SCORE The Supplemental Complex Repository for Examiners Biotechnology/Chemical/Pharmaceutical Partnership June 2006

2 What is SCORE? Supplemental Complex Repository for Examiners Official repository for complex application data (biosequences, mathematical data, design drawings, 3-D protein crystal data, chemical drawing files, search results, etc.) Cost-efficient repository for mega information submitted with applications Pilot repository for text file wrapper data

3 Why SCORE? Challenges faced with image-based processing of complex data –Prosecution and Publication Images of complex data are not efficient Complex data must be rendered in proper format (text, drawing, proprietary software) –Data Management Supplemental data must be printed or soft- scanned and manually processed Mega portions (possibly 1,000,000+ pages) difficult to store and use

4 Accomplishments to Date SCORE 1.0 deployed August Repository is populated with: –All USPTO biosequence listings –Biosequence search results back to June 2005 –All design drawings received via electronic filing –QBE search results pilot initiated –Beginning to load artifact backfile –Other complex information as needed Interface with eDAN enabled PAIR interface enabled

5 Immediate Future Automate data entry of supplemental file wrapper information upon receipt from applicant Automate biosequence validation, error processing, and report dissemination Automate internal text document handling (e.g., search results) Automate data export to publication contractor and public database partner (NCBI) Complete Electronic Records Management certification

6 Dataflow

7 SCORE Long–Term Objectives Accept all file formats allowed with applications Maintain complex data in proper format for use and export (to search systems, to publication contractor, and/or to public database partners) Provide Examiners with multiple display options Assist with Trilateral exchange of complex data Support growing mega data storage needs Support USPTO electronic file wrapper and electronic workflow solutions

8 Examiner Access (eDAN) Clicking on the SCORE double helix icon opens the SCORE browser and displays the SCORE Table of Contents for this application.

9 SCORE Table of Contents

10 Automated Biotechnology Sequence Search (ABSS) Results Page Files may be viewed when the hyperlink is selected. The file extension identifies the database searched. The header information in the results also identifies the database searched. Files may be saved to a workstation..rge = GenEmbl

11 ABSS Search Results Page This information appears when the file US rge is selected. These results are from a search of the GenBank/EMBL/DDBJ database.

12 ABSS Search Result Example The top 45 hits are shown in the table.

13 ABSS Alignment Example The top 15 alignments are shown in the results.

14 PLUS Search Results Page Again, files can be either viewed or saved to a workstation. When the *.east file download button is selected, the EAST application browser is invoked and executes an EAST search.

15 EAST Search Results Example

16 PLUS Search Results Example Clip of the _CLS.txt file. Clip of the _CLSTITLES.txt file. Clip of the _WDS.txt file. Clip of the _QUAL.txt file.

17 3-D File Page The file may be viewed or saved to a workstation.

18 SCORE 3-D Text Data Page The SCORE team is in the process of determining the appropriate 3-D viewing software. An example of the PDB (Protein Data Bank) viewer, providing an example of viewing capabilities, follows.

19 PDB Viewer Example

20 Accessing PAIR PAIR can be found via the USPTO web site ( Hyperlink

21 SCORE Content via PAIR After Application Number entry The presence of the Supplemental Content tab indicates SCORE content in the file wrapper

22 SCORE Content via PAIR SCORE Content tab was selected This application has a Sequence Listing and Search Results Note the Hyperlinks

23 Sequence Listing via PAIR Once the Sequence Listing is selected, a version may be chosen The Sequence Listing may also be downloaded

24 Sequence Listing via PAIR Navigation tools for the Sequence Listing are provided Header information appears with SEQ ID NO: 1

25 ABSS Search Results via PAIR Multiple sequence searches have been performed in this application A results set may be chosen for viewing or download

26 ABSS Search Results via PAIR Browser functions may be used to navigate the results set

27 PLUS Search Results via PAIR Each version is one set of PLUS (QBE) search results

28 PLUS Search Results via PAIR Search results may be printed

29 Computer Program Data via PAIR

30 Computer Program Data via PAIR

31 Mega Tables via PAIR PAIR download limit is 650 Mb. Please contact the Office of Public Records for copies of files over this limit.

32 Questions? Lisa J. Hobbs, Ph.D. Project Manager Search and Information Resources Administration