Linking chemistry: wider lessons for how we publish research

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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

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

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?

RSC Prospect – semantic publishing

What were we trying to improve? Discoverability Use Understanding Linking

Steering how the chemical sciences develop on the web...

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

Do we know what’s going on?

Vision …

http://www.optimumengineering.com.au/cyclone_silos/cyclone_silo_4.jpg

Market Research

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.

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”

Industrial Researchers

“Need to find information any way we can” “Don’t have access to expensive systems”

Most ingenious and sophisticated users.

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”

Key Findings

Key Findings

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.

The article of the future

PDFs

Dumbing down can be good

Lowest common denominator PDF Word & ChemDraw JPG

Enables participation, exchange & comparison familiarity for the user

Authors?

number

tech ability/interest of authors & readers

Rzepa,H.

• 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

<?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

We forget our place

We assume our readers spend their lives in our platforms

www.visitingdc.com

media.obsessable.com

As few interfaces as possible

What do humans want?

What do computers want?

Web services

flickr.com/photos/microcosmos

What is ChemSpider?

+ +

Free to use

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

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

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

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

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

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

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

ChemSpider as chemistry portal

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?

Micropublication?

Nanopublication?

Slide from Jan Velterop

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

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.