Linking chemistry: wider lessons for how we publish research
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Transcript of Linking chemistry: wider lessons for how we publish research
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Linking chemistry: wider lessons for how we publish research
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Anomalocarisfloreslivroselua.files.wordpress.com
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What have we gained?
Very interesting Very clever
We’re all innovating into niches, growing extra legs, fins, ears...
news.sky.com
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Who has this been for?
US!
All good publicity, shows we’ll all good at our jobs, pats on the back all round
Have any of these widgets solved any more research problems? Saved time? Money?
And how much are they used? Really?
But helps become flexible to try out new things, test models, approaches, technologies
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OK, what do we think? 2007 version
Publishing methods are changing Reading methods are changing We know what our readers want We know how the researchers work
How many did we get right?
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RSC Prospect – semantic publishing
What were we trying to improve? Discoverability Use Understanding Linking
Steering how the chemical sciences develop on the web...
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What do we learn with Prospect?
This is probably the way to go How do we cover all subjects? Scale-up in manual QA Scale-up during huge growth and scope
How to use all that real chemistry data Pump prime to change what
we ask from authors Is our vision the day-glo article?
“Free headache for every user”
blogs.guardian.co.uk
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Do we know what’s going on?
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Vision …
http://www.optimumengineering.com.au/cyclone_silos/cyclone_silo_4.jpg
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Market Research
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Students
“Starting point for finding information is Wikipedia” “I’d like to use images from articles” “Colleagues tell me about papers so I don’t really
need to go looking for them”
Not very sophisticated outlook: have access to expensive services and content but don’t use.
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Academic Faculty
“Too busy to spend much time online” “My students tell me about everything that I need
to know” “I use email alerts to find content”
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Industrial Researchers
“Need to find information any way we can” “Don’t have access to expensive systems”
Most ingenious and sophisticated users.
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Librarians
“Don’t change any URLs” “Users are confused when they don’t have access
to all the content” “When things go wrong, we have to sort it out” “I need my customers to know that the library has
paid for this content”
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Key Findings
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Key Findings
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So what have we built?
Simple interface to fulfill the main use – come in, find a paper
RSC Publishing platform
All our journal, books, databases XML, in Marklogic. Normalised. A single query interface.
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The article of the future
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PDFs
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Dumbing down can be good
Lowest common denominator PDF Word & ChemDraw JPG
Enables participation, exchange & comparison familiarity for the user
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Authors?
number
tech ability/interest of authors & readers
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Rzepa,H.
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• Phil Bourne
• Lynn Fink
Source code and binary:http://research.microsoft.com/ontology/
Relationships: Ontology browser
Relationships: Ontology browser
Intent: Term recognition & disambiguation based on OBO or OWL formats
Intent: Term recognition & disambiguation based on OBO or OWL formats
John WilbanksServices: Ontology download web service
Ontology Add-in for Word 2007
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<?xml version="1.0" ?><cml version="3" convention="org-synth-report" xmlns="http://www.xml-cml.org/schema"> <molecule id="m1"> <atomArray> <atom id="a1" elementType="C" x2="-2.9149999618530273" y2="0.7699999809265137" /> <atom id="a2" elementType="C" x2="-1.5813208400249916" y2="1.5399999809265137" /> <atom id="a3" elementType="O" x2="-0.24764171819695613" y2="0.7699999809265134" /> <atom id="a4" elementType="O" x2="-1.5813208400249912" y2="3.0799999809265137" /> <atom id="a5" elementType="H" x2="-4.248679083681063" y2="1.5399999809265137" /> <atom id="a6" elementType="H" x2="-2.914999961853028" y2="-0.7700000190734864" /> <atom id="a7" elementType="H" x2="-4.248679083681063" y2="-1.907348645691087E-8" /> <atom id="a8" elementType="H" x2="1.0860374036310796" y2="1.5399999809265132" /> </atomArray> <bondArray> <bond atomRefs2="a1 a2" order="1" /> <bond atomRefs2="a2 a3" order="1" /> <bond atomRefs2="a2 a4" order="2" /> <bond atomRefs2="a1 a5" order="1" /> <bond atomRefs2="a1 a6" order="1" /> <bond atomRefs2="a1 a7" order="1" /> <bond atomRefs2="a3 a8" order="1" /> </bondArray> </molecule></cml>
<?xml version="1.0" ?><cml version="3" convention="org-synth-report" xmlns="http://www.xml-cml.org/schema"> <molecule id="m1"> <atomArray> <atom id="a1" elementType="C" x2="-2.9149999618530273" y2="0.7699999809265137" /> <atom id="a2" elementType="C" x2="-1.5813208400249916" y2="1.5399999809265137" /> <atom id="a3" elementType="O" x2="-0.24764171819695613" y2="0.7699999809265134" /> <atom id="a4" elementType="O" x2="-1.5813208400249912" y2="3.0799999809265137" /> <atom id="a5" elementType="H" x2="-4.248679083681063" y2="1.5399999809265137" /> <atom id="a6" elementType="H" x2="-2.914999961853028" y2="-0.7700000190734864" /> <atom id="a7" elementType="H" x2="-4.248679083681063" y2="-1.907348645691087E-8" /> <atom id="a8" elementType="H" x2="1.0860374036310796" y2="1.5399999809265132" /> </atomArray> <bondArray> <bond atomRefs2="a1 a2" order="1" /> <bond atomRefs2="a2 a3" order="1" /> <bond atomRefs2="a2 a4" order="2" /> <bond atomRefs2="a1 a5" order="1" /> <bond atomRefs2="a1 a6" order="1" /> <bond atomRefs2="a1 a7" order="1" /> <bond atomRefs2="a3 a8" order="1" /> </bondArray> </molecule></cml>
Relationships: Navigate and link referenced chemistry
Relationships: Navigate and link referenced chemistry
Available soon:http://research.microsoft.com/chem4word/
Data: Semantics stored in Chemistry Markup Language
Data: Semantics stored in Chemistry Markup Language
Intent: Recognizes chemical dictionary and ontology terms
Intent: Recognizes chemical dictionary and ontology terms
Author and edit 1D and 2D chemistry. Author and edit 1D and 2D chemistry.
Intelligence: Verifies validity of authored chemistry
Intelligence: Verifies validity of authored chemistry
Authoring: Chem4Word – Chemistry Drawing in Word
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We forget our place
We assume our readers spend their lives in our platforms
www.visitingdc.com
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media.obsessable.com
As few interfaces as possible
What do humans want?
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What do computers want?
Web services
flickr.com/photos/microcosmos
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What is ChemSpider?
+ +
Free to use
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Quick history Launched 2007 with a vision Bedroom project for 2 years Acquired by RSC in 2009
Since acquisition Infrastructure and development resource Community and user support added Integration with RSC Publishing resources Engagement with RSC’s community of influence
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ChemSpider as aggregator Public and non-public compound sets Publications Domain resources – DailyMed, Wikipedia Personal data sets SureChem patents Multimedia additions, blogs, Open Notebook Sci
Data normalised, errors rejected
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ChemSpider as chemical search
Single search across 400 data sources Text, structure and substructure search tools
Simple and very advanced Validated names for external search expansion
Google Scholar, PubMed, RSC, Google patents Links to original sources Mobile version
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ChemSpider as wikiAdds quality and quantity
Users can comment, others action Registered users can curate
names, add links, spectra, data and multimedia resources
Depositors can load data sets, curated on load
Curators and Master Curators approve additions and decide what is the correct structure
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ChemSpider as resource Download and reuse structures Download and reuse search structure set 2D and 3D images Embed and link - never draw a structure again Predicted properties
Physical, Environmental, Biological Spectra, crystal structures ChemSpider SyntheticPages Spectral game
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ChemSpider as compound hub Extensive web services
Utility conversion services MassSpec services Name + structure lookups Prediction services
Validated name:structure pairs provides public disambiguation service
InChI Resolver – links InChIKeys to compounds: MYPYJXKWCTUITO-LYRMYLQWSA-N
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For the RSC (more selfishly) Critical mass for a chemistry portal
Support for semantic developments Proven user need to search for compounds Shop window for our other publications
Ability to test other business models (some of which are a little scary)
Engagement with new publishing methods
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ChemSpider as chemistry portal
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What will the RSC be doing?
Facilitating scientific communication
Publish articles – with the semantics
But what else can be part of this?
Partial publication syntheses, blogs, unpublished data
How does all this sit alongside traditional articles?
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Micropublication?
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Nanopublication?
Slide from Jan Velterop
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Exploring standards and extraction of semantic assertions
Pistoia Alliance“An initiative to provide an open foundation of data
standards, ontologies and web-services to streamline the Pharmaceutical Drug Discovery workflow”
Semantic Enrichment of the Scientific Literature (SESL) Oct09-Oct10
Pistoia Alliance-funded EBI Elsevier, NPG, OUP, RSC
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Do we know what the answer is?
Probably not, but RSC Publishing & ChemSpider allows us to cover pretty much everything. Serve existing behaviours Allow experimentation
Science – keying into the readers as well as the researchers is more important than the technology.
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