gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
Security Assessment
About gene-database
The gene-database skill enables users to query the NCBI Gene database using the E-utilities and Datasets API, allowing for comprehensive searches of gene information by symbol or ID. It effectively addresses the need for researchers and bioinformaticians to access detailed gene data, including reference sequences, gene ontology annotations, and phenotypic associations. This skill simplifies the retrieval and analysis of gene-related information, facilitating functional analyses and gene annotation tasks.
FAQ
How do I search for a gene using its symbol?
You can use the `scripts/query_gene.py` script with E-utilities ESearch, specifying the gene symbol and organism.
What format can I expect the gene information to be returned in?
You can retrieve gene information in JSON, XML, or text format depending on your query.
What are the rate limits for using the APIs?
Without an API key, the rate limit is 3 requests/second for E-utilities and 5 requests/second for Datasets API. With an API key, it increases to 10 requests/second for both.
Can I perform batch lookups for multiple genes?
Yes, you can use the `scripts/batch_gene_lookup.py` to process multiple gene symbols or IDs simultaneously.
What should I do if I encounter a rate limit error?
If you exceed the rate limit, you should retry your requests with exponential backoff.
Install gene-database
Quick Setup:
- Copy the skill folder to
.claude/skills/ - Claude will automatically detect and use the skill
Repository
davila7/claude-code-templates