Manifest Checklists

An overview of each checklist is provided below. Some checklists are adapted from sample checklists and annotation checklists from European Nucleotide Archive (ENA).

The Manifests page provides a list of all available manifest templates supported by COPO.

Tip

To view the description of each checklist type on the Manifests page:

Identify the type in the Category column.
Click the dropdown menu in the Manifest/Checklist Type column. A popover will appear with a list of types.
Hover over the type to view its description in a popover.

Barcoding Manifest Checklists

Hint

To view the entire description of a checklist, collapse the description by clicking the button below.

ERT000020 - COI gene

For mitochondrial cytochrome oxidase subunit 1 genes.

ERT000002 - RNA Gene

For ribosomal RNA genes from prokaryotic, nuclear or organellar DNA. All rRNAs are considered partial.

Sample Manifest Checklists

COPO samples

Available COPO Sample Manifest Types
Checklist Identifier	Manifest/Checklist	Description	Current version
COPO_DWC	DwC sample checklist	Minimum information required for Darwin Core (DwC) samples	–
COPO_FAANG	FAANG sample checklist	Minimum information required for Functional Annotation of Animal Genomes (FAANG) sample	–

ENA samples

Refer to the European Nucleotide Archive (ENA) sample checklists for the full list of sample types accepted.

Available ENA Sample checklists
Checklist identifier	Manifest/Checklist	Description	Current version
ERC000011	ENA default sample checklist	Minimum information required for the sample	–
ERC000012	GSC MIxS air	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000013	GSC MIxS host associated	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000014	GSC MIxS human associated	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000015	GSC MIxS human gut	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000016	GSC MIxS human oral	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000017	GSC MIxS human skin	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000018	GSC MIxS human vaginal	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000019	GSC MIxS microbial mat biolfilm	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000020	GSC MIxS plant associated	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000021	GSC MIxS sediment	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000022	GSC MIxS soil	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000023	GSC MIxS wastewater sludge	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000024	GSC MIxS water	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000025	GSC MIxS miscellaneous natural or artificial environment	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000026	EGA default checklist	The minimum sample requirements for EGA	–
ERC000027	ENA Micro B3	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/).	–
ERC000028	ENA prokaryotic pathogen minimal sample checklist	Minimum information required for a prokaryotic pathogen sample	–
ERC000029	ENA Global Microbial Identifier reporting standard checklist GMI_MDM:1.1	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/	–
ERC000030	ENA Tara Oceans	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.	–
ERC000031	GSC MIxS built environment	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000032	ENA Influenza virus reporting standard checklist	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). The ENA Influenza sample checklist is based on standards in use at the Influenza Research Database.	–
ERC000033	ENA virus pathogen reporting standard checklist	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.	–
ERC000034	ENA mutagenesis by carcinogen treatment checklist	Minimum Information required for reporting samples associated with genomic data, derived from carcinogen induced animal tumours. This minimum metadata standard was developed in collaboration with Duncan Odom lab for the Mouse Liver Cancer Evolution Project.	–
ERC000035	ENA Crop Plant sample enhanced annotation checklist	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.	–
ERC000036	ENA sewage checklist	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.	–
ERC000037	ENA Plant Sample Checklist	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.	–
ERC000038	ENA Shellfish Checklist	Shellfish contextual information associated with molecular data. The checklist has been developed in collaboration with EMBRIC Project partners.	–
ERC000039	ENA parasite sample checklist	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).	–
ERC000040	ENA UniEuk_EukBank Checklist	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.	–
ERC000041	ENA Global Microbial Identifier Proficiency Test (GMI PT) checklist	Minimum information to standardise metadata related to samples used in GMI PT (Global Microbial Identifier Proficiency Test). A checklist for reporting metadata of GMI PT samples associated with molecular data. This minimum metadata standard was developed by the COMPARE platform and can be used for submission of sample metadata derived from Campylobacter coli, Campylobacter jejuni, Listeria monocytogenes, Klebsiella pneumoniae, Salmonella enterica, Escherichia coli and Staphylococcus aureus.	–
ERC000042	ENA RNA-Seq Checklist	Minimum information to standardise metadata related to samples used in RNA seq experiments. Useful for downstream services to select RNA-Seq read data for appropriate alignment processing and display. Also useful for external users to select RNA-Seq read files, their alignments and structured metadata describing the source material.	–
ERC000043	ENA Marine Microalgae Checklist	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.	–
ERC000044	COMPARE-ECDC-EFSA pilot human-associated reporting standard	A checklist for reporting metadata of human-associated pathogen samples for the COMPARE-ECDC-EFSA reporting system.	–
ERC000045	COMPARE-ECDC-EFSA pilot food-associated reporting standard	A checklist for reporting metadata of food-borne pathogen samples for the COMPARE-ECDC-EFSA reporting system.	–
ERC000046	Pan Prostate sample checklist	Minimal Information required for reporting samples associated with molecular data into the Pan Prostate Cancer Project (http://panprostate.org/).	–
ERC000047	GSC MIMAGS	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000048	GSC MISAGS	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000049	GSC MIUVIGS	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000050	ENA binned metagenome	Minimum information to standardise metadata of binned metagenome samples. Ensures binned and MAG metagenome assembly metadata is compatible.	–
ERC000051	PDX Checklist	Minimum information required for reporting samples associated with patient-derived xenograft (PDX) models or patient samples	–
ERC000052	HoloFood Checklist	Minimum information required for reporting HoloFood samples. HoloFood is a	–
ERC000053	Tree of Life Checklist	Minimum information required for reporting samples associated with the Tree of Life Programme (https://www.sanger.ac.uk/programme/tree-of-life/).	–
ERC000055	GSC MIxS agriculture	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000056	GSC MIxS Food and Production	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms. This package is a combination of the four food extensions (MIxS-food-animal and animal feed, MIxS-food-farm environment, MIxS-food-food production facility, MIxS-food-human foods).	–
ERC000057	GSC MIxS Symbiont	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–
ERC000058	GSC MIxS Hydrocarbon	Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from relevant subsets of the GSC terms.	–

Image Manifest Checklists

Sample images

Sample images are based on samples submitted under the Tree of Life (ToL) [1] programme. They relate to the following ToL projects:

Aquatic Symbiosis Genomics (ASG) [2]
Darwin Tree of Life (DToL) [3]
Darwin Tree of Life Environmental (DToL_ENV)
European Reference Genome Atlas (ERGA) [4]

Refer to Uploading Sample Images for more information.

Image metadata

Available image manifest types
Checklist identifier	Manifest/Checklist	Description	Current version
version_rembi	REMBI images	REcommended Metadata for Biological Images (REMBI) provides a way to explain how images have been generated, providing enough context to allow others to interpret them without reference to external sources.	–
version_dwc_stx_fish	Darwin Core metadata	Spatial transcriptomics using Fluorescence In Situ Hybridisation (FISH), adhering to Darwin Core (DwC) standards for describing biodiversity related features.	–
version_mixs_stx_fish	Minimum Information about any Sequence metadata	Spatial transcriptomics using Fluorescence In Situ Hybridisation (FISH), Minimum Information about any (x) Sequence (MIxS) standard for contextual data about sequencing and sampling.	–
version_tol_stx_fish	Tree of Life metadata	Spatial transcriptomics via Fluorescence In Situ Hybridisation (FISH), with metadata based on the Tree of Life (ToL) initiative’s goals to explore the origins and diversity of life through advanced genomic technologies.	–

Footnotes