Linked Data and Cochrane Reviews

Report
Linked Data and
Cochrane Reviews
A report from the ‘Star Trek’ Crew
Chris Mavergames
Web Operations Manager/Information Architect
Cochrane Collaboration Web Team
 Intro
to linked data and what it
means for Cochrane
 "Star Trek" stream of work so far
 What'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.
Structure of this talk

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
Cochrane Reviews are fantastic
BUT…
Search for “Prozac” – no reviews
 Search for “fluoxetine” – 25 reviews

Searching The Cochrane Library

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?
Ideally we’d restructure our
content for different users
How did Bing read 3 different
weather sites & bring me the data
I need?
If so, what might we be able to accomplish?
Could we do similar magic with
our Cochrane reviews?
Linked data
Semantic Web
is made up of:
Linked Data & Web of Data
Which all together comprise
Web 3.0
What is linked data?
Current web = Web of documents
Docs are linked not data in docs
Data on the web is meant for human
consumption
 Machines need the data to be structured
 Once structured, information can be more
easily shared within datasets and across
web pages

Machines aren‘t good at reading
web pages
Cochrane Reviews
and Linked data
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">........
Cochrane Reviews
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.
Data
point
Data
point
Data
point
Data
point
Cochrane Reviews
Data
point
Data
point
Cochrane Register of Studies
Lack of unique study IDs a real problem
 CRS solves this by providing a unique ID
for all studies that can be referenced
 Better linking of data about trials and
possibilities with linking to external
sources such as PubMed (example later)

Links to the CRS



OWL (Web Ontology Language)
RDF (Resource Description Framework)
SPARQL (RDF query language)
Model Cochrane Reviews in OWL
Transform them into RDF and add to triple
store
 Query them with SPARQL


OR, simply...
Linked data technologies
Use the gears!
Subject ->
Property -> Object
<Gerd Antes> has-role <Director German Ctr>
<Director German Ctr> works-in <Freiburg, Germany>
<Gerd Antes> works-in <Freiburg, Germany>
Triple store = Way we think!
All
Reviews
in Archie
A Copy of
the
Review
XML
Standard tools have been
developed to facilitate this
process
A
Model
of the
Data
Using “the gears”
A Machine
Readable
“Triple
Store”
A
Question
A Machine
Generated
Answer
A Machine
Readable
“Triple
Store”
Using “the gears”
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
Cochrane Review ontology
Cochrane Review ontology
Cochrane Review ontology
Cochrane Review ontology
Findings ontology from Lorne
A
Question
A Machine
Generated
Answer
A Machine
Readable
“Triple
Store”
What sorts of things could we do
with this?
Gears!
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 search
 Make it easier for people to find Cochrane
Reviews

We can…
Ask questions that use data from
several different reviews
Enhancing the User Experience
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.
A question using multiple reviews




Search for the relevant Reviews
Read the reference lists to find included trials
Compare with my trial search
Eliminate the new references that are
additional publications from trials already
included in a Review.
OR…
Finding the answer the old way
My list of
trials
A
”studified”
list from
the CRS
The
Cochrane
Review
“Triple
Store”
The “Star Trek” Way
A Machine
Generated
list of
trials not
yet
included
in a
review
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
What are the risks of bias for the entire set
of trials assessing the effectiveness of a
particular intervention?
Another question using multiple
Reviews
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)
Finding the answer the old way
The
Cochrane
Review
“Triple
Store”
The “Star Trek” Way
A Machine
generated
summary of
the Risk of
Bias
assessments
for the
relevant
trials
RoB Summary for Cochrane Reviews on
dementia
These figures summarize
Risks of Bias from the
trials included in the
reviews in your search
Question 2 visualized
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">........
Cochrane Reviews
Make search work better
Enhancing the User Experience

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, UniAce, Valorin
You Say “Paracetamol”
I Say “Acetaminophen”
LinkedLifeData.com
LinkedLifeData.com
DrugBank
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">........
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">........
Cochrane Reviews
Make it easier for people to find
Cochrane Reviews
Enhancing the User Experience
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

Enhancing news content
Super Star Trek
How applicable is this
Review in my part of the world?
Super Star Trek
A list of the drugs in comparisons of
malaria in Reviews and the geographic
extent of their effectiveness
Geographical relevance
Map of Artemisin Resistance
The future
Structured and linked data can help make
our content “nimble”
Nimble content can:
• Travel Freely
• Retain Context Meaning
• Create New Products
- R. Lovinger, Razorfish
Making our content nimble
"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
Structured data
Implementing semantic and linked
data technologies should be:
• Non-invasive
• Agile
• Low impact (on staff – hopefully,
high impact on users!)
Incremental development
What would Cochrane data “look
like” outside of it’s container, the
Review?
Looking to the future
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.
Risk of Bias in PubMed
RoB assessment in PubMed






Linked Data or Web 3.0 is here
How can we leverage these tools to further
our mission
Requires that we think differently about the
“container“ of the Review
Our data needs to become “nimble“ to meet
future user needs
We should proceed slowly, incrementally
What are the “quick wins“ – Links to CRS?
Across-Review queries? Links to external
datasets
Summary
CDSR
CRS/
CENTRAL
HTAs
DARE
CMR
EbHC Semantic Platform
CRS/
CENTRAL
CDSR
Drug
Bank
DARE
Symptom
Ontology
UMLS
HTAs
Diseasome
CMR
* BBC
Health
Ontology
EbHC Semantic Platform
* Not yet created
Cochrane and EbHC ontology?
Will Cochrane have a bubble
here someday?
Muchas Gracias!

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