The Sequence EMO-BON Ontology

A sequencing run activity

• Activity ^c
• obi:0000070

• associated batch ^op
• relevant standard operating procedures for the sequencing work ^op
• relevant electronic resources for the sequencing work ^dp
• correspoding prokaryotes mock community sequencing reads filename ^op
• correspoding eukaryotes mock community sequencing reads filename ^op
• sequencing reads filename ^op
• has ENA run accession number ^dp
• dna concentration after extraction ^op
• dna quantity after extraction ^op
• pcr conditions ^dp
• pcr primers ^dp
• library layout ^dp
• target gene ^dp
• target gene ^dp
• target subfragment ^dp
• nucleic acid extraction ^dp
• nucleic acid amplification ^dp
• library reads sequenced ^dp
• sequencing method ^dp
• sequence quality check ^dp
• adapters ^dp
• multiplex identifiers ^dp

A batch in a sequencing run

• associated sample ^op
• batch processing ready ^dp
• batch production deployment ^dp
• batch sender ^dp
• batch receiver ^dp
• batch number ^dp
• batch status ^dp
• shipping date ^dp
• arrival date ^dp

A sequencing-reads file

• correspoding prokaryotes mock community sequencing reads filename ^op
• correspoding eukaryotes mock community sequencing reads filename ^op
• sequencing reads filename ^op

The batch associated with as sequencing run

The sample associated with a batch

• sosa:Sample
• Entity ^c

Standard operating procedures used in the sequencing molecular work

Filename given by the sequencing centre to the sequencing reads produced by the prokaryote mock community included in the same sequencing run as the sample

• A sequencing-reads file ^c
• schema:CreativeWork

Filename given by the sequencing centre to the sequencing reads produced by the eukaryote mock community included in the same sequencing run as the sample

• A sequencing-reads file ^c
• schema:CreativeWork

Filename given by the sequencing centre to the sequencing reads produced

• A sequencing-reads file ^c
• schema:CreativeWork

DNA concentration measured, using a specified DNA concentration measurement method, after DNA extraction

Total DNA quantity calculated from the DNA concentration measured after extraction

• sosa:Result
• qudt:QuantityValue

Indication whether batch is processing ready

Indication whether batch is ready for production deployment

The sender of a batch

The receiver of a batch

The batch number

The status of the batch

The date when the batch was shipped

The date when the batch arrived

Relevant electronic resources for the sequencing molecular work. Resources may be provided for any of the steps/methods followed

• xsd:string
• xsd:anyURI

ENA run accession number associated to the sequencing run.

Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'. If the sample is used for metagenomics add 'metag'

PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters. If the sample is used for metagenomics add 'metag'

Specify whether to expect single, paired, or other configuration of reads

Analysis workflow followed

Targeted gene or locus name for marker gene studies (e.g. for metabarcoding). If the sample is used for metagenomics add 'metag'

Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA. If the sample is used for metagenomics add 'metag'

A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample

A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids. If the sample is used for metagenomics add 'metag'

Total number of clones sequenced from the library

Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid

Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA

Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters

Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters