Check species, reference genome and chromosome identifiers
Worked example Identify human GRCh38.p14 chromosome 1
Confirm organism, versioned assembly and chromosome aliases before combining records from different databases. The output is an identity table for one chromosome, with the original source responses.
Before starting, follow Scientific databases to enable the required Connectors. Use a connected model and an available Notebook runtime.
1. Query the organism, assembly and chromosome
- Enable Genomes in Settings → Connectors. Open a session with a connected model and available Notebook runtime. This v0.31.1 example used Codex subscription.
- Query the organism, versioned assembly and sequence in that order. Send:
Use Genomes through Session Notebook. Load its connector instructions.
Call ncbi_resolve_taxon with query human and max_matches 10.
Call ncbi_get_assembly_info with assembly_accession GCF_000001405.40.
Call ncbi_get_sequence_aliases with assembly_accession GCF_000001405.40,
sequence chr1 and max_sequences 200. Save the complete responses as
ncbi-human-taxon.json, ncbi-grch38-assembly.json and ncbi-chr1-aliases.json.
Save ncbi-reference-identity.csv and ncbi-reference-notes.md with the
query, identity, ambiguity and truncation flags, and source URLs.
Preserve accession versions and RefSeq/GenBank differences. Do not perform
coordinate liftover or invent results. Keep everything in English.
2. Compare the returned identifiers
Open the notes and compare the returned IDs across the three JSON files. All three calls succeeded in this example.
| Check | This example's result |
|---|---|
| Organism | Homo sapiens, TaxID 9606; one match, ambiguous: false |
| Requested/current assembly | GCF_000001405.40, GRCh38.p14, UCSC name hg38 |
| Paired GenBank assembly | GCA_000001405.29; the returned record reports differences from RefSeq |
| Chromosome 1 aliases | 1, chr1, RefSeq NC_000001.11, GenBank CM000663.2 |
| Selected sequence | 248956422 bp, Primary Assembly; one match, matches_truncated: false |
3. Retain the identity table and source records
Query notes · Identity table · Taxon response · Assembly response · Sequence response
This is a completed lookup for one selected chromosome, not an export of every assembly sequence. Keep ambiguous matches and truncation flags when changing the query. An assembly name alone cannot replace its versioned accession, and a returned current accession does not authorize silently replacing a historical version. Sequence aliases describe names within an assembly; they do not perform coordinate liftover between builds. Exact inputs