[Corpora-List] Biomedical Linked Annotation Hackathon 2015: Call for contributions

Jin-Dong Kim jdkim at dbcls.rois.ac.jp
Wed Oct 15 20:07:16 CEST 2014


Apologies for multiple posting -----

Dear Colleagues,

We are pleased to announce the 1st Biomedical Linked Annotation Hackathon (BLAH2015), which is to take place in Kashiwa-no-ha City, Japan, 27th February, 2015.

BLAH2015 is being organized to establish community collaboration for a shared collection of integrated, harmonized, and linked literature annotation resources in the life sciences.

With various annotated literature data which already exist, and also ongoing efforts for annotation, we believe it is time to seek linking of these invaluable resources. It will open a new era of text mining, enabling us to explore heterogeneous perspectives represented in the annotations.

For more details of the event, please take a look at the homepage: http://2015.linkedannotation.org/

[Important Dates] - Submission due: 12th (Fri) Dec, 2014 - Notification: 12th (Mon) Jan, 2014 - Hackathon: 23rd (Mon) - 26th (Thu) Feb, 2015 - Symposium: 27th (Fri) Feb, 2015

[Confirmed Keynote Speakers] - Lawrence Hunter, University of Colorado - Pierre Zweigenbaum, LIMSI-CNRS

For the event, we calls for three types of contributions.

1. Call for proposals

We solicit extended abstracts of proposals (up to 1000 words with figures and tables) to present innovative use cases of linked annotation resources. Particularly, biologically or medically meaningful use cases which cannot be achieved using single annotation data sets are desired. Submissions will be peer-reviewed, and accepted ones will be presented in the symposium, included in the proceedings and invited to the co-authorship of joint papers.

2. Call for annotation data sets

We solicit annotation data sets that have been made to PubMed or PubMed Central (open access subset) articles. Contributed annotations will be aligned with others, and will be openly provided to the public for investigation. Also, all the annotations will be indexed using semantic web technology and will become searchable and accessible through SPARQL and REST API. Being aligned with others, any annotation data set will find a significantly improved value of its own (like any document linked with others in WWW). The contributors will retain the full credit and full right over their data sets. Any usage of the data sets will be asked to make proper citations.

Prospective contributors are asked to submit a description of the data sets (1-2 pages) which have to present

- how the based texts are collected - how the annotations are developed, e.g., manually or automatically - a small piece of example and a detailed description of it - reference to relevant publications or web pages if any - license policy (in terms of creative commons, hopefully)

Successful contributions will be listed in the Hackathon homepage and in the joint paper. Expected type of annotation may include, but not limited to:

- Manual or automatic annotations - Semantic or syntactic annotations - Bio-medical or clinical annotations

3. Call for tools

We also solicit tools and systems to be integrated in the hackathon environment. Prospective contributors will have to collaborate with the organizers to make their tools inter-operable with other tools (mainly through REST API and JSON). Successful contributions will be provided to the participants (and also to the public), listed in the hackathon homepage and in the joint paper. Any usage of the tools will be asked to make proper citations. The contributors will retain full credit and right over their tools and systems. The contributors will retain full credit and right over their tools and systems.

Expected type of contribution will include, but not limited to:

- Visualization - Analysis - Format conversion - Mining

Prospective contributors are asked to submit a description of the tools (1-2 pages) with reference to relevant publications if any.

Successful contributions must

- be web-based applications, - guarantee free access without restriction by the public,

: open-source software is desired. - provide RESTful APIs for programmable access, and - provide online comprehensive documentation.

We look forward a wide participation from the community. Should you have any question or comment, please contact to admin at linkedannotation.org.

Organizing Committee

- Jin-Dong Kim, DBCLS - Kevin Cohen, University of Colorado - Nigel Collier, EBI - Zhiyong Lu, NCBI - Pontus Stenetorp, University of Tokyo

Program Committee (confirmed so far)

- Olivier Bodenreider, LHNCBC, NLM, NIH - Karën Fort, University Paris-Sorbonne - Filip Ginter, University of Turku - Jung-Jae Kim, Nanyang Technological University - Martin Krallinger, CNIO - Robert Leaman, NCBI, NLM, NIH - Hongfang Liu, Mayo Clinic - Makoto Miwa, Toyota Technological Institute - Claire Nédellec, Institut National de Recherche Agronomique - Aurélie Névéol, CNRS - Tomoko Ohta, textimi - Jong C. Park, KAIST - Sampo Pyysalo, University of Turku - Fabio Rinaldi, IFI, University of Zurich - Karin Verspoor, The University of Melbourne - W. John Wilbur, Computational Biology Branch, NCBI, NLM, NIH -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/html Size: 6666 bytes Desc: not available URL: <https://mailman.uib.no/public/corpora/attachments/20141016/58cadc14/attachment.txt>



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