#BLAHmuc
Munich September 19-23, 2016
Biomedical text mining & APIs,
for real use cases
Biomedical text mining & APIs,
for real use cases
#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 |
|---|---|---|---|---|
|
Registration Symposium Social Dinner |
Keynote Hackathon Social Dinner |
Hackathon |
Hackathon |
Hackathon Grand Wrap-Up |
| Monday 19th, Symposium | |
|---|---|
| 08:3009:00 | Registration |
| 09:0009:05 | Welcome remark: Prof. Dr. Burkhard Rost |
| 09:0509:15 | Introduction to #BLAHmuc; Juan Miguel Cejuela; slides |
| 09:1510:15 | Featured Speech: Dr. Jin-Dong Kim Toward community-driven shared literature annotation resources; slides |
| 10:1510:45 | Coffee Break |
| 10:4511:00 | Valentin Grouès; University of Luxembourg Information extraction from biomedical literature for community sharing; slides |
| 11:0011:15 | Dr. Kevin Bretonnel Cohen; U. Colorado School of Medicine Towards the Last Annotation Tool; slides |
| 11:1511:30 | Juan Miguel Cejuela; Rostlab, tagtog tagtog: manual and automatic annotations tool |
| 11:3011:45 | Prof. Dr. Lars Juhl Jensen; University of Copenhagen Text-mining-based retrieval of protein networks; slides |
| 11:4512:00 | Dr. Matúš Kalaš; University of Bergen EDAM ontology and Bio.Tools registry; slides |
| 12:0014:00 | Lunch |
| 14:0015:00 | Keynote: Prof. Dr. Lars Juhl Jensen STRING: Protein networks from data and text mining; slides |
| 15:0015:15 | Dr. Fabio Rinaldi; IFI, University of Zurich The Bio Term Hub: an integrated resource of biomedical terminology; slides |
| 15:1515:30 | Madhukar Sollepura Prabhu Shankar; Technische Universität München LocText: relationship extraction of Proteins to Subcellular Localizations; slides |
| 15:3015:45 | Dr. Mariana Neves; Hasso Plattner Institute Text Mining to Support Data Curation for SABIO-RK; slides |
| 15:4516:00 | Nikola Milosevic; University of Manchester RichAnnotator - Annotation Tool For Rich Web Documents; slides |
| 16:0018:00 | Brainstorming and forming of groups |
| 18:0020:30 | Welcome Dinner |
| Tuesday 20th, Hackathon | |
|---|---|
| 09:0010:00 | Keynote: Prof. Dr. Burkhard Rost Personalized health – harnessing the power of diversity |
| 10:0012:30 | Hacking |
| 12:3013:30 | Lunch |
| 13:3015:45 | Hacking |
| ~15:0017:00 | Going to Munich Center |
| 17:0020:00 | Oktoberfest |
| Wednesday 21st, Hackathon | |
|---|---|
| 09:0012:30 | Hacking |
| 12:3013:30 | Lunch |
| 13:3017:00 | Hacking |
| 17:0018:00 | Day Wrap-Up |
| 18:0020:00 | (Non-organized) Dinner |
| Thursday 22nd, Hackathon | |
|---|---|
| 09:0012:30 | Hacking |
| 12:3013:30 | Lunch |
| 13:3017:00 | Hacking |
| 17:0018:00 | Day Wrap-Up |
| 18:0020:00 | (Non-organized) Dinner |
| Friday 23rd, Hackathon | |
|---|---|
| 09:0012:30 | Hacking |
| 12:3013:30 | Lunch |
| 13:3016:00 | Hacking |
| 16:0018:00 | Grand 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.
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 €2.20that we pay for hackathon-accepted participants ;-)