Improving the Display of Type Material in the NCBI TaxBrowser

Have you ever been confused by multiple taxonomic names for a single organism? You’re not alone! It’s one of the challenges in maintaining any biological database. Recently we updated the NCBI TaxBrowser to assist with this.

Let’s start with a brief word about how investigators name species in the first place. For any new species, the reporting author declares a “type.” They then deposit a specimen, or “type material,” in a publicly available biorepository. This type material is tied to the new species name and serves as a reference for future comparisons. Researchers can then use DNA sequences obtained from type material to identify other samples from the same species. NCBI currently uses such an approach to verify the taxonomic assignment of prokaryotic genomes.

Our Taxonomy group has been curating type material records in the Taxonomy database since 2013 using a common vocabulary accepted by our international partners (the INSDC). For example, the Entrez query “type material[prop]” in the Taxonomy database will return all type material at NCBI.

So what are the improvements to the TaxBrowser?

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The NCBI BioCollections database links specimen vouchers and sequence records to home institutions

A paper in the January 2018 issue of Database describes the NCBI BioCollections database, a curated dataset of metadata for culture collections, museums, herbaria and other natural history collections connected to sequence records in GenBank. The BioCollections database was established to allow the association of specimen vouchers and related sequence records to their home institutions. This process also allows back-linking from the home institution for quick identification of all records originating from each collection.

The rapidly growing set of GenBank submissions frequently includes records that are derived from specimen vouchers.  Correct identification of the specimens studied, along with a method to associate the sample with its institution, is critical to the outcome of related studies and analyses.

New repository records are added to the database if they are submitted to the International Nucleotide Sequence Database Collaboration (INSDC) along with sequence data. Each record now provides information about the institution that houses the collection, standard Institution Code, mailing address, and associated webpage if available.

The BioCollections database is maintained and curated by the Taxonomy group at NCBI.