All In One Example

Below you’ll find an example of a basic submission that:

Is attached to a project named “blueprint”
Has a root section with a single file, a files table, and a single link attached to it
Some of the attributes in the root section have name and value attributes
Has a section table
Has a subsection with a links table

Submission	S-IHECRE00000919.1
Title	venous blood, Monocyte
ReleaseDate	2016-06-07
RootPath	S-IHECRE00000919.1
DataSource	BLUEPRINT
AttachTo	blueprint

Study	SECT-001
Title	venous blood, Monocyte
Project	CEEHRC (McGill)
Status	Incomplete
Organism	Homo sapiens
Tissue type	venous blood
[Ontology]	UBERON
(Tissue)	Blood
Donor ID	McGill0139
Biomaterial Type	primary cells
Cell Type	Monocyte
[Ontology]	CL
Disease	Systemic Lupus Erythematosus
[Ontology]	EFO
Experiment type	Single donor

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

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

Link	IHECRE00000919.1
Type	EpiRR

Data[SECT-001]	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

Stranded Total RNA-Seq	SUBSECT-001	SECT-001

Links	Type	Assay type	Experiment type	Primary id
EGAD00001001282	EGA	RNA-Seq	Stranded Total RNA-Seq	EGAX00001273202
EGAD00001001283	EGA	RNA-Seq	Stranded Total RNA-Seq	EGAX00001273203

{
  "accno": "S-IHECRE00000919.1",
  "attributes": [{
    "name": "RootPath",
    "value": "S-IHECRE00000919.1"
  }, {
    "name": "Title",
    "value": "venous blood, Monocyte"
  }, {
    "name": "ReleaseDate",
    "value": "2016-06-07"
  }, {
    "name": "DataSource",
    "value": "BLUEPRINT"
  }, {
    "name": "AttachTo",
    "value": "blueprint"
  }],
  "section": {
    "accno": "SECT-001",
    "attributes": [{
      "name": "Title",
      "value": "venous blood, Monocyte"
    }, {
      "name": "Project",
      "value": "CEEHRC (McGill)"
    }, {
      "name": "Status",
      "value": "Incomplete"
    }, {
      "name": "Organism",
      "value": "Homo sapiens"
    }, {
      "name": "Tissue type",
      "value": "venous blood",
      "nmqual": [{
        "name": "Tissue",
        "value": "Blood"
      }],
      "valqual": [{
        "name": "Ontology",
        "value": "UBERON"
      }]
    }, {
      "name": "Donor ID",
      "value": "McGill0139"
    }, {
      "name": "Biomaterial Type",
      "value": "primary cells"
    }, {
      "name": "Cell Type",
      "value": "Monocyte",
      "valqual": [{
        "name": "Ontology",
        "value": "CL"
      }]
    }, {
      "name": "Disease",
      "value": "Systemic Lupus Erythematosus",
      "valqual": [{
       "name": "Ontology",
       "value": "EFO"
      }]
    }, {
      "name": "Experiment type",
      "value": "Single donor"
    }],
    "files": [{
      "path": "plates/J_Sero_plate_keys.xlsx",
      "attributes": [{
        "name": "Description",
        "value": "Summary data"
      }, {
        "name": "Type",
        "value": "XLSX File"
      }]
    }, [{
      "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"
      }]
    }]],
    "links": [{
      "url": "IHECRE00000919.1",
      "attributes": [{
        "name": "Type",
        "value": "EpiRR"
      }]
    }],
    "subsections": [{
      "accno": "SUBSECT-001",
      "links": [[{
        "url": "EGAD00001001282",
        "attributes": [{
          "name": "Type",
          "value": "EGA"
        }, {
          "name": "Assay type",
          "value": "RNA-Seq"
        }, {
          "name": "Experiment type",
          "value": "Stranded Total RNA-Seq"
        }, {
          "name": "Primary id",
          "value": "EGAX00001273202"
        }]
      }, {
        "url": "EGAD00001001283",
        "attributes": [{
          "name": "Type",
          "value": "EGA"
        }, {
          "name": "Assay type",
          "value": "RNA-Seq"
        }, {
          "name": "Experiment type",
          "value": "Stranded Total RNA-Seq"
        }, {
          "name": "Primary id",
          "value": "EGAX00001273203"
        }]
      }]],
      "type": "Stranded Total RNA-Seq"
    }, [{
      "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"
    }]],
    "type": "Study"
  },
  "type": "submission"
}

<submission accno="S-IHECRE00000919.1">
  <attributes>
    <attribute>
      <name>RootPath</name>
      <value>S-IHECRE00000919.1</value>
    </attribute>
    <attribute>
      <name>Title</name>
      <value>venous blood, Monocyte</value>
    </attribute>
    <attribute>
      <name>ReleaseDate</name>
      <value>2016-06-07</value>
    </attribute>
    <attribute>
      <name>DataSource</name>
      <value>BLUEPRINT</value>
    </attribute>
    <attribute>
      <name>AttachTo</name>
      <value>blueprint</value>
    </attribute>
  </attributes>

  <section accno="SECT-001" type="Study">
    <attributes>
      <attribute>
        <name>Title</name>
        <value>venous blood, Monocyte</value>
      </attribute>
      <attribute>
        <name>Project</name>
        <value>CEEHRC (McGill)</value>
      </attribute>
      <attribute>
        <name>Status</name>
        <value>Incomplete</value>
      </attribute>
      <attribute>
        <name>Organism</name>
        <value>Homo sapiens</value>
      </attribute>
      <attribute>
        <name>Tissue type</name>
        <value>venous blood</value>
        <nmqual>
          <name>Tissue</name>
          <value>Blood</value>
        </nmqual>
        <valqual>
          <name>Ontology</name>
          <value>UBERON</value>
        </valqual>
      </attribute>
      <attribute>
        <name>Donor ID</name>
        <value>McGill0139</value>
      </attribute>
      <attribute>
        <name>Biomaterial Type</name>
        <value>primary cells</value>
      </attribute>
      <attribute>
        <name>Cell Type</name>
        <value>Monocyte</value>
        <valqual>
          <name>Ontology</name>
          <value>CL</value>
        </valqual>
      </attribute>
      <attribute>
        <name>Disease</name>
        <value>Systemic Lupus Erythematosus</value>
        <valqual>
          <name>Ontology</name>
          <value>EFO</value>
        </valqual>
      </attribute>
      <attribute>
        <name>Experiment type</name>
        <value>Single donor</value>
      </attribute>
    </attributes>
    <files>
      <file>
        <path>plates/J_Sero_plate_keys.xlsx</path>
        <attributes>
          <attribute>
            <name>Description</name>
            <value>Summary data</value>
          </attribute>
          <attribute>
            <name>Type</name>
            <value>XLSX File</value>
          </attribute>
        </attributes>
      </file>
      <table>
        <file>
          <path>plates/J_Sero_plate_keys.xlsx</path>
          <attributes>
            <attribute>
              <name>Description</name>
              <value>Summary data</value>
            </attribute>
            <attribute>
              <name>Type</name>
              <value>Library File</value>
            </attribute>
          </attributes>
        </file>
        <file>
          <path>plates/Plate01.csv</path>
          <attributes>
            <attribute>
              <name>Description</name>
              <value>Data for Plate 01</value>
            </attribute>
            <attribute>
              <name>Type</name>
              <value>Plate Details File</value>
            </attribute>
          </attributes>
        </file>
      </table>
    </files>
    <links>
      <link>
        <url>IHECRE00000919.1</url>
        <attributes>
          <attribute>
            <name>Type</name>
            <value>EpiRR</value>
          </attribute>
        </attributes>
      </link>
    </links>

    <subsections>
      <section accno="SUBSECT-001" type="Stranded Total RNA-Seq">
        <attributes/>
        <links>
          <table>
            <link>
              <url>EGAD00001001282</url>
              <attributes>
                <attribute>
                  <name>Type</name>
                  <value>EGA</value>
                </attribute>
                <attribute>
                  <name>Assay type</name>
                  <value>RNA-Seq</value>
                </attribute>
                <attribute>
                  <name>Experiment type</name>
                  <value>Stranded Total RNA-Seq</value>
                </attribute>
                <attribute>
                  <name>Primary id</name>
                  <value>EGAX00001273202</value>
                </attribute>
              </attributes>
            </link>
            <link>
              <url>EGAD00001001283</url>
              <attributes>
                <attribute>
                  <name>Type</name>
                  <value>EGA</value>
                </attribute>
                <attribute>
                  <name>Assay type</name>
                  <value>RNA-Seq</value>
                </attribute>
                <attribute>
                  <name>Experiment type</name>
                  <value>Stranded Total RNA-Seq</value>
                </attribute>
                <attribute>
                  <name>Primary id</name>
                  <value>EGAX00001273203</value>
                </attribute>
              </attributes>
            </link>
          </table>
        </links>
      </section>
      <table>
        <section accno="DT-1" type="Data">
          <attributes>
            <attribute>
              <name>Title</name>
              <value>Group 1 Transcription Data</value>
            </attribute>
            <attribute>
              <name>Description</name>
              <value>The data for zygotic transcription in mammals group 1</value>
            </attribute>
          </attributes>
        </section>
        <section accno="DT-2" type="Data">
          <attributes>
            <attribute>
              <name>Title</name>
              <value>Group 2 Transcription Data</value>
            </attribute>
            <attribute>
              <name>Description</name>
              <value>The data for zygotic transcription in mammals group 2</value>
            </attribute>
          </attributes>
        </section>
      </table>
    </subsections>
  </section>
</submission>

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{ "accno": "S-IHECRE00000919.1", "attributes": [{ "name": "RootPath", "value": "S-IHECRE00000919.1" }, { "name": "Title", "value": "venous blood, Monocyte" }, { "name": "ReleaseDate", "value": "2016-06-07" }, { "name": "DataSource", "value": "BLUEPRINT" }, { "name": "AttachTo", "value": "blueprint" }], "section": { "accno": "SECT-001", "attributes": [{ "name": "Title", "value": "venous blood, Monocyte" }, { "name": "Project", "value": "CEEHRC (McGill)" }, { "name": "Status", "value": "Incomplete" }, { "name": "Organism", "value": "Homo sapiens" }, { "name": "Tissue type", "value": "venous blood", "nmqual": [{ "name": "Tissue", "value": "Blood" }], "valqual": [{ "name": "Ontology", "value": "UBERON" }] }, { "name": "Donor ID", "value": "McGill0139" }, { "name": "Biomaterial Type", "value": "primary cells" }, { "name": "Cell Type", "value": "Monocyte", "valqual": [{ "name": "Ontology", "value": "CL" }] }, { "name": "Disease", "value": "Systemic Lupus Erythematosus", "valqual": [{ "name": "Ontology", "value": "EFO" }] }, { "name": "Experiment type", "value": "Single donor" }], "files": [{ "path": "plates/J_Sero_plate_keys.xlsx", "attributes": [{ "name": "Description", "value": "Summary data" }, { "name": "Type", "value": "XLSX File" }] }, [{ "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" }] }]], "links": [{ "url": "IHECRE00000919.1", "attributes": [{ "name": "Type", "value": "EpiRR" }] }], "subsections": [{ "accno": "SUBSECT-001", "links": [[{ "url": "EGAD00001001282", "attributes": [{ "name": "Type", "value": "EGA" }, { "name": "Assay type", "value": "RNA-Seq" }, { "name": "Experiment type", "value": "Stranded Total RNA-Seq" }, { "name": "Primary id", "value": "EGAX00001273202" }] }, { "url": "EGAD00001001283", "attributes": [{ "name": "Type", "value": "EGA" }, { "name": "Assay type", "value": "RNA-Seq" }, { "name": "Experiment type", "value": "Stranded Total RNA-Seq" }, { "name": "Primary id", "value": "EGAX00001273203" }] }]], "type": "Stranded Total RNA-Seq" }, [{ "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" }]], "type": "Study" }, "type": "submission" }

<submission accno="S-IHECRE00000919.1"> <attributes> <attribute> <name>RootPath</name> <value>S-IHECRE00000919.1</value> </attribute> <attribute> <name>Title</name> <value>venous blood, Monocyte</value> </attribute> <attribute> <name>ReleaseDate</name> <value>2016-06-07</value> </attribute> <attribute> <name>DataSource</name> <value>BLUEPRINT</value> </attribute> <attribute> <name>AttachTo</name> <value>blueprint</value> </attribute> </attributes> <section accno="SECT-001" type="Study"> <attributes> <attribute> <name>Title</name> <value>venous blood, Monocyte</value> </attribute> <attribute> <name>Project</name> <value>CEEHRC (McGill)</value> </attribute> <attribute> <name>Status</name> <value>Incomplete</value> </attribute> <attribute> <name>Organism</name> <value>Homo sapiens</value> </attribute> <attribute> <name>Tissue type</name> <value>venous blood</value> <nmqual> <name>Tissue</name> <value>Blood</value> </nmqual> <valqual> <name>Ontology</name> <value>UBERON</value> </valqual> </attribute> <attribute> <name>Donor ID</name> <value>McGill0139</value> </attribute> <attribute> <name>Biomaterial Type</name> <value>primary cells</value> </attribute> <attribute> <name>Cell Type</name> <value>Monocyte</value> <valqual> <name>Ontology</name> <value>CL</value> </valqual> </attribute> <attribute> <name>Disease</name> <value>Systemic Lupus Erythematosus</value> <valqual> <name>Ontology</name> <value>EFO</value> </valqual> </attribute> <attribute> <name>Experiment type</name> <value>Single donor</value> </attribute> </attributes> <files> <file> <path>plates/J_Sero_plate_keys.xlsx</path> <attributes> <attribute> <name>Description</name> <value>Summary data</value> </attribute> <attribute> <name>Type</name> <value>XLSX File</value> </attribute> </attributes> </file> <table> <file> <path>plates/J_Sero_plate_keys.xlsx</path> <attributes> <attribute> <name>Description</name> <value>Summary data</value> </attribute> <attribute> <name>Type</name> <value>Library File</value> </attribute> </attributes> </file> <file> <path>plates/Plate01.csv</path> <attributes> <attribute> <name>Description</name> <value>Data for Plate 01</value> </attribute> <attribute> <name>Type</name> <value>Plate Details File</value> </attribute> </attributes> </file> </table> </files> <links> <link> <url>IHECRE00000919.1</url> <attributes> <attribute> <name>Type</name> <value>EpiRR</value> </attribute> </attributes> </link> </links> <subsections> <section accno="SUBSECT-001" type="Stranded Total RNA-Seq"> <attributes/> <links> <table> <link> <url>EGAD00001001282</url> <attributes> <attribute> <name>Type</name> <value>EGA</value> </attribute> <attribute> <name>Assay type</name> <value>RNA-Seq</value> </attribute> <attribute> <name>Experiment type</name> <value>Stranded Total RNA-Seq</value> </attribute> <attribute> <name>Primary id</name> <value>EGAX00001273202</value> </attribute> </attributes> </link> <link> <url>EGAD00001001283</url> <attributes> <attribute> <name>Type</name> <value>EGA</value> </attribute> <attribute> <name>Assay type</name> <value>RNA-Seq</value> </attribute> <attribute> <name>Experiment type</name> <value>Stranded Total RNA-Seq</value> </attribute> <attribute> <name>Primary id</name> <value>EGAX00001273203</value> </attribute> </attributes> </link> </table> </links> </section> <table> <section accno="DT-1" type="Data"> <attributes> <attribute> <name>Title</name> <value>Group 1 Transcription Data</value> </attribute> <attribute> <name>Description</name> <value>The data for zygotic transcription in mammals group 1</value> </attribute> </attributes> </section> <section accno="DT-2" type="Data"> <attributes> <attribute> <name>Title</name> <value>Group 2 Transcription Data</value> </attribute> <attribute> <name>Description</name> <value>The data for zygotic transcription in mammals group 2</value> </attribute> </attributes> </section> </table> </subsections> </section> </submission>