Sample checklists

When submitting samples to ENA, there is a minimal amount of information that is required.  The information required, depends on the type of sample being described, with different communities having different requirements.  In these pages we describe those checklists that have been prepared in collaboration with these communities.

Micro B3

The Micro B3 checklist is a multi-disciplinary standard developed by the Micro B3 Consortium for description of marine microbial sampling. Content of the standard is grouped into six categories covering various aspects of marine microbial sampling.

Tara Oceans

The Tara Oceans sample description at the ENA consists of core set of sample attributes that uniquely characterise each sample and map to the Tara Oceans Sample Registry at the PANGAEA.

Influenza

The Influenza checklist is intended for reporting metadata of Influenza virus samples associated with genomic data. It is the first reporting standard developed by the COMPARE platform ((COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe). This minimum metadata standard supports submission of avian, human and mammalian surveillance data as well as serology and virus isolate information (where available).

MIxS

The MIxS is a unified standard developed by the Genomic Standards Consortium (GSC) for reporting of minimum information about any (x) nucleotide sequence. It consists of MIGS, MIMS and MIMARKS* standards and describes fifteen environments.

GMI:MDM

The MDM (minimal data for matching) is the reporting standard developed by the Global Microbial Identifier initiative (GMI) for submissions of genome-scale pathogen sequence data. The checklist includes minimal fields of information to be reported for such studies. The scope of this checklist is submissions relating to next generation sequencing platforms used in high-throughput genome-scale projects of pathogens in clinical, animal and environmental samples.

Virus Pathogen

The virus pathogen reporting standard checklist can be used for reporting metadata of virus pathogen samples associated with genomic data and supports submission of virus surveillance and outbreak data (such as Ebola) as well as serology and virus isolate information. This checklist was developed by the COMPARE platform ((COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe).

List of all currently available ENA sample checklists

Checklist name Checklist ID Checklist description
GSC MIxS packages (http://www.ebi.ac.uk/ena/submit/mixs-checklists)
GSC MIxS air ERC000012

The MIxS is a unified standard developed by the Genomic Standards Consortium (GSC) for reporting of minimum information about any (x) nucleotide sequence.

Currently, fifteen environments are described. By choosing an environmental package, a selection of fields can be made from relevant subsets of GSC terms.

 

GSC MIxS host associated ERC000013
GSC MIxS human associated ERC000014
GSC MIxS human gut ERC000015
GSC MIxS human oral ERC000016
GSC MIxS human skin ERC000017
GSC MIxS human vaginal ERC000018
GSC MIxS microbial mat biolfilm ERC000019
GSC MIxS plant associated ERC000020
GSC MIxS sediment ERC000021
GSC MIxS soil ERC000022
GSC MIxS wastewater sludge ERC000023
GSC MIxS water ERC000024
GSC MIxS miscellaneous natural or artificial environment ERC000025
GSC MIxS built environment ERC000031
Other Environmental Checklists
ENA sewage checklist ERC000036 Minimum information about sewage samples. A checklist for reporting of sewage surveillance samples associated with sequence data from metagenomic sequencing projects. This minimum metadata standard was developed by the COMPARE platform.
ENA UniEuk_EukBank Checklist ERC000040  Minimum information required for reporting samples associated with the UniEuk EukBank initiative. This checklist aims to capture contextual metadata associated with V4 18S SSU rRNA molecular data.
Micro B3 Sample description
(http://www.ebi.ac.uk/ena/submit/microb3-checklist)
 ENA Micro B3 ERC000027 Minimum information about a Micro B3 sample.
A checklist for reporting metadata of marine microbial samples associated with genomics data.
NOTE: Non-genomics data, i.e. oceanographic environmental data and morphology-based biodiversity data, should be submitted to the appropriate National Oceanographic Data Centre according to established reporting practices maintained by oceanographic community experts.
Major National Oceanographic Data Centres from countries bordering the North-East Atlantic, and its adjacent seas: the Mediterranean, the Black Sea, the Baltic, the North Sea and the Arctic are listed at http://www.seadatanet.org/Overview/Partners. For the Ocean Sampling Day campaign, non-genomics data shall be reported to the PANGAEA (http://www.pangaea.de/submit/)
Tara Oceans Sample description
(http://www.ebi.ac.uk/ena/submit/tara-oceans-checklist)
ENA Tara Oceans ERC000030

Minimum information about a Tara Oceans sample. A checklist for reporting metadata of oceanic plankton samples associated with genomics data from the Tara Oceans Expedition. This sample checklist is compliant to the Micro B3 reporting standard.

Other Marine Sample descriptions
ENA Shellfish Checklist ERC000038 Shellfish contextual information associated with molecular data. The checklist has been developed in collaboration with EMBRIC Project partners.
ENA Marine Microalgae Checklist ERC000043 Marine microalgae contextual information. The checklist has been developed in collaboration with EMBRIC Project partners and is suitable for reporting metadata related to environmental samples and those in culture collections.
Pathogen Sample description
ENA prokaryotic pathogen minimal sample checklist ERC000028 Minimum information required for a prokaryotic pathogen sample.
ENA Global Microbial Identifier reporting standard checklist ERC000029 Minimum Data for Matching (MDM). A checklist for reporting metadata of pathogen samples for the Global Microbial Identifier (GMI) reporting system. More about GMI can be found here http://www.g-m-i.org/
For more details also see: http://www.ebi.ac.uk/ena/submit/pathogen-surveillance
ENA Influenza virus reporting standard checklist ERC000032 Minimum information about an Influenza virus sample. A checklist for reporting metadata of Influenza virus samples associated with genomic data. This minimum metadata standard supports submission of avian, human and mammalian surveillance data as well as serology and viruse isolate information (where available).
ENA virus pathogen reporting standard checklist ERC000033 Minimum information about a virus pathogen. A checklist for reporting metadata of virus pathogen samples associated with genomic data. This minimum metadata standard was developed by the COMPARE platform for submission of virus surveillance and outbreak data (such as Ebola) as well as virus isolate information.
ENA parasite sample checklist ERC000039

Minimum information about parasite samples. A checklist for reporting metadata of parasite samples associated with molecular data. This standard was developed by the COMPARE platform and can be used for submission of sample metadata derived from protozoan parasites (e.g. Cryptosporidium) and also multicellular eukaryotic parasites (e.g. Platyhelminthes and Nematoda).

COMPARE-ECDC-EFSA pilot human-associated reporting standard ERC000044 A checklist for reporting metadata of human-associated pathogen samples for the COMPARE-ECDC-EFSA reporting system.
COMPARE-ECDC-EFSA pilot food-associated reporting standard ERC000045 A checklist for reporting metadata of food-borne pathogen samples for the COMPARE-ECDC-EFSA reporting system.
Other Sample descriptions
ENA Plant Sample Checklist ERC000037 ENA implementation of plant specimen contextual information associated with molecular data. The checklist has been developed in collaboration with the NCBI-GenBank and iPlant data resources under the umbrella of the Genomic Standards Consortium (GSC).
ENA Crop Plant sample enhanced annotation ERC000035 The ENA Crop sample enhanced checklist has been developed in collaboration with a number of EMBL-EBI teams to capture enriched annotation of published crop plant samples that lack sufficient reported metadata and are typically associated with systematic transcriptomic realignment-based analyses.
ENA default sample checklist ERC000011 Minimum information required for the sample.
This sample checklist follows the INSDC Feature Table convention.