ABSS BNJ SSJ - Executed_Redacted.pdf

Form # USPTO-OP-071.v1.0 (01/2020) 1 Brand Name Justification

BRAND NAME JUSTIFICATION (BNJ)

(41 U.S.C. 1903, PTAG 6.1.1, PM 2016-02)

SECTION I. COMPLETED BY THE PROGRAM OFFICE

Program Office: OCIO/IEO/ESSD Program Office

POC:

John Lau / Johanna Cruz

Title of Procurement: FY20 Automated Biotechnology Sequence Search (ABSS) System

Estimated Value (including options) Contracting Officer: Jonathan E. Bettis

Contracting Officer Phone: (571) 270-5803 Acquisition Package

Number: ACQ-20-0716

1. Program Office Anticipated Type of BNJ (select from the drop-down box) [ o Brand Name and Sole Source (limited to one vendor who can fulfill the brand name (FAR subpart 8.4, subpart 13.5, subpart 16.505 or PTAG 6.1.1)) ]

2. Description of the Action

This justification supports the acquisition of software licenses and maintenance for Automated Bio-sequence Search System (ABSS). The procurement will result in a Firm-Fixed Price contract with an estimated price for the supplies and services described in Item 3 below as follows:

Base Year: 05/01/2020 - 04/30/2021

Unit Price Information

Total Cost Total UnitsCLIN Labor Category Units/Hour Rate

FY20 Automated Bio-sequence Search System (ABSS) SW License and Support (O&M)

1 unit 1 unit

0002 Contractor Support- FTE (CIF) 1920 hours 1920 hours

Grand Total

Option Year 1: 05/01/2021 - 04/30/2022

Units CLIN Labor Category Units Rate

Form # USPTO-OP-071.v1.0 (01/2020) 2

FY20 Automated Bio-sequence Search System (ABSS) SW License and Support (O&M)

1 1

2002 Contractor Support- FTE (CIF) - (Optional Clin) 1920

Option Year 2: 05/01/2022 - 04/30/2023

Units CLIN Labor Category Units Rate

FY20 Automated Bio-sequence Search System (ABSS) SW License and Support

1 1

3002 Contractor Support- FTE (CIF) (Optional Clin) 1920

Option Year 3: 05/01/2023 - 04/30/2024

Units CLIN Labor Category Units Rate

FY20 Automated Bio-sequence Search System (ABSS) SW License and Support

1 $ 1

0002 Contractor Support- FTE (CIF)(Optional Clin) 1920

Option Year 4: 05/01/2024- 04/30/2025

Units CLIN Labor Category Units Rate

FY20 Automated Bio-sequence Search System (ABSS) SW License and Support

1 1

Form # USPTO-OP-071.v1.0 (01/2020) 3

0002 Contractor Support- FTE (CIF) (Optional Clin) 1920

GRAND

TOTAL

3. Description of the Supplies/Services The procurement will include all aspects of ABSS software system including Software Licenses, maintenance services, installations, training, transition plan, and Premiere Operational Support (responses 24 hours a day and including a three hour response time from initial call).

Base Period: 05/01/2020 - 04/30/2021 Option Year 1: 05/01/2021 - 04/30/2022 Option Year 2: 05/01/2022 - 04/30/2023 Option Year 3: 05/01/2023 - 04/30/2024 Option Year 4: 05/01/2024 - 04/30/2025

4. Unique Vendor Qualifications or Nature of the Acquisition Biocceleration's products are part of USPTO's ABSS system. The Biocceleration team has delivered, integrated, and has been upgrading and maintaining the ABSS system since 1998. In cooperation with the PTO staff, the team has introduced several upgrades and improvements to the system over the years.

The current ABSS system is based on Biocceleration's GenCore-6 optimized software package that delivers burst performance of more than 3000 BCPS when run on the ABSS Linux cluster, more than 100 fold improvement over the original system. In addition, many upgrades and improvements have been introduced to the user interface system, the queuing management infrastructure, search results and interfaces to external databases, compatibility with various sequence database formats, and almost every other aspect of the system. These improvements have been developed through close and daily cooperation with the PTO search and technical staff, while maintaining the 24/7 availability of the ABSS system, and continuously improving the usability and effectiveness of the system for the PTO users.

Attachment 1 to this justification includes a Statement of Required Functionality that outlines extensive characteristics that only the Biocelleration software suite is capable of providing. Those characteristics are not repeated in this section but are incorporated in full as unique characteristics and capabilities that warrant the Biocelleration brand requirement and the issuance of a sole-source award directly to Biocelleration.

5. Other Facts Supporting the Justification If the USPTO is not able to renew its licensing for the subject software, then a large portion

Form # USPTO-OP-071.v1.0 (01/2020) 4 of Patent Examiners in Technology Center 1600 – the examiner corps responsible for the fields of Biotechnology and Organic Chemistry – will be unable to perform their jobs because they will lack biochemical and organic chemical data provided by the ABSS software suite required to examine patent applications. Therefore, failure to acquire the ABSS software suite will significantly limit the USPTO’s ability to fulfill its core mission of fostering innovation, competitiveness and economic growth, domestically and abroad, by providing high quality and timely examination of patent and trademark applications, guiding domestic and international intellectual property (IP) policy, and delivering IP information and education worldwide.

6. Listing of sources that expressed interest in writing None.

SECTION II. COLLABORATION BETWEEN THE PROGRAM OFFICE AND OP

7. Adjudicated Type of BNJ (select from the drop-down box) [ o Brand Name and Sole Source (limited to one vendor who can fulfill the brand name (FAR subpart 8.4, subpart 13.5, subpart 16.505 or PTAG 6.1.1)) ]

8. Statutory Authority This action is being executed for a combination of Brand Name and Sole Source used in accordance with the authority of 41 U.S.C. §1901: no other company can provide the necessary product and support services required and no other brand name can satisfy the requirement for the request explained in Item 4 above.

9. Efforts to solicit as many potential sources as possible The USPTO posted a synopsis on March 24, 2020 which included the required language in FAR Part 5 inviting interested parties to submit a capability statement in accordance with FAR 5.207(c)(16)(ii). The USPTO will continue to explore additional capabilities as they come to market in order to support the Examiner corps.

10. Market Research

Technical teams have assessed the availability of comparable products on the market by searching the internet and by searching GSA schedules for comparable products. None exist that would provide the degree of support that the USPTO requires.

11. Actions to remove or overcome barriers to competition The USPTO will continue to assess the extent to which is able to migrate to non-brand name products particularly as the agency stabilizes and modernizes its current IT infrastructure.

Form # USPTO-OP-071.v1.0 (01/2020) 5

SECTION III. COMPLETED BY OP

12. Determination by the Contracting Officer that estimated cost will be fair and reasonable The Contracting Officer will finalize a price reasonableness determination, appropriate to the contract type, prior to contract award. Detailed documentation and justification of price reasonableness will be provided in the Acquisition Form Documentation (AFD) to be prepared upon completion of negotiations.

SECTION IV. REVIEW AND APPROVAL

1. Technical Certification

By signature below, the Technical Representative certifies that the supporting data necessary to form the basis for this justification is accurate and complete to the best of their knowledge and belief. Furthermore, the Technical Representative certifies that the justification has been adjudicated by the Program Office and OP.

Technical Representative Name

Technical Representative Signature Date

2. Contracting Officer’s Certification

By signature below, the Contracting Officer certifies that this justification is accurate and complete to the best of their knowledge and belief.

Contracting Officer Name

Contracting Officer Signature Date

3. Bureau Procurement Official (BPO)/ Director of OP (or Designee) (required for actions valued at or >$700K)

By signature below, the ordering activity BPO/Director of OP certifies that this justification is accurate and complete to the best of their knowledge and belief.

Form # USPTO-OP-071.v1.0 (01/2020) 6

BPO/Director of OP (or Designee) Name

BPO/Director of OP (or Designee) Signature Date

Competition Advocate Certification:

Approval (required for actions valued from $700K to $13.5M) Concurrence (required for actions valued above $13.5M)

By signature below, the Competition Advocate certifies that they have reviewed this justification and has determined that sufficient facts exist to support the justification.

Competition Advocate Name (Deputy Chief Financial Officer)

Competition Advocate Signature Date

SECTION V. ATTACHMENTS

Attachment 1: Statement of Required Functionality

, Digitally signed by Users, Date: 2020.04.22 11:55:06 -04'00'

Date: 2020.04.22 17:01:29 -04'00'

STATEMENT OF REQUIRED FUNCTIONALITY

Automated Biotechnology Sequence Search (ABSS) System Software and Maintenance Support

1. Background

1.1. The Automated Bio-sequence Search System (ABSS) is the current system used by the U.S.

Patent and Trademark Office (USPTO) since 1997 to examine claims including bio-sequences.

The purpose of the ABSS is to sustain USPTO business function of performing prior-art searching of polynucleotide and polypeptide sequences claimed in patent applications examined by its Technology Center 1600 (Biotechnology). ABSS is designed to accept and store electronic sequence listing data submitted by applicants, and support searching of polynucleotide sequences using data stored from both applicant submissions and public and commercial databases of published sequence information.

1.2. In addition, this product is also required for USPTO’s upcoming project, Patents End-2-End (PE2E) Biosequence System Phase 4 (Project ID# 102267).

2. Objective

To renew ABSS Software for continued license maintenance services, installation, trainings (if needed), premier operation support (24/47 with three-hour response time from initial call (to include all requirements specified under Section 4).

3. Scope

The purpose of this is to acquire Automated Biotechnology Sequence Search Software and Maintenance Support in accordance with the requirements listed sin Section 4.

4. Requirements The USPTO has a requirement for Automated Biotechnology Sequence Search (ABSS) system Software and Maintenance Support in accordance with the specifications listed below.

Specifications:

1.1. Capability to perform one-to-one nucleotide and protein sequence alignment searching against large databases e.g. single sequence vs. GenBank Nucleotide Collection databases.

1.1. Using at least the following sequence alignment algorithms/heuristics or their equivalents, including Smith-Waterman and BLAST, for local alignments; Needleman-Wunsch for global alignments; and Hidden Markov Model, including creating HMM profiles.

For nucleotide searches, search both the query sequence and its complement (searched in the 5’ to 3’ direction, a.k.a. reverse complement).

In all search results, each hit to a complement identified as such in both a table of scores and alignments, see 1.5.

1.1.1.Capability to search a nucleotide query against a nucleotide database (n2n search) and against a protein database (“n2p search”). Alignments displayed in search results for n2p searches must align three letter abbreviations for amino acids with their corresponding codon.

1.1.2.Capability to search a protein query against a protein database (p2p search) and against a nucleotide database (“p2n search”). Alignments displayed in search results for p2n searches must align three letter abbreviations for amino acids with their corresponding codon.

1.1.3.Capability to add and run a search using any other alignment algorithm/heuristic.

1.1.4.All algorithms and heuristics must be subject to independent, public review for soundness.

1.1.4.1. Algorithms and heuristics must be optimized so as to minimize computational requirements (e.g. SSE extensions for Smith-Waterman).

1.2. Capability to search databases stored in common formats, at least IG, FASTA, and BLAST formats.

1.3. Capability to set a specific algorithm/heuristic and set of search input and output parameters as the default condition for each of n2n, n2p, p2n, and p2p searches.

Must be configurable at an administration level.

1.4. Capability to set a default set of search input and output parameters as the default conditions for each alternative algorithm/heuristic available for n2n, n2p, p2n, and p2p searches.

1.5. Capability to set one or more alternative sets of search input and output parameters for each available algorithm/heuristic as alternative defaults for each of n2n, n2p, p2n, and p2p searches.

1.6. Capability to rank and save hits based upon “% Query Match” parameter.

% Query Match = 100*(score/length of query sequence)

1.7. Capability to rank and save hits based upon “% Database Match” parameter.

% Database Match = 100*(score/length of database sequence)

This parameter is similar to % Query Match.

1.8. Capability to rank and save hits based upon “Score” parameter.

1.9. Capability to search with a fragment of a database sequence as query, where the position numbering from the original sequence is maintained and displayed in the alignment output.

1.10.Capability to filter database sequences by minimum and/or maximum length. E.g. database sequences that are not from 15-100 residues in length are excluded from the search.

1.11.Capability to score pairings between an ambiguity symbol and a corresponding defined residue as a match, conservative mismatch or mismatch.

E.g. X in protein query paired with A in database sequence; y in nucleotide query paired with c or t in database sequence.

1.12.Capability to search sequence patterns with following capabilities (currently using

EMBOSS/Jemboss in-house):

1.12.1. Search PROSITE-style patterns in nucleotide or amino acid sequences, equivalent to EMBOSS “fuzznuc” & “fuzzpro”

1.12.2. Search regular expression patterns in nucleotide or amino acid sequences, equivalent to

EMBOSS “dreg” and “preg”.

1.12.3. Search with a query containing alternate residues at each of one or more positions.

For example, position 5 can be Ala, Leu, Gly; and position 20 can be Arg or Lys.

1.12.4. Search with a query that excludes a specified residue or string of residues at a specified location.

For example, position 5 is anything except His; position 10 is anything except Glu or Phe;

position 15 is followed by anything other than the string Pro-Ser-Lys.

1.12.5. Search with a query with the beginning and/or the end of the sequence being marked.

E.g. the N-terminus must be Gly; the C-terminus must be Thr; the N-terminus is Val and the C-terminus must be Trp.

1.12.6. Search with a query containing a wildcard residue at each of one or more positions.

E.g. position 13 is any amino acid.

1.12.7. Capability to specify the size of a gap in a query.

E.g. 0-20 repeats of any amino acid; 3-5 repeats of Trp

1.12.8. Search with a query containing a specified number of perfect or imperfect repeats (as with EMBOSS “dreg” and “preg”.)

E.g. 3-10 consecutive copies of an imperfect repeat that is gatc or gatt.

1.12.9. Capability to combine any or all of these features:

A combination of features/capabilities provided under items 1.12.1-1.12.5.

1.12.10. The output must display each alignment along with the bibliographic and annotation information associated with the database sequence(s). Not like FindPatterns output.

1.12.11. Capability to select multiple databases to search a query in a single operation, as opposed to entering a separate search for each database – applies to general searching and EMBOSS.

1.13.Capability to create and search a 'mini-database' of specified sequences retrieved from nucleic and protein databases.

1.14. Capability to display a local alignment in context by displaying a specified number of residues adjacent to the region of best local similarity.

1.15. The output file for the search results must be printable and in a defined format:

o Search input information;

o Table of scores (output statistics) for database sequences;

o Alignments, output statistics, and annotations associated with database sequences.

1.15.1. Output results saved in customer defined format (relational tables, XML, etc.).

1.16. Capability of filtering out specified database sequence records from a results set. Primarily for instances where many sequence records from a large family of related patents contain the same sequence. Need to see the results for only one representative patent, and mask the rest.

Filter by assigned sequence identifier for the records"

1.17. Capability to set default naming of search output files. Must be configurable at an administration level.

1.17.1. Part of file name structure can include user input for part of filename.

1.18. Capability to provide search output results to end-users.

1.18.1. Provide end-user with estimate of time of completion for a search that has been entered.

1.18.2. Provide end-user with access to search output results files, i.e. view and download.

1.18.2.1. Must be configurable with USPTO systems.

1.18.2.2. Capability to select multiple EMBOSS search results files to copy to a user designated location.

1.18.3. Access to search output results files to be available within 20 min of completion of search.

1.19. Capability to store more results (hits) for a search than is to be provided in an initial results set. See Requirements 1.15, 1.15.1, 3.1.9, and 3.2.7.

1.20. Capability to sort and filter search results.

1.21. Capability to select patent numbers or PGPub numbers from sequence search result sets and generate a query from these identifiers to initiate a search in USPTO designated databases.

Sequence Analysis tools

2.1. Capability to perform global or local pairwise sequence alignments between specified database sequences.

2.1.1.Algorithms/heuristics for pairwise sequence alignments to include Needleman-Wunsch, Smith-Waterman, BLAST, and Hidden Markov Model.

2.1.2.Capability to add and run alignments using any other pairwise alignment algorithm/heuristic.

2.2. Capability to perform multiple sequence alignments between specified database sequences, and when required create a “consensus sequence” from multiple sequences.

2.2.1.Algorithms/heuristics for multiple sequence alignments to include ClustalW or equivalent, EMBOSS “emma” or equivalent.

2.2.2.Capability to add and run alignments using any other multiple sequence alignment algorithm/heuristic.

2.3. Capability to map restriction enzyme cleavage sites in a nucleotide sequence.

Output to show sites in context of nucleotide sequence, and also translated amino acid sequence. Equivalent to EMBOSS “remap”.

2.4. Capability to translate a nucleotide sequence and backtranslate a protein sequence, and also allow the use of such translations as queries in a search.

E.g. EMBOSS “transeq” and “backtranseq“

2.5. Capability to predict antigenic sites within an amino acid sequence. E.g. EMBOSS “antigenic”

2.6. Capability to calculate a hydropathy plot for an amino acid sequence.

E.g. EMBOSS “pepwindow”

2.7. Capability to determine protein statistics, including molecular weight, number and mole fraction for each amino acid.

E.g. EMBOSS “pepstats”

2.8. All alignments must be run in the distributed environment (no single point of failure or execution).

2.9. Capability to compare different search results sets to identify hits common to all sets (i.e.

intersection).

User-friendly Search Entry Interface:

3.1 Search Entry Interface for search staff.

3.1.1 Input and output parameters for the chosen algorithm/heuristic to be configurable by the user. E.g. gap penalties, scoring matrix, word size, scores and alignments to save.

When entering a new search, the default parameters should be displayed (see Requirements 1.3-1.5), and further configurable by the user.

3.1.1.1 Interface must not retain any user-configured input/output parameters from a preceding search session, but shall display default algorithm/heuristic and default input/output parameters for a new search.

3.1.2 Capability to upload existing sequences from a sequence database record as query from any given storage device, e.g. network storage.

3.1.3 Capability to upload existing sequences from a local file as query.

3.1.4 Capability to import query sequence from Sequence Editor. See Section 4.

3.1.5 Capability for user to display several sequences from a patent application and select them to search. Applies only to sequences from in-house patent application sequence databases.

All queries searched with same algorithm/heuristic and set of parameters.

3.1.5.1 Capability to select multiple sequences in different ways for batch searching:

o selecting a range of sequences, e.g. 1-8;

o selecting various sequences, e.g. 2, 4, 7;

o combination of a range and various, e.g. 12, 53-55, 75-80, 121;

See Requirement 3.1.5.

3.1.5.2 Capability to select multiple fragments of a single sequence from a patent application to be searched. See Requirement 3.1.5.

3.1.6 Provide for length-limited searches, including minimum length, maximum length and a range of length options. Length limitations apply to database sequences excluded.

3.1.7 Capability for user to see progress and estimated completion time for searches that have been entered. See Requirement 1.18 et seq.

3.1.8 Capability for user to access results output for completed search requests. See

Requirement 1.18 et seq.

3.1.9 Capability to retrieve more results (hits) for a previously run search than was provided in an initial results set without having to re-enter the search. See Requirements 1.15, 1.15.1, and 1.19.

3.1.10 Capability to sort and filter search results.

3.1.11 Capability to select patent numbers or PGPub numbers from sequence search result sets and generate a query from these identifiers to initiate a search in USPTO designated databases.

3.1.12 Capability to choose among sets of databases to further do a combined text search based on the sequence result output.

3.2 Search Entry Interface for examiners

3.2.1 Capability for user to select sequences from a patent application for search. Applies only to sequences from in-house patent application sequence databases. All queries searched with same algorithm/heuristic and set of parameters.

3.2.2 Capability for user to select algorithm, Smith-Waterman or BLAST.

3.2.2.1 Capability for user to choose a pre-determined set of search parameters, e.g.

standard or oligomer.

3.2.2.2 Capability for user to choose the number of scores and alignments to save.

Limit to be set by administrator.

3.2.2.3 Capability for users to access and use BLAST to search NCBI databases through the cloud.

3.2.3 Capability for user to choose among sets of databases to search.

3.2.4 Interface must not retain any user-configured input or output parameters from a preceding search session.

3.2.5 Capability for user to see progress and estimated completion time for searches that have been entered. See Requirement 1.18 et seq.

3.2.6 Capability for user to access results output for completed search requests. See

Requirement 1.18 et seq.

3.2.7 Capability to retrieve more results (hits) for a previously run search than was provided in an initial results set without having to re-enter the search. See Requirements 1.15, 1.15.1, and 1.19.

Query Sequence Editor with the following minimum capabilities: For creating custom query sequences

4.1 Capability to generate new and/or edit search query sequences.

4.2 Capability to retrieve a specified sequence from nucleic or protein databases into text editor window

4.3 Provide system-created numbers for residue positions. Residue position numbers are to be system created.

4.4 Display residue-position number when the cursor is hovered over a residue.

4.5 Move the cursor to the correct residue when its position number is typed in. When a number is typed in, the system moves the cursor to a residue with that number.

4.6 Copy a sequence or part of a sequence from another source and paste it into the editor window.

4.6.1 Strip or filter non-sequence characters (numerals) and white space, if present, from a pasted sequence.

4.6.2 Convert case of residue symbols in a pasted sequence.

4.6.3 Convert 3-letter amino acid sequence to 1-letter, and vice versa.

4.7 Delete a residue or a block of residues by typing in a range and not having to delete one by one.

4.8 Capability to insert new residues within an existing sequence without overwriting.

4.9 Capability to replace one or more residues with another one or more residues.

4.10 Capability to name the final product as desired, and the file so created can be used as a query in any of the search tools.

4.11 Capability to construct fuzzpro, fuzznuc, preg, and dreg (EMBOSS) and pattern match (STN) query-patterns (i.e. allows syntax characters (special characters and numbers) in addition to letters) as a separate mode from construction of queries containing only letters.

System requirements

5.1 System must run on heterogeneous commodity hardware.

5.2 System must have no single points of failure.

5.3 System must be portable to commercial/private clouds on demand with no re-work.

System must have ability to recover from compute node failure without reloading all data to all nodes.

5.4 System must be highly scalable with little to no configuration changes.

System must provide user defined reporting statistics on demand.

Data management

6.1 Data must be replicated across compute nodes to user configurable level.

6.2 Data management must be distributed to compute nodes.

System must maintain data integrity.

6.3 System must allow for partial reloads and updates.

Job management/queuing

7.1 System must be able to ensure completion/re-execution of all requests without manual intervention.

7.2 System must be able to provide different queue management for customer-defined job populations -- rush, default, etc.

7.3 System must be configurable to either attain minimum runtime for individual jobs or equal allocation of resources to all jobs.

7.3.1 System must be adaptive to varying loads and allocate compute and storage resources accordingly.

Relative light loads would change number of resources available to jobs. If only one job queued at historically light load time, all resources allocated to that one job.

ADDITIONAL Specifications required for USPTO Project ID 102267

Note: Items 2,3,6,7,8,9 & 28 will require support from the ABSS developer

Phase 4 High Level Requirements

1. Development of the SLIC Admin Module and Automate all existing manual processes related to

Documentum to enable access and control via the admin module.

2. Update SLIC to process Standard (ST) ST.23, ST.25 and ST.26 files for Automated Biotechnology

Sequence Search System (ABSS).

3. Update SLIC/ABSS to enable examiners enhanced processing, sorting and analysis of ABSS Search

Result data sets including sorting result sets by, for example, patent no, pgpub no, date order, sequence length or organism. Enable more examiner flexibility in how searching is performed, how results are displayed and ability to sort and further search results.

a. Ability to extract and export data, including Patent No., Pre-Grant Publication (PGPub) No, (Phase 4)

i. Export to Examiner’s Automated Search Tool (EAST) and/or Web-based Examiner’s Search Tool (WEST) and/or Search for Patents (Search4P) and generate query

b. Capability for user to choose among sets of ABSS search results databases to further do a combined text search based on the sequence result output, e.g., East similar to first one for patent numbers, but this is to extract text to create search string for East/West.

c. Ability sort on fields like sequence length, date (of record or within record), organism.

This will allow NCBI

d. to begin identify hit that are not prior art

e. Ability to robustly text search ABSS hit sets using operators similar to as in EAST or WEST

f. Capability to compare different results sets to identify hits common to all sets. This is useful for when claim requires two or more sequences that have to be searched separately

4. Update SLIC to enable examiners enhanced functionality such as comparison of sequence listing files, selectable by application no. and version no. from same case or different case to help examiners identify new matter issues. (H)

5. Complete changes needed to Publication Site for Issued and Published Sequences (PSIPS) SLIC/

PSIPS for publication and viewing of ST.26 sequence listings in addition to ST.23 and ST.25, including mega-sequence listings in raw xml or human readable form. (H)

6. Update SLIC/ ABSS to work with eDRS. (H)

7. Update SLIC/ ABSS to complete changes needed for Certified Copies in Certified Copy Center

(CCC) or Order Entry Management System (OEMS). (H)

8. Update all SLIC / ABSS export work including but not limited to exports for ABSS, Reed Technology Information Services (RTIS), NCBI, PSIPS, On Demand to OEMS for certified copies, PCT Contractor and WIPO. (H)

9. Update all SLIC / ABSS scripts for sequence listing processing and enable access and control via the admin module including makepat, makepub, allow script, sssaddnew, score splitter, ptoform script, etc. (H)

10. Activate “SLIC Load Status” panel? (H)

11. Complete all Enhancements and bug fixes to existing SLIC Modules as needed based on development work during this phase. (H)

12. In ABSS, Enable BLAST searching as well as user modification of search algorithm parameters.

Implement a sequence query editor for ABSS sequence searching. Ability on examiner search tool to pull up a SEQ ID NO, and then have automated entry of that sequence into NCBI BLAST or other publicly available search tools, such as EMBOSS. A simple selection button shown in the ABSS interface which allows the capability for users to select Smith-Waterman algorithm or BLAST algorithm. (H)

13. Work with Enterprise Application Integration Hub (EAI Hub) EAI Hub / SLIC related functionality-funding needed for EAI-Hub as no active project currently in place. EAI Hub- new queues for ST.26 XML files. (H)

14. Patent Application Locating Monitoring (PALM) and Docket Application Viewer (DAV)

PALM/DAVchanges to alert examiner when there is a CRFD as most recent submission (M)

15. Warning to Science Technology Information Center (STIC) staff when title in 120 field does not match title in PALM. (M)

16. Updates to OC / PALM PreExam / MPEP for ST.26 related form para changes (H)

17. PALM Pre Exam interface to be updated to handle ST.26 including new form paragraphs (H)

18. Update data exchange process with RTIS as needed for ST.23, ST.25 and ST.26 sequence listings including any changes that will be needed for RedBook, YellowBook, and GreenBook data files (H)

19. Update World Intellectual Property Organization (WIPO) ST.26 Validator tool as new releases become available.(H)

20. Routinely test existing Supplemental Complex Repository for Examiners (SCORE) SCORE validator and compare files with SLIC validator to ensure parity for ST.23 and ST.25 validation (H)

21. Transfer all documentation, procedures to Operations and Maintenance Team and train them accordingly (H)

22. Update all System Development Life Cycle and operation documents System Design Document, Dynamic Operational Support Plan, and User Manual to reflect the current SLIC system. (H)

23. Update SLIC Workflow Management System (WMS), which uses USPTO’s Hierarchical Finite

State Machine with end-to-end progress tracking modules. (H)

24. Update Sequence listing Review module as needed to accommodate ST.26 validation. (H)

25. Update SLIC’s integration of handling of PCT and 371 sequence listings with PALM Patent

Cooperation Treaty Operations (POWER). (H)

26. Capability to identify and group identical sequences (M). For example: for instances where many sequence records from a large family of related patents contain the same sequence. Need to see the results for only one representative patent, and mask the rest. Filter by assigned sequence identifier for the records.

27. Provide end-user with estimate of time of completion for a search that has been entered. (L)

28. Improve efficiency of ABSS such that Access to search output results files to be available within

20 min of completion of search. (M)

5. Period of Performance:

The period of performance will be a one-year base period with four one-year options.

Base Period: 05/01/2020 - 04/30/2021 Option Year 1: 05/01/2021 - 04/30/2022 Option Year 2: 05/01/2022 - 04/30/2023 Option Year 3: 05/01/2023 - 04/30/2024 Option Year 4: 05/01/2024 - 04/30/2025

6. Deliverables

ITEM SUPPLIES / SERVICES QTY UNIT OF

MEASURE

0001 ABSS Software System to include all aspects of ABSS software system per Section 4 ~ including Software License(s), maintenance services, installations, training, transition plan, Premiere Operational Support:

24-7 with 3-hour response time from initial call.

1 EA