GSCID/BRC Project and Sample Application Standard
Sequencing Assay
v1.4
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 |
Field Name: | Sample ID - Sequencing Facility |
Description: | Unique identifier used by the relevant sequencing center to identify the sample submitted by the sample provider. |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | SRA* |
OBO Foundry Synonym: | specimen identifier assigned by sequencing facility |
OBO Foundry ID: | http://purl.obolibrary.org/obo/OBI_0001901 |
OBI Mapping Comments: | |
Definition (OBI): | A specimen identifier which is assigned by a sequencing facility |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Sample Shipment |
Allowed Values: | free text |
Unknown/Not Applicable/Censored Allowed: | |
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 |
2. Nucleic Acid Extraction Method | |
Sequencing Assay Field ID: | SA2 |
Field Name: | Nucleic Acid Extraction Method |
Description: | Experimental procedure used to derive the nucleic acid fraction from the submitted sample used for the sequencing reaction. |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | SRA* |
OBO Foundry Synonym: | nucleic acid extraction |
OBO Foundry ID: | http://purl.obolibrary.org/obo/OBI_0666667 |
OBI Mapping Comments: | |
Definition (OBI): | 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. |
MIxS Equivalent: | sample material processing |
Other Synonyms: | Nucleic acid preparation - extraction method |
Data Categories: | Sequencing Sample Preparation |
Allowed Values: | OBI, http://bioportal.bioontology.org/ontologies/40832 |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | Illumina suggested standard method; CTAB/phenol/chloroform |
Data Source: | Sample Provider or GSCID |
Comments: | |
3. Nucleic Acid Preparation Method | |
Sequencing Assay Field ID: | SA3 |
Field Name: | Nucleic Acid Preparation Method |
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. |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | SRA* |
OBO Foundry Synonym: | sample preparation for sequencing assay |
OBO Foundry ID: | http://purl.obolibrary.org/obo/OBI_0001902 |
OBI Mapping Comments: | |
Definition (OBI): | 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. |
MIxS Equivalent: | sample material processing |
Other Synonyms: | Nucleic acid preparation by GSC; including amplification procedure |
Data Categories: | Sequencing Sample Preparation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | Standard 454 LC |
Data Source: | GSCID |
Comments: | required with not applicable as an allowed value |
4. Sequencing Method | |
Sequencing Assay Field ID: | SA4 |
Field Name: | Sequencing Method |
Description: | Experimental procedure used to derive sequence data from the input assay sample including both method and device. Type of sequencing used based on approach (pyrosequencing) and technology (454). |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | SRA* |
OBO Foundry Synonym: | sequencing assay |
OBO Foundry ID: | http://purl.obolibrary.org/obo/OBI_0600047 |
OBI Mapping Comments: | |
Definition (OBI): | 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. |
MIxS Equivalent: | sequencing method |
Other Synonyms: | Sequencing method (e.g. dideoxysequencing, pyrosequencing, polony) |
Data Categories: | Sequencing Assay |
Allowed Values: | OBI, http://bioportal.bioontology.org/ontologies/40832 |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | Consensus or Intra-Host |
Example Values: | Pyrosequencing |
Data Source: | GSCID |
Comments: | |
5. Assembly Name | |
Sequencing Assay Field ID: | SA5 |
Field Name: | Assembly Name |
Description: | A unique name given to a specific assembled genome build. |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Assembly Name |
OBO Foundry Synonym: | IAO:'written name' denotes some 'sequence assembly' |
OBO Foundry ID: | |
OBI Mapping Comments: | sequence assembly' has been submitted to OBI |
Definition (OBI): | |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Data Transformation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | |
Data Source: | |
Comments: | Newly-proposed GenBank Structured Comment Field ID |
6. Assembly Method | |
Sequencing Assay Field ID: | SA6 |
Field Name: | Assembly Method |
Description: | The name and version of the software or pipeline used to assemble individual sequence reads into larger contigs. Any dependencies such as reference genome files should be listed. |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Assembly Method* |
OBO Foundry Synonym: | software pipeline |
OBO Foundry ID: | http://purl.obolibrary.org/obo/OBI_0001943 |
OBI Mapping Comments: | |
Definition (OBI): | A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. |
MIxS Equivalent: | assembly |
Other Synonyms: | Assembly (Assembly method, estimated error rate and method of calculation) |
Data Categories: | Data Transformation |
Allowed Values: | pick list |
Unknown/Not Applicable/Censored Allowed: | |
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: | |
7. Depth of Coverage - Average | |
Sequencing Assay Field ID: | SA7 |
Field Name: | Depth of Coverage - Average |
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. |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Genome Coverage* |
OBO Foundry Synonym: | average depth of sequence coverage |
OBO Foundry ID: | http://purl.obolibrary.org/obo/OBI_0001618 |
OBI Mapping Comments: | |
Definition (OBI): | 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. |
MIxS Equivalent: | finishing strategy |
Other Synonyms: | average depth of sequence coverage |
Data Categories: | Data Transformation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | 45X average |
Data Source: | GSCID |
Comments: | core, but not available until genome submitted - average? min? max? |
8. Annotation Algorithm | |
Sequencing Assay Field ID: | SA8 |
Field Name: | Annotation Algorithm |
Description: | Computational algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Annotation Algorithm |
OBO Foundry Synonym: | sequence annotation algorithm |
OBO Foundry ID: | http://purl.obolibrary.org/obo/OBI_0001625 |
OBI Mapping Comments: | |
Definition (OBI): | A plan specification which 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. |
MIxS Equivalent: | |
Other Synonyms: | Annotation source |
Data Categories: | Data Transformation |
Allowed Values: | pick list |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | free text |
Example Values: | RAST v4.0; reference annotation transfer |
Data Source: | GSCID |
Comments: | required with not applicable as an allowed value; core, but not available until genome submitted |
9. Annotation Provider | |
Sequencing Assay Field ID: | SA9 |
Field Name: | Annotation Provider |
Description: | |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Annotation Provider |
OBO Foundry Synonym: | (organization or 'Homo sapiens') and participates_in some 'sequence annotation' |
OBO Foundry ID: | |
OBI Mapping Comments: | sequence annotation' has been submitted to OBI |
Definition (OBI): | |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Data Transformation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | |
Data Source: | |
Comments: | Newly-proposed GenBank Structured Comment Field ID |
10. Annotation Status | |
Sequencing Assay Field ID: | SA10 |
Field Name: | Annotation Status |
Description: | |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Annotation Status |
OBO Foundry Synonym: | report is_about some (is_specified_output_of some 'sequence annotation') |
OBO Foundry ID: | |
OBI Mapping Comments: | sequence annotation' has been submitted to OBI |
Definition (OBI): | |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Data Transformation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | |
Data Source: | |
Comments: | Newly-proposed GenBank Structured Comment Field ID |
11. Annotation Version | |
Sequencing Assay Field ID: | SA11 |
Field Name: | Annotation Version |
Description: | |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Annotation Version |
OBO Foundry Synonym: | version number' and is_about some (is_specified_output_of some 'sequence annotation') |
OBO Foundry ID: | |
OBI Mapping Comments: | sequence annotation' has been submitted to OBI |
Definition (OBI): | |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Data Transformation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | |
Data Source: | |
Comments: | Newly-proposed GenBank Structured Comment Field ID |
12. Annotation Pipeline | |
Sequencing Assay Field ID: | SA12 |
Field Name: | Annotation Pipeline |
Description: | |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Annotation Pipeline |
OBO Foundry Synonym: | software pipeline' and 'is concretized as' some ('is realized by' some 'sequence annotation') |
OBO Foundry ID: | |
OBI Mapping Comments: | software pipeline' and 'sequence annotation' have been submitted to OBI |
Definition (OBI): | |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Data Transformation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | |
Data Source: | |
Comments: | Newly-proposed GenBank Structured Comment Field ID |
13. Annotation Method | |
Sequencing Assay Field ID: | SA13 |
Field Name: | Annotation Method |
Description: | |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Annotation Method |
OBO Foundry Synonym: | protocol and 'is concretized as' some ('is realized by' some 'sequence annotation') |
OBO Foundry ID: | |
OBI Mapping Comments: | sequence annotation' has been submitted to OBI |
Definition (OBI): | |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Data Transformation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | |
Data Source: | |
Comments: | Newly-proposed GenBank Structured Comment Field ID |
14. Features Annotated | |
Sequencing Assay Field ID: | SA14 |
Field Name: | Features Annotated |
Description: | |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | Features Annotated |
OBO Foundry Synonym: | sequence_feature |
OBO Foundry ID: | http://purl.obolibrary.org/obo/SO_0000110 |
OBI Mapping Comments: | |
Definition (OBI): | An extent of biological sequence. |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Data Transformation |
Allowed Values: | |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | |
Example Values: | |
Data Source: | |
Comments: | Newly-proposed GenBank Structured Comment Field ID |
15. GenBank Record ID | |
Sequencing Assay Field ID: | SA15 |
Field Name: | GenBank Record ID |
Description: | Unique identifier of the submitted GenBank sequence record(s). |
Privacy Risks: | No |
GenBank Structured Comment Synonym: | |
OBO Foundry Synonym: | GenBank ID |
OBO Foundry ID: | http://purl.obolibrary.org/obo/OBI_0001614 |
OBI Mapping Comments: | |
Definition (OBI): | An information content entity that consists of a CRID symbol and additional information about which CRID registry it belongs. |
MIxS Equivalent: | |
Other Synonyms: | |
Data Categories: | Data Transformation |
Allowed Values: | free text |
Unknown/Not Applicable/Censored Allowed: | |
Syntax: | free text |
Example Values: | |
Data Source: | GSCID |
Comments: | core, but not available until genome submitted |
Content last reviewed on October 5, 2016