Qualifying Online Information Resources for Chemists
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Transcript of Qualifying Online Information Resources for Chemists
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…