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Merge pull request #3166 from antgonza/fix-3160
fix #3160
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‎qiita_pet/support_files/doc/source/checklist-for-ebi-ena-submission.rst

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.. role:: red
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.. _checklist-for-ebi-ena-submission:
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Making data Public in Qiita and/or send data to EBI-ENA
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=======================================================
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data can be submitted to EBI and can be kept private and simply make public when
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the paper is accepted. Note that EBI/ENA takes up to 15 days to change the status
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from private to public, so consider this when submitting data and your manuscript.
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If need help send an email to `[email protected] <mailto:[email protected]>`__
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and please include your study ID.
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.. note::
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For convenience Qiita allows you to upload a QIIME mapping file to process your data. However,
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Checklist
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---------
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For each preparation that needs to be uploaded to EBI-ENA we will check:
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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:
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1. Data processing
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3. *sample_type*
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4. *taxon_id* - needs to match *scientific_name* value
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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”
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6. *env_biome*, *env_feature*, *env_material*, *env_package*, for options `visit the ENVO section in <http://ols.wordvis.com/>`__
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6. *env_biome*, *env_feature*, *env_material*, *env_package*, for options `visit ENVO <http://ols.wordvis.com/>`__
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7. *elevation*, *latitude*, *longitude*
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8. *empo_1*, *empo_2*, *empo_3*
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8. *physical_specimen_location*
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9. *collection_timestamp*
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10. *empo_1*, *empo_2*, *empo_3*
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.. table::
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:widths: auto
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9. *instrument_model*
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10. *sequencing_method*
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.. note::
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The current valid values for instrument_model per platform are - please contact us if you would like to add yours to this list:
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| Platform | Valid instrument_model options |
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+=====================+==========================================================================================================+
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| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, |
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| | ``454 GS Junior`` or ``unspecified`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| ``Illumina`` | ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, |
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| | ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``, |
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| | ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``, |
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| | ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``, |
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| | ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or ``unspecified`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| ``Ion_Torrent`` | ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| ``PacBio_SMRT`` | ``PacBio RS``, ``PacBio RS II``, ``Sequel``, ``Sequel II`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| ``Oxford_Nanopore`` | ``GridION`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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c. Additional minimal columns, if possible:
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1. *pcr_primers*

‎qiita_pet/support_files/doc/source/gettingstartedguide/index.rst

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You can download an example sample information file from
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`here <ftp://ftp.microbio.me/pub/qiita/sample_prep_information_files_examples.tgz>`__.
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EBI-ENA NULL values vocabulary
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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For all public studies including those being submitted to EBI, no blanks are allowed in the sample information.
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We support the following null values: *not applicable*, *not collected*, *not provided*,
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*restricted access*.
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For the latest definitions and explanation visit the `EBI/ENA Missing value reporting <http://www.ebi.ac.uk/ena/about/missing-values-reporting>`__.
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.. warning::
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Column names in your information files cannot be named as a Postgres reserved word. For example, a column cannot be named
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`CONDITION`, but could instead be named `DISEASE_CONDITION`. For a full list of these reserved words, see this
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`link <https://www.postgresql.org/docs/9.3/static/sql-keywords-appendix.html>`__.
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Sample information file
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~~~~~~~~~~~~~~~~~~~~~~~
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| | | characters are alphabetic ``[A-Za-z]``, numeric ``[0-9]``, and periods ``.``. |
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+-------------------+-----------------------------+-------------------------------------------------------------------------------+
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Required fields for EBI submission
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Required fields for EBI submission and to make a study public
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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In order to submit your data to EBI, please review :ref:`checklist-for-ebi-ena-submission`.
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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".
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Attaching the Sample Information to the Study
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---------------------------------------------
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| | | match the sample_name in the sample template. |
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+-------------------+-------------------------------+------------------------------------------------------------------------+
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Required fields for EBI submission
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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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".
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For all valid values for instrument_model per platform, view the values in the table below:
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| Platform | Valid instrument_model options |
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+=====================+==========================================================================================================+
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| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, |
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| | ``454 GS Junior`` or ``unspecified`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| ``Illumina`` | ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, |
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| | ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``, |
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| | ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``, |
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| | ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``, |
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| | ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or ``unspecified`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| ``Ion_Torrent`` | ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| ``PacBio_SMRT`` | ``PacBio RS``, ``PacBio RS II``, ``Sequel``, ``Sequel II`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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| ``Oxford_Nanopore`` | ``GridION`` |
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+---------------------+----------------------------------------------------------------------------------------------------------+
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Required fields for pre-processing target gene data
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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