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RE: Minutes from BioRDF/LODD telcon Monday 06/12/2012

From: Lin MD, Simon <LINMD.SIMON@mcrf.mfldclin.edu>
Date: Fri, 15 Jun 2012 13:19:50 +0000
To: "rdb20@pitt.edu" <rdb20@pitt.edu>, Matthias Samwald <matthias.samwald@meduniwien.ac.at>
CC: M005994 <Jiang.Guoqian@mayo.edu>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>, "M. Scott Marshall" <mscottmarshall@gmail.com>, "Zhu, Qian" <Zhu.Qian@mayo.edu>
Message-ID: <A5BD550FC766564987DA2A59779890300D502BC9@MCL-EXMB02.mfldclin.org>
Hi Rich and Matthias,

It is indeed a challenging problem, but critical to the daily operation of the pharmacy, clinic, pharmaceutical industry, and regulatory agencies!

I hope there is an international committee to orchestrate the semantics of drug labels!

For SNOMED, there is multi-lingual support. Anything similar for drugs to start with?

Simon 

==================================================
Simon Lin, MD
Director, Biomedical Informatics Research Center 
Marshfield Clinic Research Foundation 
1000 N Oak Ave, Marshfield, WI 54449 
Office 715-221-7299 
Lin.Simon@mcrf.mfldclin.edu 
www.marshfieldclinic.org/birc

For scheduling assistance, please contact
      Crystal Gumz, Administrative Secretary
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      715-221-6403

-----Original Message-----
From: Richard Boyce [mailto:rdb20@pitt.edu] 
Sent: Friday, June 15, 2012 6:28 AM
To: Matthias Samwald
Cc: M005994; public-semweb-lifesci@w3.org; M. Scott Marshall; Zhu, Qian
Subject: Re: Minutes from BioRDF/LODD telcon Monday 06/12/2012

On 06/14/2012 04:37 PM, Matthias Samwald wrote:
> I would also be interested in extending this with data extracted from 
> European product labels. Compared to the US and Dailymed, this is far 
> trickier. The data is not openly available for many countries, content 
> has different languages, and structured product labels are even harder 
> to come by.
This does sound very challenging. While in different languages, do you know if all 12 Euro countries follow the regulations regulated by Article 11 of Directive 2001/83/EC on the "Summary of Product Characteristics"? If so, it seems possible that the Article 30 (p32) of the that directive would be relevant (see attached). Note especially item #2:

"In order to promote harmonisation of authorisations for medicinal products authorised in the Community, Member States shall, each year, forward to the coordination group a list of medicinal products for which a *harmonised summary of product characteristics should be drawn up.*" 
(emphasis mine)

The "coordination group" here is the Committee for Medicinal Products for Human Use (CHMP) <http://tinyurl.com/7qcqqva>. Their webpage states:

"The CHMP publishes a European public assessment report (EPAR) for every centrally authorised medicine that is granted a marketing authorisation, setting out the scientific grounds for the Committee's opinion in favour of granting the authorisation, plus a 'summary of product characteristics' (SPC), labelling and package leaflet (patient/user information leaflet) for the medicine, and details of the procedural steps taken during the assessment process. "

EPARs are available here: http://tinyurl.com/c8hua94

It looks like a whole bunch of harmonized SPCs (i.e., EU product labels, if I understand correctly) are available from this site. For example, I downloaded the attached SPC for Abilify (aripriprazole).

Hopefully, there is a standard structure to the document sections. 
Rimichi in [1] says that they are...

"Accordingly, SPCs of specialty medicines for human use are organized into 12 sections: name, therapeutic categories, active ingredient, excipients, indications, contraindication/side effects, undesired effects, posology, storage precautions, warnings, interactions, and use in case of pregnancy and nursing"

...but the one I looked at only has 10 sections. Any ways, it might be interesting to contact EPAR and see if you can get the documents used to create these SPC PDFs. Otherwise, one might wget all PDFs from the site, convert to text, and then fit the content into a SPL-like structure (in terms of sections) and provide as RDF.

-Rich

[1] Rubrichi S, Quaglini S. Summary of Product Characteristics content extraction for a safe drugs usage. J Biomed Inform. 2012 Apr;45(2):231-9. Epub 2011 Nov 10. PubMed PMID: 22094356.
> A Viennese startup called http://www.diagnosia.com/de/ recently made 
> package insert texts from 12 European countries openly available. I 
> plan to contact them and see if they would also be interested in 
> cooperating with research projects. We might not end up with a 
> resource that can be shared without restrictions, but at least we 
> could end up with something that allows us to run SPARQL queries for analysis and research.
>
> Other ideas for how such a multilingual, pan-European ressource are welcome!
>
> Cheers,
> Matthias
>
>
>> Hi, Richard,
>>
>> Very nice work. Building the linked data source for SPLs is very 
>> important for facilitating its wide use. It is impressive that you 
>> keep the source updated once per week.
>>
>> As you have pointed out that the SPLs are semi-structured, the 
>> combination of NLP and standard terminologies will be crucial for 
>> producing structured data out of the SPLs. As you know, our team at 
>> Mayo Clinic is investigating the SPLs from the perspective of Adverse 
>> Drug Events. We would like to collaborate to see whether we could 
>> link our ADEpedia data
>> (http://adepedia.org) with your LinkedSPLs.
>>
>> The following are our preliminary works,
>>
>> 1)  Jiang G, Solbrig H, Chute CG. ADEpedia: a scalable and 
>> standardized knowledge base of Adverse Drug Events using semantic web 
>> technology. AMIA Annu Symp Proc. 2011;2011:607-16. Epub  2011 Oct 22.
>> http://www.ncbi.nlm.nih.gov/pubmed?term=adepedia
>>
>> 2) Zhu Q, Jiang G, Chute CG. Profiling Structured Product Labeling 
>> using RxNorm and NDF-RT. ICBO 2012 Workshop (to be held in July 21-25, 2012).
>>
>> Best regards,
>>
>> Guoqian
>>
>>
>> Guoqian Jiang, M.D., Ph.D.
>> ===========================================
>> Assistant Professor of Medical Informatics Division of Biomedical 
>> Statistics&  Informatics, Mayo Clinic College of Medicine
>> 200 First Street, SW,
>> Rochester, MN, 55905
>> Tel: 1-507-266-1327
>> Fax: 1-507-284-0360
>> Email: jiang.guoqian@mayo.edu
>> ===========================================
>>
>>
>>
>>
>> On 6/14/12 12:47 PM, "Richard Boyce"<rdb20@pitt.edu>  wrote:
>>
>>> Minutes from BioRDF/LODD telcon Monday 06/12/2012
>>>
>>> Rich Boyce (University of Pittsburgh) presented "LinkedSPLs - a 
>>> dynamically updated and comprehensive linked data node for US drug 
>>> package inserts"
>>>
>>> Link to his slides:
>>> <http://www.slideshare.net/boycer/linkedsplsinitialhclspresentation0
>>> 6082012>
>>>
>>> Summary of discussion:
>>>
>>> Richard: Purpose of presenting is to attract 
>>> collaborators...consider Linked Structured Product Labels an 
>>> important data resource to keep up to date and improved, hopefully with partners.
>>>
>>> Richard: Structured Product Labels are the standard in the U.S.
>>> Medscape, Micromedex echo product labels and add information that is 
>>> missing. If a recent IOM report (http://tinyurl.com/cxovshm) is 
>>> acted on, we should see some progress in how the product labels are 
>>> formed in the next few years
>>>
>>> ericP: q+ to ask if the SPLs reflect the areas of concensus and that 
>>> affects the degree to which not being on the SPL indicates variation 
>>> of information from the various resources
>>>
>>> Richard: (answering EricP): Interesting question. Warfarin is an 
>>> example of how consensus from the community ended up in the product 
>>> label. Often the information is not complete and it is left up to 
>>> third parties to complete - dynamic process.
>>>
>>> Richard: FDA wrote laws the dictate the types of claims that should 
>>> be present in each section. This gives us an opportunity to link to 
>>> related resources such as for evidence.
>>>
>>> Richard: FDA wrote laws the dictate the types of claims that should 
>>> be present in each section.
>>> ..This gives us an opportunity to link to related resources such as 
>>> for evidence.
>>> ..[slide8]DailyMed is the public source of SPLs ..[slide9] "SPL IDs 
>>> are not static, so a label's URL may change if ..the label is 
>>> updated. However, DailyMed provides permanent ..URLs to view or 
>>> download the latest version of an SPLē
>>>
>>> Richard: LinkedSPLs started with Anja's PHP for DailyMed and ported 
>>> to python
>>>
>>> EricP: correcting for multiple active ingredients require modeling 
>>> changes?
>>> Richard: Modeling changes
>>> UNII -
>>> Unique Ingredient Identifier
>>> sounds like Unicode when spoken!
>>> CODE: http://swat-4-med-safety.googlecode.com/svn/trunk/linkedSPLs/
>>>
>>> JoanneLuciano Health Care Delivery Grants from ???
>>>
>>> Simon Lee: Maybe use for AHRQ grants
>>>
>>> JoanneLuciano NIN NLM grants
>>> JoanneLuciano I'm thinking this can be linked with Safety-Code.org
>>>
>>> Richard: Think it's a little early for AHRQ grants, more research 
>>> necessary
>>>
>>> Simon: agree.
>>> Simon: need working prototype.
>>> Simon Lin - Marshfield Clinic
>>>
>>> michel DrugBank is the best to link to, i think michel they then 
>>> link out to many other sources
>>>
>>> JoanneLuciano safety-code.org
>>>
>>> michel BTW - I've built a new parser for drugbank michel 
>>> http://bio2rdf.semanticscience.org:8022/describe/?url=http%3A%2F%2Fb
>>> io2rdf.org
>>> %2Fdrugbank%3ADB00975&sid=5
>>>
>>> michel we're in the process of adding this to bio2rdf mscottm asks 
>>> michel - adding what?
>>> ericP zakim, please disconnect ericP Zakim EricP is being 
>>> disconnected
>>>
>>>
>>> gamble @boycer I'm interested in data quality / Minimum information 
>>> checklist validation potential for this data. Versioning is also 
>>> interesting. I don't have a mic so I'll follow up by email.
>>> michel adding my parse of drugbank to bio2rdf
>>
>>
>>


--
Richard Boyce, PhD
Assistant Professor of Biomedical Informatics Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research and Training Program Scholar, Comparative Effectiveness Research Program University of Pittsburgh rdb20@pitt.edu
412-648-9219 (W), 206-371-6186 (C)
Twitter: @bhaapgh

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Received on Friday, 15 June 2012 13:20:33 GMT

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