kira-biodata-manager (kira-bm)

Reproducible bio-data manager with a project-local store and a shared global cache. kira-bm it's like npm/cargo/pip for bioinformatics.

Prerequisites

• Rust 1.91+ (Edition 2024)
• Network access to NCBI GEO/Datasets, RCSB PDB, UniProt, GO, KEGG, Reactome

Installation

Install from crates.io (Rust 1.91+ / Windows / Linux / MacOS):

cargo install kira-biodata-manager

Or

Build from source (Rust 1.91+):

cargo build --release

Config (kira-bm.json)

It's like package.json/Cargo.toml

{
  "schema_version": 1,
  "proteins": [
    "1LYZ",
    { "id": "4V6X", "format": "pdb" }
  ],
  "genomes": [
    {
      "accession": "GCF_000005845.2",
      "include": ["genome", "gff3", "protein", "seq-report"]
    }
  ],
  "srr": [
    "SRR014966",
    { "id": "SRR123456", "format": "fasta", "paired": true }
  ],
  "uniprot": [
    "P69905",
    { "id": "Q9Y263" }
  ],
  "doi": [
    "10.1038/s41586-020-2649-2"
  ],
  "expression": [
    "GSE102902"
  ],
  "expression10x": [
    "GSE115978"
  ]
}

Notes:

• schema_version defaults to 1 if omitted.
• Protein format defaults to cif. Supported: cif, pdb, bcif.
• Genome include defaults to ["genome","gff3","protein","seq-report"].
• SRR format defaults to fastq. Supported: fastq, fasta.
• UniProt accepts accessions like P69905 or Q9Y263.
• DOI accepts full DOI strings like 10.1038/s41586-020-2649-2.
• GEO expression datasets accept GSE accessions (expression, expression10x).
• Knowledge bases are available as singletons: go, kegg, reactome (use CLI fetch).
• SRR datasets require NCBI SRA Toolkit (prefetch + fasterq-dump). See kira-bm tools install-sra.

Usage

Fetch from config (kira-bm.json) in the current directory:

kira-bm fetch
or just
kira-bm

In case you have no kira-bm.json file in project and run kira-bm -- you'll see an interactive terminal user interface.

Fetch a specific dataset (add dataset to project's dataset directory):

kira-bm fetch protein:1LYZ
kira-bm fetch genome:GCF_000005845.2
kira-bm fetch srr:SRR014966
kira-bm fetch uniprot:P69905
kira-bm fetch expression:GSE102902
kira-bm fetch expression10x:GSE115978
kira-bm fetch go
kira-bm fetch kegg
kira-bm fetch reactome

Routing:

• Protein structures (protein:<PDB_ID>) are fetched from RCSB PDB.
• Genomes and SRR runs are fetched from NCBI.
• UniProt accessions (uniprot:<ACCESSION>) are fetched from UniProt.
• DOI-based discovery (doi:<DOI>) resolves metadata via Crossref and hydrates public dataset IDs.
• GEO expression datasets (expression:<GSE>, expression10x:<GSE>) are fetched from NCBI GEO.
• Knowledge bases (go, kegg, reactome) are fetched from their official sources.

List datasets (JSON in non-interactive mode):

kira-bm list --non-interactive

Show dataset info:

kira-bm info protein:1LYZ --non-interactive

Clear project store:

kira-bm clear

DOI-driven dataset discovery

kira-bm can resolve a DOI into public repository identifiers (GEO/SRA/BioProject/Assembly/PDB/UniProt) using structured metadata from Crossref, then hydrate and download the resolved datasets.

What it does:

• Resolves Crossref metadata (title/abstract/references/links).
• Extracts known identifiers via strict regex matching.
• Validates identifiers using public APIs.
• Hydrates hierarchies (e.g. GSE -> GSM -> SRR, BioProject -> SRR/assemblies).
• Writes doi_resolution.json provenance to the project store.

What it does NOT do:

• No PDF parsing.
• No publisher HTML scraping.
• No fuzzy matching or probabilistic inference.

Example:

kira-bm fetch doi:10.1038/s41586-020-2649-2

Storage layout

Project store:

./.kira-bm/
  proteins/<ID>/<ID>.<ext>
  proteins/<ID>/metadata.json
  proteins/<ID>/metadata.raw.json
  genomes/<ACCESSION>/...
  srr/<SRR_ID>/reads.fastq
  srr/<SRR_ID>/reads_1.fastq
  srr/<SRR_ID>/reads_2.fastq
  srr/<SRR_ID>/metadata.json
  uniprot/<ACCESSION>/<ACCESSION>.fasta
  uniprot/<ACCESSION>/metadata.json
  uniprot/<ACCESSION>/raw.json
  doi/<ENCODED_DOI>/doi_resolution.json
  expression/<GSE>/...
  expression/<GSE>/metadata/metadata.json
  expression10x/<GSE>/... (10x bundles preserved)
  expression10x/<GSE>/metadata/metadata.json
  metadata/<TYPE>/<ID>.json
  metadata/go/go-basic.obo
  metadata/go/metadata.json
  metadata/kegg/...
  metadata/kegg/metadata.json
  metadata/reactome/...
  metadata/reactome/metadata.json

Global cache:

~/.cache/kira-biodata-manager/
  proteins/<ID>/<ID>.<ext>
  proteins/<ID>/metadata.json
  proteins/<ID>/metadata.raw.json
  genomes/<ACCESSION>/...
  srr/<SRR_ID>/reads.fastq
  srr/<SRR_ID>/reads_1.fastq
  srr/<SRR_ID>/reads_2.fastq
  srr/<SRR_ID>/metadata.json
  uniprot/<ACCESSION>/<ACCESSION>.fasta
  uniprot/<ACCESSION>/metadata.json
  uniprot/<ACCESSION>/raw.json
  expression/<GSE>/...
  expression/<GSE>/metadata/metadata.json
  expression10x/<GSE>/... (10x bundles preserved)
  expression10x/<GSE>/metadata/metadata.json
  metadata/go/go-basic.obo
  metadata/go/metadata.json
  metadata/kegg/...
  metadata/kegg/metadata.json
  metadata/reactome/...
  metadata/reactome/metadata.json
  metadata/<TYPE>/<ID>.json

Output contracts

--non-interactive mode:

• list and info output JSON to stdout.
• fetch and clear output JSON summaries.
• Errors go to stderr with non-zero exit codes.

Optional external tools

kira-bm may optionally invoke externally installed third-party tools (e.g. NCBI SRA Toolkit https://github.com/ncbi/sra-tools ). These tools are not bundled, not distributed, and are subject to their own licenses. Users are responsible for installing and complying with those licenses.