Make sure all INSDC are represented

Author: fmaguire

PHA4GE Contextual Data SOP.docx

@@ -3,7 +3,7 @@ bioproject umbrella accession,Optional,The INSDC umbrella accession number of th
 bioproject accession,Optional,The INSDC accession number of the BioProject(s) to which the BioSample belongs.,Bioproject_ID,PRJNA12345,"Required if submission is linked to a BioProject. BioProjects are an organizing tool that links together raw sequence data, assemblies, and their associated metadata. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345 and is created once at the beginning of a new sequencing project. Your laboratory can have one or many BioProjects."
 biosample accession,Recommended,The identifier assigned to a BioSample in INSDC archives.,Biosample_ID,SAMN14180202,"Store the accession returned from the BioSample submission. NCBI BioSamples will have the prefix SAMN, while EBI BioSamples will have the prefix SAMEA."
 SRA accession,Optional,"The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.",SRA_ID,SRR11177792,"Store the accession assigned to the submitted ""run"". NCBI-SRA accessions start with SRR, while EBI-ENA runs start with ENA."
-GenBank accession,Optional,The GenBank identifier assigned to the sequence in the INSDC archives.,Genbank_ID,MN908947.3,Store the accession returned from a GenBank submission (viral genome assembly).
+GenBank accession,Optional,The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.,Genbank_ID,MN908947.3,Store the accession returned from a GenBank submission (viral genome assembly).
 GISAID accession,Optional,The GISAID accession number assigned to the sequence.,GISAID_ID,EPI_ISL_123456,Store the accession returned from the GISAID submission. 
 specimen collector sample ID,Required,The user-defined name for the sample.,String,SARS-CoV-2/human/USA/CA-CDPH-001/2020;hCoV-19/USA-CDPH-001/2020,"Chose one of the following naming conventions for SARC-CoV-2 samples:
 1) ICTV compliant name for INSDC submission: ""SARS-CoV-2/host/location/isolate/date""
@@ -83,4 +83,4 @@ diagnostic pcr Ct value 1,Optional,The Ct value result from a diagnostic SARS-Co
 gene name 2,Optional,The name of the gene used in the diagnostic RT-PCR test.,String,RNA-directed RNA Polymerase (RdRP),Provide the full name of another gene used in an RT-PCR test. The gene symbol (short form of gene name) can also be provided. Standardized gene names and symbols can be found in the Gene Ontology using this look-up service: https://bit.ly/2Sq1LbI
 diagnostic pcr protocol 2,Optional,The name and version number of the protocol used for diagnostic marker amplification.,String,AllTheTestingPCRingRdRpGene v. 3,The name and version number of the protocol used for carrying out a second diagnostic PCR test. This information can be compared to sequence data for evaluation of performance and quality control.
 diagnostic pcr Ct value 2,Optional,The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.,Int,36,Provide the CT value of the sample from the second diagnostic RT-PCR test.
-authors,Recommended,"Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.",String,"Tejinder Singh, Fei Hu, Johnny Blogs","Include the first and last names of all individuals that should be attributed, separated by a comma."
+authors,Recommended,"Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.",String,"Tejinder Singh, Fei Hu, Johnny Blogs","Include the first and last names of all individuals that should be attributed, separated by a comma."

PHA4GE SARS-CoV-2 Contextual Data Template.xlsx

@@ -35,7 +35,7 @@
             ]
         },
         "genbank_accession": {
-            "description": "The GenBank identifier assigned to the sequence in the INSDC archives.",
+            "description": "The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.",
             "type": "string",
             "pattern": "^([a-zA-Z]{2})\\d*.\\d{1}",
             "examples": [