Talk given during the symposium session of the 2016 Biohackathon

1. Project: Drug Safety
Portal
J U A N M . B A N D A P H . D .
R E S E A R C H S C I E N T I S T
N I G A M S H A H ’ S L A B
S T A N F O R D C E N T E R F O R
B I O M E D I C A L I N F O R M A T I C S

2. Acknowledgements
- Travel sponsorship from the National Bioscience Database
Center (NBDC) and the Database Center for Life Science
(DBCLS)
- Drug Safety input: Shah Lab and Rave Harpaz
- Semantic Web input: Michel Dumontier & Tobias Kuhn

3. What is Drug Safety Portal?
- Easy to use portal that allows researchers and regular
users to verify if two drugs have any reported and/or
predicted possible adverse events
- Central repository of over 7 published and publicly
available datasets
- A bridge between the scientific world and the average
Internet user

4. Origins of Drug Safety Portal
- Moving from Astroinformatics to Biomedical Informatics in
2014, my first project was to prioritize a list of around 2,000
drug-drug interactions …. sounds easy……. I was so… so wrong
- Multiple resources have drug-drug interaction information… but
they don’t talk to each other
- Multiple vocabularies for drugs (NDC, NDFRT, RxNorm, etc.)
- Multiple names for the same drug
- Multiple names for the adverse events (SNOMED, MeSH, etc.)

5. Building Blocks (1):
- J. M. Banda, T. Kuhn, N.H. Shah, M. Dumontier “Provenance-Centered Dataset of
Drug-Drug Interactions”. In Lecture Notes in Computer Science: The Semantic Web
- ISWC 2015, Volume 9367, 2015, pp. 293-300, Springer International Publishing,
ISBN: 978-3-319-25009-0. DOI: 10.1007/978-3-319-25010-6_18.

6. Building Blocks (2):
- J. M. Banda, A. Callahan, R. Winnenburg, H. Strasberg, A. Cami, B. Reis, S. Vilar, G.
Hripcsak, M. Dumontier, N.H. Shah. “Feasibility of prioritizing Drug-Drug-Event
Associations Found in Electronic Health Records”. Drug Safety Vol. 39(1) pp. 45-57,
2016. DOI: 10.1007/s40264-015-0352-2.

7. Motivation behind Drug Safety Portal?
- Not just another academic resource that only a handful of
people use
- People are blindly looking at what the drugs they are
taking can do to them… just Google any drug and be
amused with the amount of miss information
- Other researchers spend hours curating resources for
analyses… and they rarely get re-used
- Other resources available (i.e. drugs.com) are too
complicated

8. http://idodrugs.club/

9. Drug Safety Portal v 1.0 – idodrugs.club
- Released: September 20th, 2015 – at TechCrunch Disrupt 2015.
- This project was considered one of the top 50 hacks of the Hackathon (over
350 teams participated/presented) and got some nice press coverage
(http://techcrunch.com/2015/09/20/hack-helps-patients-prevent-adverse-
drug-reactions/ )

10. Drug Safety Portal V 1.0 features
- Supports 2 drug interactions (limited) and 1 drug interactions
(restricted)
- NLP translation of drug user queries via NCBO BioPortal
- Drug normalization via RxNorm API
- Mesh Normalization via NLM Mesh on demand API for
PubMed/Medline queries
- Literature verification of drug interactions via Medline API
- Literature extraction via PubMed API
- DDI sources querying via MySQL database backend

11. Drug Safety Portal V 1.0 - Stack
- Boostrap front-end
- Javascript/PHP/MySQL backend
- Code: https://github.com/jmbanda/DrugSafetyPortal

12. What is missing?
- Proper linkage to linked data resources (only linkage to
MeSH via bio2rdf)
- Underlying dataset is available in linked data format (with
provenance information)
- Ability to download interaction reports
- Ability to tweet to the resource to get results
- Ability to expand resource (more drugs, more adverse
events)

13. Objectives during BioHackathon 2016
1) Proper linkage with open linked data resources
2) Further standardization of resource
3) Enable researchers to upload (and automatically standardize)
their published DDI resources
4) Provide facilities to download data
5) Allow people to Tweet to Drug Safety Portal
6) Keep track of user queries for investigation of possibly new
DDIs

14. Objective 1: Proper linkage with open
linked data resources
- Back-end dataset is derived from LIDDI
(https://datahub.io/dataset/linked-drug-drug-interactions-
liddi) which includes provenance information and is
available as nanopublications
- Allow linkage to Mesh RDF and Bio2RDF

15. Objective 2: Further standardization of
resource
- We currently have around 6 different mappings between
data sources
- Using the standardization used for:
J. M. Banda, L. Evans, R. S. Vanguri, N. P. Tatonetti, P. B. Ryan &
N. H. Shah. “A curated and standardized adverse drug event
resource to accelerate drug safety research”. Scientific Data 3,
Article number: 160026 (2016) ​doi:10.1038/sdata.2016.26
• Using the OMOP/OHDSI common vocabulary for this

16. Objective 3: Enable researchers to upload (and
automatically standardize) their published DDI
resources
- Keep the resource growing by allowing published datasets
to be uploaded
- Automagically standardize their drug/adverse effects
names
- Verify upload is available via PubMed for this

17. Objective 4: Provide facilities to download
data
- Allow users to download the results of their query
- Allow the extraction of all DDI information per
drug/adverse event

18. Objective 5: Allow people to Tweet to Drug
Safety Portal
- Make it even easier for general purpose users to get quick
information via social media

19. Interested in helping out?
- Email: jmbanda@stanford.edu
- Twitter: @drjmbanda