Searching the Patent Chemistry Database A Supplement to Searching CrossFire Databasesbased on CrossFire Beilstein

Training Guide

Training Guide CrossFire® Commander Version 7.1

Searching the Patent Chemistry Database A Supplement to Searching CrossFire Databasesbased on Crossfire Beilstein

Training Guide

CrossFire® Commander Version 7.1 Training Guide CrossFire Software Copyright © 1995-2008, Elsevier Information Systems GmbH. CrossFire Beilstein Database: Copyright © 2007-2008, Elsevier Information Systems GmbH. Gmelin Database: Copyright © 2000-2008, Gesellschaft Deutscher Chemiker, licensed to Elsevier Information Systems GmbH; © 1988-1999, Gmelin Institut fuer Anorganische Chemie und Grenzgebiete der Max-Planck-Gesellschaft zur Förderung der Wissenschaften. All rights reserved. ®

This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in other ways, and storage in data banks. Duplication of this publication or parts thereof is only permitted under the provisions of the German Copyright Law of September 9, 1965, in its version of June 24, 1985, and a copyright fee must always be paid. Violations fall under the prosecution act of the German Copyright Law. The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and are therefore free for general use. ®

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Furthermore the Elsevier CrossFire system is subject to the license agreement and the terms and conditions for the CrossFire Beilstein data and database system. Training Guide: May 2008, for Elsevier CrossFire Commander Version 7.1

TABLE OF CONTENTS

INTRODUCTION Searching the Patent Chemistry Database...................................................... 1-1 Patent Chemistry Database ............................................................................ 1-2 Course Objectives .......................................................................................... 1-3 Patent Chemistry Database sources ............................................................... 1-4 Compound Types ........................................................................................... 1-5

SEARCHING BIBLIOGRAPHIC DATA Searching Bibliographic Data ........................................................................ 2-1 Database Selection ......................................................................................... 2-2 Database Structure ......................................................................................... 2-3 Factual Search Comparisons.......................................................................... 2-4 Scenario #1 – Search specific fields .............................................................. 2-5 Query.............................................................................................................. 2-6 Results – Grid View....................................................................................... 2-7 Results – Details View................................................................................... 2-8 View Patent Family Members........................................................................ 2-9 View Compounds with Bioactivity or Application Data ............................. 2-10 Return to the Citation Record ...................................................................... 2-11 View Markush Structure .............................................................................. 2-12 View Markush Display and Referencing compounds.................................. 2-13 What is a Prophetic Compound? ................................................................. 2-14 Determine which Compounds are Prophetic ............................................... 2-15 View Prophetic compounds ......................................................................... 2-16 PRACTICE EXERCISES Find Patented Information by Scientific Area ............................................. 2-17 Export the Citations to an Excel Spreadsheet .............................................. 2-22

SEARCH FOR A SPECIFIC TRANSFORMATION Search for a specific transformation .............................................................. 3-1 Scenario #2 – Reaction processes in patents .................................................. 3-2 Create and Launch the Reaction Query.......................................................... 3-3

View Reaction Details ................................................................................... 3-4 View the Citation Record............................................................................... 3-5 InfoChem ClassCodes.................................................................................... 3-6 Find Similar reactions – Narrow.................................................................... 3-7 Find Similar reactions – Broad ...................................................................... 3-8 Review the Reaction Details .......................................................................... 3-9 PRACTICE EXERCISES Retrieve patent information for a Class of Reactions .................................. 3-11 Use InfoChem Classification Codes to Retrieve Similar Reactions ............ 3-16 Export Reactions to a Report ....................................................................... 3-18

SEARCH FOR SPECIFIC PROPERTIES Search for Specific Properties........................................................................ 4-1 Scenario #3 – Data/structure Search............................................................... 4-2 Create the Query ............................................................................................ 4-3 Search Results – Markush Structure .............................................................. 4-4 Use the Tree Pane to Return to Previous Results .......................................... 4-5 View Bioactivity and Application Data ......................................................... 4-6 View the Original Patent................................................................................ 4-7 View Patent Classification............................................................................. 4-8 View Preparation Reactions........................................................................... 4-9 Retrieve all Related Citations ...................................................................... 4-10 PRACTICE EXERCISES Search for information in a specific class of Compounds ........................... 4-11 Retrieve Preparation Reactions for an Active Compound ........................... 4-15

Introduction

Searching the Patent Chemistry Database

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Welcome to Searching the Patent Chemistry Database, A Supplement to Searching CrossFire Databases- based on CrossFire Beilstein. In this module, you will use the CrossFire Commander 7.1 to search the Patent Chemistry database to retrieve information from organic chemistry patents. The focus of this course is to present information that is unique to the Patent Chemistry Database. General information about how to use the CrossFire Commander can be found in “Searching CrossFire Databasesbased on CrossFire Beilstein.

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Searching the Patent Chemistry Database

Patent Chemistry Database

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Powerful and easy-to-use tool – for research scientists and information professionals – to access structure searchable reactions, compounds and compound property data from selected organic chemistry patents. The ONLY database – to index not only reactions and compounds with data, but also prophetic compounds and analogous reactions including Markush reaction display

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PCD is a structure-searchable CrossFire database used by research scientists and information professionals . It was specifically designed for chemists and is indispensable in synthesis and lead discovery. It is the only database that indexes reactions/compounds with data and prophetic compounds and analogous reactions mentioned in the patent. It is the first database to offer Markush structure displays. PCD is updated biweekly. It contains > 4.8 million compounds/ 4.7 million reactions excerpted from > 400,000 patents (as of March 2008). Yearly growth is 800,000 compounds a year, 500,000 reactions/year, and 35,000 patents/year.

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Introduction

Course objectives

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Use your knowledge of searching with the CrossFire Commander to retrieve information from PCD View bioactivity, application, patent classification, and preparation information Find similar reactions using InfoChem Class Codes View Markush structures and referencing compounds View prophetic compounds Retrieve all related citations for your results Link to patent documents

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In this course, you will view desired patent information resulting from structure, reaction, and data queries. You will use the “Find Similar Reactions” link to retrieve similar reactions in the PCD database using InfoChem ClassCodes. You will learn how to navigate to integrated data, including the original patent document. You will learn how to view Markush structures and prophetic compounds.

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Searching the Patent Chemistry Database

Patent Chemistry Database sources

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International Patent Classes

- C07 - A61K

Organic Chemistry*

Preparations for medical, dental, cosmetic purposes

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- A01N - C09B

Biocides (Agrochemicals, Disinfectants) Dyes and related compounds

Patent Agencies***

- World (WO), United States (US), European (EP) patents

Bio-sequences indexed by name - from Dec. 2003 onwards. *Polymers are indexed, when mentioned in these 4 IPC’s (e. g. formulations). **Main 33 patent agencies deeply indexed.

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Notes The Patent Chemistry Database indexes the main IPC classes which refer to low molecular weight organic chemistry (C07, A61K, A01N, C09B). The Patent Chemistry database covers the World (WO), United States (US), and European (EP) patent agencies from 1976 onwards. The Patent Chemistry database indexes experimental bioactivity and application data as well as physical data. The Patent chemistry database is complementary to CrossFire Beilstein which covers experimental data from historical patent documents from 1886 until 1980.

Introduction

Compound types

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Low molecular weight organic compounds Inorganic compounds* Organometallic compounds*,** Polymeric compounds*,** Prophetic compounds Markush structure display** Markush structures correlated with defined structures

* When mentioned in the four selected IPC classes **Chemical structures available for patent documents published 2003 onwards; (before 2003, only chemical names for polymers and organometallics).

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PCD indexes low molecular weight organic compounds, as well as polymeric molecules, inorganic com-pounds, and organometallic compounds (when mentionned in the 4 IPC classes) From 2003 onwards, the database indexes organic reactions, as well as inorganic and organometallic reactions. The database indexes defined compounds with data, as well as “Prophetic Compounds”, where the author states they can be prepared analogously to given preparation methods (there is no yield or physical properties listed for such compounds). From 2003, graphical representations of Markush structures (linked to the correlated defined structures within the Patent document) are included.

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Searching Bibliographic Data

Searching bibliographic data In this section, you will learn how to:

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View the datastructure of PCD View Use and Bioactivity data View Markush structure

View prophetic compounds

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In this section, you will view the datastructure of the Patent Chemistry Database. You will use the Search All Text and the Search Fields grids to create and launch data queries and view results in various contexts.

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You will view bioactivity data.

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You will view a Markush structure.

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You will group results to display prophetic compounds.

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Searching the Patent Chemistry Database

Database Selection

Once connected, the “Connect” button is replaced with the “Select Database” button. The selected database is displayed.

If you select more than 1 database, the available search fields are adjusted to only those fields common to the chosen databases.

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It is possible to select multiple data sources in order to perform multiple database searches. When multiple databases are selected, you will receive a message in the note area informing you that the All Search Fields area only allows you to search fields common to all the databases selected. The database list box varies based on the databases licensed at your site. The choices are the Patent Chemistry Database, Beilstein, and Gmelin databases. We will search only PCD in this module.

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Searching Bibliographic Data

Datastructure Citations Publication Data Application Data* Priority DataInventor Assignee Title, Abstract, Claim Markush Structures(display only)* Cited Patents

Substances Application Data* Bioactivity Data * Formulation* Metabolism*

Reactions Reaction Scheme Example Text Reaction Conditions InfoChem Reaction Class Codes Markush Reactions (display only)*

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Citation records are produced from the complete frontpage data, including patent inventors, assignees, main patent family members, and the claims text. Substance records provide the chemical structures (including Markush), application data, and property data (bioactivity, spectral, physical, and toxicological) derived from various patent documents. Reaction records provide a reaction scheme that was generated from the Example text, the reaction conditions, and the markush representations for data indexed from 2003 onwards. The asterisk shows items only available for data indexed from 2003 onwards.

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Toxicological Data * Physical Data Spectral Data Markush Structure(diplay only)*

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Searching the Patent Chemistry Database

Factual search comparisons

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Search All Text (Search Basic Indexes) is recommended when:  you do not know the specific field name  the search string can appear in multiple data fields, e.g. application or bioactivity data  the search string can appear in different contexts e.g. in the citation record (title, abstract, claim) and also in the substance record (bioactivity data, but only for PY>=2003) Search Fields is recommended when:  you know the field name and the search string can appear only in one data field, e. g. bibliographic data (inventor, patent assignee, patent application number)

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There are 2 ways to do a data search: Search Text/Field or select a data field. The Search Text/Field conducts a search over all of the basic indexes: - Citations (BICIT) Data fields that cover frontpage (bibliographic data, title, abstract) data and claims text. - Substance (BISUB) Substance identification and property data. - Reactions (BIREA) (reactant, product, selectivity, topic, etc.). When you select a data field, only that field is searched. Use Search Text/Field when you do not know the field name, when the query can appear in multiple data fields or in different contexts. Use Search Text/Field when you know the field name and the query can appear in only 1 field.

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Searching Bibliographic Data

Scenario #1 – Search specific fields

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In the course of a planned joint venture, you are interested in retrieving patent information for the company Aventis Cropscience and any information about fungicides in the patent claims/frontpages.

When the results are retrieved, view the claim text, patent family members, bioactivity data, application data, Markush structure, and prophetic structure.

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Notes You are interested in retrieving patent information for the company Aventis Cropscience and any information about fungicides in the patent claims/frontpage. You will conduct a search and then view the desired claims text, patent family members, Markush structure, bioactivity, and application data.

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Searching the Patent Chemistry Database

Query

Searches the Basic Indexes fields

Use the “Contains” operator to maximize the number of hits

Click to expand your selection

Query is displayed

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Enter the combined text/data query as shown, using the All Text field, the Assignee data field, and the appropriate operators. Use the Find Field or Form button to find and select the Assignee field. Use the List functionality to expand your data selection. Choose Citations as the context for your results. After starting the search, the Search Status Report displays the query analysis and number of hits for the chosen context.

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Searching Bibliographic Data

Results- Grid view in citation context 44 citations retrieved

Click to view details for the list of 44 citations

Click a detail to jump to a specific section in this citation record

Click to view the citation record for this citation in the list

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The resulting list of citations is displayed in Grid view. Click the View Details button to scroll trough the details of each citation; or click Full text to link to the original patent" Right click in the Tree pane to jump to a specific detail in a specific record, group or sort the list, or retrieve a list of structures or reactions.

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Searching the Patent Chemistry Database

Results – Details view

Choose View all > Hit only to view the Patent Assignees and the Title/Abstract/Claims data.

View > Highlight Hit Terms makes it easier to view the queried terms.

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View the details for EP1204323. Choose View All> Hit Only to view only those fields that contain terms or values matching your serach criteria (the patent assignees and claims text). View> Highlight Hit Terms makes viewing easier. It is recommended that you activate the option View> Highlight Hit Terms, as it increases the visibility of the requested results. It is saved with your profile when you disconnect from the Commander.

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Searching Bibliographic Data

View Patent Family members

For WO and EP patents the designated countries are also given.

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For the same basic invention, an inventor can apply for a patent in different countries and at different patent offices. Depending on the legal status, each patent office creates new document types (published document, granted patent, etc.) from the original application document. All these documents, derived from the same invention, form a patent family. Within each patent family, the database indexes only one patent family member, most often the first published patent document or an English language equivalent.

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Searching the Patent Chemistry Database

View compounds with bioactivity or application data 58 substances retrieved

Click to jump to bioactivity data for the first compound in the list

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The “Compounds with Use/Bio” link allows you to retrieve all of the compounds included in the citation that contain application or bioactivity data. Double click a structure or use the Tree pane to view the details. In this example, the Bioactivity Data lists “fungicidal” in the Effect field.

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Searching Bibliographic Data

Return to the citation record Use the Back button or the Tree Pane to return to the citation record

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We would like to return to the citation record to see if there are any Markush displays of the structures. After viewing the list of compounds, return to the citation record by clicking the back button. Alternatively, you can click on the link for EP1204323 in the Tree pane.

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Citation record

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Searching the Patent Chemistry Database

View Markush structure A Markush structure is a generic structure that represents defined compounds with data (or prophetic compounds). It is often used to describe the claim of the patent.

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A Markush structure is a generic structure that can represent hundreds of different defined compounds with data or prophetic compounds. It is often used to describe the claim of the patent. Markush structures are displayed in a compressed form showing only the generic structure scaffold in a standardized form. Look for “Markush Structures” in the Field Availability List and click to view the substance record for the Markush structure.

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Searching Bibliographic Data

View Markush display and referencing compounds Right click markush structure to display Markush viewer

Display Referencing compounds

226 referencing compounds

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Markush structures are displayed in a compressed form showing only the generic structure scaffold in a standadized form. Right-click the Markush structure window to open a second window that displays the Markush structure with the definition of all substituents. The symbols used for the substituents are the same as those used by the inventor in the patent document. To view all of the defined compounds for the Markush structure, click the link for Referencing Compounds. (Alternatively, you can click the link for Substance type).

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Searching the Patent Chemistry Database

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What is a Prophetic compound?

A prophetic compound is a compound specifically mentioned in a patent where the inventor states that it could be prepared or used analogously to a given example.

Prophetic compounds have neither been synthesized, nor has their existence been proven. In PCD prophetic compounds are marked with a flag, which is not searchable, but can be used in grouping/sorting. A substance may be prophetic in patent A and “real” (with data) in patent B.

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A patent may contain different types of substance representations: defined compounds that have specific data available (such as an experimental section for a reaction process, physical data and bioactivity data) and Prophetic Compounds. Prophetic compounds are compounds that are legally relevant compounds, for which the inventor states that they can be prepared analogously to described methods, but they do not need supporting data (yield, spectral data) to prove their existence. Prophetic compounds are important for low molecular weight organic chemistry where about 20% of the compounds mentioned in a patent are considered as “prophetic."

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Searching Bibliographic Data

Determine which compounds are prophetic Return to citation record Group by Compound Status in Patent

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The citation record for EP1204323 tells us that 270 substances are contained in this patent. Which ones are prophetic?

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Click the “Get” button to retrieve the list of substances.

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Group the list by “Compound Status in Patent” to create a list of prophetic compounds.

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Searching the Patent Chemistry Database

View prophetic compounds

Prophetic compounds can have experimental data

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View the details for your list of prophetic compounds. A prophetic compound may be considered prophetic in one patent and be shown as a “real” compound with supporting data in another patent. Therefore, the substance record for a prophetic compound may contain experimental data.

Searching Bibliographic Data

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Find patented information by scientific area Exercise 1

Find the field name

Conduct a search to retrieve patents from Novo Nordisk that contain information about cardiovascular disorders in the claim. 1. Click the Query tab. 2. Click the Search Fields tab in the Tree pane. 3. Click the Find Field or Form button and type assignee in the Search Field Name in Hierarchy box. Click OK.

4. Double-click the Patent Assignees entry to add this field to the Search Text/Fields grid. 5. In the Relation column, select starts with from the drop-down list. 6. In the Field content box, type novo. 7. Click the List button. Verify the occurrence of the term “novo” in the database. Click Cancel.

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Searching the Patent Chemistry Database

Search All Text

Select the search context

8. Type cardio* in the All Text box. Verify that and is selected as the operator.

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Select Citations in the drop-down menu next to As result I want to get.

10. Click the Start Search button.

11. Click the View button.

Display the full record

View the indexed patent

12. Click the View Details button for the hit below.

13. Under Field Availability, click the IND (Indexed Patent) hyperlink.

Searching Bibliographic Data

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14. Click the home button to return to the top of the page. View the claims text

15. Under Field Availability, click the CONT (Title/Abstract/Claims) hyperlink.

16. Click the View menu and confirm that View> Highlight Hit Terms is checked. Scroll through the Title/Abstract/Claims section to find your highlighted term. 17. Click the Home button to return to the top of the page. View the Markush structure – scaffold only

18. Under Field Availability, click the MSTR (Markush Structures) hyperlink.

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Searching the Patent Chemistry Database

19. Click the View menu and confirm that View>Structures Included is checked. You should see the compressed Markush structure.

View the substituent definitions

Open the substance record for the Markush structure

Display all related compounds

20. Right click the compressed Markush structure to view the substituent definitions. Click OK.

21. Click the Markush PRN link located above the compressed Markush structure.

22. Click the Referencing Compounds link.

Searching Bibliographic Data

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23. Click the View button.

24. Click the Details button to view the full display for the first record. 25. Click the Previous screen hyperlink to go back to the original substance record.

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Searching the Patent Chemistry Database

Export the citations to an Excel spreadsheet Exercise 2

Export hits from Exercise 1 to an Excel spreadsheet. Use the predefined export setting “Citations…to Table”. 1. Using the Tree View, click to select the list of citations from Exercise 1.

Use the Export Hits button

2. Click the Export Hits button and then choose “Citations…..to Table”.

3. Click the radio button for Specify Hits or Range. Enter 1 to 4. Click Start.

Searching Bibliographic Data

4. In the Save Export File As dialog box, type Export in the File name box. Click Save.

5. View the Excel spreadsheet.

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Search for a Specific Transformation

Search for a specific transformation In this section, you will learn how to:

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Search for a compound as a product

Find similar reactions using InfoChem ClassCodes

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PCD contains about 4736454 structure searchable reactions from 457977 patents (Database PA080103PA). It is the first end user patent database to display Markush reactions(from 2003 on). You can search this database using a full or partial reaction. All reactions are indexed with InfoChem ClassCodes that enable users to retrieve similar reactions from all of the CrossFire databases. In this section, you will search for a compound as a product and find similar reactions in the Patent Chemistry Database.

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Searching the Patent Chemistry Database

Scenario #2 – Reaction processes in patents

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You are interested in retrieving information on the details of the preparation process for a specific compound. You are interested in whether this information can be found in a published patent. O

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View the reaction details.

View the Frontpage/Claim/Abstract

Find similar reactions in the Patent Chemistry Database

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In this example, you are interested in retrieving patent information about reactions where a defined compound is the product. Additionally, you are interested in the patented reaction details that are defined in the experimental section of the retrieved reaction.

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Search for a Specific Transformation

Create and launch the reaction query

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A partial reaction search can be created using one of the structure editors or the Structure Search Options area located to the right of the Structure/Reaction Search box. Draw the structure shown above.

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Clicking “as reactant” will retrieve reactions where the defined structure is a starting material.

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Click “as product” to retrieve reactions where the structure is prepared.

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Select Reactions from the drop-down menu near As result I want to get. Click Start Search.

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Searching the Patent Chemistry Database

View reaction details

Original heading and experimental description of the reaction from the patent.

Spectral data from the patent.

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The Example Title is the original heading of the reaction text inside the original patent. This field is useful as a display field, making it easier to find the reaction in the original patent. The Example Text contains the text for the reaction example (experimental section, receipt). It is an exact copy from the original patent text. Reaction conditions (temperature, pressure, and time) are indexed in separate data fields.

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Search for a Specific Transformation

View the citation record

View frontpage and claim of the patent.

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Patent documents are indexed by a reaction scheme where the products and reactants are structure-searchable. Reagents and solvents will often have a structure associated with them, whereas organometallic compounds and catalysts are indexed by structure when they are commercially available. If they are not commercially available, they are entered by name only. Analogous reactions are often indexed as half-reactions with a product structure only and the corresponding example text.

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Searching the Patent Chemistry Database

InfoChem ClassCodes Reaction Similarity Broad Only reaction centers are compared.

Reaction Similarity Medium Reaction centers and the alpha atoms and bonds are compared.

Reaction Similarity Narrow Reaction centers and the alpha and beta atoms and bonds are compared

Reactions in the CrossFire databases are indexed using InfoChem ClassCodes. Similar reactions have the same ClassCodes in these databases.

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We can use the InfoChem ClassCodes to retrieve similar reactions in any of the 3 CrossFire databases. The CLASSIFY algorithm is used to categorize reactions by the type of chemical transformations they represent. Reactions are grouped based on the structural environment at the reaction centers and the kind and hybridization grade of the alpha/beta-atoms. The reactions are analyzed and are assigned a reaction ClassCode. The class codes are: Broad- same reaction centers. Medium- reaction centers and alpha atoms and bond types are the same. Narrow-reaction centers and alpha & beta atoms and bond types are same.

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Search for a Specific Transformation

Find similar reactions – Narrow Use the back button to return to the Reaction record

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We retrieved one interesting reaction from our initial search. We want to generalize the query to retrieve additional information about this type of reaction. Click the “Find Similar Reactions” link to use InfoChem ClassCodes to retrieve similar reactions. The Reaction Similarity Search dialog box opens, displaying an area to select the appropriate database and an area to access all the similarity levels. You can select the individual similarity feature or you can select All Choices (it searches the selected database comprehensively for the Broad, Medium and Narrow ClassCodes).

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Searching the Patent Chemistry Database

Find similar reactions – Broad Use the Tree Pane to return to the Reaction record

This hit was not retrieved by the Narrow search.

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Use the Tree Pane to return to the Reaction record. The procedure for conducting a Broad similarity search is the same as it was for the Narrow similarity search; you will receive different results due to the measurement involved in the process. Typically, the list for a broad search will be larger than a search for the Medium or Narrow searches. Double click a structure in your list to view the Reaction Details.

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Search for a Specific Transformation

Review the reaction details These fields facilitate retrieval of the reaction details in the original patent.

This is the name that the author, or inventor, of the patent has used for this example.

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There are a series of fields, found under Reactions Details, which facilitate the viewing of reaction information in the original patent. Example Name is the name that the author/inventor has used for the reaction text in the patent document. Example Title is the original heading of the reaction text inside the original patent. Location in Patent contains the location of the example text in the original patent.

Indicates the location of the example text within the patent.

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Search for a Specific Transformation

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Retrieve patent information for a class of reactions Exercise 1

You want to retrieve patent information about ring opening reactions of oxirane compounds to the corresponding 1hydroxy-, 2-substituted products. Conduct a reaction search, and then group the results by narrow reaction classification code. View the reaction description for a specific reaction. View the claim information from the patent document. 1. Click the Query tab. Click the Clear Query button.

2. Double-click the Structure/Reaction Search box.

3. Draw the backbone of the reaction query.

O

O

4. Click the Edit tool.

Apply the Beilstein Generic group

5. Click the terminal carbon atom on the product. Type G in the Atom Attributes box under Symbol and press Enter. O

O G

6. Click the Select tool. Apply maximum free sites

7. Control-click to select the four carbon atom positions where free sites are to be applied.

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Searching the Patent Chemistry Database

8. Choose Options > Define Atom. Choose Max next to Free Sites. Click OK.

9. Using the Edit tool, click one of the positions for the aryl group. Type ary into the Atom Attributes box under Symbol. Click OK. Repeat for the other aryl group position.

10. Click the Reaction Mode button.

11. Use the Select tool to select the product. Click the Product button. Select the reactant. Click the Reactant button.

Map the reaction

12. Using the Edit tool, click the carbon atom in the reactant. Draw a line to the corresponding atom in the product. Repeat for the second set of carbon atoms.

Search for a Specific Transformation

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13. Click the to Commander button.

14. Under Allow, check the boxes for addl. rings, isotopes, charges and radicals.

15. For the Search Context, choose Reactions.

16. Click Start Search.

17. Click View.

18. Click the Sort/Groupbutton.

Group the results

19. Click the Group tab. Select Narrow Class Code (RX.NCODE) from the drop-down list. Click OK.

Examine the resulting groups

20. In the Tree View, click a + to open a group. Click a product name to open the record.

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Searching the Patent Chemistry Database

View the reaction description

21. View the Example Name (that is the name of the reaction that the author/inventor has defined in the original patent), Example Title (the header for the reaction description), and Example Text (the full reaction description).

22. Scroll to the reference information. Click the View Details button for Frontpage/Claim. The corresponding citation record is displayed.

View the abstract and claims information

23. In the Field Availability box click the CONT hyperlink.

Search for a Specific Transformation

Return to the Results list

24. Use the Tree pane to view the details for another group in the results list.

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Searching the Patent Chemistry Database

Use InfoChem Classification Codes to retrieve similar reactions Exercise 2

Use the results obtained in Exercise 1. Retrieve similar reactions from the Beilstein database.

1. Using the Tree View, click to select a reaction.

Find Similar Reactions

Select the Beilstein database

2. Click the Find Similar Reactions hyperlink.

3. Select Beilstein from the “Find Similar Reactions in” drop-down list.

Conduct the similarity search

4. Under All Choices, click find all.

View only the narrow precision results

5. In the Search Status Report dialog box, uncheck the boxes for the broad and medium precision level hitsets (found under query. RX.BCODE and RX.MCODE).

Search for a Specific Transformation

6. Click View. In the next exercise you will use the Tree pane to return to the Patent Chemistry Database.

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Export reactions to a report Exercise 3

Use the results obtained in Exercise 1. Create a user-defined report which contains reactions and data exported from the first four records in the group. Include the following information in the HTML report: the reaction structure, a list of all of the references, the patent assignee information, and the reaction details.

1. Using the Tree pane, click to select the hitset containing the grouped reactions. The gridview of the groups will appear showing the group number and the number of reactions contained within the group.

2. Using the Tree pane, right-click the same hitset and select Sort/Group from the list. Ungroup the Hitset

Sort the Hitset

3. Select (no_grouping) from the dropdown menu under the Group tab. Click OK.

4. Click the Sort/Group button. Under the Sort tab, select Yield (percent) from the dropdown menu. Select the radio button for Descending.Click OK.

Search for a Specific Transformation

5. Select the first four reactions by using a checkmark. Create a new export setting

6. Click the Export Hits button.

7. Click the New button. Export – Define Content

8. In the Define Export Format category, click the radio buttons for Browser [HTML] and List [Report].

9. Click the Next button.

10. Check the box for Include images of title structures/reactions. If necessary, uncheck other choices.

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11. Under Facts, check the box for Facts. Set the occurrences per fact to 5.

12. Under Facts, click the Select facts to View button.

Define a new user view

13. In the Define User View dialog box, click New.

14. Click the plus (+) sign to expand Citations in the Available Fields pane. Double-click Indexed Patent to add it to the Selected Fields pane. Double-click Patent Inventors to add it to the Selected Fields pane.

15. Click the plus (+) sign to expand Reactions in the Available Fields pane. Double-click Reaction Details to add it to the Selected Fields pane.

Search for a Specific Transformation

16. Click OK.

Save the user view

17. Enter Reactions_to_HTML_Patent_References for the file name. Click Save.

18. In the Define User View dialog box, click Apply.

19. Under Additional Data, check the box for incl. References.

20. In the Export – Define Content dialog box, click Next.

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Enter a comment

21. In the Export – Finish dialog box, enter Reactions, Patent info, and References to HTML report for the comment.

22. Click Finish.

Save the export setting

23. Enter mysetting as the export setting name.

Search for a Specific Transformation

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24. Click Save.

Apply the new export setting

25. Click the Start export button.

26. In the “Export data from the following hits” dialog box, click the radio button for Selected hits Only.

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27. Click the Start button.

28. Enter a name for the file. Click Save.

Search for a Specific Properties

Search for specific properties In this section, you will learn how to:

• • • • •

Search for a compound with specific activity

View Markush structures and all the referencing compounds View the patent

View bioactivity, application, patent classification, and preparation information Retrieve all related citations for your results

Key points 



 

In this section, you will learn how to search for a compound with specific activity. You will view the related Markush structures and other referencing compounds. You will retrieve the related citations. You will view the patent document using OpenURL linking .

Notes

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Scenario #3 – Data/structure search

•

You are interested in retrieving comprehensive information on whether a defined compound has a written claim for a specific application or bioactivity, in particular whether it exhibits antiviral (or virucidal) activity. O

N

O

N

O N

Cl

O

•

When the substance and citation data are retrieved, view the bioactivity and application data, claim text, Markush structure, patent classification, and preparation reactions.

Notes Key points 



You are interested in retrieving comprehensive information on whether a defined compound has a written claim for a specific application or bioactivity. View the bioactivity and application data, the claim text, the Markush structure, the patent classification, and the preparation reactions.

Search for a Specific Properties

Create the query Select to allow retrieval of mixtures and Markush structures

Antivir*; viru*

All Text is Antivir*; viru* is the same as (bisub="antivir*" or bisub="viru*")

All Text Searches all 3 Basic Indexes when the query does not include a structure or reaction

Key points 







The Patent Chemistry Database supports two structure search options that are not available within the Beilstein or Gmelin database: the ability to search for mixtures and the presence of Markush structures. Markush structures are structures that are indexed only for display from patents that have been published from the year 2003 and onwards. These structures are not explicitly searchable. The “Search All Text” area allows you to conduct a search over all of the Basic Indexes. The indexes are: BICIT (citations), BISUB (substances), and BIREA (reactions). When a structure or reaction is coupled with an All Text search, the BISUB or BIREA basic index is searched.

Notes

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Search results – Markush structure

Double click and select Referencing Compounds to view the structures

Right click to display Markush Viewer

Key points 

 





The retrieved substance list displays two compounds. One is the exact match and the other is the Markush structure. Both compounds have bioactivity data. Markush structures are displayed in a compressed form only showing the generic structure. Double-click the Markush structure to change to the Substance Characterization information for the Markush structure. To view all structures that have been correlated to a Markush structure, click the Referencing Compounds hyperlink.

Notes

Search for a Specific Properties

Use the Tree pane to return to previous results Single click to open substance record in Details View

Notes Key points 



We would now like to take a closer look at the query results and review the bioactivity data for the second compound . After viewing the Markush structure and its referencing compounds, use the Tree Pane to open the substance record for the second compound in the list.

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View bioactivity and application data

Notes Key points  

The use for this substance is as an antiviral drug. This substance has been tested for antiviral activity in the HCMV Polymerase assay.

Search for a Specific Properties

View the original patent

Location in Patent makes it easier to retrieve the information in the original patent. Click the Full Text hyperlink to view the patent.

Notes Key points 





The “Location in Patent” field contains the location of the data within the patent making it easier to find the information in the original patent document, especially within a large patent. The display most often represents the page number or the page column (US patents). Here we see that the method details can be found in columns 7-8 in the patent.

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View patent classification View the details of the patent from within the CrossFire Commander

Notes Key points 



The Patent Classification (CLS) data field displays information about the patent classification in terms of content. It is a hierarchical classification system used to classify and search patent documents. Two patent classification systems are in use: The International Patent Classification Code (IPC) and the US Patent Classification Code.

Search for a Specific Properties

View preparation reactions View > Substance as Product only

Use the back button to return to the substance record

Notes Key points 





In the scenario description, we indicated that we would like to know which preparation reactions are available. To view only preparation reactions, choose View > Substance as Product only. Only those reactions showing the synthesis of this compound will be displayed. To view the details of these preparation reactions, use the RX hyperlink found in the Field Availability List.

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Retrieve all related citations Right-click in the Tree pane or

Notes Key points  





In Substance view, you can right-click a hitset to obtain all the related citations. Alternatively, you can choose Get All related Citations, and make the same selections. A new hitset is created, containing all citations referencing the selected compound. The new hitset is represented in the Tree View as a linked list and is prefaced with the indicator “L”.

Search for a Specific Properties

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Search for bioactivity/application information in a specific class of compounds Exercise 1

Create the query

Conduct a search to retrieve patents that report substances containing the 8-hydroxy-4-quinolinone substructure. Require that the substances show antiherpetic activity.

1. Click the Query tab. Click the Clear Query button.

2. Draw the structure.

Define the structure search options

3. Under Free Sites, check the box for all atoms. To include Markush structures, check the box for relat. Markush under Allow.

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Enter the data constraint

Select the context

4. Type herp or antiherp for the All Text field. Choose Starts with as the relation.

5. Select Substances in the drop-down menu next to As Result I want to get.

6. Click the Start Search button.

7. Click View.

8. From the list of retrieved substances, right-click the first Markush structure. Click OK. Double-click the structure to view the details.

View the hit data

View all fields

9. Click View all > Hit only. Scroll through the record to find the terms from your query.

10. Click View hit > All Fields.

Search for a Specific Properties

Export structures and data

11. Click Export Hits > Substances-IdentificationApplication-Bioactivity-to Report.

12. Click the radio button for All, and then click Start.

13. Name the file Exercise1. Click Save.

14. View the file. Close the browser window.

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View the citations hitset

15. Use the Tree pane to retrieve a list of citations from the substance hitset. Right-click the hitset and select Get All Related Citations.

16. Click the radio button for the current hitset and click OK. Link to the Full Text

17. Click the Full Text button to link to the patent for the first citation in the list. Then, click the link for Espacenet.

Search for a Specific Properties

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Retrieve preparation reactions for an active compound Exercise 2

Retrieve preparation reactions and associated data for a substance retrieved in Exercise 1.

1. Using the Tree View, click to open the hitset containing the list of substances retrieved in Exercise 1. Click the 9th substance in the list to view the full record.

View all reaction details

View only preparation reactions

2. In the Field Availability box, click the (Reaction Identification) hyperlink. 3. From the View menu choose View > Substance as Product only.

4. In the Field Availability box, click the RX (Reaction Identification) hyperlink.

View the reaction scheme

5. Choose View > Structures included. Scroll to the reaction scheme.

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View preparation reaction details

6. Review the reaction description provided in the Example Text section.

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