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.
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.
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.
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).
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.
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.
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
|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
|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.