galaxyproject / galaxyproject/brc-analytics

[GA2] update data to include more assembly information

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GA2 ga2 roadmap item
Dominant language
TypeScript
Stars
7
Forks
11
Avg merge
2d 12h
Merged PRs (30d)
16

Description

Using NCBI Rest Api we can extract the more assembly data.

```bash
curl https://api.ncbi.nlm.nih.gov/datasets/v2/genome/accession/GCA_009859065.2/dataset_report
```

will give us the following response

```json
{
"reports": [
{
"accession": "GCA_009859065.2",
"current_accession": "GCA_009859065.2",
"source_database": "SOURCE_DATABASE_GENBANK",
"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",
"assembly_name": "bTaeGut2.pri.v2",
"assembly_type": "haploid",
"bioproject_lineage": [
{
"bioprojects": [
{
"accession": "PRJNA489186",
"title": "Taeniopygia guttata (zebra finch) genome sequencing and assembly, female, primary haplotype, v1",
"parent_accessions": [
"PRJNA533101"
]
},
{
"accession": "PRJNA533101",
"title": "Taeniopygia guttata (zebra finch) genome assembly, bTaeGut2",
"parent_accessions": [
"PRJNA489243",
"PRJNA489244"
]
},
{
"accession": "PRJNA489243",
"title": "Vertebrate Genomes Project",
"parent_accessions": [
"PRJNA533106"
]
},
{
"accession": "PRJNA489244",
"title": "B10K Reference Genome Project"
},
{
"accession": "PRJNA533106",
"title": "Earth BioGenome Project (EBP)"
}
]
}
],
"bioproject_accession": "PRJNA489186",
"release_date": "2020-04-01",
"submitter": "Vertebrate Genomes Project",
"linked_assemblies": [
{
"linked_assembly": "GCA_009859025.1",
"assembly_type": "alternate_pseudohaplotype_of_diploid"
}
],
"sequencing_tech": "PacBio Sequel I; 10X genome; Bionano Genomics; Arima Genomics Hi-C",
"assembly_method": "FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; scaff10x v. 2.1; Bionano Solve 2 enzyme v. 3.2.1; Salsa2 v. 2.0; smrtanalysis Arrow polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2019-11-12; VGP standard assembly pipeline v. 1.0",
"biosample": {
"accession": "SAMN09946140",
"last_updated": "2023-08-23T12:25:19.680",
"publication_date": "2019-09-11T00:00:00.000",
"submission_date": "2018-09-02T11:47:05.227",
"sample_ids": [
{
"label": "Sample name",
"value": "Female zebra finch (Taeniopygia guttata) BioSample"
},
{
"db": "SRA",
"value": "SRS18699827"
}
],
}
```

I would at least like to add:

- [ ] release_date

and preferably the following data could also be extracted:
- [ ] sequencing_tech
- [ ] assembly_method

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by locating the TypeScript entry point that imports assembly data from the NCBI Datasets REST API, using the dataset_report endpoint and the GCA_009859065.2 example. Add release_date, and if supported, sequencing_tech and assembly_method; done means these fields are extracted from the response and made available with the existing assembly data.

Written by the indexing model from the issue text.

Assessment

Tech stack
typescript
Domain
backend-api-design
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
50/100

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