Creating IP Reports Integrating Sequence, Family, and Hit Structure data with BizInt Smart Charts

Transcription

1 Patents & IP Sequences Clinical Trials Drug Pipelines Creating IP Reports Integrating Sequence, Family, and Hit Structure data with BizInt Smart Charts PIUG 2019 Biotechnology Conference, Boston MA John Willmore 19 February

2 doxifun.com/puppies 2019 BizInt Solutions, Inc 2

3 Agenda IP Sequence reports Hit Structure reports Summary Record exports Reference Rows BizInt.com/slides for other presentations 2019 BizInt Solutions, Inc 3

4 Agenda IP Sequence reports Hit Structure reports Summary Record exports Reference Rows 2019 BizInt Solutions, Inc 4

5 IP Sequence Databases Provide data on sequences filed in patents GQ Life Sciences GenomeQuest (Geneseq, GQ-PAT) STN (USGENE, DGENE, PCTGEN) 2019 BizInt Solutions, Inc 5

6 Sequence Databases on STN DGENE, USGENE, PCTGEN Jim Brown s workshop this morning provided step-by-step instructions for searching D BIB SCORE ALIGN Import your transcripts into BizInt Smart Charts Each row is a sequence from a patent pub. Don t skip Validate Sequences step! 2019 BizInt Solutions, Inc 6

7 Sequence Databases on STN 2019 BizInt Solutions, Inc 7

8 Sequence Databases on STN CAplus Not supported yet Save both your transcript D BIB HITRN and your Alignment report (.xss) 2019 BizInt Solutions, Inc 8

9 Sequence Databases on GenomeQuest GQPat, GENESEQ Results filters now apply to BizInt exports (e.g. top results per query) 2019 BizInt Solutions, Inc 9

10 Sequence Databases on GenomeQuest CAS Biosequences Watch this space! 2019 BizInt Solutions, Inc 10

11 Export your search results 2019 BizInt Solutions, Inc 11

12 Export from GenomeQuest 2019 BizInt Solutions, Inc 12

13 Added Unique Family Sequence ID Possible development: each unique sequence only appears once per family Added Sequence Listing Equivalents Useful in publication-level reports 2019 BizInt Solutions, Inc 13

14 Features of IP Sequences in BizInt reports Each row corresponds to a sequence in the context of a query. Columns contain bibliographic data, sequence details, and query results. You may see the same sequence more than once in a report. Family equivalents are not removed BizInt Solutions, Inc 14

15 BizInt Smart Charts Sample sequence data report Show a sample report with sequence data

16 BizInt Smart Charts Sample sequence data report - features Show a sample report with sequence data Bibliographic Data

17 BizInt Smart Charts Sample sequence data report - features Show a sample report with sequence data Sequence Data

18 BizInt Smart Charts Sample sequence data report - features Show a sample report with sequence data Query Results

19 About the Alignment Column The Alignment column appears in the same default font as all columns You might be tempted to change the font to Courier New DON T! Text menu Fixed Width (e.g. Alignment) is the correct technique Preserves runs of whitespace when exporting to HTML, Word, or Excel 2019 BizInt Solutions, Inc 19

20 Features of IP Sequences in BizInt reports 2019 BizInt Solutions, Inc 20

21 Features of IP Sequences in BizInt reports 2019 BizInt Solutions, Inc 21

22 Non-Patent Sequence Databases Can support as needed e.g. SWISSPROT, DrugBank Can be combined with IP sequences Cannot be grouped with patent families No tools for deduplication 2019 BizInt Solutions, Inc 22

23 Sequences in Literature Most collections are structed around sequences with multiple citations per seq CAplus is organized by document, with multiple sequences per doc 2019 BizInt Solutions, Inc 23

24 Improved Literature Support -- Project Goals Bring literature support up to the same level as drug pipelines, clinical trials, patents, and IP sequences Collecting user priorities to help set our development plans Focus of development for the next year BizInt Solutions, Inc 24

25 Improved literature support - summary Identify Common Citation to allow Reference Rows operations and deduplication Literature support in all products Combine literature with patents OR trials Options for Citation formats, exports Support for additional sources Additional fields for analysis Improved hyperlink generation 2019 BizInt Solutions, Inc 25

26 Agenda IP Sequence reports Hit Structure reports Summary Record exports Reference Rows 2019 BizInt Solutions, Inc 26

27 Deliver reports in HTML, Word, Excel Link to Link record to web resource in the export (like fileuspto) Link to record on source platform 2019 BizInt Solutions, Inc 27

28 Summary Record export in Word Fields are the columns in chart Content, like hyperlinks, is included in the Summary Record 2019 BizInt Solutions, Inc 28

29 Summary Record export with Hit Structures Text from CAplus record Each hit substance identified Structures with annotations including multi page images Index Terms 2019 BizInt Solutions, Inc 29

30 A structure oriented Index of Hit Structures Structures with annotations Each hit substance identified Links to references for each structure Multiple images (continuation) or mixtures 2019 BizInt Solutions, Inc 30

31 Option: Index of Hit Structures 2019 BizInt Solutions, Inc 31

32 Option: Hit Structures 2019 BizInt Solutions, Inc 32

33 Option: Index Terms 2019 BizInt Solutions, Inc 33

34 Importing transcripts with hit structures (STNext) Make sure that Classic Display is on Start new transcript before displaying BizInt Solutions, Inc 34

35 BIB vs. IBIB We recommend using tagged (BIB), rather than indented (IBIB), display formats Some field contents (table headings) appear before the label in IBIB Indent levels in RTF are more reliably detected in BIB 2019 BizInt Solutions, Inc 35

36 Agenda IP Sequence reports Hit Structure reports Summary Record exports Reference Rows 2019 BizInt Solutions, Inc 36

37 Summary Record export in Word Fields are the columns in chart Content, like hyperlinks, is included in the Summary Record 2019 BizInt Solutions, Inc 37

38 Summary Records Table of Contents Add a table of contents in Word 2019 BizInt Solutions, Inc 38

39 Summary Records Table of Contents Sections are marked up for headings First column in chart is used as TOC entry 2019 BizInt Solutions, Inc 39

40 Summary Records Table of Contents Can collapse the Index of Hit Structures (in recent versions of Word) 2019 BizInt Solutions, Inc 40

41 Option: Claims + Hit Structures 2019 BizInt Solutions, Inc 41

42 Link sequence results with hit structures Follow Cookbook recipe to create a summary of sequence hits for each 2019 BizInt Solutions, Inc 42

43 Option: Alignments + Hit Structures 2019 BizInt Solutions, Inc 43

44 Option: Alignments + Hit Structures 2019 BizInt Solutions, Inc 44

45 Agenda IP Sequence reports Hit Structure reports Summary Record exports Reference Rows 2019 BizInt Solutions, Inc 45

46 Patent Databases Provide data on patents filed worldwide STN Classic, STNext, & New STN Questel Orbit.com Minesoft PatBase Innovation, Cortellis IP, Integrity Patents LexisNexis TotalPatent GQ LifeSciences LifeQuest 2019 BizInt Solutions, Inc 46

47 Tools for integrating patent data Combine charts using File Combine command Identify related records using the Identify Common Patent Family tool BizInt Solutions, Inc 47

48 Tools for integrating patent data Combine charts using File Combine command Identify related records using the Identify Common Patent Family tool. Use BizInt Smart Charts Reference Rows to summarize related records in a single row BizInt Solutions, Inc 48

49 Combining Charts You can combine two or more charts into a single report BizInt Smart Charts usually removes duplicate rows when combining Combining different queries? Use the Combine without removing duplicates option in the Combine wizard See 2013 PIUG Biotech presentation for more details (@ bizint.com/slides) 2019 BizInt Solutions, Inc 49

50 Combining multiple queries Show the combine option to not remove duplicates 2019 BizInt Solutions, Inc 50

51 Preserving Multiple Queries First combine non-sequence charts with standard options (remove duplicates) Then combine the resulting non-sequence chart with the sequence results (without removing duplicates) Only use without removing duplicates option when you want to see variations on a row side by side 2019 BizInt Solutions, Inc 51

52 Common Patent Family Identify Common Patent Families tool 2019 BizInt Solutions, Inc 52

53 Minimum effort with Reference Rows Save chart in BizInt Smart Charts for Patents Send to Reference Rows 2019 BizInt Solutions, Inc 53

54 Minimum effort with Reference Rows Generate Common Patent Family (if needed) 2019 BizInt Solutions, Inc 54

55 Minimum effort with Reference Rows Simply Finish on step two 2019 BizInt Solutions, Inc 55

56 Minimum effort with Reference Rows File Export Word - summary records 2019 BizInt Solutions, Inc 56

57 Reference Rows: Selection View Unique fields are easily integrated in BizInt Smart Charts Reference Rows 2019 BizInt Solutions, Inc 57

58 Reference Rows: HTML exports As seen in the fully integrated view 2019 BizInt Solutions, Inc 58

59 Integrate data from related records 2019 BizInt Solutions, Inc 59

60 Reference Rows: user-defined rules 2019 BizInt Solutions, Inc 60

61 Summarize data from related records 2019 BizInt Solutions, Inc 61

62 Sequence Summary Recipe Recipe for creating the sequence summary table at bizint.com/cookbook Create Subtable from any columns you want NOTE: alignment loses fixed width formatting In Reference Rows, choose Summarize All Values column rule Export chart 2019 BizInt Solutions, Inc 62

63 Summary Record export 2019 BizInt Solutions, Inc 63

64 Summarize at Patent or Sequence Level Always start with Tools Identify Common Patent Family to create the Common Family column (this is a magic column) Replace contents of the Common Family column with the data you want to group by Select column, copy Select Common Family, paste Patent level: Patent Number Sequence level: Sequence ID (pub+seqidno) 2019 BizInt Solutions, Inc 64

65 Questions?