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

Note

The EBI-ENA submission returns two accessions - the primary starts with PRJ and the secondary with ERP; they can be used interchangeably. We suggest that you add at least one of them to your manuscript, together with the Qiita Study id. Please do not forget to cite Qiita (https://doi.org/10.1038/s41592-018-0141-9). This information should be sufficient for your manuscript but if you would like to add direct links to your data, once they are public, you can use the EBI-ENA: https://www.ebi.ac.uk/ena/browser/view/[accession] or the Qiita Study id: https://qiita.ucsd.edu/public/?study_id=[study-id]

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. If need help send an email to 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, 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

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

  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 ENVO

  7. elevation, latitude, longitude

  8. physical_specimen_location

  9. collection_date

  10. country

    Note

    The EBI-ENA submission requires to have a geographic location (country and/or sea) so during submission Qiita will automatically replace country to match that requirement.

  11. empo_1, empo_2, empo_3, empo_4, more info: Earth Microbiome Project Ontology (EMPO)

empo_1

empo_2

empo_3

empo_4

Examples

Control

Negative

Sterile water blank

Sterile water blank

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

Control

Positive

Mock community

Mock community

known mixed community used as positive control

Control

Positive

Single strain

Single strain

known single strain used as positive control

Free-living

Free-living (non-saline)

Aqueous (non-saline)

Aerosol (non-saline)

aerosolized dust or liquid

Free-living

Free-living (non-saline)

Aqueous (non-saline)

Surface (non-saline)

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

Free-living

Free-living (non-saline)

Aqueous (non-saline)

Water (non-saline)

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

Free-living

Free-living (non-saline)

Solid (non-saline)

Sediment (non-saline)

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

Free-living

Free-living (non-saline)

Solid (non-saline)

Soil (non-saline)

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

Free-living

Free-living (non-saline)

Solid (non-saline)

Subsurface (non-saline)

deep or subsurface environment

Free-living

Free-living (non-saline)

Solid (non-saline)

Surface (non-saline)

dust or biofilm from dry surface such as floors, keyboards, door handles, and filters

Free-living

Free-living (saline)

Aqueous (saline)

Aerosol (saline)

seaspray or other aerosolized saline material (>5 psu)

Free-living

Free-living (saline)

Aqueous (saline)

Hypersaline (saline)

water from hypersaline sample or brine (>50 psu)-

Free-living

Free-living (saline)

Aqueous (saline)

Surface (saline)

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

Free-living

Free-living (saline)

Aqueous (saline)

Water (saline)

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

Free-living

Free-living (saline)

Solid (saline)

Sediment (saline)

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

Free-living

Free-living (saline)

Solid (saline)

Soil (saline)

saline or hypersaline soil from forest, grassland, tundra, desert, etc.

Free-living

Free-living (saline)

Solid (saline)

Subsurface (saline)

deep or subsurface saline environment

Host-associated

Host-associated (non-saline)

Animal (non-saline)

Animal corpus (non-saline)

tissue, carcass, etc., or whole small terrestrial or freshwater animal

Host-associated

Host-associated (non-saline)

Animal (non-saline)

Animal distal gut (non-saline)

feces, stool from terrestrial or freshwater animal

Host-associated

Host-associated (non-saline)

Animal (non-saline)

Animal proximal gut (non-saline)

gut intestine, gizzard, crop, lumen, mucosa from terrestrial or freshwater animal

Host-associated

Host-associated (non-saline)

Animal (non-saline)

Animal secretion (non-saline)

saliva, breast milk, vaginal secretion from terrestrial or freshwater animal

Host-associated

Host-associated (non-saline)

Animal (non-saline)

Animal surface (non-saline)

skin, sebum, mucus, slime from terrestrial or freshwater animal

Host-associated

Host-associated (non-saline)

Fungus (non-saline)

Fungus corpus (non-saline)

tissue of fruiting body or thallus or other fungal structure; terrestrial or freshwater

Host-associated

Host-associated (non-saline)

Fungus (non-saline)

Fungus surface (non-saline)

biofilm of fruiting body or thallus or other fungal structure; terrestrial or freshwater

Host-associated

Host-associated (non-saline)

Plant (non-saline)

Plant detritus (non-saline)

root/holdfast, stem, leaf/blade/bulb, flower, fruit, seed, algal interior/tissue; terrestrial or freshwater

Host-associated

Host-associated (non-saline)

Plant (non-saline)

Plant rhizosphere (non-saline)

plant root system, may include some soil; terrestrial or freshwater

Host-associated

Host-associated (non-saline)

Plant (non-saline)

Plant secretion (non-saline)

pollen, sap; terrestrial or freshwater

Host-associated

Host-associated (non-saline)

Plant (non-saline)

Plant surface (non-saline)

root/holdfast, stem, leaf/blade/bulb, flower, fruit, seed, algal surface biofilm; terrestrial or freshwater

Host-associated

Host-associated (saline)

Animal (saline)

Animal corpus (saline)

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

Host-associated

Host-associated (saline)

Animal (saline)

Animal distal gut (saline)

feces, stool from marine animal

Host-associated

Host-associated (saline)

Animal (saline)

Animal proximal gut (saline)

gut intestine, gizzard, crop, lumen, mucosa from marine animal

Host-associated

Host-associated (saline)

Animal (saline)

Animal secretion (saline)

saliva, breast milk, vaginal secretion from marine animal

Host-associated

Host-associated (saline)

Animal (saline)

Animal surface (saline)

skin, sebum, mucus, slime from marine animal

Host-associated

Host-associated (saline)

Fungus (saline)

Fungus corpus (saline)

tissue of fruiting body or thallus or other fungal structure; marine

Host-associated

Host-associated (saline)

Fungus (saline)

Fungus surface (saline)

biofilm of fruiting body or thallus or other fungal structure; marine

Host-associated

Host-associated (saline)

Plant (saline)

Plant detritus (saline)

root/holdfast, stem, leaf/blade/bulb, flower, fruit, seed, algal interior/tissue; marine

Host-associated

Host-associated (saline)

Plant (saline)

Plant rhizosphere (saline)

plant root system, may include some soil; marine

Host-associated

Host-associated (saline)

Plant (saline)

Plant secretion (saline)

pollen, sap; marine

Host-associated

Host-associated (saline)

Plant (saline)

Plant surface (saline)

root/holdfast, stem, leaf/blade/bulb, flower, fruit, seed, algal surface biofilm; marine

not applicable

not applicable

not applicable

not applicable

information is inappropriate to report, can indicate that the standard itself fails to model or represent the information appropriately

missing

not collected

not collected

not collected

information of an expected format was not given because it has not been collected

missing

not provided

not provided

not provided

information of an expected format was not given, a value may be given at a later stage

missing

restricted access

restricted access

restricted access

information exists but can not be released openly because of privacy concerns

  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: “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

  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

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, 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, Sequel IIe, Revio, Onso

Oxford_Nanopore

GridION

  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