Request for Information Attachment 2 - Biosequence Search Statement of Objectives

Draft Statement of Objectives (SOO)
Next-Generation Super Intelligence (SI)-Assisted Biosequence Search System

1. Purpose

The United States Patent and Trademark Office (USPTO) seeks to acquire and implement a next-generation, commercially available biological sequence search system. The objective is to utilize Super Intelligence (SI)-assisted capabilities to modernize the architecture, increase the efficiency, and improve the quality of biological sequence searches (e.g., DNA, RNA, proteins, peptides, antibodies) conducted during patent examinations.

2. Background

The USPTO examines patent applications to determine whether the claimed invention satisfies U.S. patentability requirements. Biotechnology examination often involves applications that disclose biological sequences in a sequence listing and recite those sequences in the claims.

Draft

A claim may be narrow, such as one exact listed sequence, or broad, such as a sequence having at least a stated percent identity to one of many listed sequences. Claims may also cover fragments, fused sequences, variants, alternative residues, and related structural forms. As a result, sequence examination is not simply a document search. Automated Biotechnology Search System (ABSS) is the USPTO’s current sequence-search system. It supports searching nucleotide and amino acid query sequences against a set of patent-sequence and non-patent-sequence databases. The examiner may run a basic search directly through the self-service ABSS interface or a more customized search executed by internal search support resources. ABSS currently employs the SmithWaterman algorithm and performs sequence searches on information from various database including GenBank, GeneSeq, and Swiss-Prot, then stores the search results as exports to other USPTO systems integrated with ABSS.
The USPTO requires a modernized, cloud-based platform that reduces examiner burden, improves search focus, and leverages SI to assist in strategy generation and result prioritization while keeping the examiner as the ultimate decision-maker.

3. Scope

The scope of this acquisition includes the software, platform, integration, and SI capabilities necessary to provide end-to-end biosequence search and alignment. This includes ingesting patent documents (claims, specifications, sequence listings), executing

complex searches across massive biological databases, and providing SI-driven analysis and summarization of the results in a secure, USPTO-hosted AWS cloud environment.