tag:blogger.com,1999:blog-44158879864511626552024-03-14T07:23:40.538+01:00Linked Data for EnterprisesKeeping myself up to date on the practical use of Linked Data in Enterprises and related topicsAnonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.comBlogger52125tag:blogger.com,1999:blog-4415887986451162655.post-38662368861377597592016-12-15T21:55:00.002+01:002016-12-19T22:23:25.698+01:00Wikipedia pages for clinical trials<div style="text-align: justify;">
<em style="background: none rgb(255, 255, 255); box-sizing: border-box; color: #333333; font-family: "Sitka Text", Georgia, Times, "Times New Roman", serif; font-size: 19px;">What would add value to have on Wikipedia pages for clinical trials? How could they support for example in recruiting and retaining patients? How could the underlying structured data in Wikidata be useful?</em></div>
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I had hoped to explore these questions during an internal innovation day. However, I had the chance to look more into another interesting thing: <a href="http://kerfors.blogspot.se/2015/06/jupyter-notebooks.html">Jupyter Notebooks</a>. Something I have been eager to do since last summer.<br />
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Anyhow, I hope to get involved in this interesting during 2017. I see great opportunities to both contribute and leverage from this in the work I do internally on a master list for clinical studies. I have started by engaging in two issues: <a href="https://github.com/opentrials/opentrials/issues/353">Normalize study_phase values see a Issue on OpenTrials Git</a> and also in a discussion about study identifiers (<a href="https://github.com/opentrials/opentrials/issues/552">OpenTrials issue on github</a>). Below some background to having clinical trials on Wikipedia, and in the data backbone called Wikdata, and also a note about OpenTrials.</div>
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Today (November 2016) a few studies have Wikipedia pages e.g. Lilly's <a href="https://en.wikipedia.org/wiki/PARAMOUNT_trial" style="background: transparent; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">PARAMOUNT study</a>. 16 studies, including the Lilly study, are typed as <a href="https://www.wikidata.org/wiki/Q30612" style="background: transparent; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">Clinical Trial (Q30612)</a> in Wikidata (<a href="https://query.wikidata.org/#SELECT%20?item%20?itemLabel%20WHERE%20%7b%0a%20%20?item%20wdt:P31%20wd:Q30612.%0a%20%20SERVICE%20wikibase:label%20%7b%20bd:serviceParam%20wikibase:language%20%22en%22.%20%7d%0a%7d%0aLIMIT%20100" style="background: transparent; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">SPARQL query</a>). The Wikidata identifier for the Lilly study is Q17148583 and its URI is<br />
<a href="http://www.wikidata.org/entity/Q17148583" style="background: transparent; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">http://www.wikidata.org/entity/Q17148583</a> </div>
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Wikidata is the backbone of Wikpedia where the entities behind Wikipedia pages are registered, such as compounds e.g. the Wikidata entity <a href="https://www.wikidata.org/wiki/Q415159" style="background: transparent; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">rosuvastatin </a><a href="https://www.wikidata.org/entity/Q415159" style="background: transparent; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">(Q415159)</a>hold some of the core structured data behind the infobox to the right on the <a href="https://en.wikipedia.org/wiki/Rosuvastatin" style="background: transparent; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">Wikipedia page for Rosuvastatin</a>. </div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiAo8D9HyymTA3ktWiraWZnfhxd5q0KUy70c4bBhUmycRbRZGj700a7NuUuz-db7esViGAvrRDj9K-GlWJ8oqk_98Q6mHCSMAgGEK5rlllTIT-piuvLCtlDnwMnwU-VLCAmWky8yLDBREQ/s1600/wikidata+and+wikipedia+illustration.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="220" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiAo8D9HyymTA3ktWiraWZnfhxd5q0KUy70c4bBhUmycRbRZGj700a7NuUuz-db7esViGAvrRDj9K-GlWJ8oqk_98Q6mHCSMAgGEK5rlllTIT-piuvLCtlDnwMnwU-VLCAmWky8yLDBREQ/s320/wikidata+and+wikipedia+illustration.png" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Wikidata entity and Wikipedia page for Rosuvastatin (also know as Crestor) </td></tr>
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Examples of structured data for Rosuvastatin in Wikidata: it is classified as a pharmaceutical drug (<a href="https://www.wikidata.org/entity/Q12140" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">Q12140</a>), and is a subclass of statin (<a href="https://www.wikidata.org/entity/Q954845" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">Q954845</a>) and what ATC code it has a property (<a href="https://www.wikidata.org/wiki/Property:P267" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">P267</a>). The structured data in Wikidata can be queries using SPARQL, a queary language for data structured as so calles RDF. The <a href="http://tinyurl.com/hd4f3x7" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">live SPARQL query</a> to get the ATC codes for statins.</div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjn958VhwgVg7lotVoL_psGbmkkjfQV6DuCjy9ilX4MNTOVAOOM82IdwWzntSDBIb430ge2KZOW3y_KW78gtWkLRd05kjuZErwk3hW_NV8_4WMirLiBXbh4JGo5KX1Qq8UpPQKR_IeeHDs/s1600/SPARQL+for+ATCcodes+for+statins.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="224" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjn958VhwgVg7lotVoL_psGbmkkjfQV6DuCjy9ilX4MNTOVAOOM82IdwWzntSDBIb430ge2KZOW3y_KW78gtWkLRd05kjuZErwk3hW_NV8_4WMirLiBXbh4JGo5KX1Qq8UpPQKR_IeeHDs/s320/SPARQL+for+ATCcodes+for+statins.png" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Live link to the SPARQL example live via: http://tinyurl.com/hd4f3x7</td></tr>
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The data for drugs and chemical compounds are sourced from Drugbank using a so called bot (see <em style="background-attachment: initial; background-clip: initial; background-image: none; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box;">A simple way to write Wikidata bots </em>[<a href="http://sulab.org/2015/09/a-simple-way-to-write-wikidata-bots/" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">blog post</a>] and <em style="background-attachment: initial; background-clip: initial; background-image: none; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box;">Drug and Chemical compound items in Wikidata as a data source for Wikipedia infoboxes</em>[<a href="https://youtu.be/U6llqWixxM4" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">video</a>]).</div>
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There are plans to integrate OpenTrials info into WikiData. That is, all studies registered in CT.gov/EudraCT, available via <a href="https://explorer.opentrials.net/" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">OpenTrials Explorer</a>. For more <a href="http://kerfors.blogspot.se/2016/11/opentrials.html" style="background-attachment: initial; background-clip: initial; background-image: initial; background-origin: initial; background-position: initial; background-repeat: initial; background-size: initial; box-sizing: border-box; color: #0072c6; text-decoration: none;" target="_blank">info about OpenTrial see my recent blog pos</a>t.</div>
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<span style="background-color: white; color: #333333; font-family: "sitka text" , "georgia" , "times" , "times new roman" , serif; font-size: 19px;">A first part of that work is</span><span style="background-color: white; color: #333333; font-family: "sitka text" , "georgia" , "times" , "times new roman" , serif; font-size: 19px;"> to develop a </span><a href="https://www.wikidata.org/wiki/Wikidata:WikiProject_Medicine/Data_models/Trials" style="background: rgb(255, 255, 255); box-sizing: border-box; color: #0072c6; font-family: "Sitka Text", Georgia, Times, "Times New Roman", serif; font-size: 19px; text-decoration: none;" target="_blank">Data model i Wikidata for Trials</a><span style="background-color: white; color: #333333; font-family: "sitka text" , "georgia" , "times" , "times new roman" , serif; font-size: 19px;">. using the </span><a href="https://prsinfo.clinicaltrials.gov/definitions.html" style="background: rgb(255, 255, 255); box-sizing: border-box; color: #0072c6; font-family: "Sitka Text", Georgia, Times, "Times New Roman", serif; font-size: 19px; text-decoration: none;" target="_blank">data elements for ClinicalTrials.gov</a><span style="background-color: white; color: #333333; font-family: "sitka text" , "georgia" , "times" , "times new roman" , serif; font-size: 19px;">. One example is how the NCT number, the identifier of studies, have been defined as a WikiData property (<a href="https://www.wikidata.org/wiki/Property:P3098">P3098</a>)</span><span style="color: #333333; font-family: "sitka text" , "georgia" , "times" , "times new roman" , serif;"><span style="font-size: 19px;"> with statements about it such as the Format as a regular expression: </span></span><span style="background-color: white; color: #252525; font-family: sans-serif; font-size: 14px;">NCT(\d{8}) </span><span style="color: #333333; font-family: "sitka text", georgia, times, "times new roman", serif; font-size: 19px;">and properties describing clinical trials like study phases.</span>Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-11162840818197755202016-11-05T16:19:00.001+01:002016-11-08T19:35:44.312+01:00OpenTrialsI have followed the development of <a href="http://opentrials.net/">OpenTrials </a>(<a href="https://twitter.com/opentrials">@opentrials</a>) since Ben Goldacre's (<a href="https://twitter.com/bengoldacre">@bengoldacre</a>) first comments about the lack of an open infrastructure to improve the sharing of information about clinical trials. See my blog post from 2013 <a href="http://kerfors.blogspot.se/2013/03/talking-to-machines.html">Talking to machines</a>.<br />
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It was nice to be able to give some initial feedback on the <i>human user interface</i> earlier this year. And very happy to see the API for <i>programmatic data access.</i> In this blog post I ask for some clarifications about <b>Study URIs </b>as a key enabler to link information about studies.<br />
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Intro to OpenTrials</h3>
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Hello <a href="https://twitter.com/hashtag/opendata?src=hash">#opendata</a> fans! Have you tried <a href="https://t.co/0I5xFcGDm1">https://t.co/0I5xFcGDm1</a> yet? It brings together all data and documents about all <a href="https://twitter.com/hashtag/clinicaltrials?src=hash">#clinicaltrials</a> <a href="https://t.co/E0LwdAUvJN">pic.twitter.com/E0LwdAUvJN</a></div>
— OpenTrials (@opentrials) <a href="https://twitter.com/opentrials/status/793901335586414592">November 2, 2016</a></blockquote>
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<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
I couldn't make it to the recent<a href="https://www.eventbrite.com/e/opentrials-hack-day-tickets-27046834811#"> Hack day in Berlin</a> just before <a href="http://opentrials.net/2016/10/10/opentrials-launches-beta-version-today-at-the-world-health-summit/">beta version was launched at the World Health Summit</a>. But it was great to follow the two events via the Twitter feed.</div>
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For a short intro to OpenTrials, watch this <a href="http://opentrials.net/2016/10/10/ben-goldacre-on-the-beta-launch-of-opentrials/">short video from the launch with Ben Goldacre</a>.<br />
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<iframe allowfullscreen="" frameborder="0" height="270" src="https://www.youtube.com/embed/EP2JXMYzOME" width="480"></iframe></div>
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<span style="font-size: large;">Human user access and Programmatic data access</span></h3>
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The user access to search the 300.000+ trials is via <a href="https://explorer.opentrials.net/">https://explorer.opentrials.net/</a>. For <a href="http://opentrials.net/2016/10/18/opentrials-api-information/">programmatic access via APIs I find the blog post</a> from the hack day excellent. It includes links to the API documentation (in Swagger), to a notebook showing sample code (Python) and to another example using R.</div>
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<tr><td style="text-align: center;"><a href="http://opentrials.net/files/2016/10/20161008_160858.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="240" src="https://opentrials.net/files/2016/10/20161008_160858.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Code from the OpenTrials Hack Day in Berlin (photo by benmeg / CC BY)</td></tr>
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I point colleagues in industry to this, and also to the <a href="https://open.fda.gov/">OpenFDA</a>, as two great examples of access to data both for humans and for programs. We have lots to learn from these two open data initatives, both when we define requirements and develop solutions.</div>
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I was also glad to see a comment from Ben Meghreblian (<a href="https://twitter.com/benmeg">@benmeg</a>), OpenTrials community manager, in an<a href="http://opentrials.net/2016/11/03/alltrials-interview-ben-meghreblian-opentrials-community-manager/"> interview for the AllTrials initative</a> the other day: "While API access is very useful, the best way a registry can offer its entire database is as a regular download, similar to what the FDA does with its OpenFDA website."</div>
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Study URIs</h3>
In the same interview Ben also concluded:<br />
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<a href="https://twitter.com/hashtag/OpenTrials?src=hash">#OpenTrials</a> community manager <a href="https://twitter.com/benmeg">@benmeg</a> on the change needed for greater <a href="https://twitter.com/hashtag/clinicaltrials?src=hash">#clinicaltrials</a> <a href="https://twitter.com/hashtag/transparency?src=hash">#transparency</a>: <a href="https://t.co/FwlLQ7Ma8S">https://t.co/FwlLQ7Ma8S</a> <a href="https://twitter.com/hashtag/alltrials?src=hash">#alltrials</a> <a href="https://t.co/QZswPpIdBD">pic.twitter.com/QZswPpIdBD</a></div>
— OpenTrials (@opentrials) <a href="https://twitter.com/opentrials/status/794176933374332929">November 3, 2016</a></blockquote>
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<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
One thing we (IMHO), both in open data initatives and in industry, "need to spend a little on making sure the information is discoverable, machine readable, and impactful" is to establish persistent URIs as Identifiers of studies. So, instead of a text string such as "D5135C00001" as a secondary/sponsor identifier in e.g. <a href="https://clinicaltrials.gov/">CT.gov</a>. I am pushing for study http-based URIs such as:</div>
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<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">http://clinicaltrials.astrazeneca.net/study/D5135C00001</span><br />
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A first step is an internal process to assign URIs to both old and new studies, and also an internal study look-up API service. This study lock-up API provide basic study descriptions, such as study phase and acronym and is presented on a study "home" page with the same http address as the URL. On this page we also provide other identifiers for the same study e.g. <a href="https://clinicaltrials.gov/">CT.gov</a>'s NCT number: "NCT01732822" and link to it using the URL.<br />
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<a href="https://clinicaltrials.gov/ct2/show/NCT01732822" style="font-family: "courier new", courier, monospace; font-size: small; text-align: start;">https://clinicaltrials.gov/ct2/show/NCT01732822</a></div>
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I have argued for study URIs from <a href="https://clinicaltrials.gov/">CT.gov</a> but my understanding from interactions with some of the people behind it - they see their URLs as pragmatic, persistent study URIs. So Study URIs = study Page URLs.</div>
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I would like to also include the identifier for the same study represented in OpenTrials. Either as a study URI distinct from the study page URL, or deliberately using the same http schema for them. I may think the current ones are locating study pages (URLs) rather than identifying studies (URIs), for example:<br />
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<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;"><a href="https://explorer.opentrials.net/trials/9b48fd6a-2c6c-4455-bcc2-b1aff574298e">https://explorer.opentrials.net/trials/9b48fd6a-2c6c-4455-bcc2-b1aff574298e</a></span><br />
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It would be great to have some clarifications about this. What I would like to have are namespaces for study identifiers (e.g. azct, nct, and opentrials) so I make assertions like these about the same study.</div>
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<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;"><azct:D5135C00001> <owl:sameAs> <nct:NCT01732822><br /><azct:D5135C00001> <owl:sameAs> <opentrials:9b48fd6a-2c6c-4455-bcc2-b1aff574298e> </span><br />
<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;"><azct:D5135C00001> <azct:hasAcronym> "EUCLID"</span><br />
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I have also posted this as an issue (<a href="https://github.com/opentrials/opentrials/issues/552">#552</a>) on <a href="https://github.com/opentrials">OpenTrials Github</a></div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-55990517536749005162016-05-22T11:36:00.000+02:002016-05-22T21:03:57.857+02:00Awesome graphic as Graphs<div style="text-align: justify;">
The classic continuum from Data via Information to Knowledge is nicely visualized in a three part graphic. I've seen it shared many times the last couple of years on Twitter and LinkedIn. Today I saw it extended with Insight and Wisdom. It made it even more awesome.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSrxrIH-6UpELOwFqSDc23NXWDBnkJhrULrG-OlwidH35X1WSE446HCVAu6RDObYZEdTCDDBeBiJIfUxmVkFbd76qw-bvyL4R0a9COaPWzS09avR4re2CM7bsedokWhQbki3EV9ClcYxs/s1600/IMG_0155.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="130" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjSrxrIH-6UpELOwFqSDc23NXWDBnkJhrULrG-OlwidH35X1WSE446HCVAu6RDObYZEdTCDDBeBiJIfUxmVkFbd76qw-bvyL4R0a9COaPWzS09avR4re2CM7bsedokWhQbki3EV9ClcYxs/s400/IMG_0155.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Original graphic by Hugh MacLeod @hughcards<br />
extended by David Sommerville @smrvl </td></tr>
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It was my friend and former colleague Martin Börjesson <a href="https://twitter.com/futuramb">@futuramb</a> that did a Re-Tweet of a tweet from John Hagel <a href="https://twitter.com/jhagel">@jhagel</a>, management consultant and author. It took me to the creator of the original graphic, Hugh MacLeod <a href="https://twitter.com/hughcards">@hughcards</a>, cartoonist and co-founder of <a href="https://twitter.com/gapingvoid">@gapingvoid</a>. The extension of it is done by David Sommerville <a href="https://twitter.com/smrvl">@smrvl</a> Digital Design Director for <a href="https://twitter.com/TheAtlantic">@TheAtlantic</a>.</div>
<br />
So, I started to think about representing the five pieces as executable and querayable graphs:<br />
<br />
<ul>
<li>1 DataPoint class</li>
<li>21 DataPoints</li>
<li>2 InfoClasses (represented by the green and lilac labels) </li>
<li>21 Classifications </li>
<li>1 type of Relationship</li>
<li>18 relationsships</li>
<li>1 new InfoClass (yellow) </li>
<li>2 new Classifications</li>
<li>1 Relationship Query</li>
</ul>
<div>
<br />
<b>RDF </b>triples, RDF Schema and SPARQL would be one option.</div>
<div>
<br /></div>
<div>
<b>Neo4j </b>Property Graph and Cypher, another option.</div>
<div>
<br /></div>
<div>
Well, will see if I can find the time to do it, or convince some graphs and linked data friends to have a go at it :-)</div>
<br />
<br />
<br />Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com2tag:blogger.com,1999:blog-4415887986451162655.post-51721443057067679542016-05-19T22:15:00.000+02:002016-05-22T21:27:52.078+02:00Global, persistent and resolvable identifiers for clinical data<div style="text-align: justify;">
Yesterday two thought leaders in clinical data standards publised great blog posts. Dave Ibersen-Hurst (<a href="https://twitter.com/Assero_UK">@Assero_UK</a>) and Armando Oliva (<a href="https://twitter.com/nomini">@nomini</a>). Dave's post has the title <a href="http://www.assero.co.uk/2016/wear-sunscreen/">Wear Sunscreen</a> but it's really about "CDISC 2.0". Armando's post has the title <a href="http://aolivamd.blogspot.se/2016/05/improving-study-data-tabulation-model.html">Improving the Study Data Tabulation Model</a></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
Discussions threads on Twitter and LinkedIn today made me write this post about one the many great proposals in the two blog posts: <i>1. SDTM should incorporate unique identifiers for each record in each domain.</i></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
In today's clinical data standards for 2-dimensional/tabular data exchange, e.g. CDISC SDTM, keys are either natural keys, e.g. STUDYID, USUBJID, LBTESTCD in a dataset of labdata according to SDTM, or surrogat keys, e.g LBSEQ. A define.xml file should be the source for study specific Key Variables for each dataset. For more details about SDTM keys and the challenges of this see <a href="http://www.pharmasug.org/proceedings/2016/TT/PharmaSUG-2016-TT18.pdf">Duplicate records - it may be a good time to contact your data management team</a>, PharmaSUG 2016, Sergiy Sirichenko and Max Kanevsky (<a href="https://twitter.com/pinnacle_21">@pinnacle_21</a>)</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
Armando details the proposal in his blog post as he says that the identifiers should be "globally unique".</div>
<blockquote class="twitter-tweet" data-lang="en">
<div dir="ltr" lang="en">
"Ideally, the identifier is globally unique. This brings us closer to creating a web of clinical data." <a href="https://t.co/Qbeabqb61k">https://t.co/Qbeabqb61k</a> HT <a href="https://twitter.com/nomini">@nomini</a></div>
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/733349635419430912">May 19, 2016</a></blockquote>
<div style="text-align: justify;">
This is a discussion I have looked forward to since I urged CDISC to consider semantic web standards and linked data principles in my presentation at CDISC EU conference in 2011.</div>
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWpDfsqn1UVYy5PoSaAzW2oETylTY4YOdaIy0WS-1Mv25rJcxj5SCx-I0jlpVjzNe4bM6hFJeJV-5iYtdNpuOqKF8NtZNNsAj_klVfChG-7uEllJo5CnNeLhv2dSUd1OtrkSRpihSjjfY/s1600/Linked+Data+URIs.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="296" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWpDfsqn1UVYy5PoSaAzW2oETylTY4YOdaIy0WS-1Mv25rJcxj5SCx-I0jlpVjzNe4bM6hFJeJV-5iYtdNpuOqKF8NtZNNsAj_klVfChG-7uEllJo5CnNeLhv2dSUd1OtrkSRpihSjjfY/s400/Linked+Data+URIs.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://www.slideshare.net/kerfors/linking-clinical-data-standards">Linking Clinical Data Standards</a><br />My presentation at CDISC EU Interchange 2011</td></tr>
</tbody></table>
I now see how smart programmers and informatians use checksums as record identifiers as a practical way to get around this problem and simplify the integration and reviewing of clinical data. <br />
<br />
A phrase we often use talking about linking data and semantic web standards is: "globally, persistent and resolvable identifiers".<br />
<br />
<ul>
<li>A http URI schema makes identifiers possible to resolve. An example of the URI that has a resolver service is <span style="font-size: x-small;"><span style="font-family: "courier new" , "courier" , monospace;"><a href="http://data.ordnancesurvey.co.uk/id/postcodeunit/SO160AS">http://data.ordnancesurvey.co.uk/id/postcodeunit/SO160AS</a></span> </span>the URI for the UK postcode SO160AS 1). </li>
<li>While the URIs assigned to CDISC standard items such as <span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">http://rdf.cdisc.org/std/sdtmig-3-1-3#Column.LB.LBSTRES</span> for the standard lab result variable in CDISC SDTM do (yet) not resolve.</li>
</ul>
<br />
<div style="text-align: justify;">
So how would a URI look like for a single data point in a clinical study? HL7 FHIR use so called UUID. Trusty URI:s use hash values "URIs that contain a certain kind of hash value that can be used to verify the respective resource" <a href="http://trustyuri.net/">http://trustyuri.net/</a> </div>
<div style="text-align: justify;">
<span style="text-align: center;"><br /></span></div>
<div style="text-align: justify;">
<span style="text-align: center;">I am eager to learn more about the potential of using URIs in combinations with Blockchains. This presentation on using blockchain technology and semantic standards for provenance across the supply chain made me think ...</span></div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="485" marginheight="0" marginwidth="0" scrolling="no" src="//www.slideshare.net/slideshow/embed_code/key/sTCu4l7tRBbeeU" style="border-width: 1px; border: 1px solid #ccc; margin-bottom: 5px; max-width: 100%;" width="595"> </iframe> </div>
<div style="margin-bottom: 5px;">
<div style="text-align: center;">
<strong> <a href="https://www.slideshare.net/christopherbrewster/20150617-tno" target="_blank" title="Semantic Blockchains in the Supply Chain">Semantic Blockchains in the Supply Chain</a> </strong> from <strong><a href="https://www.slideshare.net/christopherbrewster" target="_blank">Christopher Brewster</a></strong> </div>
</div>
<div style="text-align: center;">
<br /></div>
<br />
<div style="text-align: justify;">
... about <i>Semantic blockchains in the Clinical Data Supply Chain</i>. With identifiers assigned to each data point through the the supply chain of clinical data captured in EHR and smartphones, fed into clinical trial records, aggregated into summary level TLFs and later on included in secondary use analyses.</div>
<br />
Thoughts?<br />
<br />
1) <a href="https://www.ordnancesurvey.co.uk/education-research/research/linked-data-web.html">https://www.ordnancesurvey.co.uk/education-research/research/linked-data-web.html </a><br />
2) CDISC2RDF see <a href="https://github.com/phuse-org/rdf.cdisc.org">https://github.com/phuse-org/rdf.cdisc.org</a>Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com1tag:blogger.com,1999:blog-4415887986451162655.post-5253992804777311552016-05-06T18:48:00.001+02:002016-05-06T20:51:03.176+02:00Twitter Feeds and Blog posts from Conferences Conferences is a great way to meet interesting people and learn new things. Always nicest when you can attend IRL but interesting also following remotely via Twitter feeds, live blogging and reports and presentations blog post.<br />
<br />
<h3>
Conference Live Blogging</h3>
When I can attend conferences IRL I like to take notes using Twitter and I try to gather links and tweets using Storify as a kind of live blogging. Check out <a href="https://storify.com/kerfors/">Storify/kerfors</a> from events such as the recent Linked Data in Sweden, 2016 (<a href="https://storify.com/kerfors/ldsv2016">ldsv2016</a>) and HL7 FHIR workshops at Vitails, eHealth conference (<a href="https://storify.com/kerfors/vitalis2016">Vitails2016</a>).<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhh-__4fdhsiLV59wv0sH2XF609gPWIVAxaTItgV4yn2afI_dXVYObb0wkV71pMU971VEZP0eDd4OTzQ9jnpsz0R_NVi6pOM5olBLRBoQU5UTTO1GBYWq72A7LhJYBY5duVPODTDrtQXOE/s1600/LiveBlogging.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="239" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhh-__4fdhsiLV59wv0sH2XF609gPWIVAxaTItgV4yn2afI_dXVYObb0wkV71pMU971VEZP0eDd4OTzQ9jnpsz0R_NVi6pOM5olBLRBoQU5UTTO1GBYWq72A7LhJYBY5duVPODTDrtQXOE/s320/LiveBlogging.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Me in action live blogging</td></tr>
</tbody></table>
<br />
When I can not attend I like to follow conferences on a distance and read peoples blog reports.<br />
<br />
This week I've been following the great <a href="https://twitter.com/hashtag/csvconf?vertical=default&src=hash">#csvconf </a>feed from "a data conference that's not literally about CSV file format but rather what CSV represents to our community: data interoperability, hackability, simplicity,etc" The most interesting Twitter feeds from onferences I've seen so far.<br />
<blockquote class="twitter-tweet" data-lang="en">
<div dir="ltr" lang="en">
And one the best conferences I have followed remotely - Thanks all for a great <a href="https://twitter.com/hashtag/csvconf?src=hash">#csvconf</a> feed <a href="https://t.co/P0bIGl4h0g">https://t.co/P0bIGl4h0g</a></div>
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/728610476054171649">May 6, 2016</a></blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
Many thanks to some of the people tweeting from the event: <span class="username js-action-profile-name" data-aria-label-part="" style="background: rgb(245 , 248 , 250); color: #8899a6; direction: ltr; font-family: "arial" , sans-serif; font-size: 13px; line-height: 18px; text-decoration: none; unicode-bidi: embed;"><a class="account-group js-account-group js-action-profile js-user-profile-link js-nav" data-user-id="14697496" href="https://twitter.com/tomayac" style="background: rgb(245, 248, 250); color: #8899a6; font-family: Arial, sans-serif; font-size: 14px; line-height: 18px; text-decoration: none;"><span style="color: #b1bbc3;">@</span>tomayac</a>, @<a href="https://twitter.com/_inundata">_inunddata</a>, <a href="https://twitter.com/EmilyGarfield">@EmilyGarfield </a>(</span>Emily also posted some very nice drawings from the event.)<br />
<br />
<br />
<h3>
Conference Reports as blog posts</h3>
The recent CDISC Europe conference in Vienna <a href="https://twitter.com/hashtag/CDISCEurope?src=hash">#CDISCEurope</a> did have a pretty thin feed but with some great tweets from Magnus Wallberg (<a href="https://twitter.com/CMWallberg">@CMWallberg</a>), Technology Evangelist at WHO Uppsala Monitoring Center, posted a few tweets.<br />
<blockquote class="twitter-tweet" data-lang="en">
<div dir="ltr" lang="en">
William Stevens <a href="https://twitter.com/UniofOxford">@UniofOxford</a> showing how <a href="https://twitter.com/hashtag/OWL?src=hash">#OWL</a> <a href="https://twitter.com/hashtag/RDF?src=hash">#RDF</a> can be used to classify Adverse Events <a href="https://twitter.com/CDISC">@CDISC</a> <a href="https://twitter.com/UMCGlobalSafety">@UMCGlobalSafety</a> <a href="https://t.co/3hT78KOTe6">pic.twitter.com/3hT78KOTe6</a></div>
— Magnus Wallberg (@CMWallberg) <a href="https://twitter.com/CMWallberg/status/725612433063202817">April 28, 2016</a></blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
Magnus also wrote an excellent report as a blog post: <a href="http://carlmagnuswallberg.wix.com/home#!A-great-mix-of-standards-and-great-visions-when-CDISC-met-in-Vienna/c1mbt/572702ed0cf26b6d6848b83f">A great mix of standards and great visions when CDISC met in Vienna</a><br />
<br />
Update: Just after I published this blog post I saw Wayne Kubick's (<a href="https://twitter.com/WayneKubick">@WayneKubick)</a>, CTO for HL7 and former CTO for CDISC, blog post <a href="https://waynekubick.com/2016/05/06/hl7s-fhir-and-biopharma/">HL7’s FHIR and BioPharma </a>and article in Applied Clinical Trial: <a href="http://www.appliedclinicaltrialsonline.com/building-fhir-pharmaceutical-research">Building on FHIR for Pharmaceutical Research</a> from a HL7 event I recently followed: Partners in Interoperability workshop in Washington DC.<br />
<br />
<h3>
Conference Presentations accompanying blog posts </h3>
I also very much like when presenters quickly post their conference presentations on e.g. Slideshare. And it's also very nice to see accompanying blog posts with the speakers notes and additional material. I very much liked Dave Iberson-Hurst (<a href="https://twitter.com/Assero_UK">@assero_UK</a>) blog post with his CDISC Europe presentation this year. It is a post on his Semantic Web & Metadata series: <a href="http://www.assero.co.uk/2016/cdisc-standards-assessing-the-impact-of-change/">CDISC Standards: Assessing the Impact of Change</a><br />
<br />
I tried something similar when I wrote a blog post to prepare for my presentation "<a href="http://www.slideshare.net/kerfors/linked-data-efforts-for-data-standards-in-biopharma-and-healthcare">Linked Data efforts for data standards in biopharma and healthcare</a>" at the Linked Data in Sweden, 2016 meeting a week ago: <a href="http://kerfors.blogspot.se/2016/04/linked-data-in-sweden-2016.html">Linked Data in Sweden 2016</a><br />
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<br />Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-46798735687283862982016-04-21T21:52:00.000+02:002016-04-26T11:00:59.367+02:00Linked Data in Sweden 2016<div style="text-align: justify;">
It's time for the 5th "<a href="https://www.eventbrite.com/e/lankade-data-i-sverige-2016-registrering-23430125135">Linked Data in Sweden</a>" event, Tuesday 26 April. Last year I was organizing <a href="http://ait.gu.se/informatik/linked-data">the meeting in Gothenburg</a> together with Fredrik Landqvist. This year we are back in Stockholm, this time at the <a href="http://livrustkammaren.se/en">Royal Armoury.</a> I just learned that it is the oldest museum in Sweden. It was established by King Gustav II Adolph in 1628.<br />
<br />
Several interesting presentations on the agenda from e.g Scania, Nobel Media, Wikimedia, Findwise and National Library of Sweden. I will give a short update on <i>Linked Data efforts for data standards in biopharma and healthcare</i>. So, I have started to think about things I would like to cover and will tweet an item per day to things I find interesting. Below the emerging list of links and a video presentation per item. Not much spare time, so I will shape them into a couple of slides on the train up to Stockholm, see slides in the end of this blog post.</div>
<div style="text-align: justify;">
<h2 style="text-align: start;">
Standards represented as Linked Data</h2>
<div>
The first items on my list are examples of when the authoritative sources of the content, in this case traditional standard organisations, publish linked data versions of their own content. This is very much what I was hoping for in my key at the Semantic Web Applications Tools for Life Sciences (SWAT4LS) workshop in late 2013: <a href="http://www.slideshare.net/kerfors/pushing-back-standards-and-standard-organizations-in-a-semantic-web-enabled-world">Pushing back, standards and standard organizations in a Semantic Web enabled world</a>.</div>
</div>
<ul>
<li>CDISC in RDF</li>
<li>HL7 FHIR in RDF</li>
<li>MeSH in RDF</li>
<li>ICD-11 in OWL</li>
<li>Others standards e.g. ATC, WHO Drug and MedDRA</li>
</ul>
<h3>
CDISC in RDF</h3>
<div style="text-align: justify;">
In 2011 I presented; <a href="http://kerfors.blogspot.se/2011/05/linking-clinical-data-standards.html">Linking Clinical Data Standards</a>, at the CDISC (Clinical Data Interchange Standards Consortium) EU conference in Brussels. A year later, in Stockholm, Frederik Malfait (IMOS Consulting and consult at Roche) and I together presented <a href="http://kerfors.blogspot.se/2012/05/semantic-models-for-cdisc-based.html">Semantic models for CDISC based standard and metadata management</a>. At the <a href="http://lanyrd.com/2013/lankade-data-i-sverige/">2nd Linked Data in Sweden meeting in 2013</a> I presented; <a href="http://lanyrd.com/2013/lankade-data-i-sverige/sckcxf/">Länkade kliniska data standards</a> (Linked clinical data standards).<br />
<br />
The same spring the CTO of CDISC, Wayne Kubick, agreed to make this a task for the <a href="http://www.phuse.eu/">PhUSE </a>organisation (PhUSE Association Programming Pharmaceutical Users Software Exchange). The <a href="http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology">PhUSE Semantic Technology project</a> started later that year.<br />
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<br />
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/skEcerECfuE" width="560"></iframe>
</div>
<div style="text-align: center;">
Overview of PhUSE Semantic Technology Project<br />
by Frederik Malfait (21:16 - 37:00)</div>
<div style="text-align: center;">
<br /></div>
In the summer 2015 <a href="http://www.cdisc.org/rdf">CDISC published their standards in RDF</a>. In the future, representation of CDISC standards in RDF will be one of the outputs of CDISC's metadata registry (SHARE).</div>
<h3>
HL7 FHIR in RDF</h3>
<div style="text-align: justify;">
The Fast Healthcare Interoperability Resources (FHIR, pronounced "fire") proposed st<span id="goog_1651215461"></span><span id="goog_1651215462"></span><a href="https://www.blogger.com/"></a>andard describing data formats and elements (known as "resources"). It is an Application Programming Interface (API) for exchanging Electronic health records. The standard was created by the Health Level Seven International (HL7) health-care standards organization. And it is hot! I recently attended a FHIR workshop organised by <a href="http://hl7.se/">HL7 Sweden</a> at the Swedish eHealth conference Vitalis (see my <a href="https://storify.com/kerfors/vitalis2016">Storify Vitalis2016</a>).<br />
<br /></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
The HL7 FHIR project and the W3C Semantic Web Health Care and Life Sciences Interest Group work on RDF representations of FHIR. The <a href="https://hl7-fhir.github.io/rdf.html">HL7 work </a>lead by Graham Grieve, one of the creators of FHIR, and the <a href="http://w3c.github.io/hcls-fhir-rdf/spec/rdf.html">W3C HCLS group</a> lead by, David Both the initiator of the so called Yosemite project, will be aligned.<br />
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<br />
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/GCPLd-wIvZU" width="560"></iframe>
</div>
<h3>
MeSH in RDF</h3>
<div style="text-align: justify;">
The Medical Subject Headings (MeSH) is the National Library of Medicine's controlled vocabulary thesaurus. It is used to index the biomedical journals. The rational and design of <a href="https://id.nlm.nih.gov/mesh/">MESH in RDF</a> is described in a good article: <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419968/">Desiderata for an authoritative Representation of MeSH in RDF</a><br />
<br />
<br /></div>
<div style="text-align: justify;">
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/yB4oNQJqZDU" width="560"></iframe>
</div>
</div>
<div style="text-align: justify;">
<div style="text-align: center;">
<br /></div>
</div>
<div style="text-align: justify;">
<h3>
ICD-11 in OWL</h3>
The 11th revision of the International Classification of Diseases (ICD-11) is based on a content model encoded in OWL that takes it beyond the long list of terms in ICD10. Excellent introduction by Mark Musen to both ICD11 and to how the ontology tool called <a href="http://icat.stanford.edu/">iCAT</a>, based on <a href="http://icat.stanford.edu/">WebProtege</a>, has been used to represent ICD-11. While most editors want to stick to Excel spread sheets. This is a shared experience for all data standards mentioned here.<br />
<br />
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/-y9WRTgLwuA" width="560"></iframe>
</div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
See also <a href="http://yosemiteproject.org/2016/webinars/musen/">http://yosemiteproject.org/2016/webinars/musen/</a></div>
</div>
<h3 style="text-align: justify;">
Other standards e.g. ATC, WHO Drug, MedDRA</h3>
<div>
There are several other standards I would like to see RDF/OWL versions of to make our use of them in biopharma more robust. For example ATC (Anatomical Therapeutic Chemical Classification System), WHO Drug Dictionary and MedDRA (Medical Dictionary for Regulatory Activities). Early 2015 I was invited to WHO Uppsala Monitoring Center to talk about the value of this.<br />
<br /></div>
<div>
<br /></div>
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="485" marginheight="0" marginwidth="0" scrolling="no" src="//www.slideshare.net/slideshow/embed_code/key/iSJX7H1dEfBEXg" style="border-image: none; border: 1px solid rgb(204, 204, 204); margin-bottom: 5px; max-width: 100%;" width="595"> </iframe> </div>
<div style="margin-bottom: 5px;">
<div style="text-align: center;">
<strong> <a href="https://www.slideshare.net/kerfors/linked-data-presentation-for-who-umc-21-jan-2015" target="_blank" title="Linked data presentation for who umc 21 jan 2015">Linked data presentation for who umc 21 jan 2015</a> </strong> from <strong><a href="https://www.slideshare.net/kerfors" target="_blank">Kerstin Forsberg</a></strong> </div>
</div>
<br />
<br />
In the same way as it took CDISC almost 5 years, from early ideas on using semantic web standards and linked data principles to actually applying them, I think it will take some years more before we have:"Standardized the Standards", quote from David Booth leading the Yosemite project (see below).<br />
<br /></div>
<h3 style="text-align: justify;">
New initiatives outside the traditional standard organisations</h3>
<div style="text-align: justify;">
<div style="text-align: justify;">
Here a couple of interesting initiatives I wanted to also cover but will probably not have the time to do. </div>
</div>
<div>
<ul>
<li>Schema.org <a href="https://www.w3.org/community/schemed/">Health Vocabulary Community Group</a> working on <a href="http://heatlh%20and%20lifesciences%20extension/">Heatlh and Lifesciences Extension</a></li>
<li><a href="http://bioschemas.org/">BioSchemas </a>Promoting the use of Schema.org for sharing and exchanging information in the life sciences</li>
<li><a href="http://yosemiteproject.org/">Yosemite Roadmap for Healthcare Information Interoperability</a></li>
<li><a href="https://www.youtube.com/watch?v=4JgTzZGRrKY&feature=youtu.be&t=22m54s">Semantic Technology 101 for Pharma</a></li>
</ul>
<div>
<br /></div>
</div>
<div>
See my <a href="https://storify.com/kerfors/ldsv2016">Storify LDSV2016</a> with notes and links from the event.<br />
<br />
And here are the slides for my presentation in the afternoon that I did put together on the train from Gothenburg to Stockholm this morning.<br />
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="485" marginheight="0" marginwidth="0" scrolling="no" src="//www.slideshare.net/slideshow/embed_code/key/xA8uktmqIWb27G" style="border-width: 1px; border: 1px solid #ccc; margin-bottom: 5px; max-width: 100%;" width="595"> </iframe> </div>
<div style="margin-bottom: 5px;">
<div style="text-align: center;">
<strong> <a href="https://www.slideshare.net/kerfors/linked-data-efforts-for-data-standards-in-biopharma-and-healthcare" target="_blank" title="Linked Data efforts for data standards in biopharma and healthcare">Linked Data efforts for data standards in biopharma and healthcare</a> </strong> from <strong><a href="https://www.slideshare.net/kerfors" target="_blank">Kerstin Forsberg</a></strong> </div>
</div>
<br /></div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-10152041795404063122015-12-09T00:04:00.006+01:002015-12-09T00:10:34.188+01:00SWAT4LS 2015 Industry streamIt's been a great first day at SWAT4LS and I have been buying a few books in the lovely Cambridge University bookstore and had a nice conference dinner.<br />
<br />
I'm now preparing for tomorrow's task to be the chair for the industry stream in SWAT4LS (see my previous <a href="http://kerfors.blogspot.se/2015/12/swat4ls-2015.html">blog post for more information about this event</a>). So, here's a list of the 6 abstracts, companies and projects/tools that I'll introduce tomorrow morning:<br />
<ol>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/industry_sub_36.pdf">The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing</a>, <a href="http://gnode1.mib.man.ac.uk/team.html">Text Mining/NLP research group</a> within the School of Computer Science at the University of Manchester together with <a href="https://www.unilever.com/">UniLever</a>, BioHub Knowledge Base (BioHubKB)</li>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/industry_sub_48.pdf">Customizing “General SPARQL” for visualisation of in-house data in Cytoscape</a>, <a href="http://www.generalbioinformatics.com/">General Bioinformatics</a>, <a href="http://apps.cytoscape.org/apps/generalsparql">General SPARQL</a></li>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/industry_sub_49.pdf">GraphScope – smart data access for the life sciences</a>, <a href="http://searchhaus.net/en/">SearchHaus</a>, <a href="https://www.graphscope.io/">GraphScope</a></li>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/industry_sub_53.pdf">Semantic Technologies Make Sense for Life Sciences</a>, <a href="http://www.smartlogic.com/">SmartLogic</a></li>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/industry_sub_52.pdf">Advancing Knowledge Discovery for Alzheimer’s Disease: The Alzforum Experience</a>, <a href="http://www.alzforum.org/">Alzforum</a></li>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/industry_sub_54.pdf">Everybody a Translational Data Scientist</a>, <a href="http://www.ontoforce.com/">Ontoforce</a>, <a href="http://www.ontoforce.com/tour/disqover-finding-life-changing-data-faster-smarter-and-simpler/">DISQOVER </a></li>
</ol>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-18624556052088110162015-12-01T22:01:00.002+01:002015-12-06T18:34:41.431+01:00SWAT4LS 2015Monday, 7th December, I will fly to Cambridge to attend the <b>Semantic Web Applications and Tools for Life Sciences (<a href="http://www.swat4ls.org/workshops/cambridge2015/">SWAT4LS</a>) conference</b> and also visit colleagues at the new AstraZeneca site. The conference <a href="http://www.swat4ls.org/workshops/cambridge2015/programme/">programme </a>looks interesting and the venue, Clare College, fantastic ("Harry-Potter-land" was my husband's comment when he saw the pictures :-).<br />
<div>
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="http://www.swat4ls.org/wp-content/uploads/2015/04/800px-20130808_Castle_End_from_Kings_Bridge-300x200.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://www.swat4ls.org/wp-content/uploads/2015/04/800px-20130808_Castle_End_from_Kings_Bridge-300x200.jpg" /></a></div>
<br />
<br />
I am very glad to be the chair for the Industry session on Wednesday morning. Here are a few items on the <a href="http://www.swat4ls.org/workshops/cambridge2015/programme/">programme </a>I find extra interesting, from my clinical and RWE data perspective:</div>
<div>
<ul>
<li><a href="http://www.swat4ls.org/workshops/cambridge2015/programme/tutorials/#wikidata">Tutorial on using Wikidata in the life sciences</a> on Monday morning and the <a href="http://www.swat4ls.org/wp-content/uploads/2015/10/SWAT4LS_2015_paper_38.pdf">short paper</a> presentation on Wednesday </li>
<li><a href="http://www.swat4ls.org/workshops/cambridge2015/programme/tutorials/#trialdata">Semantic Representations of Clinical Care and Clinical Trial Data</a> tutorial on Monday afternoon and a poster Feasibility of Modeling HL7 FHIR Profiles Using RDF Shape Expressions Language</li>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/SWAT4LS_2015_paper_38.pdf">ODM on FHIR: Towards Achieving Semantic Interoperability of Clinical Study Data </a>in the main conference on Thuesday</li>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/SWAT4LS_2015_paper_6.pdf">Cochrane PICO Annotator and PICOfinder: Using semantically-enabled evidence to find what works in health care</a> demo on Wednesday</li>
<li><a href="http://www.swat4ls.org/wp-content/uploads/2015/10/SWAT4LS_2015_paper_29.pdf">A new Ontology Lookup Service at EMBL-EBI</a> demo on Wednesday </li>
<li>Discussion panel on Wednesday with interesting participants, e.g. Harold Solbrig – Mayo Clinic, and Egon Willighagen – Maastricht Universit</li>
<li>The <a href="http://www.swat4ls.org/workshops/cambridge2015/programme/hackathon/">hackathon </a>at European Bioinformatics Institute on Thursday. (I'll not attend as I will meet colleagues onsite in the new offices.) </li>
</ul>
Will be great fun to meet friends and colleagues in the Semantic Web community.</div>
<div>
<br /></div>
<div>
Checkout my Storify: <a href="https://storify.com/kerfors/swat4ls2015">SWAT4LS2015</a></div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-41654819708596485952015-06-25T21:40:00.003+02:002015-12-02T21:23:05.327+01:00Jupyter Notebooks<div style="text-align: justify;">
<div class="separator" style="clear: both;">
<br /></div>
Last week I followed the feed from the <a href="http://spark-summit.org/2015/">Spark Summit 2015</a> event and several tweets talked about using Notebooks. Two tweets especially:</div>
<blockquote class="twitter-tweet" lang="en">
<div dir="ltr" lang="en">
Paco Nathan: Notebooks as fundamental a change as spreadsheets were. Speaks to collab of teams involving non-data scientists <a href="http://twitter.com/hashtag/SparkInsight?src=hash">#SparkInsight</a></div>
— IBM Big Data (@IBMbigdata) <a href="http://twitter.com/IBMbigdata/status/610658646180040704">June 16, 2015</a></blockquote>
<blockquote class="twitter-tweet" lang="en">
<div dir="ltr" lang="en">
Ever wondered what might disrupt Excel or Tableau for analytics? I'm starting to think the Notebook format is a strong contender</div>
— Edd Dumbill (@edd) <a href="http://twitter.com/edd/status/611245014283325440">June 17, 2015</a></blockquote>
<div>
<div style="text-align: justify;">
So I got curios in <a href="http://jupyter.org/">Jupyter</a>, the lab notebooks used in the edX/DataBricks MOOC I'm following (<a href="http://www.edx.org/course/introduction-big-data-apache-spark-uc-berkeleyx-cs100-1x">Introduction to Big Data with Apache Spark</a>). And yes, I do agree with Paco Nathan (<a href="http://twitter.com/pacoid">@pacoid</a>) and Edd Dumbill (<a href="http://twitter.com/edd">@edd</a>); Notebooks do look like a real game changer: </div>
</div>
<ul>
<li>VisiCalc and Lous 1-2-3 in the early 80ies. </li>
<li>Mosaic and Netscape in the mid 90ies. </li>
<li>I get a similar feeling now, in the mid 2010ies, when I see Jupyter Notebooks.<br />(Yes, I know it's old news for all Mathematica users :)</li>
</ul>
<div class="separator" style="clear: both; text-align: center;">
</div>
<br />
<div style="text-align: justify;">
The first 20 mins of this great video with Min Ragan-Kelley (<a href="http://twitter.com/minrk">@minrk</a>) one of the core contributor to IPython and now to Jupyter, he gives a nice intro and in the following 30 mins he describes several cool examples of Notebooks, e.g. the <a href="http://notebooks.codeneuro.org/">CodeNeuro notebooks</a> using <a href="http://thunder-project.org/">Thunder </a>based on <a href="http://spark.apache.org/">Spark</a>.</div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<iframe allowfullscreen="" frameborder="0" height="315" src="http://www.youtube.com/embed/QkGSj24Qs-g" width="560"></iframe>
</div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: center;">
<br /></div>
<div style="text-align: left;">
Excellent <a href="http://podcastinit.com/episode-10-brian-granger-and-fernando-perez-of-the-ipython-project.html">podcast interview</a> with two other key contributors to iPython/Jupyter: Brian Granger (<a href="http://twitter.com/ellisonbg">@ellisonbg</a>) and Fernando Perez (<a href="http://twitter.com/fperez_org">@fperez_org</a>)<br />
<br />
<br />
Hmm, I need to think more about the combinations of Notebooks (reproducible research) and Linked Data (processable data) ... ...</div>
<br />
<div style="text-align: center;">
<br /></div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-14975398115237845082015-04-22T23:01:00.000+02:002015-05-04T20:54:44.223+02:00CSVW for Tabular Clinical Trial Data and Metadata <div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
W3C has developed a set of <a href="http://www.w3.org/blog/data/2015/04/16/csv-on-the-web-seeking-comments-and-implementations/">working drafts for tabular data and metadata called CSV on the Web (CSVW) </a>and are now seeking comments and implementations.</div>
<br />
The drafts describes:<br />
<ul>
<li><b>Metadata vocabular for tabular data</b><br />A JSON-based format for expressing metadata about tabular data to inform validation, conversion, display and data entry for tabular data<br /></li>
<li><b>Model for tabular data and metadata</b><br />An abstract model for tabular data, and how to locate metadata that enables users to better understand what the data holds; this specification also contains non-normative guidance on how to parse CSV files.<br /></li>
<li><b>Procedures and rules to be applied when converting tabular data into JSON and RDF </b></li>
</ul>
<div style="text-align: justify;">
These are based on a <a href="http://w3c.github.io/csvw/use-cases-and-requirements/index.html">series of use cases and recommendations</a> including for example Publication of National Statistics and Analyzing Scientific Spreadsheets. I can see some interesting opportunities in this for tabular Clinical Trial Datasets.<br />
<br />
<h3>
A small example</h3>
</div>
<div style="text-align: justify;">
Check out Ed Summers' (<a class="ProfileHeaderCard-screennameLink u-linkComplex js-nav" href="https://twitter.com/edsu" style="background: rgb(245, 248, 250); color: #8899a6; font-family: Arial, sans-serif; font-size: 14px; line-height: 14px; text-decoration: none !important;">@<span class="u-linkComplex-target">edsu</span></a>) very nice, small <a href="http://edsu.github.io/csvw-template/">csvw example</a> mentioning one of the authors of the drafts; Dan Brickley (<a class="ProfileHeaderCard-screennameLink u-linkComplex js-nav" href="https://twitter.com/danbri" style="background: rgb(245, 248, 250); color: #8899a6; font-family: Arial, sans-serif; font-size: 14px; line-height: 14px; text-decoration: none !important;">@<span class="u-linkComplex-target">danbri</span></a>, Developer Advocate at Google). Below the CSV example, related Metadata and the Annotated, linked data.</div>
<br />
<b>CSV</b><br />
<span style="font-family: Courier New, Courier, monospace;">isbn,title,author</span><br />
<span style="font-family: Courier New, Courier, monospace;">0470402377,"Bricklin on Technology","Dan Bricklin"</span><br />
<br />
<b>Metadata</b><br />
<pre style="white-space: pre-wrap; word-wrap: break-word;">{
"@context": {
"@vocab": "http://www.w3.org/ns/csvw#",
"dc": "http://purl.org/dc/terms/"
},
"@type": "Table",
"url": "example.csv",
"dc:creator": "Dan Bricklin",
"dc:title": "My Spreadsheet",
"dc:modified": "2014-05-09T15:44:58Z",
"dc:publisher": "My Books",
"tableSchema": {
"aboutUrl": "http://librarything.com/isbn/{isbn}",
"primaryKey": "isbn",
"columns": [
{
"name": "isbn",
"titles": "ISBN-10",
"datatype": "string",
"unique": true,
"propertyUrl": "http://purl.org/dc/terms/identifier"
},
{
"name": "title",
"titles": "Book Title",
"datatype": "string",
"propertyUrl": "http://purl.org/dc/terms/title"
},
{
"name": "author",
"titles": "Book Author",
"datatype": "string",
"propertyUrl": "http://purl.org/dc/terms/creator"
}
]
}
}</pre>
<pre style="white-space: pre-wrap; word-wrap: break-word;"></pre>
<b><br /></b>
<b>Annotated, linked data </b><br />
(RDF modeled serialized in JSON-LD)<br />
<pre style="white-space: pre-wrap; word-wrap: break-word;"> "@context": {
"csvw": "http://www.w3.org/ns/csvw#",
"dc": "http://purl.org/dc/terms/",
"prov": "http://www.w3.org/ns/prov#",
"xsd": "http://www.w3.org/2001/XMLSchema#"
},
"@graph": [
{
"@id": "_:g69960879269460",
"@type": "prov:Usage",
"prov:entity": {
"@id": "example.csv-metadata.json"
},
"prov:hadRole": {
"@id": "csvw:tabularMetadata"
}
},
{
"@id": "_:g69960879270660",
"@type": "prov:Usage",
"prov:entity": {
"@id": "example.csv"
},
"prov:hadRole": {
"@id": "csvw:csvEncodedTabularData"
}
},
{
"@id": "_:g69960879273280",
"@type": "prov:Activity",
"prov:endedAtTime": {
"@value": "2015-04-22T20:21:11Z",
"@type": "xsd:dateTime"
},
"prov:qualifiedUsage": [
{
"@id": "_:g69960879270660"
},
{
"@id": "_:g69960879269460"
}
],
"prov:startedAtTime": {
"@value": "2015-04-22T20:21:10Z",
"@type": "xsd:dateTime"
},
"prov:wasAssociatedWith": {
"@id": "http://rubygems.org/gems/rdf-tabular"
}
},
{
"@id": "_:g69960879277480",
"@type": "csvw:Row",
"csvw:describes": {
"@id": "http://librarything.com/isbn/0470402377"
},
"csvw:rownum": {
"@value": "1",
"@type": "xsd:integer"
},
"csvw:url": {
"@id": "#row=2"
}
},
{
"@id": "_:g69960879413940",
"@type": "csvw:Table",
"csvw:row": {
"@id": "_:g69960879277480"
},
"csvw:url": {
"@id": "example.csv"
},
"dc:creator": "Dan Bricklin",
"dc:modified": "2014-05-09T15:44:58Z",
"dc:publisher": "My Books",
"dc:title": "My Spreadsheet"
},
{
"@id": "_:g69960879425260",
"@type": "csvw:TableGroup",
"csvw:table": {
"@id": "_:g69960879413940"
},
"prov:wasGeneratedBy": {
"@id": "_:g69960879273280"
}
},
{
"@id": "http://librarything.com/isbn/0470402377",
"dc:creator": "Dan Bricklin",
"dc:identifier": "0470402377",
"dc:title": "Bricklin on Technology"
}
]
}</pre>
<pre style="white-space: pre-wrap; word-wrap: break-word;"></pre>
<pre style="white-space: pre-wrap; word-wrap: break-word;"></pre>
<h3>
A clinical trial data example?</h3>
Tabular data has been the traditional way to organize how clinical trial data is captured, stored and submitted. So, I think that this would be very interesting to explore to be able to bind data to it's metadata in a similar way. That is to, make things like variable labels, date/time formats etc. explicit.<br />
<ul>
<li>How could the metadata for a small, example of e.g. demographic data look like?</li>
<li>How would the annotated, linked data look for such a small example like?</li>
</ul>
<div>
<div style="text-align: justify;">
I would love to see some early ideas on how this could be implemented in the two main language/environments we use today for clinical data: SAS and R. Similar to the early implementation of <a href="http://greggkellogg.net/2015/04/implementing-csv-on-the-web/">CSVW in Ruby</a> described in a nice blog post from Greg Kellogg (<span class="screen-name" style="background: rgb(255, 255, 255); color: #66757f; font-family: Arial, sans-serif; font-size: 14px; line-height: 18px; text-decoration: none;"><a class="pretty-link js-nav" data-send-impression-cookie="true" dir="ltr" href="https://twitter.com/Gkellogg" style="background: rgb(255, 255, 255); color: #3b88c3; font-family: Arial, sans-serif; font-size: 14px; line-height: 18px; text-decoration: none;">@Gkellogg</a>, </span>one of the authors of the drafts).<br />
<br />
Such a first example I think would trigger an interesting ideas for best practices and potential extensions to the metadata vocabular and model, and also to the procedures and rules to create annotated JSON and RDF representations such as:<br />
<ul>
<li>Templates for the URIs to be assigned to each captured and derived data point?</li>
<li>Representing implied formats in varchar fields such as dates and precision.</li>
<li>Making explicit the implied metadata from the actual data such as encoded labtest codes and units.</li>
<li>How to leverage the <a href="https://github.com/phuse-org/rdf.cdisc.org">RDF schemas representing CDISC standards</a>?</li>
<li>How to best use <a href="http://www.w3.org/TR/prov-overview/">W3C's Provenance ontology</a> to capture the life cycle of a data point in a clinical trial?</li>
</ul>
</div>
<div style="text-align: justify;">
I think questions as these are important to address, especially in the context of transparency and reuse of clinical trial data, see also an earlier blog post: <a href="http://kerfors.blogspot.se/2015/02/clinical-trial-data-transparency-and.html">Clinical Trial Data Transparency and Linked Data</a>.<br />
<br />
So, I hope this blog post will spark some interesting responses from the SAS and R communities, and discussions in groups like CDISC and PhUSE Semantic Technology project.</div>
</div>
<div>
<br /></div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-62364098539918628732015-02-16T19:03:00.001+01:002015-03-08T20:50:17.770+01:00Clinical Trial Data Transparency and Linked Data<div style="text-align: justify;">
I've with great interest been following the discussions about clinical trial transparency and sharing of clinical trial data for the last three years. More precisely - my first tweet about this is from early 2012:</div>
<div style="text-align: justify;">
<br /></div>
<blockquote class="twitter-tweet" lang="en">
RT <a href="https://twitter.com/bmj_latest">@bmj_latest</a>: Editorial: Missing clinical trial data <a href="http://t.co/YOCWi7RD">http://t.co/YOCWi7RD</a> via <a href="https://twitter.com/researchremix">@researchremix</a><br />
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/154604081351106560">January 4, 2012</a></blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
<br />
<div style="text-align: justify;">
There has been a lot of debates over these years of how much of results of clinical trial results being published - is 50% or much more? Journal article publications vs trial registries? A lot of issues around summary level data vs. patient level data, and around de-identification of data and redaction of documents etc.<br />
<br />
All interesting topics but my interest in all of this is the opportunities in making data in, about and related to clinical trials, useful using semantic web standards and linked data principles. In the spring 2013 I wrote a <a href="http://kerfors.blogspot.se/2013/03/talking-to-machines.html">post on my blog: Talking to Machines</a>, about this after listening to Ben Goldacre, one of the key people behind the <a href="http://www.alltrials.net/">AllTrials </a>initiative where he also acknowledged this:<br />
<br /></div>
<blockquote class="twitter-tweet" lang="en">
“Talking to machines: Why are not all clinical trial data structured .. in RDF” <a href="https://twitter.com/bengoldacre">@bengoldacre</a> <a href="http://t.co/ne21HkF9xS">http://t.co/ne21HkF9xS</a> [28.30-39.00]<br />
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/315079348547883009">March 22, 2013</a></blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
<br />
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<br />
Here are a couple of recent events, early 2015, related to Clinical Trial Data Transparency and Linked Data:</div>
<ul>
<li>AAAS Panel on Innovations in Clinical Trial Registry</li>
<li>Public consultation EMA Clinical trial database</li>
<li>IoM report: Sharing Clinical Trial Data: Maximizing Benefits, Minimizing Risk</li>
</ul>
<h3>
AAAS Panel on Innovations in Clinical Trial Registry</h3>
<div style="text-align: justify;">
So, I really liked what I saw in the program for a session yesterday evening (15 February, 2015) from the American Association for the Advancement of Science annual meeting in San Jose (#AAASmtg) in a panel on <a href="https://aaas.confex.com/aaas/2015/webprogram/Session9579.html">Innovations in Clinical Trial Registers</a></div>
<blockquote class="tr_bq">
<div style="text-align: justify;">
<span style="font-family: Verdana, sans-serif;">Documents relating to trials -- protocols, regulatory summaries of results, clinical study reports, consent forms, and patient information sheets -- are scattered in different places. It is difficult to track the information that is available, in order to audit for gaps in information and for doctors and regulators to be sure they have all the information they need to make decisions about medicines. There is an unprecedented opportunity to refine how clinical trial data are shared and linked.</span></div>
</blockquote>
<div>
<h3>
Public consultation EMA Clinical trial database</h3>
<div style="text-align: justify;">
This is similar to what I wrote last week when I tried to "act courageously" and responded to "the <a href="http://www.ema.europa.eu/ema/index.jsp?curl=pages/news_and_events/news/2015/01/news_detail_002253.jsp&mid=WC0b01ac058004d5c1">public consultation</a> on how the transparency rules of the European Clinical Trial Regulation will be applied in the new clinical trial database is launched by the European Medicines Agency (EMA)."</div>
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<span style="font-family: Verdana, sans-serif;">Make use of modern data standards and access methods to <i>make the access to the clinical trial database developer-friendly</i>, <i>data machine-processable</i> and the <i>trials and their components linkable</i>. Leverage initiatives and use principles, such as <a href="http://www.cdisc.org/standards/dataexchange">CDISC Standards in RDF (under review)</a>, that uses modern data standards from W3C stack of semantic web standards, openFDA that uses developer-friendly REST APIs JSON (<a href="https://open.fda.gov/api/reference/">openFDA API reference</a>), and the linked data principles.</span></div>
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<h3>
IoM report: Sharing Clinical Trial Data: Maximizing Benefits, Minimizing Risk</h3>
<div style="text-align: justify;">
A couple of weeks ago the Institute of Medicine (IOM) released an excellent report: <a href="http://www.iom.edu/reports/2015/sharing-clinical-trial-data">Sharing Clinical Trial Data: Maximizing Benefits, Minimizing Risk.</a></div>
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Short summary, as I interpret the core message of the report: Instead of just designing and planning a study, scientists need to plan and document how they're going to share the data from that study so that its usable to others who may want to re-analyze it.<br />
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The report has a well written section on “legacy trials” and an interesting listing of challenges:</div>
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<span style="font-family: Verdana, sans-serif;">• <b>Infrastructure challenges</b>—Currently there are insufficient platforms to store and manage clinical trial data under a variety of access models. </span></div>
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<span style="font-family: Verdana, sans-serif;">• <b>Technological challenges</b>—Current data sharing platforms are not consistently discoverable, searchable, and interoperable. Special attention is needed to the development and adoption of common protocol data models and common data elements to ensure meaningful computation across disparate trials and databases. A federated query system of “bringing the data to the question” may offer effective ways of achieving the benefits of sharing clinical trial data while mitigating its risks. </span></div>
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<span style="font-family: Verdana, sans-serif;">• <b>Workforce challenges</b>—A sufficient workforce with the skills and knowledge to manage the operational and technical aspects of data sharing needs to be developed. </span></div>
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<span style="font-family: Verdana, sans-serif;">• <b>Sustainability challenges</b>—Currently the costs of data sharing are borne by a small subset of sponsors, funders, and clinical trialists; for data sharing to be sustainable, costs will need to be distributed equitably across both data generators and users.</span></div>
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And for a ”clinical trial data and metadata nerd” as me this is like music :-)<br />
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<span style="font-family: Verdana, sans-serif;">Just because data are accessible does not mean they are usable. Data are usable only if an investigator can search and retrieve them, can make sense of them, and can analyze them within a single trial or combine them across multiple trials. Given the large volume of data anticipated from the sharing of clinical trial data, the data must be in a computable form amenable to automated methods of search, analysis, and visualization.</span></div>
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<span style="font-family: Verdana, sans-serif;">To ensure such computability, data cannot be shared only as document files (e.g., PDF, Word). Rather, data must be in electronic databases that clearly specify the meaning of the data so that the database can respond correctly to queries. If data are spread over more than one database, the meaning of the data must be compatible across databases; otherwise, queries cannot be executed at all, or are executable but elicit incorrect answers. In general, such compatibility requires the adoption of common data models that all results databases would either use or be compatible with.</span></div>
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Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-1216856917800368092014-11-05T00:39:00.000+01:002015-12-02T21:29:18.323+01:00ISWC2014 Trip Report <div style="text-align: justify;">
A few highlights from five intensive days at the International Semantic Web Conference (<a href="http://iswc2014.semanticweb.org/">ISWC2014</a>) in lovely Riva del Garda. See also my previous blog post <a href="http://kerfors.blogspot.se/2014/10/preparing-for-iswc2014.html">Preparing for ISWC2014</a> and my <a href="https://storify.com/kerfors/iswc2014">live blog from all five days using Storify</a>.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIPM9OINl61c4pNPE0BBCDV-VFMuHzXzXILrd67_43Fv4YPhEinF3NtaURdYjUhPGqFNV_LqehrcRbiIAV1WNqxJ7H9VnnA0nm4U5NWpFBWkYpf2pL1tp2_S4uth5Ly_e0S11EXLRgOyc/s1600/iswc2014+storofy.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="261" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIPM9OINl61c4pNPE0BBCDV-VFMuHzXzXILrd67_43Fv4YPhEinF3NtaURdYjUhPGqFNV_LqehrcRbiIAV1WNqxJ7H9VnnA0nm4U5NWpFBWkYpf2pL1tp2_S4uth5Ly_e0S11EXLRgOyc/s400/iswc2014+storofy.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="https://storify.com/kerfors/iswc2014" style="font-size: medium; text-align: justify;">ISWC2014 Storify</a></td></tr>
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<h3>
Strong industry presence</h3>
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ISWC is a research focused conference. However, this year it had a strong industry prescence with a full day Industry track, Semantic Developer workshop and many of the Lighning Talks came from industry. It was great to meet Business Analysts and Information Architects from large companies such as Roche, Genentech and NXP Semiconductors and also from small companies such as the Danish StatGroup.</div>
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<ul>
<li><span style="text-align: justify;">All five Information Architects in the Data Standards Office at Roche / Genentech attended all five days to learn more about latest in semantic web research, especially traceability and provenance. Frederik Malfait, working for Roche and FDA/Phuse, described their RDF implementations of clinical trial data standards is the basis for a model driven architecture enabling computable protocols, component based authoring and automation of setting up clinical trial databases and generating submission datasets.</span></li>
<li style="text-align: justify;">Marc Andersen, one of the two founders of StatGroup, presented the experience of the Pharmaceutical Users Software Exchange (PhUSE) developing a semantic representation of statistical results based on RDF and OWL. Providing clinical trial results as linked data will facilitate traceability, data sharing and integration, data mining and meta-analysis benefiting industry, regulatory authorities and the general public.</li>
<li style="text-align: justify;">A business analyst described how NXP Semiconductor is making use of Semantic Web technology such as RDF and SPARQL to manage a product taxonomy for marketing purposes that forms the key navigation of the NXP website. </li>
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<blockquote class="twitter-tweet" lang="en">
Announcing <a href="http://t.co/8amKPgaca9">http://t.co/8amKPgaca9</a> our linked data portal <a href="https://twitter.com/hashtag/iswc2014?src=hash">#iswc2014</a><br />
— NXP data (@NXPdata) <a href="https://twitter.com/NXPdata/status/525217307694727168">October 23, 2014</a></blockquote>
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<h3>
Hot topics: Developer friendly, Linked Data Fragments, Provenance and Semantics for Sensors</h3>
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<li><div style="text-align: justify;">
The Semantic Developer Workshop and the conference program included many examples of RDF and SPARQL support in traditional programming languages, such as Java, Perl, C# and Javascript, as well as in data science languages, such as Python and R. The Semantic Developer of the Year, Kjetil Kernsmo, from Oslo University, presented RDF/Linked Data for Perl. JSON-LD was refereed to as the the developer-friendly serialization of RDF.</div>
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<li><div style="text-align: justify;">
Many of the presentations described how they applied the Provenance standard from W3C for "information about entities, activities, and people involved in producing a piece of data or thing, which can be used to form assessments about its quality, reliability or trustworthiness." One example was how the standards had been used event based traceability in pharmaceutical supply chains via automated generation of linked pedigrees.</div>
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Semantics for Sensors for every-thing from smart building diagnostic, traceability in pharmaceuticals supply chain, and traffic diagnosis to predicting frost in vineyards on Tasmania.</div>
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<li><div style="text-align: justify;">
"Everyone" talked about the work presented on the best awarded poster: Linked Data Fragments "so light-weight that even a Raspberry Pi can publish DBpedia (Wikipedia structured content) with high availability" <a href="http://fragments.dbpedia.org/">http://fragments.dbpedia.org/</a> </div>
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<blockquote class="twitter-tweet" lang="en">
Brilliant <a href="https://twitter.com/hashtag/demo?src=hash">#demo</a> about <a href="https://twitter.com/LDFragments">@LDFragments</a> by <a href="https://twitter.com/RubenVerborgh">@RubenVerborgh</a> at <a href="https://twitter.com/hashtag/iswc2014?src=hash">#iswc2014</a> <a href="http://t.co/BVaj4FRUsl">pic.twitter.com/BVaj4FRUsl</a><br />
— Enrico Daga (@enridaga) <a href="https://twitter.com/enridaga/status/524847332597436416">October 22, 2014</a></blockquote>
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<h3>
Best workshop paper award</h3>
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It was very nice to present our joint EHR4CR, Open PHACTS, SALUS and W3C HCLS paper. It got a best paper award in the pre-conference workshop: <a href="http://www.macs.hw.ac.uk/~fm206/cim14/">Context, Interpretation and Meaning</a> for the Semantic Web.</div>
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<iframe allowfullscreen="" frameborder="0" height="355" marginheight="0" marginwidth="0" scrolling="no" src="https://www.slideshare.net/slideshow/embed_code/40448087" style="border: 1px solid rgb(204, 204, 204); margin-bottom: 5px; max-width: 100%;" width="425"></iframe></div>
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<strong><a href="https://www.slideshare.net/kerfors/cim2014" target="_blank" title="A Justification-based Semantic Framework for Representing, Evaluating and Utilizing Terminology Mappings">A Justification-based Semantic Framework for Representing, Evaluating and Utilizing Terminology Mappings</a> </strong>from <strong><a href="https://www.slideshare.net/kerfors" target="_blank">Kerstin Forsberg</a></strong><br />
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<h3>
Other ISWC2014 reports</h3>
<ul>
<li><a href="http://thinklinks.wordpress.com/2014/10/29/trip-report-iswc-2014/">From Paul Groth (@pgroth)</a></li>
<li><a href="http://blog.tomayac.com/index.php?date=2014-10-27&time=13:01:35&perma=International+Semant.html">From Thomas Steiner (@tomayac)</a></li>
<li><a href="http://ruben.verborgh.org/blog/2014/10/30/the-year-of-the-developers/">From Ruben Verborgh (@RubenVerbrogh)</a></li>
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Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-21276579973018725272014-10-28T20:59:00.001+01:002014-11-14T17:08:19.316+01:00RDF as a Universal Healthcare Exchange Language<div style="text-align: justify;">
Here's a short post about a nice webinar serie: Yosemite Manifesto proposing RDF as a Universal Healthcare Exchange Language. It is provided by Semantic Technology & Business (<a href="https://twitter.com/semanticweb">@semanticweb</a>).</div>
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Here are a couple of tweets I posted during <a href="http://semanticweb.com/webinar-yosemite-project-part-1-rdf-roadmap-healthcare-information-interoperability-video_b44757">Part 1 (video and slides)</a> with David Booth.</div>
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<blockquote class="twitter-tweet" lang="en">
140+ attendees now in <a href="https://twitter.com/SemanticWeb">@SemanticWeb</a> webinar The Yosemite Project: An RDF Roadmap for Healthcare Information Interop <a href="http://t.co/BEtTSgVR0S">http://t.co/BEtTSgVR0S</a><br />
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/523176001128636416">October 17, 2014</a></blockquote>
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<blockquote class="twitter-tweet" lang="en">
How RDF Helps Standards -- David Booth, Yosemite Project A Roadmap for Healthcare Info Interop <a href="http://t.co/65RPpx3SfQ">http://t.co/65RPpx3SfQ</a> <a href="http://t.co/uKDCYdWGDO">pic.twitter.com/uKDCYdWGDO</a><br />
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/523178530084225024">October 17, 2014</a></blockquote>
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<blockquote class="twitter-tweet" lang="en">
How RDF Helps Translations -David Booth Yosemite Project A Roadmap for Healthcare Info Interop <a href="http://t.co/65RPpx3SfQ">http://t.co/65RPpx3SfQ</a> <a href="http://t.co/gj7oTuFgZQ">pic.twitter.com/gj7oTuFgZQ</a><br />
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/523179821065850880">October 17, 2014</a></blockquote>
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<blockquote class="twitter-tweet" lang="en">
Roadmap for Interop --David Booth Yosemite Project A Roadmap for Healthcare Info Interop <a href="http://t.co/65RPpx3SfQ">http://t.co/65RPpx3SfQ</a> … <a href="http://t.co/pQZbBRpD1N">pic.twitter.com/pQZbBRpD1N</a><br />
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/523182001973903360">October 17, 2014</a></blockquote>
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The Yosemite manifesto has been critized. I recommend a "very civil discussion, in the face of clear disagreement" between David Booth, Thomas Beale (<a href="https://twitter.com/wolands_cat">@wolands_cat</a>) and Dean Allemang (<a href="https://twitter.com/WorkingOntology">@WorkingOntology</a>): <a href="http://wolandscat.net/2014/08/08/rdf-for-universal-health-data-exchange-correcting-some-basic-misconceptions/">RDF for universal health data exchange? Correcting some basic misconceptions…</a></div>
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I look forward to <a href="http://semanticweb.com/new-webinar-announced-yosemite-project-part-2_b44764">Part 2, Friday 7 November</a> evening (8pm CET), when Conor Dowling, Caregraph will talk about: "Lab tests and results have many dimensions from substances measured to timing to the condition of a patient. This presentation will show how RDF is the best medium to fully capture this highly nuanced data."</div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-37489347097356050282014-10-14T20:45:00.002+02:002015-12-02T21:35:56.348+01:00Preparing for ISWC2014<div style="text-align: justify;">
Next week I’ll have the great pleasure to attend my first Int. Semantic Web Conference (<a href="http://iswc2014.semanticweb.org/">ISWC</a>). I've been fascinated by the power of the semantic web stack of standards for many years. Standards all based on the RDF model to represent and link data, as well as schemas, models and terminologies. I heard <a href="http://www.w3.org/Talks/1999/05/www8-tbl/Overview.html">Tim Berners-Lee talk about the Semantic Web for the first time at the WWW8 conference</a> back in 1999 in Toronto, Canada.<br />
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<tr><td style="text-align: center;"><a href="http://iswc2014.semanticweb.org/sites/iswc2014.fbk.eu/themes/professional_theme/images/slide-image-1.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://iswc2014.semanticweb.org/sites/iswc2014.fbk.eu/themes/professional_theme/images/slide-image-1.jpg" height="176" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="text-align: justify;"><span style="font-size: x-small;">13th International Semantic Web Conference, <a href="http://iswc2014.semanticweb.org/">ISWC 2014</a>, <br />will take place in Riva del Garda, Terentino, Italy</span></span><span style="font-size: small; text-align: justify;">.</span></td></tr>
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At ISWC2014 I’ll present a follow-up paper to the one I presented in early September at the Medical Informatics Europe conference (see my earlier blog post: <a href="http://kerfors.blogspot.se/2014/08/preparing-for-mie2014.html">Preparing for MIE2014</a>). It is a joint paper with colleagus from IMI EHR4CR, Open PHACTS, FP7 SALUS, W3C HCLS. Now with more details on the use of nanopubs and linksets in <a href="http://www.macs.hw.ac.uk/~fm206/cim14/cim20140_submission_2.pdf">A Justification-based Semantic Framework for Representing, Evaluating and Utilizing Terminology Mappings</a>. It will be discussed on Sunday in a pre-conference workshop organized by Alasdair Gray (<a href="https://twitter.com/gray_alasdair">@gray_alasdair</a>), Paul Groth (<a href="https://twitter.com/pgroth">@pgroth</a>) et al. <a href="http://www.macs.hw.ac.uk/~fm206/cim14/">Workshop on Context, Interpretation and Meaning</a></div>
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I'm also also looking forward to participate in the <a href="http://semstats2014.wordpress.com/">Semantic Statistics workshop</a> to learn more about things like the Data Cube for statistical data. This is a highly relevant topic for FDA/PhUSE and CDISC as representing clinical trial analysis results data as RDF Data Cubes is a topic at the ongoing PhUSE conference (presentation from UCB) and at the upcoming CDISC Interchange (presentation from DIcore Group, LLC, SAS Data Submission Consulting Services).</div>
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Tuesday evening I’ve been asked by James Malone (<a href="https://twitter.com/jamesmalone">@jamesmalone</a>) from EBI to sit on a panel at the European Ontology Network (EUON) Town Hall meeting together with Mark Musen, Stanford Center for Biomedical Informatics Research (I’m star strucked ;-) (Started earlier this year at the <a href="http://www.eudat.eu/euon/euon-2014-worksho">1st EUON workshop in Amsterdam</a>.)</div>
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I’m looking forward to meet interesting people from the semantic web community, and also newcombers to the community from organizations such as WHO, Roche, and CDISC. Magnus Wallberg from Uppsala Monitoring Centre WHO, working on a <a href="http://www.umc-products.com/OpenDataInitiative/">API and RDF project for Global ICSR statistics</a>. Also from the <a href="http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology">FDA/PhUSE Semantic Technology project </a>there will be presentations form Landen Bain, CDISC, and Frederik Malfait, Roche, will present at the <a href="http://iswc2014.semanticweb.org/full_program_day_two">Industry Track on Wednesday</a>.</div>
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I’ll try to keep my <a href="https://storify.com/kerfors/iswc2014">Storify-ISWC2014</a> updated during the week with interesting tweets, links and notes. And I know the Twitter-tag <a href="https://twitter.com/hashtag/iswc2014?f=realtime&src=hash">#iswc2014</a> feed will be lively as I’ve followed several earlier ISWC conferences on a distance. </div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-62265673781699399042014-08-25T21:01:00.000+02:002015-12-02T21:40:11.643+01:00Preparing for MIE2014<div style="text-align: justify;">
After a fantastic warm and sunny summer here in Sweden it's time for me to get prepared for the <a href="http://www.mie2014.org/">European Medical Informatics Conference - MIE2014</a>, Istanbul, 31 Aug. to 3 Sept.<br /><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUvph-fvSIePVwRiCXytTyxS0G8vOR-c_RGm7SJs0z5D7VuSfY27oR4v84dm53Rze3FbVo32iahETEVRB6E13i6GYGh_u_oPOfshxFe8iNr9MYdeUA3fvfG47ef2unZ5P5cDGd7zgh0Wg/s1600/MIE2014.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUvph-fvSIePVwRiCXytTyxS0G8vOR-c_RGm7SJs0z5D7VuSfY27oR4v84dm53Rze3FbVo32iahETEVRB6E13i6GYGh_u_oPOfshxFe8iNr9MYdeUA3fvfG47ef2unZ5P5cDGd7zgh0Wg/s400/MIE2014.jpg" width="279" /></a></div>
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Our joint paper co-authored by members across the IMI EHR4CR, Open PHACTS, SALUS projects and W3C HCLS community describing "<i><a href="http://ebooks.iospress.nl/volumearticle/37557">A Framework for Evaluating and Utilizing Medical Terminology Mapping</a>s</i>" has been accepted. And I have got the opportunity to present it in the main conference on the 2th September. </div>
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<iframe allowfullscreen="" frameborder="0" height="356" marginheight="0" marginwidth="0" scrolling="no" src="//www.slideshare.net/slideshow/embed_code/38325383" style="border-width: 1px; border: 1px solid #CCC; margin-bottom: 5px; max-width: 100%;" width="427"> </iframe> </div>
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<strong><a href="https://www.slideshare.net/kerfors/mie2014" target="_blank" title="MIE2014: A Framework for Evaluating and Utilizing Medical Terminology Mappings ">Slides for MIE2014: A Framework for Evaluating and Utilizing Medical Terminology Mappings </a> </strong> from <strong><a href="http://www.slideshare.net/kerfors" target="_blank">Kerstin Forsberg</a></strong> </div>
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For me the paper started from some great discussions at ICBO (Int. Conference Biomedical Ontologies) in Montreal last year with Trish Whetzel (<a href="https://twitter.com/TrishWhetzel">@TrishWhetzel</a>) and Jim McCusker (<a href="https://twitter.com/jpmccu">@jpmccu</a>) on the topic: "mappings are not sufficient - need the justifications for the mappings". We started to talk about using so called Nanopublications to capture the justification for the mapping for users to make better use of for example the mappings provided via the NCBO Bioportal.<br />
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When I came back from the ICBO conference I wrote a <a href="http://kerfors.blogspot.se/2013/09/justifications-of-mappings.html">blog post</a> outlining some more ideas on using Nanopublications and/or Linksets, both stemming from the IMI Open PHACTS project. Some nice comments and sharing of my blog post: <a href="http://kerfors.blogspot.se/2013/09/justifications-of-mappings.html">Justifications of Mappings</a> encourage me to work more on these ideas. My colleague in the EHR4CR project, Sajjad Hussain (<a href="https://plus.google.com/116764823254501886742/posts">+Sajjad Hussain</a>), pointed me to a very interesting blog post: <a href="http://www.srdc.com.tr/projects/salus/blog/?p=241">SALUS project on Terminology Mappings</a>. After some great discussion over a lunch at the SWAT4LS conference in Edinburgh with Hong Sun, from SALUS, Charlie Mead and Eric Prud'hommeaux, from W3C HCLS, Alasdair Gray (<a href="https://twitter.com/gray_alasdair">@gray_alasdair</a>) from Open PHACTS, and many more, Sajjad and I started to outline a paper decribing a framework combining solutions and ideas on evaluating and utilizing terminology mappings.</div>
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Beside presenting this paper I look forward to participate in an MIE2014 tutorial and workshop:<br />
<ul>
<li><b>Tutorial on the IEEE 11073 Standards for Personal Health Devices</b> (Wikipedia: <a href="http://en.wikipedia.org/wiki/ISO/IEEE_11073">ISO/IEEE_11073</a>). This is a standard I have been looking into earlier. It nicely combines my interest in clinical trials and health care data standards together with my previous industrial PhD studies in Mobile Informatics (see the slides presenting my PhLic thesis from 2001: <a href="http://www.slideshare.net/kerfors/mobile-newsmaking">Mobile Newsmaking</a>).</li>
<li><a href="https://www.w3.org/wiki/HCLS/workshops/iceh-2014"><b>Workshop on Interoperability Challenges for enabling secondary use of Electronic Health Records — ICEH 2014</b></a> In this workshop I look foward to meet and talk with many including the great metadata and ontology experts Gokce Laleci Ertukmen and Anil Pacaci (@aasinaci), Software Research, Development and Consultancy, Turkey.</li>
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I hope to be able to use my Twitter (<a href="https://twitter.com/kerfors">@kerfors</a>) feed to share interesting things I learn about in the conference, and from the historic city of Istanbul. And gather tweets, links, photos from each day using Storify. In the same way as I have done from eralier conferences. </div>
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So, have a look at my <a href="https://storify.com/kerfors/mie2014">MIE2014 Storify</a> for daily updates 31 Aug. to 3 Sept.</div>
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Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-74437721285670712232014-06-13T22:13:00.000+02:002015-12-02T21:43:00.438+01:00openFDA a Game Changer?<div>
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I’ve been fascinated by innovative people in the FDA organization since I had the pleasure to meet Dr Norman Stockbridge, the father of <a href="http://en.wikipedia.org/wiki/JANUS_clinical_trial_data_repository">FDA’s Janus datawarehouse model</a>, F2F back in 2005 in Washington, DC. </div>
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So when I saw some early notes about an openFDA initiative in June 2013 and early 2014 I posted a couple of tweets.</div>
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Interesting: <a href="http://t.co/A5MVm5omBd">http://t.co/A5MVm5omBd</a> Cloud-Based Initiative In The Works To House Public, Shared Data<br />
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/statuses/347104397093916672">June 18, 2013</a></blockquote>
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Very nice <a href="https://twitter.com/DrTaha_FDA">@DrTaha_FDA</a> to see <a href="http://t.co/34rnvqHVoG">http://t.co/34rnvqHVoG</a> <a href="https://twitter.com/search?q=%23openFDA&src=hash">#openFDA</a>. <a href="https://twitter.com/EMA_News">@EMA_News</a> When will we get <a href="https://twitter.com/search?q=%23opendata&src=hash">#opendata</a> <a href="https://twitter.com/search?q=%23openEMA&src=hash">#openEMA</a> <a href="http://t.co/C1QiXQlFsv">http://t.co/C1QiXQlFsv</a> ?<br />
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/statuses/444583515603365888">March 14, 2014</a></blockquote>
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In April I wrote a short blog post about <a href="http://kerfors.blogspot.se/2014/04/openfda.html">openFDA</a>. And, when I saw how the new Chief Health Informatics Officer at FDA, Taha Kass-Hout (<a href="https://twitter.com/DrTaha_FDA">@DrTaha_FDA)</a> started to count down on Twitter a couple of weeks ago I got really excited. It was nice to follow the <a href="https://twitter.com/hashtag/hdpalooza?f=realtime&src=hash">#hdpalooz feed </a>on Twitter from the health care data event in early June when openFDA was launched.</div>
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And, also to see services that directly were picking up the first openFDA API and launced services and apps to search the 3.4 million adverse <span style="text-align: center;">events, such as </span><a href="http://www.researchae.com/">Research AE</a></div>
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For a brilliant intro to what sits behind the first openFDA API I recommend Alex Howard's (<a href="https://twitter.com/digiphile">@digiphile</a>) excellent article: <a href="http://www.techrepublic.com/article/openfda-launches-open-data-platform-for-consumer-protection/">openFDA launches open data platform for consumer protection openFDA launches open data platform for consumer protection</a>.</div>
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"Instead of contracting with a huge systems integrator.. FDA worked with a tiny data science startup.. to harmonize the data, create a cutting-edge website, and write and release open source code for a data publishing platform for it [<a href="https://github.com/FDA">on GitHub</a>]"</blockquote>
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I think this will be a game changer for how we think about open data, open source and open communities in industry. And yes, I do think we will soon will see much more Open, and <a href="http://kerfors.blogspot.se/p/linked-data-resources_10.html">Linked Data</a> from FDA, and hopefully also from EMA and across industry.</div>
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<span style="font-size: x-small;">Kudos to the devlopers behind all of this great work, <br />e.g. Sean Herron (<a href="https://twitter.com/seanherron">@seanherron</a>) and Brian Norris (<a href="https://twitter.com/Geek_Nurse">@Geek_Nurse</a>)</span></div>
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Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-58295403995154290012014-04-02T21:57:00.000+02:002015-12-02T21:44:06.032+01:00openFDA<div style="text-align: justify;">
It's exiciting to see how the FDA (Food and Drug Administration) now starts to make some nice buzz about their new project called openFDA: <i> </i><i>A research project to provide open APIs, raw data downloads, documentation and examples, and a developer community for an important collection of FDA public datasets.</i></div>
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Excellent <a href="http://open.fda.gov/blog/introducing-openfda/">blog post </a>from Dr. Taha Kass-Hout (<a href="http://twitter.com/DrTaha_FDA">@DrTaha_FDA</a>), Chief Health Informatics Officer of FDA. He writes: "O<span style="background-color: white; color: #3a3a3a; font-family: "open sans"; line-height: 19.18000030517578px;">ur initial pilot project will cover a number of datasets from various areas within FDA, defined into three broad focus areas: Adverse Events, Product Recalls, and Product Labeling."</span></div>
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I do hope that the idea of not only open, but also linked data, will be part of this effort. For a quick intro to Why Linked Data? check out this nice video explaining the utility of linked data and how its being used by the UK's Ordnance Survey.</div>
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<iframe allowfullscreen="" frameborder="0" height="270" src="//www.youtube.com/embed/8qBEkW1wmEM" width="480"></iframe></div>
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I don't have the full context to all of this, but I may think there are some excellent opportunties for Dr Kass-Hout and his team to leverage linked data intitative such as these:</div>
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<ul>
<li><a href="http://aers.data2semantics.org/">Linked AERS</a></li>
<li><a href="http://dbmi-icode-01.dbmi.pitt.edu/linkedSPLs/">Linked SPL</a></li>
<li>See also <a href="http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology">FDA/PhUSE Semantic Technology project</a></li>
<li>See also <a href="http://chem-bla-ics.blogspot.nl/2014/03/linked-open-drug-data-three-years-on.html">Linked Open Drug Data: three years on</a> by Egon Willighagen (<a href="https://twitter.com/egonwillighagen">@egonwillighagen</a>)</li>
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Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-33307765508334564122014-02-27T20:12:00.002+01:002015-12-02T21:47:49.121+01:00Why I am so obsessed with this Semantic Web thing<div style="text-align: justify;">
In an <a href="http://kerfors.blogspot.se/2014/02/why-are-you-so-obsessed-with-this.html">earlier blog post </a>I reflected on the fact that it is now 25 years since the web was born. I had the opportunity to bring web technology into a large organisation. Many colleagues asked <a href="http://kerfors.blogspot.se/2014/02/why-are-you-so-obsessed-with-this.html">Why are you so obsessed by this "Web thing"?</a> (remember that this was the time when a Swedish minister said that "Internet är bara en fluga").</div>
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So, now in 2014 many ask me<i><b> Why are you so obsessed with this "Semantic Web thing"?</b></i>.</div>
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I had a good chance to reflect on this question when I was asked to be one of the keynote speaker at a very nice conference: <a href="http://www.swat4ls.org/workshops/edinburgh2013/">SWAT4LS</a>, Semantic Web Applications and Tools for Life Science, in Edinburgh. </div>
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<iframe allowfullscreen="" frameborder="0" height="356" marginheight="0" marginwidth="0" scrolling="no" src="http://www.slideshare.net/slideshow/embed_code/29053092" style="border-width: 1px 1px 0; border: 1px solid #CCC; margin-bottom: 5px; max-width: 100%;" width="427"> </iframe> </div>
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<strong>SWAT4LS 2013 keynote<br /><a href="https://www.slideshare.net/kerfors/pushing-back-standards-and-standard-organizations-in-a-semantic-web-enabled-world" target="_blank" title="Pushing back, standards and standard organizations in a Semantic Web enabled world">Pushing back, standards and standard organizations <br />in a Semantic Web enabled world</a> </strong> from <strong><a href="http://www.slideshare.net/kerfors" target="_blank">Kerstin Forsberg</a></strong> </div>
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I was also<a href="http://ecancer.org/conference/529-international-swat4ls-workshop/"> interviewed together with other speakers by the eCancer organisation in relation to the EURECA</a> (Enabling information re-Use by linking clinical REsearch and Care) project, Always scary to see, and hear yourself, but I think I managed to convey some of <a href="http://ecancer.org/conference/529-international-swat4ls-workshop/video/2647/improving-research-capabilities-with-semantic-web-technology.php">my thoughts</a>. And it is really nice to watch the interviews with <a href="http://ecancer.org/conference/529-international-swat4ls-workshop/video/2649/using-semantic-web-technology-to-improve-medical-trials-and-guidelines.php">Frank van Harmelen</a>,<a href="http://ecancer.org/conference/529-international-swat4ls-workshop/video/2648/w3c-and-maintaining-the-semantic-web-platform.php">Eric Prud'hommeaux</a>, <a href="http://ecancer.org/conference/529-international-swat4ls-workshop/video/2645/the-future-of-ontology.php">Robert Stevens</a> and <a href="http://ecancer.org/conference/529-international-swat4ls-workshop/video/2644/ibm-watson-for-healthcare.php">David Kerr</a>.</div>
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However, I think the one that best expressed the answer to the question was Charlie Mead. Charlie has been around in a long time in the standard world, working with HL7 for health care data and CDISC for clinical research data. Charlie is now a co-chair of the W3C interest group for semantic web for health care and life sciences (HCLS). I recommend this 7 minutes interview with Charlie. Below I have transcribed the last part of it as I think Charlie well express the reasons for Why I'm so obsessed by this "Semantic Web thing".</div>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTmQyf5evJftO7Fk454oN7DiGC9LvthLzkJinE9yKZ_Hx27FJepLlnzvEpM971Deuo6yOaJP-oXpcqnO9bICeoWrW1GqLHt0jYNaW0MD8TGAPuNYRYc5FPrGrvF2o_n3dtHPdTlRLp3-U/s1600/Charlie+Mead.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="158" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTmQyf5evJftO7Fk454oN7DiGC9LvthLzkJinE9yKZ_Hx27FJepLlnzvEpM971Deuo6yOaJP-oXpcqnO9bICeoWrW1GqLHt0jYNaW0MD8TGAPuNYRYc5FPrGrvF2o_n3dtHPdTlRLp3-U/s400/Charlie+Mead.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://ecancer.org/conference/529-international-swat4ls-workshop/video/2646/w3c-and-semantic-web-tecnology.php" style="font-size: 12.8px;">Charlie Mead<br />W3C HCLS semantic web interest group</a></td></tr>
</tbody></table>
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<i>"The thing that is really astonishing about the semantic web, the tools and technologies, really solve all of the core problems that we struggled with for a very long time.</i> </div>
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<i>And they solve them in a very elegant way, which almost by magic, that live on top of the Internet that we now works and have brought tremendous value.</i> </div>
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<i>And I think the real barrier to adopt these technologies is that is if more people understood what they can do I think the change curve will come faster and the resistance would melt more quickly."</i></div>
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<div style="text-align: center;">
Kudos to Scott Marshall, W3C and <a href="http://eurecaproject.eu/">EURECA</a> project, (<a href="https://twitter.com/mscottmarshall">@mscottmarshall</a>) <br />
for arranging the interviews and to the <a href="http://ecancer.org/video/index.php">eCancer TV</a> team.</div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com1tag:blogger.com,1999:blog-4415887986451162655.post-49167230928711828422014-02-06T20:09:00.000+01:002014-02-06T22:17:16.800+01:00Why are you so obsessed with this Semantic Web thingA lot of nice buzz today in sociala media when Tim Berners-Lee discusses the future of the web in the <a href="http://www.wired.co.uk/magazine/archive/2014/03">March issue of Wired UK</a>. The web turns 25 years in March.<br />
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"In 1989 I delivered a proposal to Cern for the system that went on to become the world wide web" <a href="http://t.co/fR2nyPhhss">pic.twitter.com/fR2nyPhhss</a></div>
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— Wired UK (@WiredUK) <a href="https://twitter.com/WiredUK/statuses/431416728564682753">February 6, 2014</a></div>
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It reminded me of what collegues asked me almost 20 years ago: <i><b>Why are you so obsessed with this "Web thing"??</b></i><br />
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Thanks to some great people in the Volvo business and data organisations I was exposed to "this web thing" and it made me change direction in my professional carrier. From a fancy job as Account Mananger to leading a small network of people get the Volvo Web Wave moving.<br />
<br />
Today, 2014, my collegues ask me: <i><b>Why are you so obsessed with this "Semantic Web thing"?</b></i><br />
<br />
Recently I, together with other speakers at the <a href="http://www.swat4ls.org/workshops/edinburgh2013/">SWAT4LS</a> (Application and Tools in Semantic Web for Health Care and Life Sciences) conference, had the opportunity to reflect on the main difference the semantic web can make for patients, health care and clinical research professionals in video interviews by <a href="http://ecancer.tv/">ecancer.tv</a><span id="goog_301870417"></span><span id="goog_301870418"></span><a href="https://www.blogger.com/"></a> for the<a href="http://eurecaproject.eu/"> EURECA</a> project. Stay tuned for these via my Twitter (<a href="https://twitter.com/kerfors">@kerfors</a>) feed and in a coming blog post.<br />
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-51430635791309789212013-11-17T21:09:00.002+01:002015-12-16T21:29:40.790+01:00De-identification and Informed Consent in Clinical Trials<blockquote class="twitter-tweet" lang="en">
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Thursday evening I was following the great <a href="http://twitter.com/search?q=%23PACCR&src=hash&f=realtime">#PACCR</a> feed on Twitter from a "Patients at Center of Clinical Research" discussion hosted by <a href="http://portal.lillycoi.com/">Eli Lilly Clinical Open Innovation</a> team. (Thank you Rahlyn Gossen, <a href="http://twitter.com/RebarInter" target="_blank">@RebarInter</a>, for the pointer)</div>
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A couple of interesting comments came up in some tweets on the topic of <a href="http://en.wikipedia.org/wiki/De-identification" target="_blank">de-identification</a>. As de-identification (sometimes called anonymization) is a key topic for clinical trial data transparency, I did find these quotes really interesting.<br />
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.<a href="https://twitter.com/ReginaHolliday">@reginaholliday</a> No one even asks if clinical trial participants want to be de-identified. Some people don't want to. <a href="https://twitter.com/hashtag/PACCR?src=hash">#PACCR</a></div>
— Rebar Interactive (@RebarInter) <a href="https://twitter.com/RebarInter/status/401010244866019328">November 14, 2013</a></blockquote>
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It was said in the meeting by Regina Holliday (<a href="http://twitter.com/ReginaHolliday" target="_blank">@ReginaHolliday</a>), a great tweeter promoting patients rights within medicine.</div>
<blockquote class="twitter-tweet" lang="en">
Is it ethical to remove rare/genetic diseases within De-identified Data to protect against re-identification? <a href="http://t.co/cGRxe9Kzv5">http://t.co/cGRxe9Kzv5</a> <a href="http://twitter.com/search?q=%23PACCR&src=hash">#PACCR</a><br />
— Daniel Barth-Jones (@dbarthjones) <a href="http://twitter.com/dbarthjones/statuses/401038094314782720">November 14, 2013</a></blockquote>
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Daniel Barth-Jones (<a href="http://twitter.com/dbarthjones" target="_blank">@dbarthjones</a>), Columbia University and expert in Data Privacy and De-identification Policy, asked in another tweet and referenced a very interesting blog post from Harvard Law School on <a href="http://blogs.law.harvard.edu/billofhealth/2013/10/02/ethical-concerns-conduct-and-public-policy-for-re-identification-and-de-identification-practice-part-3-re-identification-symposium/">Ethical Concerns, Conduct and Public Policy for Re-Identification and De-identification Practice</a>. </div>
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<i>"<span style="-webkit-text-size-adjust: auto; background-color: rgba(255, 255, 255, 0);"><span style="text-align: justify;">When re-identification risks are exaggerated, we need to recognize that the resulting fears cause needless harms. Such fears can push us toward diminishing our use of properly de-identified data, or distorting the accuracy of our statistical methods because we’ve engaged in ill-motivated de-identification and have altered data even in cases where there was not anything more than </span><span style="border: 0px; margin: 0px; outline: 0px; padding: 0px; text-align: justify; vertical-align: baseline;">de minimis</span><span style="text-align: justify;"> re-identification risks."</span></span></i></blockquote>
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From the same <a href="http://blogs.law.harvard.edu/billofhealth/2013/10/02/ethical-concerns-conduct-and-public-policy-for-re-identification-and-de-identification-practice-part-3-re-identification-symposium/">blog post</a> from the <a href="http://blogs.law.harvard.edu/billofhealth/2013/05/13/online-symposium-on-the-law-ethics-science-of-re-identification-demonstrations/">Online Symposium on the Law, Ethics & Science of Re-identification Demonstrations</a>, at the Bill of Health at Harvard Law School, in the fields of health law policy, biotechnology, and bioethics.<br />
<blockquote class="tr_bq">
<i style="text-align: left;">“We must achieve an ethical equipoise between potential privacy harms and the very real benefits that result from the advancement of science and healthcare improvements which are accomplished with de-identified data."</i></blockquote>
There were also a couple of interesting <a href="http://twitter.com/search?q=%23PACCR&src=hash&f=realtime">#PACCR</a> tweets on the topic of <a href="http://en.wikipedia.org/wiki/Informed_consent" target="_blank">Informed Consent</a> quoting Sharon Terry (<a href="http://twitter.com/sharonfterry" target="_blank">@sharonfterry</a>), CEO of Genetic Alliance:<br />
<blockquote class="twitter-tweet">
Informed consent information should be dynamic, granular, matrixed and contextual. <a href="http://twitter.com/sharonfterry">@sharonfterry</a> <a href="http://twitter.com/search?q=%23PACCR&src=hash">#PACCR</a> <a href="http://twitter.com/search?q=%23clinicaltrials&src=hash">#clinicaltrials</a><br />
— Lilly Clinical OI (@Lilly_COI) <a href="http://twitter.com/Lilly_COI/statuses/401080627463987201">November 14, 2013</a></blockquote>
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I would like to learn more about this thinking and how they potentially could be realized by:<br />
<blockquote class="tr_bq">
<i>Structuring and formalizing the Informed Consent content to become a semantic rich, and machine-executable, contract/policy for transparency and accountability in using clinical trial data. </i></blockquote>
For more information see:<br />
<ul>
<li>Permission Ontology for informed consent and HIPAA compliance (<a href="http://ontology.buffalo.edu/smith/ppt/CTS-Ontology_2012/WorkshopDay1/Adela_Grando_Permissions_Ontology.pdf" target="_blank">presentation in pdf</a>) in the <a href="http://ncorwiki.buffalo.edu/index.php/CTSA_Ontology_Workshop" target="_blank">CTSA Ontology Workshop, Febr 2013</a></li>
<li><a href="http://dig.csail.mit.edu/2013/07/pclob-weitzner-accountability.pdf" target="_blank">Information accountability policy whose restrictions are based on usage rules, not access or collection rules</a> testimony by Danny Weitzner (<a href="http://twitter.com/djweitzner" target="_blank">@djweitzner</a>) in the Privacy and Civil Liberties Oversight Board <a href="http://www.pclob.gov/Pages/9%20July%202013%20Public%20Workshop.aspx" target="_blank">Workshop Regarding Surveillance Programs Operated, July 2013</a></li>
</ul>
<br />
I do find all of this very interesting. And I hope such a "dynamic, granular, matrixed and contextual" approach can be part of new clinical trial data transparency policies: </div>
<blockquote class="tr_bq">
"<i>To find solutions that are 'good enough' and provide both dramatic privacy protections and useful analytic data</i>" (from the same <a href="http://blogs.law.harvard.edu/billofhealth/2013/10/02/ethical-concerns-conduct-and-public-policy-for-re-identification-and-de-identification-practice-part-3-re-identification-symposium/">blog post</a>).</blockquote>
<div style="text-align: justify;">
<ul>
</ul>
</div>
<blockquote class="twitter-tweet">
</blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script></div>
</blockquote>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-55441842713472388112013-10-07T23:00:00.003+02:002015-01-07T19:57:08.262+01:00The future of CDISC CT:s<div style="text-align: justify;">
A <a href="http://www.linkedin.com/groups/When-you-import-CDISC-Controlled-56393.S.276975726" target="_blank">poll </a>posted by Lex Jansen (<a href="https://twitter.com/lexjansen" target="_blank">@lexjansen</a>) in the LinkedIN group for CDISC (Clinical Data Interchange Standards Consortium) triggered me to write down some thoughts on the future of CDISC's so called Controlled Terminologies (CT:s):</div>
<br />
<div style="text-align: center;">
<span style="font-family: Trebuchet MS, sans-serif;">When you import CDISC Controlled Terminology from NCI EVS at <a href="http://evs.nci.nih.gov/ftp1/CDISC">http://evs.nci.nih.gov/ftp1/CDISC</a>, which format do you use?</span></div>
<div style="text-align: center;">
<span style="font-family: Trebuchet MS, sans-serif;"> (Excel, Text, ODM XML, or OWL/RDF)</span></div>
<br />
<div style="text-align: justify;">
My vote goes to the formats with the best potential for the future, that is the formats serializing RDF modeled data e.g. turtle, json-ld, n-triples, and xml (See the blog post: <a href="http://blog.swirrl.com/articles/rdf-serialisation-formats/" target="_blank">Understanding RDF serialisation formats</a>)</div>
<br />
<h3>
Today's RDF version</h3>
<div style="text-align: justify;">
The recently published OWL/RDF version of the CT:s (serialized in xml) uses the first version of the CDISC2RDF schema 1) implementing the model behind the existing export of a limit part of the content in NCI Thesaurus (NCIt). </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
It is modeled to support today's use of the CT:s only as text strings to populate variables in CDISC defined data sets (e.g. SDTM domains) with submission values.That is, it provide <i>study specific clarity</i> making it easy for humans to read the clinical data and metadata.</div>
<div style="text-align: justify;">
<br /></div>
<h3 style="text-align: justify;">
Next RDF version</h3>
<div style="text-align: justify;">
Based on very useful discussions with the terminology expert Julie James (<a href="http://www.linkedin.com/pub/julie-james/15/870/3b4" target="_blank">LinkedIn profile</a>) working for HL7, IMI EHR4CR and <a href="http://www.phusewiki.org/wiki/index.php?title=Metadata_Definition_Project" target="_blank">FDA/PhuSE Metadata definition project</a>, these are my thoughts for the next RDF version:</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
To provide <i>cross study semantic interoperability</i> making it easy for machines to directly integrate and query clinical data and metadata <i>across health care and clinical research </i>we need an enhanced model.</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
That is, a model that fully leverage the content in NCIt. And address the issues people have experienced when using the CT:s in attempts to implement them in <a href="http://www.cdisc.org/bridg" target="_blank">BRIDG</a> / <a href="http://wiki.medical-objects.com.au/index.php/ISO_21090_Datatypes_Guide" target="_blank">ISO21090</a>. Using the insights from the IMI EHR4CR project and from the development of the <a href="http://www.ihe.net/uploadedFiles/Documents/QRPH/IHE_QRPH_Suppl_DEX.pdf" target="_blank">IHE DEX profile</a> (Data Element Exchange).<br />
<br />
I think there is also an opportunity to leverage the work on binding value sets to data elements part of the <a href="http://hl7.org/implement/standards/fhir/index.html" target="_blank">HL7 FHIR</a> (Fast Healthcare Interoperability Resources) development 2). Julie also pointed me to a new ISO standards: <span style="text-align: start;">ISO/CD 17583 3) </span>The next version should also apply both the <a href="http://en.wikipedia.org/wiki/Object_identifier" target="_blank">OID </a>(Object identfier) standard and the <a href="http://en.wikipedia.org/wiki/Uniform_resource_identifier" target="_blank">URI </a>(Uniform Resource Identifier) standard to identify each value set and each value.</div>
<div style="text-align: justify;">
<br /></div>
<br />
References:<br />
1) <a href="http://www.slideshare.net/kerfors/forsberg-dils2013poster" target="_blank">CDISC2RDF poster</a> (presented at DILS 2013, Data Integration in Life Science conference) and <a href="http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology" target="_blank">FDA/PhUSE Semantic Technology project </a><br />
2) <a href="http://www.linkedin.com/redirect?url=http%3A%2F%2Fwww%2Ehl7%2Eorg%2Fimplement%2Fstandards%2Ffhir%2Fterminologies%2Ehtm&urlhash=1_qD&_t=tracking_disc" style="text-align: justify;">http://www.hl7.org/implement/standards/fhir/terminologies.htm</a><br />
3) ISO/CD 17583: Health informatics -- Terminology constraints for coded data elements expressed in (ISO 21090) Harmonized Data Types used in healthcare information interchange.Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-83315220612047830232013-09-13T00:13:00.000+02:002015-12-02T21:58:58.854+01:00Justifications of Mappings<div style="text-align: justify;">
A common theme in the Semantic Trilogy events in Montreal this summer (see <a href="http://kerfors.blogspot.se/2013/06/semantic-trilogy-preparation.html">Semantic Trilogy preparations</a> and <a href="http://kerfors.blogspot.se/2013/07/semantic-trilogy-report-part-1.html">Semantic Trilogy report part 1</a>) was mappings such as <a href="http://www.bioontology.org/wiki/index.php/BioPortal_Mappings">the mappings provided via the NCBO BioPortal</a>. </div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
For example the mappings in the Bioportal expressed as skos:closeMatch are the result of using the LOOM lexical algorithm. Examples of not so good mappings, such as this one, were highlighted:<br />
<span style="font-size: x-small;"><br /></span></div>
<div style="text-align: center;">
<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;"><NCI Thesaurus: Chairperson (subclass to Person)> </span></div>
<div>
<div style="text-align: center;">
<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;"><skos:closeMatch> </span></div>
<div style="text-align: center;">
<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;"><Int. Classification for Patient Safety: Chair (subclass to Piece of Furniture)></span></div>
<span style="font-family: "courier new" , "courier" , monospace; font-size: x-small;">
</span>
<span style="font-size: x-small;"><br /></span>One view was: ‘Don’t use them!’ (<a href="https://twitter.com/kerfors/status/353889165861064705">tweet</a>). Another view was “Give us the justification of the mappings so we can decide when it makes sense to use them.”<br />
<br />
<div>
</div>
<div style="text-align: justify;">
<h3>
Mappings in chemical informatics</h3>
</div>
<div style="text-align: justify;">
When I came back from the Semantic Trilogy and read about mappings, or linksets as they are called, in the new version of the Open PHACTS specification "<a href="http://www.openphacts.org/specs/2013/WD-datadesc-20130912/" target="_blank">Dataset Descriptions for the Open Pharmacological Space</a>" I saw some opportunities to make mappings more explicit and hence more useful.</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
I think the editor, Alasdair Gray (<a href="https://twitter.com/gray_alasdair" target="_blank">@gray_alasdair</a>), and the whole team of authors, have done a great job on this specification.</div>
<blockquote class="tr_bq">
"The <a href="http://www.openphacts.org/specs/2013/WD-datadesc-20130912/" target="_blank">Dataset Descriptions for the Open Pharmacological Space</a> is a specification for the metadata to described datasets, and the linksets that relate them, to enable their use within the Open PHACTS discovery platform. The specification defines the metadata properties that are expected to describe datasets and linksets; detailing the creation and publication of the dataset."</blockquote>
<div style="text-align: justify;">
I especially liked the part on making the justification of mappings explicit. For example, what is the justification behind stating that there is a close match (skos:closeMatch), or exact match (skos:exactMatch), between what is described in two different chemical datasets, such as the RDF datasets sourced from ChemSpider and ChEMBL.<br />
<br /></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.openphacts.org/specs/2013/WD-datadesc-20130912/chemspider-chembl-links.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://www.openphacts.org/specs/2013/WD-datadesc-20130912/chemspider-chembl-links.png" height="286" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The figure depicts four distinct linksets: two sourced from ChemSpider <br />
depicted in blue which use different link predicates; one sourced from ChEMBL <br />
depicted in red; and one sourced from a third party depicted in green. </td></tr>
</tbody></table>
<div style="text-align: justify;">
My understanding is that for the chemical informatics community the Open PHACTS specification will establish a vocabulary to express the justifications for links/mappings between chemical entities. This enables them to explicitly state justifications such as "Has isotopically unspecified parent" or "Have the same InChI key" (see B.2 Link Justification Vocabulary Terms to also get the URIs for these terms).<br />
<br /></div>
<div style="text-align: justify;">
<h3>
Mappings between medical terminologies</h3>
</div>
<div style="text-align: justify;">
Together with members of the EU projects EHR4CR and SALUS, MedDRA MSSO, and W3C HCLS, I am now exploring the idea of establishing a similar approach for the medical terminology community. That is, a vocabulary of terms to express the justifications for different mappings between concepts/terms in terminologies across healthcare and clinical research, such as ICD9, SNOMED CT and MedDRA.</div>
<div style="text-align: justify;">
</div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
This is part of a broader discussion on the use of terminologies in semantic web focused environments, with formal representations in RDF of both the terminologies themselves and of the mappings between them. Here's an example of a visualization from such a formal representations of MedDRA and SNOMED-CT terms and mappings between them in SKOS/RDF.</div>
<div>
<br /></div>
<div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVnJnABCW6D0htUnBqaJYyZTnAyKwq5ugXL0Bg7_fcYtM1ohN32Zukq7s0_wwiQKSTaHAyLqpjR9Odhj2h0vlzwgKw0FlrFnlU_mma8Jk_CfaWLL5IKNubtEa_inxwYtsyFOwM9GdnEZE/s1600/MedDRA+mappings.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="268" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhVnJnABCW6D0htUnBqaJYyZTnAyKwq5ugXL0Bg7_fcYtM1ohN32Zukq7s0_wwiQKSTaHAyLqpjR9Odhj2h0vlzwgKw0FlrFnlU_mma8Jk_CfaWLL5IKNubtEa_inxwYtsyFOwM9GdnEZE/s400/MedDRA+mappings.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div style="direction: ltr; margin-bottom: 0pt; margin-top: 0pt; unicode-bidi: embed; vertical-align: baseline;">
<span style="font-size: xx-small;"><span style="font-family: Arial;">The example show the hierarchy of
cardiac disorders in both the </span><span style="font-family: Arial;">MedDRA</span><span style="font-family: Arial;"> and</span></span></div>
<div style="direction: ltr; margin-bottom: 0pt; margin-top: 0pt; unicode-bidi: embed; vertical-align: baseline;">
<span style="font-size: xx-small;"><span style="font-family: Arial;">SNOMED-CT concept schemes,
expressed using the </span><span style="font-family: Arial;">skos:broader</span><span style="font-family: Arial;"> property. Mappings between</span></span></div>
<div style="direction: ltr; margin-bottom: 0pt; margin-top: 0pt; unicode-bidi: embed; vertical-align: baseline;">
<span style="font-size: xx-small;"><span style="font-family: Arial;">similar concepts in both concept
schemes are stated using the </span><span style="font-family: Arial;">skos:exactMatch</span><span style="font-family: Arial;"> property.<br />
From: </span><span style="font-family: Arial;"><a href="http://www.srdc.com.tr/projects/salus/docs/SALUS_D4.3.1%20Harmonized%20Ontology%20for%20Post%20Market%20Safety%20Studies%20%E2%80%93R1%20v1.0_FINAL.pdf">SALUS
Harmonized Ontology for Post Market Safety Studies</a></span></span></div>
</td></tr>
</tbody></table>
<br /></div>
</div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-41385338455785498022013-07-29T16:19:00.001+02:002015-12-02T22:03:09.103+01:00Semantic Trilogy report part 1It's been two very nice summer weeks of vacation after I got home from a week at the <a href="http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/" target="_blank">Semantic Trilogy</a> events in Montreal, Qc, Canada. (See my previous blog post:<a href="http://kerfors.blogspot.se/2013/06/semantic-trilogy-preparation.html" target="_blank"> Semantic Trilogy preparations</a>.) Here's the first part of my report from seven intensive days of conferences, tutorials, workshops and great discussions with researchers in biomedical ontologies and data integration in life sciences.<br />
<br />
It was very nice to meet colleagues from other pharma companies; Sanofi, UCB and NovoNordisk, and to discuss with early adopters in traditional software vendors, such as Siemens, and with experts from niche vendors, such as IO Informatics. It was also nice to discuss common topics, such the use of semantic web standards and linked data principles on for example clinicaltrials.gov, with key individuals such as Olivier Bodenreider, NLM (National Library of Medicine).<br />
<br />
<span style="font-size: large;">Notes</span><br />
During the two main conferences I used Twitter as my note book and in the evenings I gather tweets and related links in two Storify items:<br />
<ul>
<li><a href="http://storify.com/kerfors/icbo2013" target="_blank">ICBO2013</a><br />Storify: 4th Interational Conference on Biomedical Ontology (ICBO), 7-9 July</li>
<li><a href="http://storify.com/kerfors/dils2013" target="_blank">DILS2013</a><br />Storify: 9th Conference on Data Integration in the Life Sciences (DILS), 11-12 July </li>
</ul>
<span style="font-size: large;">My poster</span><br />
The last evening I presented a <a href="http://www.slideshare.net/kerfors/forsberg-dils2013poster" target="_blank">CDISC2RDF poster</a> on our joint AstraZeneca and Roche <a href="http://cdisc2rdf.com/" target="_blank">CDISC2RDF</a> project, now part of the <a href="http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology" target="_blank">FDA/Phuse Semantic Technology working group</a>. I really enjoyed the discussions it triggered.<br />
<br />
<blockquote class="twitter-tweet" lang="en">
<div dir="ltr" lang="en">
My <a href="https://twitter.com/hashtag/dils2013?src=hash">#dils2013</a> poster <a href="http://t.co/HWr1Yy9uQY">http://t.co/HWr1Yy9uQY</a> Thx <a href="https://twitter.com/jpmccu">@jpmccu</a> <a href="https://twitter.com/micheldumontier">@micheldumontier</a> @siv_arabandi <a href="http://t.co/NR3lrWZT6R">pic.twitter.com/NR3lrWZT6R</a></div>
— Kerstin Forsberg (@kerfors) <a href="https://twitter.com/kerfors/status/355523022691639296">July 12, 2013</a></blockquote>
<script async="" charset="utf-8" src="//platform.twitter.com/widgets.js"></script>
<div>
I'll be back in mid August, after couple of days of trecking in the Swedish mountains, with more details about the papers, presentations and discussions I did find most interesting. (For a first glimpse of two of them see this blog post from HL7 Watch by Barry Smith: <a href="http://hl7-watch.blogspot.se/2013/07/an-ogms-based-model-for-clinical.html" target="_blank">An OGMS-Based Model for Clinical Information</a>.) </div>
Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-12794647816979130342013-06-24T21:28:00.000+02:002015-12-02T22:06:19.789+01:00Semantic Trilogy preparation<div class="separator" style="clear: both; text-align: center;">
</div>
The <a href="http://en.wikipedia.org/wiki/Midsummer#Sweden" target="_blank">Swedish Midsummer weekend</a> is over and it's time to look forward. Saturday 6th to Friday 12th of July I'll attend the <a href="http://www.unbsj.ca/sase/csas/data/ws/semantic-trilogy-2013/" target="_blank">Semantic Trilogy</a> in Montreal, Qc, Canada.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
I plan to attend these events during the week:<br />
<ul>
<li>6 July, Semantic Trilogy <a href="http://www.hackathon.io/semantic3" target="_blank">Hackaton</a>, "Making big data out of small contributions"</li>
<li>7 July, Tutorial, <a href="http://ncorwiki.buffalo.edu/index.php/2013_ICBO_OBO_tutorial" target="_blank">OBO Foundry 101</a>: Collaborative ontology development, tool support and semantic web</li>
<li>8-9 July, 4th International Conference on Biomedical Ontology (<a href="http://www.unbsj.ca/sase/csas/data/ws/icbo2013/" target="_blank">ICBO 2013</a>)</li>
<li>10 July, <a href="http://ncorwiki.buffalo.edu/index.php/OGMS_Workshop" target="_blank">OGMS Workshop</a>, (<a href="https://code.google.com/p/ogms/" target="_blank">Ontology for General Medical Science</a>) and 4th Canadian Semantic Web Symposium (<a href="http://www.unbsj.ca/sase/csas/data/ws/csws2013/" target="_blank">CSCW 2013</a>)</li>
<li>11-12 July, 9th International Conference on Data Integration in the Life Sciences (<a href="http://www.unbsj.ca/sase/csas/data/ws/dils2013/" target="_blank">DILS 2013</a>) I'll present my <a href="http://www.slideshare.net/kerfors/forsberg-dils2013poster" target="_blank">poster on CDISC2RDF </a>in the poster session.</li>
</ul>
In 2011 I, together with three colleagues, attended the ICBO 2011 event (see my three blog post: Preparations <a href="http://kerfors.blogspot.se/2011/06/icbo2011-preparations.html" target="_blank">part 1</a> and <a href="http://kerfors.blogspot.se/2011/07/icbo2011-preparations-part-two.html" target="_blank">part 2</a>, <a href="http://kerfors.blogspot.se/2011/08/icbo2011-reports.html" target="_blank">report</a>). So, I look forward to reconnect with people in the <a href="http://www.obofoundry.org/" target="_blank">OBO </a>(The Open Biological and Biomedical Ontologies) community.<br />
<br />
And to meet F2F interesting people in the <a href="http://www.w3.org/wiki/HCLSIG" target="_blank">W3C HCLS</a> (Semantic Web Health Care and Life Sciences Interest Group). And people interested in ontologies and semantic web working for e.g. Sanofi, Novo Nordisk, Mayo Clinic.<br />
<div>
<br /></div>
I'm also very happy that I'll get the opportunity to attend my third semantic web related event in Canada.<br />
<ul>
<li>In 1999 I attended the W3C conference in Toronto. The <a href="http://www8.org/" target="_blank">WWW8 </a>conference where I was absolutely thrilled by the power of the simple and elegant model of RDF triples. At the WWW8 I also heard <a href="http://www.w3.org/Talks/1999/05/www8-tbl/Overview.html" target="_blank">Tim Berners-Lee talk about the Semantic Web for the first time</a>.</li>
</ul>
<ul>
<li>In 2007 I attended the <a href="http://www2007.org/" target="_blank">WWW2007 </a>conference in wonderful Banff.</li>
</ul>
<blockquote class="tr_bq">
"During the WWW2007 conference a breakthrough of the Linked Data idea happened in a session where web experts demonstrated the power of a new generation of the web, a web of data. For us attending the session it was hard to imagine the full potential on what this idea would mean for individual scientists and for a pharmaceutical company." </blockquote>
<blockquote class="tr_bq">
From <a href="http://www.slideshare.net/kerfors/linked-data-in-pharma" target="_blank">Linked Data, an opportunity to mitigate complexity in pharmaceutical research and development</a>, Bo Andersson and Kerstin Forsberg, LWDM 2011 </blockquote>
<br />
And yes, I do hope to also get some time during the weekend to visit the Jazz Festival.<br />
<div class="separator" style="clear: both; text-align: center;">
</div>
<br />Anonymoushttp://www.blogger.com/profile/14441161082622324677noreply@blogger.com0tag:blogger.com,1999:blog-4415887986451162655.post-32130403992461575512013-06-11T22:56:00.000+02:002013-12-07T18:12:24.774+01:00Standards for common aspectsThrough the last three years I have been engage with different groups working on standards, both for data exchange, such as CDISC, and for vocabularies such as MedDRA MSSO and NCI EVS. As they now start to see the value of using "standards for standards".<br />
<br />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://www.flickr.com/photos/bitpuddle/120110303/" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;" title="Push Back by bitpuddle, on Flickr"><img alt="Push Back" height="240" src="http://farm1.staticflickr.com/38/120110303_aa200ee33e_m.jpg" width="160" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><div style="direction: ltr; margin-bottom: 0pt; margin-top: 0pt; unicode-bidi: embed; vertical-align: baseline;">
<span style="font-family: Arial; font-size: 7pt;">From Flickr</span><span style="font-family: Arial; font-size: 7pt;">
</span><span style="font-family: Arial; font-size: 7pt;"><a href="http://www.flickr.com/photos/bitpuddle/120110303/">bitpuddle</a></span><span style="font-family: Arial; font-size: 7pt;"><a href="http://www.flickr.com/photos/bitpuddle/120110303/"> </a></span><span style="font-family: Arial; font-size: 7pt;"><br />
(Twitter </span><span style="font-family: Arial; font-size: 7pt;"><a href="https://twitter.com/eric_d_hancock">@</a></span><span style="font-family: Arial; font-size: 7pt;"><a href="https://twitter.com/eric_d_hancock">eric_d_hancock</a></span><span style="font-family: Arial; font-size: 7pt;">)</span></div>
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<h3>
Standards for standards</h3>
So, "I push back" to standard organisations to use semantic web standards and linked data principles to make their standards directly usable for humans and for machines. <br />
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A good example is CDISC and their growing interest in using semantic web standards (based on RDF, Resource Description Framework): <a href="http://cdisc2rdf.com/" target="_blank">CDISC2RDF</a>. For some background see <a href="http://semanticweb.com/clinical-studies-and-the-road-to-linked-data_b35252" target="_blank">Clinical studies and the road to Linked Data</a>. Today FDA, CDISC, pharma:s, CRO:s and software vendors are working together on this in a <a href="http://www.phusewiki.org/wiki/index.php?title=Semantic_Technology" target="_blank">FDA working group for Semantic Technology</a> organised by PhUSE.<br />
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<h3>
Standards for common aspects</h3>
The last year or so, I have also tried to keep up to date with groups developing RDF-based standards for common aspect such as:<br />
<ul>
<li>data descriptions (<a href="http://www.w3.org/TR/void/" target="_blank">VoID</a>)</li>
<li>data provenance and versioning (<a href="http://www.w3.org/TR/prov-overview/" target="_blank">PROV </a>and <a href="https://code.google.com/p/pav-ontology/" target="_blank">PAV</a>)</li>
<li>concept based vocabularies and value sets (<a href="http://www.w3.org/TR/skos-reference/" target="_blank">SKOS</a>)</li>
<li>multi-dimensional statistical data (<a href="http://www.w3.org/TR/vocab-data-cube/" target="_blank">RDF Data Cube</a>)</li>
</ul>
I try to ensure that we have a good view of the maturity and applicability of these standars so we can use them in our internal“integration factory”. But most of all “push back” to vendors. I foresee that we in the same way started to add requirements on web-interfaces for better end user usability back in the late 90:ies, we now should start to add requirements on web-interfaces for better machne usability. So we need to to understand how to incorporate these common aspects in our URS:s, RFI:s RFP:s etc..<br />
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For software vendors to use RDF-based standards for common aspects, for example:<br />
<ul>
<li>MediData's Rave and Perceptive's IMPACT to describe datasets using VoID.</li>
<li>Accelrys' Pipeline Pilot to use W3C PROV.</li>
<li>Microsoft's SharePoint to use term sets for tagging in SKOS.</li>
<li>SAS Institute's Drug Development to create analysis results using RDF Data Cube.</li>
</ul>
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So, this interview with Reza B'Far, Vice President of Development, Oracle on the W3C blog made me vryy glad: <a href="http://www.w3.org/QA/2013/05/interview_oracle_on_semantic_w.html" target="_blank">Oracle on Data on the Web</a><br />
<blockquote class="tr_bq">
<b>Oracle to use W3C provenance standard to create a single audit time line across systems</b></blockquote>
<blockquote class="tr_bq">
<i>"One of the hugest problems we faced was maintaining transaction audit trails in a heterogeneous environment in a standard and compatible way. Audit trails are described with literally millions of different formats in different organizations. This used to mean it was impossible to create a single audit time line. PROV solves this problem. We now provide (and consume) a PROV feed that unifies the audit trails generated by transactions across heterogeneous systems."</i></blockquote>
See also the <a href="http://www.w3.org/TR/prov-implementations/" target="_blank">Implementation report with 60+ examples of usage of the W3C Provenance specifications</a>.<br />
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For a nice intro to the W3C Provenance Specifications, see the <a href="http://www.w3.org/2001/sw/wiki/ESWC2013ProvTutorial" target="_blank">tutorial </a>by Paul Groth (<a href="https://twitter.com/pgroth" target="_blank">@pgroth</a>) at the Extended (European) Semantic Web conference.<br />
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