[Corpora-List] FINAL CALL FOR PARTICIPATION: Fifth BioCreative V.5 evaluation workshop

Martin Krallinger mkrallinger at cnio.es
Mon Apr 17 19:38:07 CEST 2017

FINAL CALL FOR PARTICIPATION: Fifth BioCreative V.5 evaluation workshop

**************************************************************** **************************************************************** Fifth BioCreative Challenge workshop, Barcelona, Spain

Home page: https://www.bsc.es/news/events/elixir-text-mining-workshop-biocreative-becalm-workshop

Challenge tasks: http://www.becalm.eu

Workshop date: April 25th, 26th and 27th, 2017

Registration: Free (see https://www.bsc.es/elixir-text-mining-workshop--biocreative-and-becalm-workshop-registration-form)

Workshop format: Keynote speech, paper presentations, group discussions.

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[Apologies for multiple postings]


*1. SCOPE* ***********

BioCreative: Critical Assessment of Information Extraction in Biology ( biocreative.org) is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain.

Advances in high-throughput technology have resulted in tremendous growth of biological data, and the number of research papers published continues to increase. This proves to be a great challenge for curators and researchers in assimilating scientific facts described in articles. This workshop aims to bring together experts in Text mining (TM), Data curation and Knowledge Management working in the Life Sciences domain, to formulate ideas on how to leverage text-mining infrastructures.

On April 25th, 26th and 27th, 2017, two text-mining workshops will be held in Barcelona: ELIXIR WP3 workshop (April, 25th & 26th), and BioCreative V.5 - BeCalm workshop (April, 26th & 27th).


*2. TOPICS* *********** Biocreative V.5 workshop (April 26th and 27th)

For BioCreative V.5., the selection of the tracks was driven in part by demands from both the text mining and biocuration communities, with the goal of addressing some of the major barriers to the adoption and use of text mining tools: evaluation, accessibility, interoperability, robustness and integration.

Two traditional BioCreative tracks focused on monitoring progress on the recognition of relevant bio-entities (chemicals and gene/proteins) and their evaluation against manually annotated.

A novel track called TIPS (Technical interoperability and performance of annotation servers) focuses on the technical aspects of the evaluation of continuous text Annotation Servers (ASs) for named entity recognition. Aspects that should be addressed in the context of this track during the workshop include:

- Continuous evaluation of text mining systems to promote more stable

annotation tools

- Facilitate the interoperability of multiple text annotation systems at

the technical level and through the design of compatible annotation schemas

- Extraction of textual content from heterogeneous sources, such as

scientific literature (PubMed abstracts) or patent abstracts

- Visualization and detailed comparative evaluation assessment of

automatic and manual annotations

- Harmonization of multiple biomedical text annotations

- Usage of standard evaluation metrics for the performance evaluation of

component-level tasks

- Management of users corresponding to developers of text annotation


With the contribution of invited speakers and panel sessions this workshop will also discuss aspects related to formats, annotations and technical integration of text mining components, the experience of text mining techniques for the DARPA Big Mechanism program and the use of web services and workflows of text processing.

Moreover, during this event the OpenMinted project (openminted.eu) and OpenMinted open call for tenders will be presented.

ELIXIR-EXCELERATE workshop (April 25th and 26th)

This workshop, in the context of ELIXIR-EXCELERATE <https://www.elixir-europe.org/> WP3, will specifically focus on:

- Identifying current practices in the TM community.

- How do we measure what is ‘good’ text mining.

- How do we share TM outputs (annotations) widely.

- Addressing gaps that prevent the uptake of TM solutions

- Identifying synergies with the larger scientific community.

Martin Krallinger,

On behalf of the BioCreative V.5. organizing committee

======================================= Martin Krallinger, Dr. Head of Biological Text Mining Unit Structural Biology and BioComputing Programme Spanish National Cancer Research Centre (CNIO) ======================================= -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/html Size: 9807 bytes Desc: not available URL: <https://mailman.uib.no/public/corpora/attachments/20170417/7ae2ecb0/attachment.txt>

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