.. _manifest-templates:

===============================
Data Templates and Instructions
===============================

A manifest [#f1]_ is a spreadsheet that helps you organise and record
metadata. Metadata is information that describes your data such as collection
date, instrument model or specimen ID.

A checklist [#f2]_ defines the metadata fields required for data submissions
based on the type of data you are submitting.

The terms *manifest* and *spreadsheet* are often used interchangeably.

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.. toctree::
   :maxdepth: 2

   /discovery/manifest-checklist

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.. _download-manifest-templates:

---------------------
Downloading Templates
---------------------

Manifest templates can be downloaded directly from the work profile component
[#f3]_ that you are working on (e.g. samples, single-cell, reads, etc.) by
clicking the |blank-manifest-download-button| button on each page. See the
:ref:`biodata-profile-components` or :ref:`tol-profile-components` sections
for more on accessing each component.

They can also be downloaded from the `Manifests page
<https://copo-project.org/manifests/index>`__ by selecting a type from the
dropdown menu then, clicking the **Download** button and choosing
**Blank template** option.

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.. _fill-blank-manifests:

---------------------------
Recording Data in Manifests
---------------------------

Each manifest follows a manual known as *Standard Operating Procedure (SOP)*
[#f4]_ which provides a detailed guidance on how to record metadata in the
manifest.

The following are various ways to retrieve a SOP for a manifest:

#. Click the |sop-download-button| button located on the COPO **Samples** page
   to download the SOP.

   See the :ref:`accessing-samples-page-tol` component section for more
   details about accessing the **Samples** page.

#. Navigate to the COPO
   `Manifests page <https://copo-project.org/manifests/index>`__ -

   * Select a manifest option from the dropdown menu in the
     **Manifest/Checklist Type** column
   * Click the **Download** button for the desired manifest to reveal the
     download options
   * Click the **Standard Operating Procedure (SOP)** option to download the
     SOP.

     Please note that if the SOP does not exist, its download option will not
     be available.

#. The SOP for the various manifests are available below.

.. list-table:: Standard Operating Procedure (SOP) for Manifests
   :widths: 15 15 20 20 25
   :width: 100%
   :align: center
   :header-rows: 1

   * - Project
     - SOP
     - GitHub repository
     - Project website
     - Note
   * -  **Aquatic Symbiosis Genomics (ASG)** [#f5]_
     - :download:`SOP <../assets/files/sops/asg-manifest-sop-v2.5.pdf>`
     -  .. centered:: -
     - |globe| `Website <https://www.sanger.ac.uk/collaboration/aquatic-
       symbiosis-genomics-project>`__
     - This follows most of the instructions outlined in the DToL SOP, with
       some minor changes and omissions.

   * -  **Darwin Tree of Life (DToL)** [#f6]_
     - :download:`SOP <../assets/files/sops/dtol-manifest-sop-v2.5.pdf>`
     - .. rst-class:: fa fa-github

          |whitespace| `GitHub repository
          <https://github.com/darwintreeoflife/metadata>`__

     - |globe| `Website <https://www.darwintreeoflife.org>`__
     - .. centered:: -

   * -  **Darwin Tree of Life Environmental Samples (DToL_ENV)**
     - .. centered:: -
     - .. centered:: -
     - .. centered:: -
     - Content is not yet available. Please check back later.

   * -  **European Reference Genome Atlas (ERGA)** [#f7]_
     - :download:`SOP <../assets/files/sops/erga-manifest-sop-v2.5.1.pdf>`
     - .. rst-class:: fa fa-github

          |whitespace| `GitHub repository <https://github.com/ERGA-
          consortium/ERGA-sample-manifest>`__

     - .. centered:: -
     - .. centered:: -

   * -  **Population Genomics (POP_GENOMICS)**
     - :download:`SOP <../assets/files/sops/popgenomics-manifest-sop-v1.1.pdf>`
     - .. centered:: -
     - .. centered:: -
     - .. centered:: -

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Related Topics
---------------

.. seealso::

   * :ref:`manifest-wizard`

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.. rubric:: Footnotes

.. [#f1] See term: :term:`Manifest`.
.. [#f2] See term: :term:`Checklist`.
.. [#f3] Also known as research object component. See term:
   :term:`Profile component`.
.. [#f4] See term: :term:`SOP`.
.. [#f5] See term: :term:`ASG (Aquatic Symbiosis Genomics) <ASG>`.
.. [#f6] See term: :term:`DToL (Darwin Tree of Life) <DToL>`.
.. [#f7] See term: :term:`ERGA (European Reference Genome Atlas) <ERGA>`.

..
    Images declaration
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.. |blank-manifest-download-button| image:: /assets/images/buttons/download-button-blank-manifest.png
   :height: 4ex
   :class: no-scaled-link

.. |collapsible-item-arrow| image:: /assets/images/icons/arrow-right.png
   :height: 2ex
   :class: no-scaled-link

.. |sop-download-button| image:: /assets/images/buttons/download-button-sop.png
   :height: 4ex
   :class: no-scaled-link

..
    Unicode declaration
..
.. |globe|  unicode:: U+1F310

.. |whitespace|  unicode:: U+0020