Program

16th
Mon
17th
Tue
18th
Wed
19th
Thu
20th
Fri
Registration
Symposium
Reception
Hackathon Hackathon
Excursion

Hackathon Hackathon
G. Wrap-up


16 (Mon) - Symposium

09:30 - 10:00 | Registration
10:00 - 10:10 | Opening remarks
| Akiko Aizawa
10:10 - 10:20 | Introduction to BLAH3 [slides]
| Jin-Dong Kim
10:20 - 11:10 | Tying it all together - From terminology integration to annotation integration [slidesKeynote
| Olivier Bodenreider
11:10 - 11:30 | Coffee Break
11:30 - 11:40 | Text-mining-based retrieval of protein networks [slides]
| Lars Juhl Jensen
11:40 - 11:50 | An overview of the MiNCor: annotation guidelines and text corpora for MicroRNA mentions in the scientific
| literature [proposal]
| Josè Camilla Sammartino, Martin Krallinger and Alfonso Valencia
11:50 - 12:00 | BioASQ and PubAnnotaion : Using linked annotations in biomedical question answering [proposal][slides]
| Anastasios Nentidis, Zi Yang, Mariana Neves, Jin-Dong Kim, Anastasia Krithara, George Paliouras and 
| Ioannis Kakadiaris
12:00 - 12:10 | Customized automatic corpus annotations using AlvisNLP/ML [proposal][slides]
| Robert Bossy, Mouhamadou Ba and Claire Nédellec
12:10 - 12:20 | Towards seamless format conversion between BioC and PubAnnotation for sharing PubMed/PubMed Central 
| documents and annotations [proposal][slides]
| Sun Kim, Donald Comeau, Rezarta Islamaj Dogan and Zhiyong Lu
12:20 - 12:30 | The Noctua Modeling Tool [slides]
Seth Carbon
12:30 - 14:00 | Lunch
14:00 - 14:50 | Scientific Paper Analysis: JST CREST Project on Big Data Application [slidesKeynote
| Yuji Matsumoto
14:50 - 15:00 | Linked Annotation Networks: Developing an Infrastructure for Inference [proposal][slides][wrapup_slides]
| Tiffany J. Callahan and Lawrence E. Hunter
15:00 - 15:10 | Data programming for PubAnnotation via Snorkel [proposal][slides]
| Juan Banda
15:10 - 15:20 | YBio M2CMT : a flexible bio-text mining tool for multi-component multi-target [proposal]
| Min Song, Sung Jeon Song, Yonghwan Kim, Kyu Bin Ahn and In Jun Baek
15:20 - 15:30 | Annotating the SIRO model and discovering experimental protocols [proposal]
| Olga Giraldo, Alexander Garcia, Tazro Ohta and Federico Lopez
15:30 - 15:50 | Coffee Break
15:50 - 16:40 | Integrating biomedical data annotation in scientific publishing [slides] Keynote
| Thomas Lemberger 
16:40 - 16:50 | Integrating PubTator in the curation pipeline of SourceData [proposal][slides][wrapup_slides]
| Lou Götz, Nancy George, Sara El-Gebali, Anastasia Chasapi, Isaac Crespo, Ioannis Xenarios, Robin Liechti
| and Thomas Lemberger
16:50 - 17:00 | BioCreative 2017 PM task: finding mutations affecting protein interactions for precision medicine
| Zhiyong Lu
17:00 - 17:10 | Building a cost-effective gold standard set for enriching PubAnnotation [proposal][slides]
| Dongseop Kwon, Chih-Hsuan Wei, Sun Kim, Robert Leaman and Zhiyong Lu
17:10 - 17:20 | Extending the interoperability of tagtog and PubAnnotation [proposal]
Juan Miguel Cejuela and Jorge Campos
17:20 - 17:25 | Closing
17:35 - 19:00 | Free (Organizers to clean the venue)
19:00 - 21:30 | Banquet

17 (Tue) - Hackathon

09:10 - 10:00 | Morning talk: Tutorial on PubAnnotation
| Jin-Dong Kim
10:00 - 12:00 | Introductions, Planning, Grouping
12:00 - 13:00 | Lunch
13:00 - 17:00 | Hacking
17:00 - 18:00 | Wrap-up
 


18 (Wed) - Hackathon

09:10 - 10:00 | Morning talk: High throughput assays and NLP
| Kevin Cohen
10:00 - 12:00 | Hacking
12:00 - 13:00 | Lunch
13:00 -  | excursion

19 (Thu) - Hackathon

09:10 - 09:40 | Morning Talk1: Tutorial on RxNorm
| Olivier Bodenreider
09:40 - 10:10 | Morning Talk2: The art of counting: scoring and ranking co-occurrences in literature [slides]
| Lars Juhl Jensen
10:00 - 12:00 | Hacking
12:00 - 13:00 | Lunch
13:00 - 17:00 | Hacking
17:00 - 18:00 | Wrap-up

20 (Fri) - Hackathon

09:00 - 12:00 | Hacking
12:00 - 13:00 | Lunch
13:00 - 15:00 | Hacking
15:00 - 17:00 | Grand Wrap-up and Discussions

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Jin-Dong Kim,
Jan 23, 2017, 5:27 PM
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Jin-Dong Kim,
Jan 13, 2017, 9:29 PM
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Jin-Dong Kim,
Jan 22, 2017, 7:30 PM
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Jin-Dong Kim,
Jan 23, 2017, 5:11 AM
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Jin-Dong Kim,
Jan 26, 2017, 7:33 PM
Ċ
Jin-Dong Kim,
Jan 23, 2017, 5:27 PM
Ċ
Jin-Dong Kim,
Jan 26, 2017, 7:33 PM
Ċ
Jin-Dong Kim,
Jan 22, 2017, 8:57 PM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:09 AM
Ċ
Jin-Dong Kim,
Jan 22, 2017, 8:57 PM
Ċ
Jin-Dong Kim,
Jan 26, 2017, 7:50 PM
Ċ
Jin-Dong Kim,
Jan 23, 2017, 5:31 AM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:10 AM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:09 AM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:10 AM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:10 AM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:09 AM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:10 AM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:10 AM
Ċ
Jin-Dong Kim,
Jan 23, 2017, 5:07 AM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:10 AM
Ċ
SD-BLAH3.pdf
(11271k)
Jin-Dong Kim,
Jan 22, 2017, 7:26 PM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:10 AM
Ċ
Jin-Dong Kim,
Jan 18, 2017, 11:06 AM
Ċ
Jin-Dong Kim,
Jan 22, 2017, 8:57 PM
Ċ
Jin-Dong Kim,
Jan 4, 2017, 12:10 AM
Ċ
Jin-Dong Kim,
Jan 22, 2017, 7:26 PM
Ċ
Jin-Dong Kim,
Jan 22, 2017, 7:26 PM