Automated database updating and curation

Inventors

Fry, Stephen • Ellis, Jeremy • Shabilla, Matthew

Assignees

Fry Laboratories LLC • Fry Laboratories LLC

Abstract

Systems and methods for retrieval of information from read-only databases that hold taxonomic-related and sequence-related data. A method may include receiving organism names from a taxonomy database and detecting new organism names. The method may also include retrieving hierarchical data and assigning the new organism names to buckets based on the hierarchical data. The method may further include receiving sequence data elements from a nucleotide database, identifying particular buckets to correspond to a screener data set, querying organism names assigned to the particular buckets with names of reference sequences of the sequence data elements, generating a mapping between the sequence data elements and organism names returned as a result of the queries, and storing the mapping.

Core Innovation

An automated curator/database management system detects that a remote taxonomy database has been updated to include an organism name that is not represented in a particular database. The particular database includes organism-name data organized using a set of buckets, where each bucket corresponds to an organism category. The system accesses metadata corresponding to the organism name stored at the remote taxonomy database.

The accessed metadata include two or more taxonomical classifications associated with the organism name, where a first taxonomical classification identifies a first organism-topology level and a second taxonomical classification identifies a second organism-topology level different from the first. The system determines an extent to which the two or more taxonomical classifications are represented on a same branch within the organism taxonomy, including determining whether the first and second organism-topology levels correspond to different organism-topology levels of the same branch. Based on that extent, the system determines which particular bucket corresponds to the organism name.

The system updates the particular database to associate the organism name with the particular bucket and receives biological sequence data. The system determines that the biological sequence data corresponds to a reference biological sequence associated with the particular bucket, supporting correspondence via mapping between sequence data elements and organism names for downstream organism detection, including accepted organism names and synonym organism names handling using similarity thresholding.

Claims Coverage

The document includes three independent claims (computer-implemented method, system, and computer-program product), each covering the same core workflow: detecting an updated remote taxonomy database, selecting a bucket for a new organism name using organism-topology information, updating the particular database, and determining correspondence between received biological sequence data and a reference biological sequence associated with the selected bucket. Across the claim set, the inventive features focus on bucket selection based on taxonomical classification representation on a shared branch and sequence-to-bucket correspondence using reference biological sequences.

Across the independent claims, the coverage centers on detecting when the remote taxonomy database introduces an organism name not represented locally, selecting the corresponding bucket by analyzing two or more taxonomical classifications and their representation on a same branch, updating the particular database to associate the organism name with that bucket, and determining that received biological sequence data corresponds to a reference biological sequence associated with the selected bucket. Dependent claims further narrow details for sequence/bucket updates and correspondence determination.

Stated Advantages

Documented Applications