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Merge branch 'master' of github.com:biocore/qiita into dev
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antgonza committed Jul 23, 2024
2 parents d85218e + 440a322 commit c98cc7e
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Expand Up @@ -65,15 +65,15 @@ Remember, metadata is the most important part for an analysis, without it we onl

2. Verify the sample information

a. Check that the sample information file complies with `the current Qiita metadata format <https://qiita.ucsd.edu/static/doc/html/gettingstartedguide/index.html#sample-information-file>`__.
a. Check that the sample information file complies with `the current Qiita metadata format <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__.
b. Minimal information:

1. *sample_name*
2. *host_subject_id*
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 ENVO <http://ols.wordvis.com/>`__
6. *env_biome*, *env_feature*, *env_material*, *env_package*, for options `visit ENVO <https://www.ebi.ac.uk/ols4/index>`__
7. *elevation*, *latitude*, *longitude*
8. *physical_specimen_location*
9. *collection_date*
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d. Double-check these fields:

1. Check the date format, should be YYYY-MM-DD (hh:mm)
1. Check the date format, should be: "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY", "YYYY-MM-DDThh:mmZ", "YYYY-MM-DDThh:mm:ssZ", "YYYY-MM-DDThhZ", "YYYY-MM-DD", or "YYYY-MM"; and that we normally submit: "YYYY-MM-DD", or "YYYY-MM" or "YYYY".
2. Check null values
3. Check that the values in each field make sense, for example that sex is not a numerical gradient, or that ph does not contain “male” or “female” values

3. Verify the preparation information

a. Check that the preparation information file complies with `the current Qiita metadata format <https://qiita.ucsd.edu/static/doc/html/gettingstartedguide/index.html#id1>`__
a. Check that the preparation information file complies with `the current Qiita metadata format <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__
b. Check that the correct Investigation type is selected on the prep info page
c. Check for fill down errors in library_construction_protocol and target_subfragment; these are common.
d. Minimal columns:
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Expand Up @@ -80,7 +80,7 @@ Example files
~~~~~~~~~~~~~

You can download an example sample information file from
`here <ftp://ftp.microbio.me/pub/qiita/sample_prep_information_files_examples.tgz>`__.
`here <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__.


Sample information file
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