Thursday, April 21, 2016

Linked Data in Sweden 2016

It's time for the 5th "Linked Data in Sweden" event, Tuesday 26 April. Last year I was organizing the meeting in Gothenburg together with Fredrik Landqvist. This year we are back in Stockholm, this time at the Royal Armoury. I just learned that it is the oldest museum in Sweden. It was established by King Gustav II Adolph in 1628.

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 Linked Data efforts for data standards in biopharma and healthcare. 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.

Standards represented as Linked Data

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: Pushing back, standards and standard organizations in a Semantic Web enabled world.
  • CDISC in RDF
  • HL7 FHIR in RDF
  • MeSH in RDF
  • ICD-11 in OWL
  • Others standards e.g. ATC, WHO Drug and MedDRA


In 2011 I presented; Linking Clinical Data Standards, 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 Semantic models for CDISC based standard and metadata management. At the 2nd Linked Data in Sweden meeting in 2013 I presented; Länkade kliniska data standards (Linked clinical data standards).

The same spring the CTO of CDISC, Wayne Kubick, agreed to make this a task for the PhUSE organisation (PhUSE Association Programming Pharmaceutical Users Software Exchange). The PhUSE Semantic Technology project started later that year.

Overview of PhUSE Semantic Technology Project
by Frederik Malfait (21:16 - 37:00)

In the summer 2015 CDISC published their standards in RDF.  In the future, representation of CDISC standards in RDF will be one of the outputs of CDISC's metadata registry (SHARE).


The Fast Healthcare Interoperability Resources (FHIR, pronounced "fire") proposed standard 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 HL7 Sweden at the Swedish eHealth conference Vitalis (see my Storify Vitalis2016).

The HL7 FHIR project and the W3C Semantic Web Health Care and Life Sciences Interest Group work on RDF representations of FHIR. The HL7 work lead by Graham Grieve, one of the creators of FHIR, and the W3C HCLS group lead by, David Both the initiator of the so called Yosemite project, will be aligned.


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 MESH in RDF is described in a good article: Desiderata for an authoritative Representation of MeSH in RDF

ICD-11 in OWL

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 iCAT, based on WebProtege, 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.

Other standards e.g. ATC, WHO Drug, MedDRA

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.

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).

New initiatives outside the traditional standard organisations

Here a couple of interesting initiatives I wanted to also cover but will probably not have the time to do. 

See my Storify LDSV2016 with notes and links from the event.

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.

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