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GSCID/BRC Project and Sample Application Standard: Sequencing Assay

v1.3
Finalized by the GSCID/BRC Metadata Working Group


How to interpret the document:
BOLD: Field Name
ITALICS: Attributes of the field

1. Sample ID - Sequencing Facility
Sequencing Assay Field ID: SA1
Description: Unique identifier used by the relevant sequencing center to identify the sample submitted by the sample provider.
Data Categories: Sample Shipment
Allowed Values: Free text
Syntax: Alphanumeric
Example Values: V506
Data Source: GSCID
Comments: This is a candidate for the key ID that would be embedded in the GenBank record as a dbxref for linkage of BRC metadata records with GenBank sequences. Required field.
OBO Foundry Synonym: specimen identifier assigned by sequencing facility
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001901
OBI Definition: A specimen identifier which is assigned by a sequencing facility
Other Synonyms: GenBank Structured Comment: SRA*

2. Nucleic Acid Extraction Method
Sequencing Assay Field ID: SA2
Description: Experimental procedure used to derive the nucleic acid fraction from the submitted sample used for the sequencing reaction.
Data Categories: Sequencing Sample Preparation
Allowed Values: OBI, http://bioportal.bioontology.org/ontologies/40832
Syntax: free text
Example Values: Illumina suggested standard method; CTAB/phenol/chloroform
Data Source: Sample Provider or GSCID
Comments: Required field with ‘not applicable’ as an allowed value
OBO Foundry Synonym: nucleic acid extraction
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0666667
OBI Definition: a protocol is a plan specification that has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
Other Synonyms: MIxS: sample material processing; GenBank structured comment: SRA*; nucleic acid preparation; extraction method

3. Nucleic Acid Preparation Method
Sequencing Assay Field ID: SA3
Description: Details about the preparation of DNA samples for sequencing including if amplification was used (e.g., in the case of sequencing a single mosquito), and any other relevant molecular biology protocols done prior to sequencing.
Data Categories: Sequencing Sample Preparation
Allowed Values: Free text
Syntax: Free text
Example Values: Standard 454 LC
Data Source: GSCID
Comments: Required field with ‘not applicable’ as an allowed value
OBO Foundry Synonym: sample preparation for sequencing assay
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001902
OBI Definition: a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
Other Synonyms: MIxS:sample material processing; GenBank structured comment: SRA*; Nucleic acid preparation by GSC; including amplification procedure

4. Sequencing Technology
Sequencing Assay Field ID: SA4
Description: The sequencing technology type(s) used to obtain the sequences
Data Categories: Sequencing Assay
Allowed Values: OBI, http://bioportal.bioontology.org/ontologies/40832
Syntax: Free text
Example Values: 454; Illumina
Data Source: GSCID
Comments: Required field
OBO Foundry Synonym: sequencing assay
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0600047
OBI Definition: a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
Other Synonyms: MIxS: sequencing method

5. Assembly Name
Sequencing Assay Field ID: SA5
Description: a unique, short name suitable for display
Data Categories: Data Transformation
Allowed Values: Free text
Syntax: Free text
Example Values: Plas_yoel_17X_V2 for Plasmodium yoellii 17X assembly version 2
Data Source: GSCID
Comments: Newly-proposed GenBank Structured Comment Field ID; Required field with ‘not applicable’ as an allowed value; ‘sequence assembly' has been submitted to OBI
OBO Foundry Synonym: sequence assembly name
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001948
OBI Definition: A textual entity that is used to denote a sequence assembly.
Other Synonyms:

6. Assembly Method
Sequencing Assay Field ID: SA6
Description: Computational algorithm used to assemble individual sequence reads into larger contigs. Assembly details including but not limited to assembler type (overlap-layout-consensus, deBrujn), assembler version, any relevant QC information such as % known genes/ESTs captured.
Data Categories: Data Transformation
Allowed Values: pick list
Syntax: free text
Example Values: Illumina GA pipeline ver1.3; Newbler MapAsmResearch-03/15/2010 -vs C_elegans -e 45; No assembly. Reads mapped to reference genome withTopHat; Newbler de novo hibrid assembly/CLC reference mapping of 454 reads; AV454 v1.0
Data Source: GSCID
Comments: Required field with ‘not applicable’ as an allowed value
OBO Foundry Synonym: sequence assembly algorithm
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001522
OBI Definition: A plan specification that describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
Other Synonyms: MIxS: assembly

7. Genome Coverage
Sequencing Assay Field ID: SA7
Description: Depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
Data Categories: Data Transformation
Allowed Values: Free text
Syntax: Free text
Example Values: 45X average
Data Source: GSCID
Comments: Required field that is generally not available until genome submitted. 'not applicable' is an allowed value.
OBO Foundry Synonym: average depth of sequence coverage
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001618
OBI Definition: An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size.
Other Synonyms: MIxS:finishing strategy

8. Annotation Provider
Sequencing Assay Field ID: SA8
Description: The name of the responsible person, group or institution providing the set of annotated features for a genome sequences that is submitted to a resource such as GenBank.
Data Categories: Data Transformation
Allowed Values: Free text
Syntax: Free text
Example Values: Broad Institute
Data Source: GSCID
Comments: Newly-proposed GenBank Structured Comment Field ID, sequence annotation' has been submitted to OBI
OBO Foundry Synonym: sequence annotation provider
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001947 OBI Definition (OBI): Person or organization report the feature annotation results of a macromolecular sequence.
Other Synonyms:

9. Annotation Method
Sequencing Assay Field ID: SA9
Description: The names and versions of the software and databases used in creating the set of annotated features that is submitted to a resource such as GenBank.
Data Categories: Data Transformation
Allowed Values: Free text
Syntax: Free text
Example Values:
Data Source: GSCID
Comments: Newly-proposed GenBank Structured Comment Field ID; sequence annotation' has been submitted to OBI
OBO Foundry Synonym: sequence annotation
OBO Foundry Purl: http://purl.obolibrary.org/obo/OBI_0001944
OBI Definition: A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data.
Other Synonyms:

10. GenBank Record ID
Sequencing Assay Field ID: SA10
Description: Unique identifier of the submitted GenBank sequence record(s).
Data Categories: Data Transformation
Allowed Values: Free text
Syntax: Free text
Example Values: KF973453
Data Source: GSCID
Comments: Required field but not available until genome submitted.
OBO Foundry Synonym: GenBank ID OBO Foundry ID: http://purl.obolibrary.org/obo/OBI_0001614
OBI Definition: An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs.
Other Synonyms: GenBank accession number

Last Updated January 07, 2014