Text Mining & Visualization

Impressions of emerging capabilities

Cynthia Barcelon-Yang (speaker)

Yun Yun Yang (speaker)
Lucy Akers

Bristol-Myers Squibb
2007 PIUG Northeast Conference
New Brunswick, New Jersey

Introduction – Text Mining &Visualization

Overview of Text Mining Tools
■ Capabilities
■ Data Sources
■ Results
■ Strengths

Summary
Why do we need a tool to do text mining?

Welcome to the age of too much information...

 Typical questions asked of IP Operations
Often, the IP Operations group within an organization provides centralized support
to a wide range of business units, and is responsible for answering the following:

How many patents do we have concerning technology ‘x’?

How does our portfolio compare with company ‘ABC’ ?

Who is citing our portfolio?

Which patents do business unit ‘xyz’ own?

Which patents should we divest as a result of selling division
XYZ?

How do our invention disclosures compare with current granted
patents?

How do we improve our patent operations?
 What is text mining?
(according to Marti Hearst of UC Berkeley School of Information)
■ The discovery of new, previously unknown information, by
automatically extracting information from different written
resources.
■ A variation on a field called data mining, that tries to find
interesting patterns from large databases.
■ Many researchers think it will require a full simulation of how the
mind works before we can write programs that read the way
people do.
■ computational linguistics (also known as natural language
processing)
■ Hearst distinguishes between "real" text mining, that discovers
new pieces of knowledge, and approaches that find overall
trends in textual data.
Text Mining Process

Courtesy of: Invention Machine Corp.

 Common Tasks

List generation (can be displayed as histograms)

List cleanup and grouping of concepts

Co-occurrence matrices and other graphing

Clustering, categorization, grouping and
extraction of text

Mapping document clusters or concepts

Adding temporal components to maps

Citation analysis

Subject/Action/Object (SAO) functions (a.k.a.
NLP)

Federated searching e.g. on Internet or Intranets
 Project Planning
■ Phase I
►Literature searches, key references, brainstorming of
text/data mining & visualization
►Identify potential tools to evaluate
►Vendor onsite demonstrations
► Summary of initial tool evaluations
■ Phase II
►Pilot selected tools
►Identify potential clients groups and interview
representative clients
Investigation & Process Approach

■ Scout the literature/internet sources & brainstorm

■ Benchmark
■ “Patinformatics – Tools and Tasks” by Tony Trippe,
World Patent Information 25 (2003) 211–221
■ “Data Visualization Tools - A Perspective from
the Pharmaceutical Industry” by Jeannette Eldridge,
World Patent Information 28 (2006) 43–49
■ Vendor demos
 Tools Initially Identified

AnaVist Matheo Patent

Anacubis OmniViz
Aureka PatAnalyst
Bioalma Quosa
BizInt Technology Watch
ClearForest Temis
Delphion VantagePoint
Entrieva (Semio) Vivisimo
GoldFire Wisdomain
Inxight Wistract
M-CAM
Vendor Tool Demonstrations
1.Quosa
2.Inxight
3.PatAnalyst
4.OmniViz
5.Temis
6.Aureka
7.Wisdomain
8.GoldFire
9.VantagePoint
10.ClearForest
11.m-CAM
12.RefViz
 * Overview of Vendor Tools

Type of Tool

Capabilities

Data Sources

Results

Strengths

Summary
* Text mining tool slides are provided courtesy of the vendors.
 Text Mining Capabilities

Keyword Analysis
■ Extracting nouns or noun phrases in text without
understanding their meaning or relationships or
counting the number of times the nouns appear

Statistical Analysis
■ Frequency-based analysis – counting the number
of times a word appears in the text

Linguistic Analysis
■ Natural language processing (NLP) – “Trained Agent”
■ Semantic analysis
 Text Mining Data Sources

■ Unstructured text
►full text document, emails
■ Structured text
►database records, such as records from STN,
pubmed
■ Hybrid content
►Patents, front page is structured, text is not
 Data Sources
I. General Data Sources (Unstructured):
ClearForest
GoldFire Innovator
Inxight
OmniViz
Temis

II. Bibliographic Data Sources (Structured):

Quosa
RefViz
VantagePoint

III. Patent-Focused (Hybrid):

Aureka
M-CAM
PatAnalyst
Wisdomain
 Evaluation Template

Type of Tool
■ Text mining software tool
■ Database content provider
■ Both

Capabilities
■ Keyword analysis
■ Statistical analysis
■ Linguistic analysis

Data Sources
■ Structured bibliographic data sources
■ Unstructured sources – full-text web, email, corporate repositories, etc.
■ Hybrid sources – patents, combination of structured/unstructured

Results
■ Lists of documents
■ Tables
■ Charts/Graphs
■ Maps

Strengths – Disclaimer: Our Impressions only!

Summary
 GoldFire Innovator

Type of tool – text mining tool

 GoldFire Innovator

Technology – Semantic Analysis
GoldFire Innovator
 GoldFire Innovator

Data Sources
■ Unstructured information from personal data,
corporate data, deep web, content, patents,
internet
►15 MM worldwide patents
►Database of over 8000 scientific effects
►3000 cross-disciplinary scientific deep web websites

Results
■ Static categorization of key concepts
■ Accurate answers to questions
■ Dynamic document summarization
 GoldFire Innovator - Strengths

Precision retrieval of targeted R&D content
►Retrieves information from context – semantic
indexing
►automated summaries and categorization
►Relevant filtering and ranking

Using natural language query to search
►Ask the right questions - How to dry paper? How to
balance diets?

Innovation Trend Analysis
► Competitive analysis
► Technology analysis
► Patent relationship analysis – citation analysis
 Inxight

Type of Tool
■ Text mining software tool.

Capability
■ Natural Language Processing
■ Contextual extractions (leaning towards semantic analysis)

Data Source
■ Unstructured text from websites, internal repositories, full-
text documents
■ Documents have to be pre-processed to extract meta-data
and identify entity types

Results
■ Hierarchical categorization
 Inxight - Strengths

Federated Search capability

Claim to have more accuracy than a
human reader

Software can work in 32 languages
and can understand 27 entity types

Can process 1.2Gigabytes per hour

Claim to have the most powerful
linguistic algorithms in the field
 Temis

Type of tool
■ Text Mining Solutions - software

Capability
■ Natural Language processing
►Insight DiscovererTM Extractor – info extraction sever powered
by Xe-LDA and used with specialized Skill Cartridges
►Insight DiscovererTM Categorizer – doc categorization sever
►Insight DiscovererTM Clusterer – automated classification sever
►XeLDA - Multilingual linguistic engine – natural language processing
►Skill Cartridge – A set of customizable knowledge components
that define the information to be extracted. The two major knowledge
components are multi-lingual dictionaries and multi-lingual
extraction rules (establish relationships between defined concepts
 Skill Cartridge Overview

Open architecture
■ Plug & Play annotation components
■ Each defines areas of interests & extraction rules
■ Extraction rules describe the sentence structure that characterizes a concept

Meaning = Acquisition
Merger &
Acquisition • Target & buyer
Insight • Amount & date
…
Plug & Play
Discoverer™ ...
Skill Cartridges™
Extractor
Positive & Meaning = Satisfaction
Negative
Sentiment • People,
Analysis companies,
Words
(any concept) Products
• Satisfaction
XeLDA™ • Support
...
Text
(any kind, any format)
 Temis

Data Sources
■ Any kind, any format, Internal & external data,
documents, literature, patents, clinical trials,
chemistry and biology, bioinformatics, internet,
email, etc

Results
■ Clusters, Rankings, Lists to discover information
trends and relationships
 Temis - Strengths

Searching by concepts
► Selecting concepts from concept tree

Specialized Skill cartridges

► Life science Skill Cartridges
– Analytics
– Text Mining 360°
– Competitive Intelligence
– Human Resources Management
► General Skill Cartridges
– Biological Entity Relationships – best selling
– Medical Entity Relationships
– Chemical Entity Relationships
– Competitive Intelligence Life Sciences Edition
 Temis - Strengths

Strong extraction, categorization, and

clustering capabilities

Robust XeLDA linguistic engine

Quick trend analysis

Chemical Document Browser – specialized
extraction module for chemical substance
nomenclature translation to chemical
structures.
 OmniViz

Type of tool
■ visual based data/text mining software

Capability
■ algorithm based statistical analysis, not semantics

Data source/type
■ numeric, text, categorical, chem. structures, sequence,
structured/unstructured text

Results
■ interactive visualizations maps such as CoMet,
Correlation, Galaxy Proximity, etc.
OmniViz
 OmniViz- Strengths

■ Interactive visualizations
■ Supports analysis of large amounts of data
(millions of documents) - numeric, categorical and
full-text analysis, including patents.
■ Broad applications including gene expression,
sequence & pathway analysis, chemical
structures, cheminformatics, clinical trial, patent
analysis, diagnosis and treatment, legal,
marketing data, regulatory compliance,
intelligence analysis, etc.
■ Flexible data import and merge capabilities
 ClearForest

Type of Tool
■ Text mining tool (text analytics solution)

Capability
■ Semantic analysis/NLP

Data Sources
■ Unstructured text – websites
■ Patents
■ Internal documents
■ Meta-data

Results
■ Structured data entities
■ List of potential solutions for identified issues
■ Visualization tools – trend graphs, category maps
►Color and font are used to show intensity of relationships
 ClearForest
Text Analytics: How it Works
Unified
Role-Based
Analysis
Interfaces

Part Problem Condition

<PartProblemCondition> Fuel Pump Fails corroded

<Part> Fuel Pump </Part>
Pump Relay Shorts Cold
Output <Problem> Fails </Problem>
DB weather
<Condition> Corroded </Condition> Headlight Fails Running hot
</PartProblemCondition>
Engine Stalls At low
XML Database speeds

Tagging Extraction
Platform Across Records
Including domain specific
entities & relationships

Unstructured Documents Database

Text, Word, Excel, DB Text Fields
Text
Email, WWW, PDF
 Clear Forest
Packaged Extraction Modules
Inputs

Patents
MicroPatent U.S. Patent Text, Word, Database
Search Search Excel, etc Fields

Outputs Structured Data Entities Entities

 Agent • Claim Element
 Application Number • Claim Invention
 Assignee • Extracted Terms
 Assignee Address • Invention Terms
 Examiner • Measurement Terms
 Filing Date • Number of Claims
 Inventor • Patent Section
 Inventor Address • Problem Solved Terms
 IPC • Problems Solved
 Issue Date • Process Technology Terms
 Number Of Claims • Technology Terms
 Patent Citations
 Patent Number
 US Class
 ClearForest - Strengths

Can be applied to a wide range of
applications as evidenced by wide variety of
available extraction modules
■ Security/intelligence gathering
■ Product/customer information
■ Corporate/People profiles
■ Patents
■ Biomedical entities

Analytics tool can discover unexpected
relationships between entities that would not
have been otherwise uncovered by standard,
manual methods.
 VantagePoint

Type of the tool
■ Text mining software mainly used for technology
assessment and company profiling

Capability
■ Uses pattern matching, rule-based, and natural language
processing techniques

Data Sources
■ Works best with structured data - text data from
bibliographic databases

Results
■ summaries, charts, matrices, maps, and graphs
 VantagePoint - Key Features

Rapid navigation in large abstract collections

Helps find relationships within your data

Visually displays relationships

Buckets documents to help in categorization

Utilities for cleaning data

User created thesauri for reducing data

Scripting capabilities to automate knowledge-
gathering

Easily exports output to other applications

Can be configured to text mine most forms of
structured bibliographic data
 VantagePoint - Strengths

List Creation and Cleanup

■ patent assignee, author, inventor
■ pre-built IPC, User created thesauri

Analytical tool box
■ rapid navigation in large abstract collections to
answer who, where, what, when but not how and
why
■ visually displays relationships

Scripting capabilities to automate
knowledge-gathering
■ configure to extract from structured databases
 RefViz

Type of tool
■ Text Analysis and Data Visualization software

Capability
■ Statistical and Linguistic analysis
►“mathematical signature” – relationship of words
►Uses a thesaurus tool

Data Sources
■ Only structured data from title, abstracts/notes
fields, or ISI Web of Science, PubMed, OCLC,
Output

Results
■ “Galaxy” & matrix visualization
 RefViz - Strengths

■ Reference Retriever™ can search multiple online

sources simultaneously
■ can be used together with EndNote, ProCite, and
Reference Manager to provide an additional level
of analysis to existing reference collections
■ analyzes large numbers of references by thematic
content
■ interactive, visual landscape
 Reveal trends and associations in references

The Galaxy view organizes references according to how they are related conceptually.

References on farming and herbs, either their Groups in the lower right focus on herbs in
cultivation or use as herbicides, are found in medicine.
the upper left region of the Galaxy.
The region in between farming and medicine contains a mix of
references about herbage diets in farm animals, herbal extracts
from plants, and research on health effects of herbicide exposure.
 Quosa

Type of tool
■ Text mining tool based on concept extraction/clustering

Capability
■ Statistical analysis (term extraction, frequency ranking,
concept extraction using dynamic extraction algorithm from
MIT/Harvard)

Data sources
■ unstructured text - PubMed, Ovid, Google Scholar
■ Patents
■ Internal documents

Results
■ Highly organized collection of documents (folders on
shared server or local machine)
■ Team sharing and annotating
 Quosa - Strengths

Full-text retrieval and management of

scientific documents
■ Get full-article from a journal or patent
gateway
► PubMed, Ovid, USPTO website
■ Document Summary from My Article
Organizer
■ Download to EndNote
 M-CAM DoorsTM

Type of tool
■ Patent database provider, with text analysis and risk management
solution

Capability
■ Linguistic & semantic-based analysis, multi lingual

Data Sources
■ Patents from over 88 patenting authorities, 50 million patent doc.
■ journal articles (by the end of the summer 2006)

Results
■ “Compass” citation view
■ “Magellan” telescope & hourglass – patent life timeline
■ Patent uniqueness and enforceability analysis
■ Competitive intelligence analysis - financial risk analysis for
merger/acquisition and stock trading
 M-CAM DoorsTM
Hourglass view – shows behavior and intent

Red bar – cited patents

Blue bar – citing patents
Green bar – concurrent art – share pendency
Purple bar – volume of uncited patents
Orange bar – volume of patents that did not cite subject patent
 M-CAM DoorsTM - Strengths

Powerful visual interface for citation analysis
with related family & legal status views

Can rate each patent for its uniqueness,
reliance on related patents, and enforcement
potential – based on Hourglass view

Can rank patent clusters by relevance to
business objectives

Competitive Intelligence/Investment
Research
■ New Patent Thursday™ , Patent Portfolio
Confidence Rating™ , Custom PPCR™
 PatAnalyst

Type of tool
■ Patent database provider – integrated source (UNIPAT) of patent
databases from US, PCT, EPO, PAJ, Germany, UK, France and
Switzerland
■ Patent search & examination service

Capability
■ No text mining algorithm

Data Sources
■ 51.5 MM patent documents – bibliographic data from 70 countries
from EPO
■ 15MM full-text documents – 8 countries/patenting authorities

Results
■ Viewer – analyze and orgnize the patent documents/families.
■ easy to use analytical colored text-highlighting of keywords
■ Organized folders of documents
 PatAnalyst - Strengths

Powerful user-interface with enhanced

display features
■ Highlight keywords are in different colors
■ Side-by-side views of full-text and standard
bibliographic data
■ Integrated IPC category trees
■ “Live” legal status & patent family tree view from
EPO Viewer (EPOQUE)
■ Combined search of full-text & bibliographic data
 Aureka

Type of tool
■ content and software tool specializing in visualization and
citation analysis

Capability
■ Keyword and Statistical Analysis

Data Sources
■ patent databases listed in MicroPatent’s FullText collection

Results
■ ThemeScape maps, hyperbolic citations trees, text clusters
 Aureka Themescape Map of

A Themescape map of
Stem Cell Technology
a large set of
documents provides an
initial view of the
content. Additional
probing and analysis of
the map will help to
reveal more insight.
 Citation Tree of Patent EP0778277
A cited patent provides insight into a corporation’s strategic intent with a patent;
build a picket fence, non-core patent, or lack of R&D interest.
 Aureka – Strengths

Strong citation analysis tool

►Interactive citation tree – intelligence analysis
and strategic planning

Annotation capabilities

Strong visualization analysis
►Patent mapping with ThemeScape
►Clustering by Vivisimo
 Wisdomain

Type of tool
■ Content and software tool. Web-based searching and
citation tool. Analysis module is local

Capability
■ Keyword analysis, citation map visualized
searching

Data Sources
■ Patents, specialized in US, EP, PCT, PAJ,
INPADOC legal and family status, China abs,
Korea abs

Results
■ Genealogy tree, Tables, charts
 Wisdomain - Strengths

Strong citation analysis capability
►backward and forward citations, more than
one nesting
►collateral citation analysis
►citation alerts

Genealogy Tree
►good in competitive analysis and licensing
strategy planning

Graphic view of the search results

 Collateral Citation
Identifying similar patents sharing the same pending period with the subject patent

APPLIED ISSUED
1990 1993
PENDING PERIOD

PATENT PATENT
PATENT PATENT
PATENT
PATENT PATENT
PATENT

SUBJECT PATENT

PATENT PATENT
PATENT

PATENT
PATENT

Key Collateral patent

7 collateral patents are identified based on indirect citation re

relations.
Vendor Name
Summary
Strength Potential User Groups
ClearForest Extraction modules Business Intelligence

GoldFire Sophisticated semantic analysis R&D scientists

tool

Inxight Extraction & Federated Search R&D Informatics

OmniViz Interactive visualization R&D scientists

Temis Extraction using Specialized Skill R&D scientists,

Cartridges Business Intelligence

Quosa Full-text retrieval & mgmt R&D scientists

RefViz Bibliographic data post- R&D scientists,

processing Information Professionals

VantagePoint Analytical tool box for technology Information Professionals,

or company assessment Business Intelligence

Aureka Patent mapping, clustering & Legal/Patent Dept., R&D scientists,

citation analysis Information Professionals,
Strategic Planning, Business
Intelligence

M-CAM Patent uniqueness & enforcement Business Intelligence, Legal/Patent

analysis Dept., Information Professionals

PatAnalyst Powerful full-text user interface Information Professionals,

with display features R&D scientists

Wisdomain Strong collateral citation analysis R&D scientists,

Information Professionals
 Path Forward

■Phase II
►Pilot selected tools
►Identify potential clients groups and interview
representative clients
Closing Remarks
 Acknowledgements
Peter Mattei Aureka
Thomas Klose ClearForest
Shelley Pavlek GoldFire/Invention Machine
Joanne Freeman Inxight
Marlene Khouri M-CAM
Heahyun Yoo OmniViz
Tony Medina PatAnalyst
Michael Rogers Quosa
Karen Stesis RefViz
Tisha Zawisky Temis
Lou Ann DiNallo VantagePoint
Mary Talmadge-Grebenar Wisdomain
Joseph Bezek
Claudia Powers
Ramesh Durvasula (Informatics)
Ronald Stoner (Mead Johnson)
Questions