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
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
Name The Name
Value The Value
(Name Attribute) The name attribute value
[Value Attribute] The value attribute value
-
Study Type RNA-seq of non coding RNA{ "attributes": [{ "name": "Study Type", "value": "RNA-seq of non coding RNA" }] } -
Study Type RNA-seq of non coding RNA [Ontology] EFO (Seq Type) RNA{ "attributes": [{ "name": "Study Type", "value": "RNA-seq of non coding RNA", "nmqual": [{ "name": "Seq Type", "value": "RNA" }], "valqual": [{ "name": "Ontlogy", "value": "EFO" }] }] } -
For this example, let's assume there's already an attribute with value "Org1"
<affiliation> Org1{ "attributes": [{ "name": "affiliation", "value": "Org1", "isReference": "true" }] } -
There are some attributes that are used as keywords.
- 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.
-
- 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.
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.
Submission AccNo
<Attributes>
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
{
"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"
}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:
- Sections can be of any type so, there's no reserved word for them
- The first section of a submission definition will be the Root Section
- Every submission should have at least a root section
Type AccNo
<Attributes>
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
{
"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"
}
}A subsection is a section contained inside another section. Any section may have several subsections.
Type AccNo ParentAccNo
<Attributes>
Data DT-1 s-E-MTAB-2950
Title Transcription Data
Description The data for zygotic transcription in mammals
{
"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"
}]
}
}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
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[]
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
{
"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"
}]]
}
}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.
Represents a single file attached to a section or subsection. The reserved word File is used to define a single file.
File Path
<Attributes>
File plates/J_Sero_plate_keys.xlsx
Description Summary data
Type XLSX File
{
"section": {
"files": [{
"path": "plates/J_Sero_plate_keys.xlsx",
"attributes": [{
"name": "Description",
"value": "Summary data"
}, {
"name": "Type",
"value": "XLSX File"
}]
}]
}
}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.
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
Files Description Type
plates/J_Sero_plate_keys.xlsx Summary data Library File
plates/Plate01.csv Data for Plate 01 Plate Details File
{
"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"
}]
}]]
}
}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.
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.
Represents a single link related to a section or subsection. The reserved word Link is used to define a single link.
Link URL
<Attributes>
Link ftp://ftp.biostudies.ebi.ac.uk/pub/S-BSMS/S-BSMS0-99/S-BSMS6/raw_data
Type Raw data
{
"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"
}]
}]
}
}Represents a group of links attached to a section or subsection. The reserved word Links is used to define a links table
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
Links Description Type
ERP007058 ENA Project ENA
ERR632210-ERR632217 ENA Runs ENA
{
"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"
}]
}]]
}
}