ERC000053

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/).

Study

A Study is a container for a sequencing investigation that may comprise multiple experiments. The Study has an overall goal, but is otherwise minimally defined in the SRA. A Study is composed of a descriptor, zero or more experiments, and zero or more analyses. The submitter may decorate the Study with web links and properties.

Field name	Cardinality	Description	Controlled vocabulary
alias	mandatory	Unique identificator for a study. this is used to link experiments to the study.
title	mandatory	Title of the study as would be used in a publication.
study_type	mandatory	The study_type presents a controlled vocabulary for expressing the overall purpose of the study.	Whole Genome Sequencing, Metagenomics, Transcriptome Analysis, Resequencing, Epigenetics, Synthetic Genomics, Forensic or Paleo-genomics, Gene Regulation Study, Cancer Genomics, Population Genomics, RNASeq, Exome Sequencing, Pooled Clone Sequencing, Transcriptome Sequencing, Other
new_study_type	optional	Optional if 'study_type' is not 'other'. to propose a new term, select other and enter a new study type.
study_abstract	optional	Briefly describes the goals, purpose, and scope of the study. this need not be listed if it can be inherited from a referenced publication.

Experiment

An experiment object serves as a metadata record encapsulating essential details about a sequencing experiment, including the experimental design, sequencing type, and relevant parameters. This information enhances the interpretation and contextual understanding of nucleotide sequences submitted to the archive.

Field name	Cardinality	Description	Controlled vocabulary
alias	mandatory	Unique identificator for each experiment. this is used to link runs to experiments.
title	mandatory	Short text that can be used to call out experiment records in searches or in displays. this element is technically optional but should be used for all new records.
study_alias	mandatory	Identifies the parent study. (from study metadata)
sample_alias	mandatory	(from sample metadata)
design_description	mandatory	Goal and setup of the individual library including library was constructed.
library_name	optional	The submitter's name for this library.
library_strategy	mandatory	Sequencing technique intended for this library.	WGS, WGA, WXS, RNA-Seq, ssRNA-seq, snRNA-seq, miRNA-Seq, ncRNA-Seq, FL-cDNA, EST, Hi-C, ATAC-seq, WCS, RAD-Seq, CLONE, POOLCLONE, AMPLICON, CLONEEND, FINISHING, ChIP-Seq, MNase-Seq, DNase-Hypersensitivity, Bisulfite-Seq, CTS, MRE-Seq, MeDIP-Seq, MBD-Seq, Tn-Seq, VALIDATION, FAIRE-seq, SELEX, RIP-Seq, ChIA-PET, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, NOMe-Seq, ChM-Seq, GBS, Ribo-Seq, OTHER
library_source	mandatory	The library_source specifies the type of source material that is being sequenced.	GENOMIC, GENOMIC SINGLE CELL, TRANSCRIPTOMIC, TRANSCRIPTOMIC SINGLE CELL, METAGENOMIC, METATRANSCRIPTOMIC, SYNTHETIC, VIRAL RNA, OTHER
library_selection	mandatory	Method used to enrich the target in the sequence library preparation	RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, repeat fractionation, size fractionation, MSLL, cDNA, cDNA_randomPriming, cDNA_oligo_dT, PolyA, Oligo-dT, Inverse rRNA, Inverse rRNA selection, ChIP, ChIP-Seq, MNase, DNase, Hybrid Selection, Reduced Representation, Restriction Digest, 5-methylcytidine antibody, MBD2 protein methyl-CpG binding domain, CAGE, RACE, MDA, padlock probes capture method, other, unspecified
library_layout	mandatory	Library_layout specifies whether to expect single, paired, or other configuration of reads. in the case of paired reads, information about the relative distance and orientation is specified.
insert_size	optional	Insert size for paired reads
library_construction_protocol	optional	Free form text describing the protocol by which the sequencing library was constructed.
platform	mandatory	The platform record selects which sequencing platform and platform-specific runtime parameters. this will be determined by the center. optional if 'instrument_model' is provided.	LS454, ILLUMINA, HELICOS, ABI_SOLID, COMPLETE_GENOMICS, BGISEQ, OXFORD_NANOPORE, PACBIO_SMRT, ION_TORRENT, CAPILLARY, DNBSEQ, ELEMENT, ULTIMA, VELA_DIAGNOSTICS, GENAPSYS, GENEMIND, TAPESTRI
instrument_model	mandatory	Model of the sequencing instrument.	454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX Titanium, 454 GS FLX+, 454 GS Junior, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, AB 5500 Genetic Analyzer, AB 5500xl Genetic Analyzer, AB 5500xl-W Genetic Analysis System, AB SOLiD 3 Plus System, AB SOLiD 4 System, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, BGISEQ-50, BGISEQ-500, Complete Genomics, DNBSEQ-G400, DNBSEQ-G400 FAST, DNBSEQ-G50, DNBSEQ-T7, Element AVITI, FASTASeq 300, GENIUS, GS111, Genapsys Sequencer, GenoCare 1600, GenoLab M, GridION, Helicos HeliScope, 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 HiSeq X, Illumina MiSeq, Illumina MiniSeq, Illumina NovaSeq 6000, Illumina NovaSeq X, Illumina iSeq 100, Ion GeneStudio S5, Ion GeneStudio S5 Plus, Ion GeneStudio S5 Prime, Ion Torrent Genexus, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, Ion Torrent S5 XL, MGISEQ-2000RS, MinION, NextSeq 1000, NextSeq 2000, NextSeq 500, NextSeq 550, Onso, PacBio RS, PacBio RS II, PromethION, Revio, Sentosa SQ301, Sequel, Sequel II, Sequel IIe, Tapestri, UG 100, unspecified

Run

A run contains a group of reads generated for a particular experiment.

Field name	Cardinality	Description	Controlled vocabulary
alias	mandatory	Unique identificator for each run.
experiment_alias	mandatory	From_experiment_metadata
file_name	mandatory	The name or relative pathname of a run data file.
file_format	mandatory	The run data file model.	sra, srf, sff, fastq, fasta, tab, 454_native, 454_native_seq, 454_native_qual, Helicos_native, Illumina_native, Illumina_native_seq, Illumina_native_prb, Illumina_native_int, Illumina_native_qseq, Illumina_native_scarf, SOLiD_native, SOLiD_native_csfasta, SOLiD_native_qual, PacBio_HDF5, bam, cram, CompleteGenomics_native, OxfordNanopore_native

Sample

A Sample defines an isolate of sequenceable material upon which sequencing experiments can be based. The Sample object may be a surrogate for taxonomy accession or an anonymized individual identifier. Or, it may fully specify provenance and isolation method of the starting material.

Field name	Cardinality	Description	Controlled vocabulary
alias	mandatory	Unique identificator for each sample.
title	mandatory	Short text that can be used to call out sample records in search results or in displays.
taxon_id	mandatory	Ncbi taxonomy identifier. this is appropriate for individual organisms and some environmental samples.
sample_description	optional	Free-form text describing the sample, its origin, and its method of isolation.
Latitude Start	optional	Latitude of the location where the sampling event started, e.g. each ctd cast, net tow, or bucket collection is a distinct event. format: ##.####, decimal degrees; north= +, south= -; use wgs 84 for gps data. example: -24.6666. (Units: DD)
Longitude Start	optional	Longitude of the location where the sampling event started, e.g. each ctd cast, net tow, or bucket collection is a distinct event. format: ###.####, decimal degrees; east= +, west= -; use wgs 84 for gps data. example: -096.1012. (Units: DD)
Latitude End	optional	Latitude of the location where the sampling event ended, e.g. each ctd cast, net tow, or bucket collection is a distinct event. format: ##.####, decimal degrees; north= +, south= -; use wgs 84 for gps data. example: -24.6643. (Units: DD)
Longitude End	optional	Longitude of the location where the sampling event ended, e.g. each ctd cast, net tow, or bucket collection is a distinct event. format: ###.####, decimal degrees; east= +, west= -; use wgs 84 for gps data. example: -096.1171. (Units: DD)
organism part	mandatory	The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells.
lifestage	mandatory	The age class or life stage of the organism at the time of collection.	adult, egg, embryo, gametophyte, juvenile, larva, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, pupa, spore-bearing structure, sporophyte, vegetative cell, vegetative structure, zygote
relationship	optional	Indicates if the specimen has a known relationship to another specimen (e.g. parental, child, sibling or other kind of relationship)
sample symbiont of	optional	Reference to host sample from symbiont. the referenced sample should already be registered in insdc. e.g. ersxxxxxx
symbiont	optional	Used to separate host and symbiont metadata within a symbiont system where the host species are indicated as 'n' and symbionts are indicated as 'y'	N, Y
sample collection method	optional	The method employed for collecting the sample. can be provided in the form of a pmid, doi, url or text.
sample coordinator affiliation	optional	The university, institution, or society affiliation of the sample coordinator.
sample same as	optional	Reference to sample(s) that are equivalent. the referenced sample(s) should already be registered in insdc. this should be formatted as one of the following. a single sample e.g. ersxxxxxx or a comma separated list e.g. ersxxxxxx,ersxxxxxx
sample derived from	optional	Reference to parental sample(s) or original run(s) that the assembly is derived from. the referenced samples or runs should already be registered in insdc. this should be formatted as one of the following. a single sample/run e.g. ersxxxxxx or a comma separated list e.g. ersxxxxxx,ersxxxxxx or a range e.g. ersxxxxxx-ersxxxxxx
project name	mandatory	Name of the project within which the sequencing was organized
barcoding center	optional	Center where dna barcoding was/will be performed.
tolid	optional	A tolid (tree of life id) is a unique and easy to communicate sample identifier that provides species recognition, differentiates between specimen of the same species and adds taxonomic context. tolids are issued by id.tol.sanger.ac.uk. they are endorsed by the earthbiogenome project (ebp) and should be assigned to any sample with association to the ebp.
collected_by	mandatory	Name of persons or institute who collected the specimen
collection date	mandatory	The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008.
geographic location (latitude)	recommended	The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD)
geographic location (longitude)	recommended	The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD)
geographic location (region and locality)	mandatory	The geographical origin of the sample as defined by the specific region name followed by the locality name.
identified_by	optional	Name of the expert who identified the specimen taxonomically
elevation	optional	The elevation of the sampling site as measured by the vertical distance from mean sea level. (Units: m)
habitat	mandatory	Description of the location of the sample material. please use envo terms where possible: https://www.ebi.ac.uk/ols/ontologies/envo
identifier_affiliation	optional	The university, institution, or society responsible for identifying the specimen.
original collection date	optional	For use if the specimen is from a zoo, botanic garden, culture collection etc. and has a known original date of collection. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008.
original geographic location	optional	For use if the specimen is from a zoo, botanic garden or culture collection etc. and has a known origin elsewhere. please record the general description of the original collection location. this should be formatted as a country and optionally include more specific locations ranging from least to most specific separated by a	character, e.g. “united kingdom
original geographic location (latitude)	optional	For use if the specimen is from a zoo, botanic garden or culture collection etc. and has a known origin elsewhere. please record the geographic location where the specimen or sample was originally taken as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD)
original geographic location (longitude)	optional	For use if the specimen is from a zoo, botanic garden or culture collection etc. and has a known origin elsewhere. please record the geographic location where the specimen or sample was originally taken as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD)
sample coordinator	optional	The name of the sample coordinator.
sex	mandatory	Sex of the organism from which the sample was obtained
geographic location (country and/or sea)	mandatory	The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html).	Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access
collecting institution	mandatory	Name of the institution to which the person collecting the specimen belongs. format: institute name, institute address
GAL	optional	The name (or acronym) of the genome acquisition lab responsible for the sample.	Biology Centre of the Academy of Sciences of the Czech Republic, Centro Nacional de Análisis Genómico, DNA Sequencing and Genomics Laboratory, Helsinki Genomics Core Facility, Dalhousie University, Dresden-concept, Earlham Institute, Functional Genomics Center Zurich, GIGA-Genomics Core Facility, University of Liege, Genoscope, Geomar Helmholtz Centre, Grigore Antipa National Museum of Natural History, Hansen Lab, Denmark, Institut de Biologia Evolutiva, CSIC-UPF, Lausanne Genomic Technologies Facility, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Lund University, Marine Biological Association, NGS Bern, NGS Competence Center Tübingen, Natural History Museum, Neuromics Support Facility, UAntwerp, VIB, Norwegian Sequencing Centre, Nova Southeastern University, Portland State University, Queen Mary University of London, Royal Botanic Garden Edinburgh, Royal Botanic Gardens Kew, Sanger Institute, SciLifeLab, Senckenberg Research Institute, Svardal Lab, Antwerp, The Sainsbury Laboratory, University of Bari, University of British Columbia, University of California, University of Cambridge, University of Derby, University of Edinburgh, University of Florence, University of Neuchatel, University of Oregon, University of Oulu, University of Oxford, University of Rhode Island, University of Vienna (Cephalopod), University of Vienna (Mollusc), West German Genome Centre, industry partner, other ERGA associated GAL
specimen_id	optional	Unique identifier used to link all data for the recorded specimen.
GAL_sample_id	optional	Unique name assigned to the sample by the genome acquisition lab.
proxy voucher	optional	For use if voucher material needs to be made from a specimen that is different than the one submitted for sequencing. please record the unique identifier that references the physical specimen and that ideally exists in a curated collection. the id should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). please note institution codes and collection codes are taken from a controlled vocabulary maintained by the insdc: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/
proxy biomaterial	optional	For use if voucher material needs to be made from a material that is different from the one submitted for sequencing. please record the unique identifier that references the biomaterial and that ideally exists in a curated collection (e.g. stock centres, seed banks, dna banks). the id should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the material id (institution_code:collection_code:material_id). please note institution codes and collection codes are taken from a controlled vocabulary maintained by the insdc: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/
bio_material	optional	Unique identifier that references the biological material from which the sample was obtained and that ideally exists in a curated collection (e.g. stock centres, seed banks, dna banks). the id should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). please note institution codes and collection codes are taken from a controlled vocabulary maintained by the insdc: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/
specimen_voucher	recommended	Unique identifier that references the physical specimen that remains after the sequence has been obtained and that ideally exists in a curated collection. the id should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). please note institution codes and collection codes are taken from a controlled vocabulary maintained by the insdc: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/
culture_or_strain_id	optional	Living, culturable, named laboratory strain that sequenced material is derived from.
depth	optional	The vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. depth can be reported as an interval for subsurface samples. (Units: mm)