Linked Data and Cochrane Reviews A report from the ‘Star Trek’ Crew Chris Mavergames Web...

Linked Data and Cochrane Reviews

A report from the ‘Star Trek’ Crew

Chris MavergamesWeb Operations Manager/Information ArchitectCochrane Collaboration Web Team

Structure of this talk

Intro to linked data and what it means for Cochrane

"Star Trek" stream of work so farWhat's possible now and in the future

* Acknowledgements to Lorne Becker and the entire Star Trek crew. Their input was invaluable in the preparation of this talk.

Cochrane Reviews are fantastic

BUT…

There are problems that limit their use by some people◦Difficult to wade through all of the text◦Difficult to understand the figures, terminology,

and other bits of the Review◦Hard to compare interventions without reading

multiple Reviews◦Can be difficult to find the Review you seek

Searching The Cochrane Library

Search for “Prozac” – no reviewsSearch for “fluoxetine” – 25 reviews

Ideally we’d restructure our content for different users

Beginning to do this now:◦Summaries.Cochrane.org for consumers◦Cochrane Clinical for clinicians

BUT◦Takes a lot of work to reformulate reviews &

authors, CRGs, etc are busy

Wouldn’t it be nice if we could automate or partially automate this?

How did Bing read 3 different weather sites & bring me the data I need?

Could we do similar magic with our Cochrane reviews?

If so, what might we be able to accomplish?

Linked data

What is linked data?

Semantic Web

is made up of:

Linked Data & Web of Data

Which all together comprise

Web 3.0

Current web = Web of documents

Docs are linked not data in docs

Machines aren‘t good at reading web pages

Data on the web is meant for human consumption

Machines need the data to be structuredOnce structured, information can be more

easily shared within datasets and across web pages

Cochrane Reviews and Linked data

Cochrane Reviews

XML <?xml version="1.0" encoding="ISO-8859-1" standalone="no"?><COCHRANE_REVIEW DESCRIPTION="For publication" DOI="10.1002/14651858.CD008440" GROUP_ID="HIV" ID="589309120202025823" MERGED_FROM="" MODIFIED="2011-05-06 12:29:46 +0100" MODIFIED_BY="Rachel Marshall" REVIEW_NO="" REVMAN_SUB_VERSION="5.1.1" REVMAN_VERSION="5" SPLIT_FROM="" STAGE="R" STATUS="A" TYPE="INTERVENTION" VERSION_NO="2.0">........

Fortunately, Cochrane Reviews are

structured – but we still need to teach the machines how to read

them, where to find data within them and how the data is related.

Cochrane Reviews

Datapoint

Datapoint

Data point

Datapoint

Datapoint Data

point

Cochrane Register of Studies

Links to the CRS

Lack of unique study IDs a real problemCRS solves this by providing a unique ID

for all studies that can be referencedBetter linking of data about trials and

possibilities with linking to external sources such as PubMed (example later)

Linked data technologies

OWL (Web Ontology Language)RDF (Resource Description Framework)SPARQL (RDF query language)

Model Cochrane Reviews in OWLTransform them into RDF and add to triple storeQuery them with SPARQL

OR, simply...

Use the gears!

Triple store = Way we think!

Subject -> Property -> Object

<Gerd Antes> has-role <Director German Ctr><Director German Ctr> works-in <Freiburg, Germany> <Gerd Antes> works-in <Freiburg, Germany>

Using “the gears”

All Reviews in Archie

A Copy of the

Review XML

A Model of the Data

A Machine Readable

“Triple Store”

Standard tools have been developed to facilitate this

process

Using “the gears”

A Question

A Machine Generated

Answer

A Machine Readable

“Triple Store”

Star Trek

Insert witty Star Trek reference here!

Cochrane Review ontology


Lots of work still needed from people with a deep understanding of Cochrane content in order to get the data model and ontology right

Findings ontology from Lorne

What sorts of things could we do with this?

A Question

A Machine Generated

Answer

A Machine Readable

“Triple Store”

Gears!

We can…

Ask questions that use data from several different reviews

Enhance the experience of our users by including data from the triple stores of others

Improve searchMake it easier for people to find Cochrane

Reviews

Ask questions that use data from several different reviews

Enhancing the User Experience

A question using multiple reviews

I’ve done a search for trials on a particular intervention for dementia.

I want to know which of the trials have been included in a Cochrane Review.

Finding the answer the old way

Search for the relevant ReviewsRead the reference lists to find included trialsCompare with my trial searchEliminate the new references that are

additional publications from trials already included in a Review.

OR…

The “Star Trek” Way

My list of trials

A Machine Generated

list of trials not

yet included

in a review

The Cochrane Review “Triple Store”

A ”studified”

list from the CRS

Links to the relevant Review for those trials that were included

INSERT IMAGE FOR QUESTION 1 HERE

Question 1: SPARQL query and partial list of results

Another question using multiple Reviews

What are the risks of bias for the entire set of trials assessing the effectiveness of a

particular intervention?

Finding the answer the old way

Search for the relevant reviews (there may be more than one)

Read the tables of included studies to find risk of bias assessments for each trial

Combine them

* (in some cases review authors may have done this for all of the trials in a single review)

The “Star Trek” Way

A Machine generated

summary of the Risk of

Bias assessments

for the relevant

trials

The Cochrane Review “Triple Store”

Question 2 visualized

These figures summarize Risks of Bias from the trials included in the reviews in your search

RoB Summary for Cochrane Reviews on dementia

Cochrane Reviews


Make search work better


You Say “Paracetamol”I Say “Acetaminophen”

Or, one could say any of these: Abenol (CA), Acephen, Anadin Paracetamol

(UK), Apo-Acetaminophen (CA), Aspirin Free Anacin, Atasol (CA), Calpol (UK), Cetaphen, Children's Tylenol Soft Chews, Disprol (UK), Exdol (CA), Feverall, Galpamol (UK), Genapap, Genebs, Infant's Pain Reliever, Mandanol (UK), Nortemp, Pain Eze, Panadol (UK), Robigesic (CA), Silapap, Tycolene, Tylenol 8 Hour, Tylenol, Tylenol Arthritis, Uni-Ace, Valorin

LinkedLifeData.com

DrugBank

Cochrane Reviews


Make it easier for people to find Cochrane Reviews


Enhancing news content

Enhancing news content

Cochrane Reviews marked up in semantic markup can be linked to news publishers

For example, BBC Health writers could be suggested related Cochrane evidence for a particular story they are writing

And, could include a link to primary source material such as a Cochrane Review

Thus driving traffic to our Reviews

Super Star Trek

Super Star Trek

How applicable is this Review in my part of the world?

Geographical relevance

A list of the drugs in comparisons of malaria in Reviews and the geographic extent of

their effectiveness

Map of Artemisin Resistance

The future

Making our content nimble

Structured and linked data can help make our content “nimble”

Nimble content can:

• Travel Freely• Retain Context Meaning• Create New Products

- R. Lovinger, Razorfish

Structured data

"Structured data allows you to preserve your value proposition over a longer distance to a much wider audience."

- Martin Hepp,creator of the Good Relations ontology

Incremental development

Implementing semantic and linked data technologies should be:

• Non-invasive• Agile• Low impact (on staff – hopefully, high impact on users!)

Looking to the future

What would Cochrane data “look like” outside of it’s container, the

Review?

Risk of Bias in PubMed

For example: someone who is looking at a study in PubMed might be interested in

seeing Cochrane’s Risk of Bias assessment of this study, regardless of

whether they are interested in the overall Cochrane Review that includes that study.

RoB assessment in PubMed

Summary

Linked Data or Web 3.0 is hereHow can we leverage these tools to further

our missionRequires that we think differently about the

“container“ of the ReviewOur data needs to become “nimble“ to meet

future user needsWe should proceed slowly, incrementallyWhat are the “quick wins“ – Links to CRS?

Across-Review queries? Links to external datasets

EbHC Semantic Platform

CDSR CRS/CENTRAL

DARE

HTAs

CMR

EbHC Semantic Platform

CDSR CRS/CENTRAL

DARE

HTAs

CMR

DrugBank

UMLS

Diseasome

SymptomOntology

* BBCHealth

Ontology

* Not yet created

Cochrane and EbHC ontology?

Will Cochrane have a bubble here someday?

Muchas Gracias!

Linked Data and Cochrane Reviews A report from the ‘Star Trek’ Crew Chris Mavergames Web...

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