription in mammals"
      }],
      "type": "Data"
    }]
  }
}

Sections Table

A sections table is used to group several sections that will be displayed as a table by the UI. Rules:

• You can place as many sections as you want in a sections table
• The sections in the table can NOT contain files, links nor subsections
• All the sections in the table will have the same type and attributes
• The parent accNo is optional
• If a parent accNo is NOT provided, every section in the table will become a new section
• If a parent accNo is provided, all the sections in the table will become subsections of the section with the provided accNo

Syntax

Type[Parent AccNo (optional)]	Attr1	Atrr2	AttrN
AccNo1	Attr1 Value	Attr2 Value	AttrN Value
AccNo2	Attr1 Value	Attr2 Value	AttrN Value
AccNoN	Attr1 Value	Attr2 Value	AttrN Value

Note: If a parent accNo is NOT provided, the brackets still need to be placed but empty: Type[]

Examples

TSV

Data[s-E-MTAB-2950]	Title	Description
DT-1	Group 1 Transcription Data	The data for zygotic transcription in mammals group 1
DT-2	Group 2 Transcription Data	The data for zygotic transcription in mammals group 2

JSON

{
  "section": {
    "accno": "s-E-MTAB-2950",
    "subsections": [[{
      "accno": "DT-1",
      "attributes": [{
        "name": "Title",
        "value": "Group 1 Transcription Data"
      }, {
        "name": "Description",
        "value": "The data for zygotic transcription in mammals group 1"
      }],
      "type": "Data"
    }, {
      "accno": "DT-2",
      "attributes": [{
        "name": "Title",
        "value": "Group 2 Transcription Data"
      }, {
        "name": "Description",
        "value": "The data for zygotic transcription in mammals group 2"
      }],
      "type": "Data"
    }]]
  }
}

Files

This element represents a file that is attached to a submission section. Whenever a file is defined, it’ll be attached to the immediately previously defined section or subsection. Files can be represented in two ways: single file or files table.

Single File

Represents a single file attached to a section or subsection. The reserved word File is used to define a single file.

Syntax

File	Path
<Attributes>

Examples

TSV

File	plates/J_Sero_plate_keys.xlsx
Description	Summary data
Type	XLSX File

JSON

{
  "section": {
    "files": [{
      "path": "plates/J_Sero_plate_keys.xlsx",
      "attributes": [{
        "name": "Description",
        "value": "Summary data"
      }, {
        "name": "Type",
        "value": "XLSX File"
      }]
    }]
  }
}

Files Table

Represents a group of files attached to a section or subsection. The reserved word Files is used to define a files table. The referenced files should be either in the user directory or attached to the submission request. Path relative to the user folder in BioStudies should be reflected with a forward slash / as the file path separator.

Syntax

Files	Attr1	Attr2	AttrN
File1 Path	Attr1 Value	Attr2 Value	AttrN Value
File2 Path	Attr1 Value	Attr2 Value	AttrN Value
FileN Path	Attr1 Value	Attr2 Value	AttrN Value

Examples

TSV

Files	Description	Type
plates/J_Sero_plate_keys.xlsx	Summary data	Library File
plates/Plate01.csv	Data for Plate 01	Plate Details File

JSON

{
  "section": {
    "files": [[{
      "path": "plates/J_Sero_plate_keys.xlsx",
      "attributes": [{
        "name": "Description",
        "value": "Summary data"
      }, {
        "name": "Type",
        "value": "Library File"
      }]
    }, {
      "path": "plates/Plate01.csv",
      "attributes": [{
        "name": "Description",
        "value": "Data for Plate 01"
      }, {
        "name": "Type",
        "value": "Plate Details File"
      }]
    }]]
  }
}

File List

A file list is an externalised Files Table which can be attached to a section by the special File List attribute. The value of this attribute is the name of the file which contains the table. An example is given in File List Example.

Links

Element used to represent links that are related to a submission section. A link doesn’t necessarily means a web page but it can also relate to other elements like genes, expressions, FTP locations, etc.

Whenever a link is defined, it’ll be attached to the immediately previously defined section or subsection. Links can be represented in two ways: single link or links table.

Single Link

Represents a single link related to a section or subsection. The reserved word Link is used to define a single link.

Syntax

Link	URL
<Attributes>

Examples

TSV

Link	ftp://ftp.biostudies.ebi.ac.uk/pub/S-BSMS/S-BSMS0-99/S-BSMS6/raw_data
Type	Raw data

JSON

{
  "section": {
    "links": [{
      "url": "ftp://ftp.biostudies.ebi.ac.uk/pub/S-BSMS/S-BSMS0-99/S-BSMS6/raw_data",
      "attributes": [{
        "name": "Type",
        "value": "Raw data"
      }]
    }]
  }
}

Links Table

Represents a group of links attached to a section or subsection. The reserved word Links is used to define a links table

Syntax

Links	Attr1	Attr2	AttrN
Link1 Url	Attr1 Value	Attr2 Value	AttrN Value
Link2 Url	Attr1 Value	Attr2 Value	AttrN Value
Link3 Url	Attr1 Value	Attr2 Value	AttrN Value

Examples

TSV

Links	Description	Type
ERP007058	ENA Project	ENA
ERR632210-ERR632217	ENA Runs	ENA

JSON

{
  "section": {
    "links": [[{
      "url": "ERP007058",
      "attributes": [{
        "name": "Description",
        "value": "ENA Project"
      }, {
        "name": "Type",
        "value": "ENA"
      }]
    }, {
      "url": "ERR632210",
      "attributes": [{
        "name": "Description",
        "value": "ENA Runs"
      }, {
        "name": "Type",
        "value": "ENA"
      }]
    }]]
  }
}