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fix #3160 #3166

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998773a
fix #3160
antgonza Nov 19, 2021
f5d7f06
adding extra comment from @maque4004
antgonza Nov 20, 2021
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33 changes: 30 additions & 3 deletions qiita_pet/support_files/doc/source/checklist-for-ebi-ena-submission.rst
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@@ -1,4 +1,5 @@
.. role:: red
.. _checklist-for-ebi-ena-submission:

Making data Public in Qiita and/or send data to EBI-ENA
=======================================================
Expand All @@ -22,6 +23,8 @@ time to request a submission is when you are writing your paper. Remember that t
data can be submitted to EBI and can be kept private and simply make public when
the paper is accepted. Note that EBI/ENA takes up to 15 days to change the status
from private to public, so consider this when submitting data and your manuscript.
If need help send an email to `qiita.help@gmail.com <mailto:qiita.help@gmail.com>`__
and please include your study ID.

.. note::
For convenience Qiita allows you to upload a QIIME mapping file to process your data. However,
Expand All @@ -43,7 +46,7 @@ For the latest definitions and explanation visit the `EBI/ENA Missing value repo
Checklist
---------

For each preparation that needs to be uploaded to EBI-ENA we will check:
Remember, metadata is the most important part for an analysis, without it we only have sequences; thus, for each preparation that needs to be uploaded to EBI-ENA or become public we will check:

1. Data processing

Expand All @@ -60,9 +63,11 @@ For each preparation that needs to be uploaded to EBI-ENA we will check:
3. *sample_type*
4. *taxon_id* - needs to match *scientific_name* value
5. *scientific_name* - needs to match *taxon_id* value - this is the name of the `metagenome <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=12908&lvl=3&srchmode=1&keep=1&unlock>`__ referenced in the column *taxon_id* and that the two values match. Submission will not work if the user puts *host_scientific_name* or *host_taxid* instead. Do not accept EBI null values. For null values use *scientific_name* “metagenome” and *taxon_id* “256318”
6. *env_biome*, *env_feature*, *env_material*, *env_package*, for options `visit the ENVO section in <http://ols.wordvis.com/>`__
6. *env_biome*, *env_feature*, *env_material*, *env_package*, for options `visit ENVO <http://ols.wordvis.com/>`__
7. *elevation*, *latitude*, *longitude*
8. *empo_1*, *empo_2*, *empo_3*
8. *physical_specimen_location*
9. *collection_timestamp*
10. *empo_1*, *empo_2*, *empo_3*

.. table::
:widths: auto
Expand Down Expand Up @@ -133,6 +138,28 @@ For each preparation that needs to be uploaded to EBI-ENA we will check:
9. *instrument_model*
10. *sequencing_method*

.. note::
The current valid values for instrument_model per platform are - please contact us if you would like to add yours to this list:
+---------------------+----------------------------------------------------------------------------------------------------------+
| Platform | Valid instrument_model options |
+=====================+==========================================================================================================+
| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, |
| | ``454 GS Junior`` or ``unspecified`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Illumina`` | ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, |
| | ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``, |
| | ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``, |
| | ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``, |
| | ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or ``unspecified`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Ion_Torrent`` | ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``PacBio_SMRT`` | ``PacBio RS``, ``PacBio RS II``, ``Sequel``, ``Sequel II`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Oxford_Nanopore`` | ``GridION`` |
+---------------------+----------------------------------------------------------------------------------------------------------+


c. Additional minimal columns, if possible:

1. *pcr_primers*
Expand Down
49 changes: 4 additions & 45 deletions qiita_pet/support_files/doc/source/gettingstartedguide/index.rst
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Expand Up @@ -87,20 +87,6 @@ Example files
You can download an example sample information file from
`here <ftp://ftp.microbio.me/pub/qiita/sample_prep_information_files_examples.tgz>`__.

EBI-ENA NULL values vocabulary
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

For all public studies including those being submitted to EBI, no blanks are allowed in the sample information.
We support the following null values: *not applicable*, *not collected*, *not provided*,
*restricted access*.

For the latest definitions and explanation visit the `EBI/ENA Missing value reporting <http://www.ebi.ac.uk/ena/about/missing-values-reporting>`__.

.. warning::
Column names in your information files cannot be named as a Postgres reserved word. For example, a column cannot be named
`CONDITION`, but could instead be named `DISEASE_CONDITION`. For a full list of these reserved words, see this
`link <https://www.postgresql.org/docs/9.3/static/sql-keywords-appendix.html>`__.


Sample information file
~~~~~~~~~~~~~~~~~~~~~~~
Expand All @@ -123,10 +109,11 @@ sample information file to be added to the system:
| | | characters are alphabetic ``[A-Za-z]``, numeric ``[0-9]``, and periods ``.``. |
+-------------------+-----------------------------+-------------------------------------------------------------------------------+

Required fields for EBI submission
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Required fields for EBI submission and to make a study public
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In order to submit your data to EBI, please review :ref:`checklist-for-ebi-ena-submission`.

In order to submit your data to EBI, certain fields are required in your sample information file. You can download a spread sheet containing these required fields on the `Knight Lab website <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__ under "MetaData Template".

Attaching the Sample Information to the Study
---------------------------------------------
Expand Down Expand Up @@ -272,34 +259,6 @@ prep information file to be added to the system:
| | | match the sample_name in the sample template. |
+-------------------+-------------------------------+------------------------------------------------------------------------+

Required fields for EBI submission
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


In order to submit your data to EBI, certain fields are required in your preparation information file. You can download a spread sheet containing these required fields on the `Knight Lab website <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__ under "Prep Template".


For all valid values for instrument_model per platform, view the values in the table below:

+---------------------+----------------------------------------------------------------------------------------------------------+
| Platform | Valid instrument_model options |
+=====================+==========================================================================================================+
| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, |
| | ``454 GS Junior`` or ``unspecified`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Illumina`` | ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, |
| | ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``, |
| | ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``, |
| | ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``, |
| | ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or ``unspecified`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Ion_Torrent`` | ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``PacBio_SMRT`` | ``PacBio RS``, ``PacBio RS II``, ``Sequel``, ``Sequel II`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Oxford_Nanopore`` | ``GridION`` |
+---------------------+----------------------------------------------------------------------------------------------------------+


Required fields for pre-processing target gene data
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down