Extract individual information from NCBI

[NoopDog]

How can we do this?

[Smeds]

From the VGP hub (https://hgdownload.soe.ucsc.edu/hubs/VGP/) you are able to see individual from 'NCBI assembly' column. The following bold part GCA_009819605.1_bSteHir1.pri . Where bSteHir is the Tree of life id and the number should be unique for an individual.

Using the following url /genome/accession/{accessions}/dataset_report from the ncbi rest api should make it possible to find the individual information. Here's example for Zebra Finch.

GCF_003957565.2

"assembly_name": "bTaeGut1.4.pri"

{
  "reports": [
    {
      "accession": "GCF_003957565.2",
      "current_accession": "GCF_003957565.2",
      "paired_accession": "GCA_003957565.4",
      "source_database": "SOURCE_DATABASE_REFSEQ",
      "organism": {
        "tax_id": 59729,
        "organism_name": "Taeniopygia guttata",
        "common_name": "zebra finch",
        "infraspecific_names": {
          "isolate": "Blue55",
          "sex": "female"
        }
      },
      "assembly_info": {
        "assembly_level": "Chromosome",
        "assembly_status": "current",
        "paired_assembly": {
          "accession": "GCA_003957565.4",
          "status": "current",
          "changed": "chromosome MT."
        },
        "assembly_name": "bTaeGut1.4.pri",
        "assembly_type": "haploid",
      }
   }
   ]
}

GCF_008822105.2

"assembly_name": "bTaeGut2.pat.W.v2",

[Smeds]

I have added some information about extraction of individual @NoopDog

[NoopDog]

Thanks, @Smeds! Are you saying that the individual name is encoded in the assembly name and is not explicitly represented in the API response?

Also, what is

"infraspecific_names": {
"isolate": "Blue55",
"sex": "female"
}

Is Blue55 also an ID for the individual? Or is this something else?

Cheers
D

[Smeds]

Could be that NCBI aren't really working with individual information, they have there different assemblies. Looks like isolate (Blue55) is something common for an organism, same value for bTaeGut2 .

{
  "reports": [
    {
      "accession": "GCF_008822105.2",
      "current_accession": "GCF_008822105.2",
      "paired_accession": "GCA_008822105.2",
      "source_database": "SOURCE_DATABASE_REFSEQ",
      "organism": {
        "tax_id": 59729,
        "organism_name": "Taeniopygia guttata",
        "common_name": "zebra finch",
        "infraspecific_names": {
          "isolate": "Blue55",
          "sex": "female"
        }
      },
      "assembly_info": {
        "assembly_level": "Chromosome",
        "assembly_status": "suppressed",
        "paired_assembly": {
          "accession": "GCA_008822105.2",
          "status": "current",
          "changed": "chromosome MT."
        },
        "assembly_name": "bTaeGut2.pat.W.v2",
      }}]}

If you look at the genome ark v1 page, they are using the TolID with a number to different between individuals, https://www.genomeark.org/vgp-all/Taeniopygia_guttata.html

[Smeds]

Also wanted to add: NOTE: there are assemblies that doesn't have correct tree of life ids, like GCF_011100685.1_UU_Cfam_GSD_1.0