Qualifying Online Information Qualifying Online Information Resources for Chemists Resources for Chemists

NFAIS-CENDI-FLICC 12/8/2008NFAIS-CENDI-FLICC 12/8/2008 Antony WilliamsAntony Williams

Building a Structure Centric Community for Chemists

Access to InformationAccess to Information

For me…For me… PhD : Libraries primary source of informationPhD : Libraries primary source of information PostDoc/Academia: Libraries and librariansPostDoc/Academia: Libraries and librarians Eastman Kodak: Software tools and Eastman Kodak: Software tools and

databasesdatabases Kodak and ACD/Labs: Replaced by the Kodak and ACD/Labs: Replaced by the

internet internet Today: The Internet enhanced by a network Today: The Internet enhanced by a network

of collaborators…of collaborators…

Librarians have become gurus in using Librarians have become gurus in using software systems to resource informationsoftware systems to resource information

Building a Structure Centric Community for Chemists

Content is KingContent is King

Chemistry “content” is big money – Chemistry Chemistry “content” is big money – Chemistry publishing and content is worth $100s of publishing and content is worth $100s of millions/yearmillions/year Patent searchingPatent searching Structures and propertiesStructures and properties Drug databasesDrug databases Literature databasesLiterature databases

Chemical Abstracts ServiceChemical Abstracts Service (CAS), a division (CAS), a division of the ACS is “Gold Standard” in Chemistry of the ACS is “Gold Standard” in Chemistry related informationrelated information 101 years of content, $260 million revenue (2006), 101 years of content, $260 million revenue (2006),

>40 million substances and 60 million sequences>40 million substances and 60 million sequences

Building a Structure Centric Community for Chemists

The Language of ChemistryThe Language of Chemistry

My language….My language….

Building a Structure Centric Community for Chemists

And its dialects….And its dialects….

Building a Structure Centric Community for Chemists

As a chemist…As a chemist…

I look for information about I look for information about chemicals/chemistrychemicals/chemistry What is a particular structure ?What is a particular structure ? What alternative names/identifiers?What alternative names/identifiers? Reaction synthesis?Reaction synthesis? Physical properties?Physical properties? Analytical data?Analytical data? Purchase?Purchase? Tell me more?Tell me more? Similar stuff – what other compounds are “like” Similar stuff – what other compounds are “like”

mine?mine?

Building a Structure Centric Community for Chemists

Why Journals?Why Journals?

Journals contain lots of information but are Journals contain lots of information but are limited – text, charts, graphs and pictures. limited – text, charts, graphs and pictures.

Text-based searches of the internet gets Text-based searches of the internet gets me to articles VERY quickly then articles me to articles VERY quickly then articles can disappoint me. can disappoint me. I use what I can I use what I can affordafford. So do others…. So do others… GoogleGoogle Google ScholarGoogle Scholar PubMedPubMed

Updating my CV recently was a breeze…Updating my CV recently was a breeze…the Internet versus other sourcesthe Internet versus other sources

Building a Structure Centric Community for Chemists

Searching and Reading Searching and Reading Articles…Articles…

Searching articles based on chemical Searching articles based on chemical structure and substructure is very expensive.. structure and substructure is very expensive.. but is changingbut is changing

The web IS “tool-ready” so when will The web IS “tool-ready” so when will publishers deliver?publishers deliver? Structures can be shownStructures can be shown Spectra can be interactiveSpectra can be interactive Graphics don’t need to be staticGraphics don’t need to be static Publishers can enhance their articles (Project Publishers can enhance their articles (Project

Prospect from the RSC is an example)Prospect from the RSC is an example)

Building a Structure Centric Community for Chemists

PublicationsPublications

Building a Structure Centric Community for Chemists

Enable Electronic Articles…Enable Electronic Articles…

Structures are the Structures are the language of language of chemistrychemistry

Show structures to Show structures to chemists and chemists and search/link from search/link from there…there…

Building a Structure Centric Community for Chemists

Allow Integration…Allow Integration…

Building a Structure Centric Community for Chemists

And Extend to Patents…And Extend to Patents…

Building a Structure Centric Community for Chemists

Structure-based Patent SearchingStructure-based Patent SearchingSureChem and IBM servicesSureChem and IBM services

Building a Structure Centric Community for Chemists

What can be done?What can be done?

Building a Structure Centric Community for Chemists

Publishers should adopt/add Publishers should adopt/add InChIsInChIs

RSC and Nature Publishing Group RSC and Nature Publishing Group have!have!

Building a Structure Centric Community for Chemists

Blogs, Wikis, Forums and Blogs, Wikis, Forums and Collaborative ScienceCollaborative Science

I have two blogs, one forum and a full blog reader…I have two blogs, one forum and a full blog reader… http://www.chemspider.com/bloghttp://www.chemspider.com/blog http://www.chemspider.com/chemunicatinghttp://www.chemspider.com/chemunicating

(ChemConnector)(ChemConnector)

http://forum.chemspider.com/http://forum.chemspider.com/ They are catalytic for collaborations, getting They are catalytic for collaborations, getting

questions answered, garnering comments and questions answered, garnering comments and feedbackfeedback

There are upsides and downsides: There are upsides and downsides: http://www.chemspider.com/blog/the-joys-and-frustrations-ofhttp://www.chemspider.com/blog/the-joys-and-frustrations-of-6-months-blogging-in-the-chemistry-community.html-6-months-blogging-in-the-chemistry-community.html

Building a Structure Centric Community for Chemists

Blogging Experience and Blogging Experience and JudgmentsJudgments

The blogging community for chemistry small The blogging community for chemistry small and tightand tight

Benefits to meBenefits to me Fast feedback – on and offlineFast feedback – on and offline Extended network, diverse skillsExtended network, diverse skills Fast way to spread news – a local PressWireFast way to spread news – a local PressWire

Most blogs are for information sharing, Most blogs are for information sharing, opinions opinions

Low in scientific content – the content is “off-Low in scientific content – the content is “off-blog” – blogs help find itblog” – blogs help find it

Small number of blogs doing real scienceSmall number of blogs doing real science

Building a Structure Centric Community for Chemists

TotallySynthetic.comTotallySynthetic.com

Building a Structure Centric Community for Chemists

Social Networking for ChemistsSocial Networking for ChemistsBlogs are the startBlogs are the start

Building a Structure Centric Community for Chemists

Collaborative Knowledge Collaborative Knowledge Management Management

for Chemists – Wikipedia, Built by for Chemists – Wikipedia, Built by a Networka Network

Building a Structure Centric Community for Chemists

Collaborative Authoring for Drug Collaborative Authoring for Drug DiscoveryDiscovery

PfizerpediaPfizerpedia

Building a Structure Centric Community for Chemists

Collaborative Authoring in Collaborative Authoring in AcademiaAcademia

Group level collaboration via WikisGroup level collaboration via Wikis

Building a Structure Centric Community for Chemists

Wikis for ScienceWikis for Science

Who in the room hasn’t used Wikipedia?Who in the room hasn’t used Wikipedia? Is it trustworthy?Is it trustworthy? What are the advantages and What are the advantages and

disadvantages of the Wiki environment?disadvantages of the Wiki environment? How suitable is it for Chemistry?How suitable is it for Chemistry?

Building a Structure Centric Community for Chemists

Wikipedia Chemistry Curation Wikipedia Chemistry Curation projectproject

Only ca. 5000 organic Only ca. 5000 organic structuresstructures

A year of work for a team of A year of work for a team of 6 people6 people

Many errors removed in the Many errors removed in the process.process.

Slow and torturous processSlow and torturous process CAS collaborating in the CAS collaborating in the

processprocess

Building a Structure Centric Community for Chemists

Wikipedia via Wikipedia via ChemSpiderChemSpider……

Building a Structure Centric Community for Chemists

Collaborative Drug Discovery, Inc. Collaborative Drug Discovery, Inc. $1.9M$1.9M from the Gates from the Gates

Foundation Foundation

Building a Structure Centric Community for Chemists

The Quality of Data Online…The Quality of Data Online…

Content is king – quality costs. Curation is Content is king – quality costs. Curation is expensive!expensive!

Data online are “filthy”. Data online are “filthy”. Gathering data is the “easy part” Gathering data is the “easy part” Structures are COMMONLY incorrectStructures are COMMONLY incorrect

Informatics tools exist alreadyInformatics tools exist already Hold millions of structures and associated dataHold millions of structures and associated data Structure/substructure/text searchingStructure/substructure/text searching Data downloads, data uploads, editing, annotationData downloads, data uploads, editing, annotation

Building a Structure Centric Community for Chemists

Rich Online Data Resources for Rich Online Data Resources for Chemists and the Life SciencesChemists and the Life Sciences

PubChemPubChem PubmedPubmed WikipediaWikipedia ChemSpiderChemSpider DrugbankDrugbank ChEBIChEBI ChemIDPlusChemIDPlus DailyMedDailyMed And many more…And many more…

Building a Structure Centric Community for Chemists

PubChemPubChem

Building a Structure Centric Community for Chemists

DailyMedDailyMed

Building a Structure Centric Community for Chemists

Caution! Question Everything!Caution! Question Everything!

Building a Structure Centric Community for Chemists

Question EverythingQuestion Everythingwww.dhmo.orgwww.dhmo.org

Building a Structure Centric Community for Chemists

Quality of Structures!!!Quality of Structures!!!

Building a Structure Centric Community for Chemists

Quality of StructuresQuality of Structures

Building a Structure Centric Community for Chemists

CrowdsourcingCrowdsourcing

Chemistry databases enhanced by Chemistry databases enhanced by crowdsourcingcrowdsourcing

Chemistry databases can be connected to Chemistry databases can be connected to articles, vendors, properties, spectra, etc.articles, vendors, properties, spectra, etc.

A platform for deposition, curation and A platform for deposition, curation and distribution ?distribution ?

This is the future… existing business This is the future… existing business models are at riskmodels are at risk

Building a Structure Centric Community for Chemists

Wendy WarrWendy Warr

“…“…some publishers are responding vigorously some publishers are responding vigorously to market forces, but to market forces, but the steady growth of the steady growth of free information resources is a real threat free information resources is a real threat to themto them.”.”

http://www.iwr.co.uk/information-world-review/features/2232039/stm-advhttp://www.iwr.co.uk/information-world-review/features/2232039/stm-advanceance

Building a Structure Centric Community for Chemists

Trademark Infringement But Trademark Infringement But Real Competition…Real Competition…

Building a Structure Centric Community for Chemists

http://http://publicaccess.nih.govpublicaccess.nih.gov//

Address CopyrightAddress Copyright

Before you sign a publication agreement Before you sign a publication agreement or similar copyright transfer agreement, or similar copyright transfer agreement, make sure that the agreement allows make sure that the agreement allows the paper to be submitted to NIHthe paper to be submitted to NIH in in accordance with the Public Access Policy. accordance with the Public Access Policy. 

Building a Structure Centric Community for Chemists

Publishers and Open AccessPublishers and Open Access

““It's clear that the academic publishing world is in It's clear that the academic publishing world is in a state of flux. Nobody's quite figured out a state of flux. Nobody's quite figured out how to how to make an open access business model workmake an open access business model work, but , but even most publishers recognize that the public and even most publishers recognize that the public and scientific community benefit from having access to scientific community benefit from having access to the research they've paid for. “the research they've paid for. “

Chemistry Publishing and Chemistry Publishing and “Structures”???“Structures”???

Building a Structure Centric Community for Chemists

PubChemPubChem

Building a Structure Centric Community for Chemists

InChIs InChIs Structure but NOT substructureStructure but NOT substructure

Building a Structure Centric Community for Chemists

The InChI ResolverThe InChI Resolver

Building a Structure Centric Community for Chemists

Peer Review and WikisPeer Review and WikisPeter Frishauf, founder of Peter Frishauf, founder of

MedscapeMedscape

““Andrew Grove, … Intel Corporation, Andrew Grove, … Intel Corporation, likens likens traditional peer-review systems to Middle traditional peer-review systems to Middle Ages guildsAges guilds. He calls for "cultural . He calls for "cultural revolution" in publishing to reinvent peer revolution" in publishing to reinvent peer review.”review.”

““That revolution will emerge as That revolution will emerge as a variant of a variant of WikipediaWikipedia. Medical publishing, peer review, . Medical publishing, peer review, research, patient care, and commerce will be research, patient care, and commerce will be transformed. And for the better.”transformed. And for the better.”

Building a Structure Centric Community for Chemists

ConclusionsConclusions

The internet enables chemistry – and at a reduced The internet enables chemistry – and at a reduced costcost

Web 2.0 is here and improving quality – to benefit Web 2.0 is here and improving quality – to benefit 3.03.0

Question Quality!Question Quality! Crowdsourcing for expansion, curation and Crowdsourcing for expansion, curation and

integrationintegration Classical models may die quite quickly – business Classical models may die quite quickly – business

models must change soon or failmodels must change soon or fail Publishers – Publishers – heed the profileration of InChIs for heed the profileration of InChIs for

ChemistryChemistry

Building a Structure Centric Community for Chemists

The End of Traditional The End of Traditional PublishingPublishing

Peter Frishauf, Peter Frishauf, The The MedscapeMedscape Journal of Medicine Journal of Medicine makes two predictionsmakes two predictions

Within 5 years, most medical journals will be Within 5 years, most medical journals will be open-open-accessaccess. […] provide access to trusted articles and . […] provide access to trusted articles and data at no cost.data at no cost.

Peer review as we know it will disappear. Rather Peer review as we know it will disappear. Rather than the secretive prepublication review process than the secretive prepublication review process followed by most publishers today, followed by most publishers today, including including MedscapeMedscape, , most peer review will occur most peer review will occur transparently, and transparently, and after publicationafter publication..

Building a Structure Centric Community for Chemists

The ChemSpider Journal – 12/2008The ChemSpider Journal – 12/2008www.chemspider.comwww.chemspider.com

Building a Structure Centric Community for Chemists

The Story of NAPEThe Story of NAPE

Building a Structure Centric Community for Chemists

NAPENAPE

Google Search of : “chemical structure of Google Search of : “chemical structure of

N-N-acylphosphatidylethanolamine”acylphosphatidylethanolamine”

Building a Structure Centric Community for Chemists

NAPENAPE

Google Search of : “chemical structure of Google Search of : “chemical structure of N-acylphosphatidylethanolamine”N-acylphosphatidylethanolamine”

Building a Structure Centric Community for Chemists

The “Lipid Library”The “Lipid Library”

Building a Structure Centric Community for Chemists

Wikipedia…Wikipedia…

Building a Structure Centric Community for Chemists

Original Source – Full loopOriginal Source – Full loop

Building a Structure Centric Community for Chemists

And now a structure…And now a structure…