Munich September 19-23, 2016

Biomedical text mining & APIs,
for real use cases

Watch now the LIVE STREAM!


#BLAHmuc is a one-week hackathon plus symposium co-organized by Rostlab, Technische Universität München, DBCLS, and tagtog. #BLAHmuc (BLAH+muc) is a sister event of BLAH (Biomedical Linked Annotation Hackathon), hosted in Munich (muc; city airport 3-letter code).

Our goal is to improve the interoperability of biomedical text mining systems and make them readily usable for final users. We invite annotation tools, developers of text mining methods, and, specially, public biomedical databases and other projects. We want independent groups to hack together practical solutions, make their tools and resources speak with each other, and complete real uses cases for the benefit of the biomedical community at large. In particular, we focus on formalizing REST APIs and exchange formats, and receive feedback from the final biomedical users to improve those. Together.

Questions that will be asked are: what exchange format should everybody support, JSON-LD / REST-OA? PubAnnotation format? BioC?; what should be the common REST parameters in API calls? how to handle computer-intensive queries? user auth?; what licenses for shared annotations and methods?; how to exchange information for full-text articles?; what is the opinion of final users?


Monday 19th Tuesday 20th Wednesday 21st Thursday 22nd Friday 23rd
Social Dinner
Social Dinner
Grand Wrap-Up
Monday 19th, Symposium
09:0009:05Welcome remark: Prof. Dr. Burkhard Rost
09:0509:15Introduction to #BLAHmuc; Juan Miguel Cejuela; slides
09:1510:15Featured Speech: Dr. Jin-Dong Kim
Toward community-driven shared literature annotation resources; slides

10:1510:45Coffee Break
10:4511:00Valentin Grouès; University of Luxembourg
Information extraction from biomedical literature for community sharing; slides
11:0011:15Dr. Kevin Bretonnel Cohen; U. Colorado School of Medicine
Towards the Last Annotation Tool; slides
11:1511:30Juan Miguel Cejuela; Rostlab, tagtog
tagtog: manual and automatic annotations tool
11:3011:45Prof. Dr. Lars Juhl Jensen; University of Copenhagen
Text-mining-based retrieval of protein networks; slides
11:4512:00Dr. Matúš Kalaš; University of Bergen
EDAM ontology and Bio.Tools registry; slides
14:0015:00Keynote: Prof. Dr. Lars Juhl Jensen
STRING: Protein networks from data and text mining; slides

15:0015:15Dr. Fabio Rinaldi; IFI, University of Zurich
The Bio Term Hub: an integrated resource of biomedical terminology; slides
15:1515:30Madhukar Sollepura Prabhu Shankar; Technische Universität München
LocText: relationship extraction of Proteins to Subcellular Localizations; slides
15:3015:45Dr. Mariana Neves; Hasso Plattner Institute
Text Mining to Support Data Curation for SABIO-RK; slides
15:4516:00Nikola Milosevic; University of Manchester
RichAnnotator - Annotation Tool For Rich Web Documents; slides
16:0018:00Brainstorming and forming of groups
18:0020:30Welcome Dinner
Tuesday 20th, Hackathon
09:0010:00Keynote: Prof. Dr. Burkhard Rost
Personalized health – harnessing the power of diversity

~15:0017:00Going to Munich Center
Wednesday 21st, Hackathon
17:0018:00Day Wrap-Up
18:0020:00(Non-organized) Dinner
Thursday 22nd, Hackathon
17:0018:00Day Wrap-Up
18:0020:00(Non-organized) Dinner
Friday 23rd, Hackathon
16:0018:00Grand Wrap-Up
18:0020:00(Non-organized) Discussions over Dinner

The exact schedule is subject to change as the date of the event approaches.


The event takes place at the Faculty of Informatics, TU München. This is in the city of Garching, northeast from Munich. Full address: Fakultät für Informatik Boltzmannstraße 3. To reach it, take the metro line U6 (U-Bahn) and get off at the last stop, Garching Forschungszentrum. The metro line takes you to the city center in 20 minutes. Please see more arrival directions here: https://rostlab.org/group/contact.

The building room for all days is: 00.13.009A.


Participants should book by themselves their preferred hotel or apartment. Please contact us if you need any help.

Online Participation

Live recordings of the symposium talks on Monday 19th and Tuesday 20th were made possible by JetBrains!

Furthermore, discussions and deliverables are captured in an open Google document.

Mailing list for all BLAH-related events (blah1, blah2, BLAHmuc, blah3, ...): http://blah.linkedannotation.org.

Please use the hashtag #BLAHmuc for all social media! :-)


At the moment we cannot guarantee to support travel expenses. If this was later confirmed, participants will be reimbursed part of the costs after the finaliziation of the event.

Social Events

We have a welcome dinner on Monday 19th to enjoy typical bavarian cuisine. The restaurant is the Gasthof Neuwirt, in Garching.

We go to the Oktoberfest on Tuesday evening. Tables are already reserved.

Participants pay themselves the costs. There is only a entry fee for the Oktoberfest of €2.20 that we pay for hackathon-accepted participants ;-)


Juanmi and Inga will be happy to assist you: