Making data Public in Qiita and/or send data to EBI-ENA

Qiita allows users to deposit their study, sample, experiment and sequence data to the European Nucleotide Archive (ENA), which is the permanent data repository of the European Bioinformatics Institute (EBI). Submitting to this repository will provide you with a unique identifier for your study, which is generally a requirement for publications. Your study will be housed with all other Qiita submissions and so we require adherence to the MiXs standard. Note that this also applies for studies in sandbox state that will become private or public.

Warning

direct BIOM uploads cannot become private or public

Here you will find a document outlining these requirements, with examples, when possible.

Note that submissions are time consuming and need full collaboration from the user. Do not wait until the last minute to request help. In general, the best time to request a submission is when you are writing your paper. Remember that the 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.

Note

For convenience Qiita allows you to upload a QIIME mapping file to process your data. However, the QIIME mapping file, in general, does not have all the EBI/ENA fields. Thus, you will need to update your information files (sample or preparation) via the update option. To simplify this process, you can download the system generated files and add/modify these fields for each file.

EBI-ENA NULL values vocabulary

We support only the following values: not applicable, not collected, not provided, restricted access.

For the latest definitions and explanation visit the EBI/ENA Missing value 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.

Checklist

For each preparation that needs to be uploaded to EBI-ENA we will check:

  1. Data processing

  1. Only datasets where raw sequences are available and linked to the preparation can be submitted. Studies where the starting point is a BIOM table cannot be submitted, since EBI is a sequence archive

  2. The data is processed and the owner confirms the data is correct and followed our Processing recommendations.

  1. Verify the sample information

  1. Check that the sample information file complies with the current Qiita metadata format.

  2. 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 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

  7. elevation, latitude, longitude

  8. empo_1, empo_2, empo_3

    empo_1

    empo_2

    empo_3

    Examples

    Free-living

    Non-saline

    Water (non-saline)

    fresh water from lake, pond, or river (<5 psu)

    Free-living

    Non-saline

    Sediment (non-saline)

    sediment from lake, pond, or river (<5 psu)

    Free-living

    Non-saline

    Soil (non-saline)

    soil from forest, grassland, tundra, desert, etc.

    Free-living

    Non-saline

    Surface (non-saline)

    biofilm from wet (<5 psu) or dry surface, wood, dust, or microbial mat

    Free-living

    Non-saline

    Subsurface (non-saline)

    deep or subsurface environment

    Free-living

    Non-saline

    Aerosol (non-saline)

    aerosolized dust or liquid

    Free-living

    Saline

    Water (saline)

    salt water from ocean, sea, estuary, mangrove, or coral reef (>5 psu)

    Free-living

    Saline

    Sediment (saline)

    sediment from ocean, sea, estuary, mangrove, or beach (>5 psu)

    Free-living

    Saline

    Hypersaline (saline)

    water from hypersaline sample or brine (>50 psu)

    Free-living

    Saline

    Surface (saline)

    biofilm from wet or underwater surface or microbial mat (>5 psu)

    Free-living

    Saline

    Aerosol (saline)

    seaspray or other aerosolized saline material (>5 psu)

    Host-associated

    Animal-associated

    Animal distal gut

    feces, stool

    Host-associated

    Animal-associated

    Animal proximal gut

    digesta

    Host-associated

    Animal-associated

    Animal secretion

    gut intestine, gizzard, crop, lumen, or mucosa

    Host-associated

    Animal-associated

    Animal surface

    skin, sebum, mucus, slime

    Host-associated

    Animal-associated

    Animal corpus

    tissue of sponge, coral, gill, siphon, carcass, etc. or whole small animal

    Host-associated

    Fungus-associated

    Fungus corpus

    tissue of mushroom or other fungi

    Host-associated

    Fungus-associated

    Fungus surface

    biofilm of mushroom

    Host-associated

    Plant-associated

    Plant secretion

    pollen or sap

    Host-associated

    Plant-associated

    Plant surface

    leaf or kelp surface biofilm

    Host-associated

    Plant-associated

    Plant rhizosphere

    plant root system, may include some soil

    Host-associated

    Plant-associated

    Plant corpus

    tissue of leaf, stem, fruit, or algae

    Control

    Negative

    Sterile water blank

    sterile water blank used as negative control for extraction, PCR, and sequencing

    Control

    Positive

    Mock community

    known mixed community used as positive control

    Control

    Positive

    Single strain

    known single strain control culture

    Unknown

    Contradictory

    Unknown (contradictory)

    unknown sample type because other metadata is contradictory

    Unknown

    Missing

    Unknown (missing)

    unknown sample type because metadata is unavailable

  1. Extra minimal information for host associated studies:

  1. host_body_habitat, host_body_site, host_body_product

  2. host_scientific_name

  3. host_common_name

  4. host_taxid, full list

  5. host_age, host_age_units

  6. host_height, host_height_units

  7. host_weight, host_weight_units

  8. host_body_mass_index (human only)

  1. Double-check these fields:

  1. Check the date format, should be YYYY-MM-DD (hh:mm)

  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

  1. Verify the preparation information

  1. Check that the preparation information file complies with the current Qiita metadata format

  2. Check that the correct Investigation type is selected on the prep info page

  3. Check for fill down errors in library_construction_protocol and target_subfragment; these are common.

  4. Minimal columns:

  1. sample_name

  2. barcode

  3. primer (include linker in this field)

  4. platform

  5. experiment_design_description

  6. center_name

  7. center_project_name

  8. library_construction_protocol

  9. instrument_model

  10. sequencing_method

  1. Additional minimal columns, if possible:

  1. pcr_primers

  2. run_prefix

  3. run_center

  4. run_date

  5. target_gene

  6. target_subfragment

  1. EBI null values for use when data is not present:

  1. not applicable

  2. missing:

  1. not collected

  2. not provided

  3. restricted access