Challenges of Developing a Global Alerting System

American Chemical Society National Meeting - ChicagoSymposium Honoring Gary Wiggins

March 25th, 2007

Leah Sandvoss

Information Scientist

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Honors

Chemical Informatics program initiation

Mentorship

Independent study on Chemical Information

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Outline

Definitions

Overview of Global Alerting System

Business Analysis – pre-project

Information Retrieval

Metadata

Users

Project limitations

Lessons Learned

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Definitions

Alerts/Selective Dissemination of Information(SDI)/Current Awareness – a stored search strategy which is run periodically against a database to return any newly added results to the end-user

Information Retrieval – the systematic storage and recovery of data, as from a file or database

Knowledge Management – refers to a range of practices used by organizations to identify, create, represent, and distribute knowledge for reuse, awareness and learning across the organization.

Business Analysis – act of gathering and translating business issues and needs into a form that can be given to appropriate people to form solutions

Metadata – data about data “Zip Code” is the metadata for the piece of data “92121” “Abstract” is the metadata for the actual abstract text

Unstructured data – data structure which is not readily machine readable

Controlled vocabulary – carefully selected list of words and phrases which are used to tag units of information to make them more retrievable by a search cancer vs neoplasm

Sources: Chicago Manual Style (CMS): information retrieval. Dictionary.com. Dictionary.com Sources: Chicago Manual Style (CMS): information retrieval. Dictionary.com. Dictionary.com Unabridged (v 1.1). Random House, Inc. http://dictionary.reference.com/browse/information Unabridged (v 1.1). Random House, Inc. http://dictionary.reference.com/browse/information retrieval (accessed: February 21, 2007). “Consulting Skills for Business Analysis” course by retrieval (accessed: February 21, 2007). “Consulting Skills for Business Analysis” course by Watermark LearningWatermark Learning

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Knowledge Management

Each company in the healthcare and pharmaceutical sector has spent an average of US$274,000 per annum on knowledge management over the past three years (ref 2001)

Dyer, G. and McDonough B. (2001) Vertical targets for knowledge management vendors. International Data Corporation. Document No. 25535

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State of Biomedical Literature Mining

Source: Jensen, L.J., Sari, J., Bork, P. Literature Mining for the biologist: from information retrieval to biological discovery Nature, vol 7, February 2006

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Current Awareness System

Common platform to deliver many types of information, providing a common process for inserting the information

Compiles results from multiple information retrieval systems

Allows for the collection, review, analysis, and summarization of information types

Export capabilities

Uses controlled vocabularies

Provides structured, actionable information

PortalPortal

PatentsPatents

LiteratureLiterature

NewsNews

BooksBooks

TOCsTOCs

InternalInternal

Integration layerIntegration layer

Key Op LeadersKey Op Leaders

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Business AnalysisBusiness Analysis

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Business Analysis

A team was formed in 2002 to look at key information products available to the end-user, coined “value-added products”

First focus was on the products providing alerts/SDIs Used online alert survey from an existing internal system to

identify user needs. Approximately 230 total respondents. Held discussions among team members about workflow based

on their experience with customer needs Conducted a per-month cost comparison of various alerting

services

Several products provided overlapping information, resulting in duplication of effort among the information scientists

Recommendations were made for a future system and workflow for managing alerts

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Business Analysis

In late 2004, a project team was formed to develop a tool to manage alerts as well as search results

First goal was to provide a repository to manage content. Tool would: Allow information scientists to contribute, manage, and disseminate

content Replace existing current awareness products Provide automation where possible to save time on the part of

information scientists

Second goal was to develop a tool to display content to the end-user in one interface with a common format

Environmental scan was performed but determined to develop product in-house Facilitate incorporating internal content

Focus of this talk is on the repository development

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Information RetrievalInformation Retrieval

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Information Retrieval– Licensing Issues

Needed to determine what was “in scope” for existing contracts

Copyright restrictions questions Vendor-produced abstracts subject to copyright restrictions? Does it violate copyright to redistribute results? Can full-text of article be used and classified? Can a screen scrape be performed on an HTML page? Can complete citation(s) be stored? If not, what fields can be stored? (ie, a

unique identifier so that user can get back to complete citation). For stored content, is there an expiration date?

Results Options Format - XML, plain text, HTML, etc Transfer type - sFTP, e-mail, HTML view

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Unstructured or Semi-structured Data – BRS/Tagged

UI 92158846 TI Cluster headache syndrome. Ways to abort or ward off attacks. [Review] AU Marks DR. Rapoport AM

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Unstructured or Semi-structured data - HTML

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Unstructured or Semi-structured data - TOC

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Information Retrieval – Process

Supported Commercial Databases

Repository

Supported News

Sources

OtherSources

Information Scientists

E-mail inbox

Rules applied for Rules applied for strategy setup and strategy setup and deliverydelivery

Parsers appliedParsers applied

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MetadataMetadata

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Source System Metadata Source system - defined set of metadata to which the vendor tags would map

To define core fields, looked at range of fields provided by all the databases of interest from the different vendors

Used Dublin Core fields where applicable

Abstract

Author

Classification

Date Granted

Device Manufacturer

Device Trade Name

Diseases

Edition Subset

External Reference ID

Gene Info

Keywords

Language

Literature Title

Literature Type

Location

Methods & Equipment

Miscellaneous

Molecular Sequence

Molecular Source Number

Open URL issn

Open URL issue

Organism Info

Patent Assignee

Patent Class

Patent Country

Patent Number

Personal Name as subject

Publish Date

Publisher

Sequence Data

Space Flight Mission

Subject Heading

Title

TOC Categories

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Metadata Mapping

Database Name Database Tag Name Target Metadata Field Name

Biosis Previews Concept Code Classification

Derwent World Patents Index

Title Index Terms and Additional Words

Keywords

Derwent World Patents Index

Derwent Accession Number External Reference ID

SciSearch Cited Work Cited Reference

CAB Abstracts Organism Descriptors Organism Info

Medline Country of Publication Location

Minimum set of fields / database standpoint

Exclude fields not used for search or retrieval (ex: Item URL, Locally Held, Local Messages, Record Owner, Update Code, Notes, Order Number, Price, Abbreviated Source, Reprint Address, etc.)

Manual process by subject matter experts (information scientists)

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Metadata - Content Objects

Content objects defined to differentiate content types on the backend Contained unique metadata as well as overlapping metadata

Choices for end-user interface

Content Objects:

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Metadata - Controlled Vocabulary

Controlled terms enhance search and retrieval capability Terms are selected by user (information scientist) for tagging content items Use preferred term, then list of synonyms Standard terminology lists as pick lists (ex: Therapeutic area, disease)

Authoritative sources were used to determine appropriate values Internal vocabularies National Library of Medicine Medical Subject Headings (MeSH) Medical Dictionary for Regulatory Activities (MedDRA)

Repository

Metathesaurus

Authoritative Classifications

MeSH

MedDRA Benzene

Internal

Benzene

Cyclohexatriene

Figure source: DATAFUSION, Inc copyright 1999Figure source: DATAFUSION, Inc copyright 1999

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UsersUsers

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Users

Information Scientists Set up alert strategies in vendor databases as

well as the source system repository Involved in interactive sessions with the tool to

discuss content needs and find bugs in the system

Information Scientists

End-Users

End-users Used the portal which displayed content Involved early on in the initial requirements

gathering, then engaged by the information scientists to test the tool

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Project LimitationsProject Limitations

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Project Limitations – Source System

For every new vendor file/database that needed to be added to the system, a manual mapping from the vendor database fields to the target metadata had to be performed

Repository interface was cumbersome Setting up a strategy was quite time-consuming as there was no auto-population

of data Opening new windows within the system was quite slow

New version of source system arrived mid-project

An approver role was required to allow an alert strategy to be set-up

System did not provide robust, boolean searching at the time

Only had one expert on the source system

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Project Limitations - Organizational

Key reasons why projects fail: Inattentiveness to organizational change Sponsorship is lost or changes Lack of budget/resources

Other Factors

Project team leaders and members changed several times throughout life of project

Other applications identified to integrate into the solution were also “new” or in development

IT resources not well supported

NO-GO decision was made near production

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Lessons Learned

For a multi-year project: Manage change

– Knowledge transfer– Sustain momentum

Sustain business sponsorship Plan the budget carefully Involve influencing parties (vendors/publishers) early

Current awareness system: Portal concept well-supported by end-users

– Flexibility on their part to manage alerts– Integrated several different content types

Common workflow supported by information scientists

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Summary

Knowledge Management is a continuous challenge

A need still exists for a global current awareness system

Follow-up plans

Currently evaluating commercially available products

Internal efforts to filter, consolidate, and analyze content for customers

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Acknowledgements

Ajit AcharyaAjit AcharyaAmy Tellez-KarstenAmy Tellez-KarstenAndrew HorganAndrew HorganAngela LiuAngela LiuAngelika Wendler-AwasthiAngelika Wendler-AwasthiAnn YoungAnn YoungBarb MillerBarb MillerBarbara BreenBarbara BreenBeverly KucharskiBeverly KucharskiBill GillickBill GillickBob BergerBob BergerBryon Tilley Bryon Tilley Cara EvansCara EvansChandra AithaChandra AithaChris Duhl, West PoleChris Duhl, West PoleChristina CarrChristina CarrChristina KeilChristina KeilChristine NgChristine NgClaire HogikyanClaire HogikyanClare ChallengerClare ChallengerCleazoe MalekCleazoe MalekDan Cooney, West PoleDan Cooney, West PoleDavid WalshDavid WalshEd PelicEd PelicElaine LoganElaine LoganEmory EmrichEmory EmrichFradwin Marmol Fradwin Marmol Francis Di BellaFrancis Di BellaGetu DiroGetu DiroHennie OswaldHennie Oswald

Ian ParsonsIan ParsonsIradj RezaIradj RezaJan CarrJan CarrJanet SmithJanet SmithJill MaddoxJill MaddoxJulie grannisJulie grannisKaren EraniKaren EraniKarl RoyerKarl RoyerKathy CornishKathy CornishKathy VanLeeuwenKathy VanLeeuwenKen DrakeKen DrakeKevin OgborneKevin OgborneKim JohnsonKim JohnsonKirsten KliwinskiKirsten KliwinskiLeah SandvossLeah SandvossMaheshkar PorandlaMaheshkar PorandlaMark MitchellMark MitchellMary SkousenMary SkousenMichele WangMichele WangMichele WolfeMichele WolfeMurali NandulaMurali NandulaNathaniel DunfordNathaniel DunfordNicola CooperNicola CooperPam KubiakPam KubiakPat BurkePat BurkePenny MillerPenny MillerPeter Dresslar, MetamaticsPeter Dresslar, MetamaticsPragati MithalPragati MithalRaj DandamudiRaj DandamudiRavneesh Sachdev Ravneesh Sachdev

Rich SteelRich SteelRichard NicholasRichard NicholasRob ExpositoRob ExpositoRob PurdueRob PurdueRobert LindeRobert LindeShuntai WangShuntai WangSimona HendlSimona HendlSrilekha Komma, Keane, IncSrilekha Komma, Keane, IncSusan SuchettaSusan SuchettaSuzan Quick, West PoleSuzan Quick, West PoleThomas KnowlesThomas KnowlesVeronica TrimbleVeronica TrimbleVishal KumarVishal Kumar

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Thanks

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Backup Slides – Requirements from VAP team

Developed Requirements. Key documents included: A proposed “alert service model” which included questions regarding alert gadget data

entry, working with clients and ROI metrics. A list of roles and responsibilities of stakeholders involved in “Global alerting process”,

including IM Colleagues and Pfizer Colleagues. A detailed description of the requirements needed for a future alerting system. It includes

requirements for processing and managing alerts, archiving/distribution/retention issues, and delivery and service to clients.

A list of all of the various types of alerts that are currently used within IM and at which location they are run is provided.

A process model that describes how an end-user might look for/subscribe to alerts. Also included is a process that would be used by the IM colleague when setting up alerts.

A “client need” summary, provided from the IM perspective

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Backup - Dublin Core Metadata Elements

Contributor

Coverage

Creator

Date

Description

Format

Resource Identifier

Language

Publisher

Relation

Rights Management

Source

Subject and Keywords

Title

Resource Type