A searchable and exportable tab-separated table of the following metadata is now available.
| metadata | definition | reference of definition[<url_to_definition>] | expected unit of measurement | examples | source |
|---|---|---|---|---|---|
| sample_name | Identifier of the sample | MIXS:0001107 | String | e.g. ISDsoil1 | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| seq_meth | Sequencing method used | MIXS:0000050 | OBI ID from the list of DNA sequencers | 454 Genome Sequencer FLX [OBI:0000702] | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”), ENA Metadata Validation: Instrument (“ENA Metadata Validation: Instrument”) |
| lib_layout | Specify whether to expect single, paired, or other configuration of reads | MIXS:0000041 | String | e.g. single-end, paired end or others | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| lib_source | The lib_source specifies the type of source material that is being sequenced | lib_source permitted values | Free text from selected list of values | e.g. GENOMIC, METAGENOMIC, TRANSCRIPTOMIC, etc. | ENA Metadata Validation: Source (“ENA Metadata Validation: Source”) |
| lib_strategy | Sequencing technique intended for this library | lib_strategy permitted values | Free text from selected list of values | e.g. WGS, Amplicon, etc. | ENA Metadata Validation: Strategy (“ENA Metadata Validation: Strategy”) |
| lib_selection | Whether any method was used to select and/or enrich the material being sequenced | lib_selection permitted values | Free text from selected list of values | e.g. RANDOM, PCR, cDNA_oligo_dT etc. | ENA Metadata Validation: Selection (“ENA Metadata Validation: Selection”) |
| sequence_count | Number of reads in the library (sequencing depth) or ‘spots’ | Defined by SRA | Integer | e.g. 32,283,453 | Adapted from NCBI-SRA (Leinonen et al. 2011) |
| basepairs_count | Number of base pairs (nucleotides) in the library or ‘bases’ | Defined by SRA | Integer | e.g. 6,400,000,000 | Adapted from NCBI-SRA (Leinonen et al. 2011) |
| average_length (optional) | basepairs_count divided by sequence_count | As defined here | Integer | e.g. 198 | Calculated as basepairs_count/sequence_count |
| sequence_q30 (optional) | Percentage of reads in the library (sequencing depth) with quality above 30 | Link to resource to calculate | Integer from 0-100 | e.g. 85 | SRA-Tinder (NCBI Hackathons) |
| basepairs_q30 (optional) | Percentage of base pairs (nucleotides) in the library with quality above 30 | Link to resource to calculate | Integer from 0-100 | e.g. 80 | SRA-Tinder (NCBI Hackathons) |
| target_gene | Targeted gene name for marker gene studies | MIXS:0000044 | String | e.g. 16S rRNA, ITS | GSC MIXS: MIMARKSSpecimen (“GSC MIXS: MIMARKSSpecimen”) |
| target_subfragment | Name of the targeted subregion | MIXS:0000045 | String | e.g. V3-V4, ITS1 | GSC MIXS: MIMARKSSpecimen (“GSC MIXS: MIMARKSSpecimen”) |
| pcr_primers | Forward and reverse primer sequences used | MIXS:0000046 | Uppercase string | e.g. FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT | GSC MIXS: MIMARKSSpecimen (“GSC MIXS: MIMARKSSpecimen”) |
| checksum | Hash value for data file integrity. This should include the name of the method used (SHA-1, SHA-256, MD5) | Checksum Verification | String following the standandards from the selected checksum method | e.g. MD5: cbc41d0e49636872a765b950cb7f410a | Data transfer and data integrity |
The publications describing the reasons for formation of The minimum information about a genome sequence (MIGS) (Field et al. 2008) and Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications (Yilmaz et al. 2011) can be found online.
“ENA Metadata Validation: Instrument.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#instrument.
“ENA Metadata Validation: Selection.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#selection.
“ENA Metadata Validation: Source.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#source.
“ENA Metadata Validation: Strategy.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#strategy.
Field, D., G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, et al. 2008. “The Minimum Information about a Genome Sequence (MIGS) Specification.” Nature Biotechnology. 2008. https://doi.org/10.1038/nbt1360.
“GSC MIXS: MIGSBacteria.” https://genomicsstandardsconsortium.github.io/mixs/MIGSBacteria/.
“GSC MIXS: MIMARKSSpecimen.” https://genomicsstandardsconsortium.github.io/mixs/MIMARKSSpecimen/.
Leinonen, R., H. Sugawara, M. Shumway, and International Nucleotide Sequence Database Collaboration. 2011. “The Sequence Read Archive.” Nucleic Acids Research 39 (Database issue): D19–21. https://doi.org/10.1093/nar/gkq1019.
NCBI Hackathons. “SRA-Tinder: A Tool to Discover Related Sequence Read Archive (SRA) Experiments.” https://github.com/NCBI-Hackathons/SRA_Tinder.
Yilmaz, Pelin et al. 2011. “Minimum Information about a Marker Gene Sequence (MIMARKS) and Minimum Information about Any (x) Sequence (MIxS) Specifications.” Nature Biotechnology 29 (5): 415–20. https://doi.org/10.1038/nbt.1823.
“Ontobee: DNA Sequencer Ontology.” http://purl.obolibrary.org/obo/OBI_0400103.