[BioNLP] Call for Participation: BioCreative V Challenge and Workshop

Islamaj, Rezarta (NIH/NLM/NCBI) [F] islamaj at ncbi.nlm.nih.gov
Mon Jan 5 12:38:11 PST 2015


Call for Participation
BioCreative V Challenge and Workshop
September 9-11, 2015 Sevilla, Spain
BioCreative: Critical Assessment of Information Extraction in Biology<http://www.biocreative.org/> <http://www.biocreative.org/> is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. Built on the success of the previous BioCreative Challenge Evaluations and Workshops ( BioCreative I, II, II.5, III, 2012 workshop, and IV) the BioCreative Organizing Committee<http://www.biocreative.org/#committee> will host the BioCreative V Challenge in Sevilla, Spain on September 9-11, 2015. One key goal of BioCreative is the active involvement of the text mining user community in the design of the tracks, preparation of corpus and the testing of interactive systems. For BioCreative V, the selection of the tracks has been driven in part by suggestions from the biocuration community, by our goal of addressing interoperability -- a major barrier to adoption to text mining tools --, and via an open call for tasks of interest to both the bioNLP and user communities.
BioCreative V will consist of five tracks. Teams can participate in one or more of these tracks. Team registration started on January 1, 2015 and will continue until final commitment is requested by the individual tracks.
To register a team go to http://www.biocreative.org/events/biocreative-v/biocreative-v-team/
Funds are available for US participants to attend BioCreative 5. Information on how to apply will follow. Women, under-represented minorities, students, and post-doctoral fellows are encouraged to apply.
•  Track 1: Collaborative Biocurator Assistant Task (BioC) – Development of BioC-compatible modules which complement each other and an integrated system that assists BioGRID curators. A non-competitive, cooperative task in which participants work together to build a better system,
Organizers:Sun Kim, Donald Comeau, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri and W. John Wilbur
Important Dates
March 2015: Deadline for participation
Mar-May. 2015: Developing individual systems and iterative system integration
June 2015: Individual systems due date
June-July 2015: Overall system evaluation
August 2015: Manuscript deadline for meeting proceedings
URL: http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/
•  Track 2: CHEMDNER patents: Identification of chemical compounds and of relevant biological context in patents.
Organizers:Martin Krallinger, Alfonso Valencia, Florian Leitner, Obdulia Rabal and Julien Oyarzabal
Important Dates
February 2015: Sample set release together with annotation guidelines
April 2015: Training set release
May 2015: Development set release
July 2015: Test set release
August 2015: The evaluated results returned to the participants
beginning of September 2015: The camera ready system description write ups
URL: http://www.biocreative.org/tasks/biocreative-v/track-2-chemdner/

•  Track 3: Chemical-disease relation (CDR) task - Automatic detection of chemical/drugs and diseases, and their relations in PubMed abstracts. In particular, the CDR task focuses on extracting the relationship of drug-induced diseases.
Organizers:Zhiyong Lu and Thomas Wiegers
Important Dates
February-March, 2015: Release of training data
April-May, 2015: Release of development data
July, 2015: Release of test data
July-August, 2015 team submissions due
August-Early September, 2015 Team workshop paper due
URL:http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/

•  Track 4: Extraction of causal network information in Biological Expression Language (BEL) - Text mining solutions to develop and test novel approaches for relation extraction in the context of pathway networks. The goal is to assess the utility of such tools for the automated annotation and network expansion, and their suitability as supporting tools for assisted curation.
Organizers:Fabio Rinaldi, Sam Ansari and Juliane Fluck
Important Dates
February 15, 2015: Release training data
April 27, 2015: Release test data
April 30, 2015: Submission of results deadline
June 15, 2015: Delivery of evaluation results
July 1, 2015: Paper submission
August 15, 2015: Camera-ready
URL: http://www.biocreative.org/tasks/biocreative-v/track-4-bel-task/

•  Track 5: Interactive Curation (IAT): Demonstration and evaluation of web-based systems addressing user-defined tasks, evaluated by curators on performance and usability.
Organizers:Catalina Oana Tudor and Cecilia Arighi
Important Dates
January 31, 2015: Submission of letter of intent by teams
March 1 2015: Submission of system document by teams
March 15 2015: Notification of accepted systems
March-May 2015: Systems development
Mid-June 2015: Individual systems ready for user testing
June-July 2015: Overall system evaluation by curators
August 2015: Manuscript deadline for meeting proceedings
URL: http://www.biocreative.org/tasks/biocreative-v/track-user-interactive-task/



From: Islamaj, Rezarta (NIH/NLM/NCBI) [F] [mailto:islamaj at ncbi.nlm.nih.gov]
Sent: Wednesday, December 24, 2014 2:34 PM
To: Cecilia Neomi Arighi; Lynette Hirschman
Cc: Comeau, Don (NIH/NLM/NCBI) [E]; Cathy H. Wu (wuc at dbi.udel.edu<mailto:wuc at dbi.udel.edu>); Kevin B. Cohen; Wilbur, John (NIH/NLM/NCBI) [E]; Lu, Zhiyong (NIH/NLM/NCBI) [E]; Thomas Wiegers; Martin Krallinger; Alfonso Valencia (valencia at cnio.es<mailto:valencia at cnio.es>); Fabio Rinaldi (rinaldi.fabio at gmail.com<mailto:rinaldi.fabio at gmail.com>); Juliane Fluck; Kim, Sun (NIH/NLM/NCBI) [E]
Subject: RE: BioCreative Telecon Thurs Dec 18, 11 AM EST NOTES + Call for participation deadlines

Happy Holidays Ceci,

Rezarta

From: Cecilia Neomi Arighi [mailto:arighi at dbi.udel.edu]
Sent: Tuesday, December 23, 2014 10:59 AM
To: Lynette Hirschman
Cc: Islamaj, Rezarta (NIH/NLM/NCBI) [F]; Comeau, Don (NIH/NLM/NCBI) [E]; Cathy H. Wu (wuc at dbi.udel.edu<mailto:wuc at dbi.udel.edu>); Kevin B. Cohen; Wilbur, John (NIH/NLM/NCBI) [E]; Lu, Zhiyong (NIH/NLM/NCBI) [E]; Thomas Wiegers; Martin Krallinger; Alfonso Valencia (valencia at cnio.es<mailto:valencia at cnio.es>); Fabio Rinaldi (rinaldi.fabio at gmail.com<mailto:rinaldi.fabio at gmail.com>); Juliane Fluck; Kim, Sun (NIH/NLM/NCBI) [E]
Subject: Re: BioCreative Telecon Thurs Dec 18, 11 AM EST NOTES + Call for participation deadlines

Hi all,
I have changed the urls for the tracks put them under tasks instead of none, except for the chemdner that is not ready.
Please when Martin is ready we need to change the CFP under Event instead of none topic and can send the emails. I will have to ask Rezarta to follow up as I am heading to snow tubing for the day and not sure when I will have access again.
Happy holidays!!!!
Thanks

Ceci
________________________________
From: "Cecilia Neomi Arighi" <arighi at dbi.udel.edu<mailto:arighi at dbi.udel.edu>>
To: "Lynette Hirschman" <lynette at mitre.org<mailto:lynette at mitre.org>>
Cc: "Rezarta 'Islamaj (NIH/NLM/NCBI) [F]'" <islamaj at ncbi.nlm.nih.gov<mailto:islamaj at ncbi.nlm.nih.gov>>, "Don 'Comeau (NIH/NLM/NCBI) [E]'" <comeau at ncbi.nlm.nih.gov<mailto:comeau at ncbi.nlm.nih.gov>>, "Cathy H. Wu (wuc at dbi.udel.edu<mailto:wuc at dbi.udel.edu>)" <wuc at dbi.udel.edu<mailto:wuc at dbi.udel.edu>>, "Kevin B. Cohen" <kevin.cohen at gmail.com<mailto:kevin.cohen at gmail.com>>, "John Wilbur (NIH/NLM/NCBI) [E] (wilbur at ncbi.nlm.nih.gov<mailto:wilbur at ncbi.nlm.nih.gov>)" <wilbur at ncbi.nlm.nih.gov<mailto:wilbur at ncbi.nlm.nih.gov>>, "Zhiyong Lu (NIH/NLM/NCBI) [E] (luzh at ncbi.nlm.nih.gov<mailto:luzh at ncbi.nlm.nih.gov>)" <luzh at ncbi.nlm.nih.gov<mailto:luzh at ncbi.nlm.nih.gov>>, "Thomas Wiegers" <twiegers at mdibl.org<mailto:twiegers at mdibl.org>>, "Martin Krallinger" <mkrallinger at cnio.es<mailto:mkrallinger at cnio.es>>, "Alfonso Valencia (valencia at cnio.es<mailto:valencia at cnio.es>)" <valencia at cnio.es<mailto:valencia at cnio.es>>, "Fabio Rinaldi (rinaldi.fabio at gmail.com<mailto:rinaldi.fabio at gmail.com>)" <rinaldi.fabio at gmail.com<mailto:rinaldi.fabio at gmail.com>>, "Juliane Fluck" <juliane.fluck at scai.fraunhofer.de<mailto:juliane.fluck at scai.fraunhofer.de>>, "Sun Kim (NIH/NLM/NCBI) [E]" <sun.kim at nih.gov<mailto:sun.kim at nih.gov>>
Sent: Friday, December 19, 2014 2:31:13 PM
Subject: Re: BioCreative Telecon Thurs Dec 18, 11 AM EST   NOTES + Call for participation deadlines
I have created the CFP page
http://www.biocreative.org/news/biocreative-v/CFP/
When everybody is ready with their individual pages we can put the final url and make it public

Ceci
________________________________
From: "Lynette Hirschman" <lynette at mitre.org<mailto:lynette at mitre.org>>
To: "Cathy H. Wu (wuc at dbi.udel.edu<mailto:wuc at dbi.udel.edu>)" <wuc at dbi.udel.edu<mailto:wuc at dbi.udel.edu>>, "Cecilia Arighi (arighi at dbi.udel.edu<mailto:arighi at dbi.udel.edu>)" <arighi at dbi.udel.edu<mailto:arighi at dbi.udel.edu>>, "Kevin B. Cohen" <kevin.cohen at gmail.com<mailto:kevin.cohen at gmail.com>>, "John Wilbur (NIH/NLM/NCBI) [E] (wilbur at ncbi.nlm.nih.gov<mailto:wilbur at ncbi.nlm.nih.gov>)" <wilbur at ncbi.nlm.nih.gov<mailto:wilbur at ncbi.nlm.nih.gov>>, "Zhiyong Lu (NIH/NLM/NCBI) [E] (luzh at ncbi.nlm.nih.gov<mailto:luzh at ncbi.nlm.nih.gov>)" <luzh at ncbi.nlm.nih.gov<mailto:luzh at ncbi.nlm.nih.gov>>, "Thomas Wiegers" <twiegers at mdibl.org<mailto:twiegers at mdibl.org>>, "Lynette Hirschman" <lynette at mitre.org<mailto:lynette at mitre.org>>, "Martin Krallinger" <mkrallinger at cnio.es<mailto:mkrallinger at cnio.es>>, "Alfonso Valencia (valencia at cnio.es<mailto:valencia at cnio.es>)" <valencia at cnio.es<mailto:valencia at cnio.es>>, "Fabio Rinaldi (rinaldi.fabio at gmail.com<mailto:rinaldi.fabio at gmail.com>)" <rinaldi.fabio at gmail.com<mailto:rinaldi.fabio at gmail.com>>, "Juliane Fluck" <juliane.fluck at scai.fraunhofer.de<mailto:juliane.fluck at scai.fraunhofer.de>>, "Sun Kim (NIH/NLM/NCBI) [E]" <sun.kim at nih.gov<mailto:sun.kim at nih.gov>>
Cc: "Rezarta 'Islamaj (NIH/NLM/NCBI) [F]'" <islamaj at ncbi.nlm.nih.gov<mailto:islamaj at ncbi.nlm.nih.gov>>, "Don 'Comeau (NIH/NLM/NCBI) [E]'" <comeau at ncbi.nlm.nih.gov<mailto:comeau at ncbi.nlm.nih.gov>>
Sent: Thursday, December 18, 2014 12:31:11 PM
Subject: BioCreative Telecon Thurs Dec 18, 11 AM EST   NOTES + Call for participation deadlines
Notes: Dec 18;
Attending:  FR, SA, CA, JW, DC, RI, SK, ZL, MK, LH

Next Meeting: Thurs Jan 8, 2015

IMPORTANT DEADLINES BELOW:  Post Call for Participation by Dec. 23, 2014 and send out to mailing lists


Funding updates

                NIH – funding will be used to recruit minorities and women to go to BC;

                                The call for participation will say that there is possibility of funding (travel, registration)

                                CA will work w KBC to craft a sentence or two to insert in call

                EU – MK – provided description to Spanish Natl Bioinformatics Inst

                                Will get back to company handling conference web site;

                                Will send around proposed numbers and inscription fee

                                Separate rates for students/post-docs vs commercial

                                Discount for participants



BC V planning

CALL FOR PARTICIPATION

Initial call will go on BioCreative web site at CNRI

                CA will set up access rights to web site for Fabio/BEL team

*** POST Call for participation (and send out info) BY DEC 23

*** Will provide 1 page description, including the tracks and consolidated time line

*** Tracks are:

                Track I – BioC (JW)

                Track 2 – Chem (MK)

                Track 3 – CTD (TW/ZL)

                Track 4 – BEL (FR/SA/JF)

                Track 5 – Interactive (CA)



For CALL for Participation--  Need from each track:

o   short descrip of track (1-2 sentences),  and

o   timeline for data release

*** CA, RI will put together draft and circulate for review (Friday Dec 19/Monday Dec. 22)

*** Post on BioCreative Web Page on Tues Dec. 23, along with pointers to full task descriptions

*** Send to mailing lists:  CA -- ISB, BioCreative;

BioNLP (Rezarta);

AMIA (John); Sun: DBWord, Machine Learning

Lynette: will check re DARPA Big Mechanism participants



                Status on task descriptions

                BioC – ready, have task on web site; JW will send URL

                MK – will send sentences and time line

Zhiyong/Tom – need to get in touch w Tom; should be able to send sentences and dates

BEL – ready, Fabio can circulate draft

CA – ready to go



Updates on BC V Tracks



Track I – BioC for BioGrid (JW)

                Created BioC files for task, web page

                Almost ready for participation

                Will release BioC key file and sample BioC files

                No training data per se; there is some data from BioGrid that will be available

                To help w format, have annotated articles (1 for now) – illustrative data

                                One article annotated in full

Track 2 -- Chem/bio patent data (MK)

                Revise the guidelines which were used for abstracts in BC IV

                Make a little more granular, also issues w hybrid mentions

Hybrid mention:  a chemical whose name is part IUPAC and part trivial

Would need to decompose into component parts to make sense out of name



                Meeting last week – EU meeting re access of articles for text mining

                Could get help from Peter Murray-Rust;

also met w Jo McEntyre, include background collection?

                                Use for silver standard corpus? Similar to BCIV

                Will meet w annotators to discuss timeline

                Structure annotations – would like subset of mentions linked to structural info

                For patents, most mentions are more systematic



Track 3 - Chem/gene/disease (TW, ZL)

                Started to annotate data; so far 100 PubMed abstracts

                Finalized guidelines, trained annotators

                Ready to do more annotations

                Looking at 100 abstracts – do some analysis to determine task difficulty



Track 4 -- BEL track (FR, SA, JF)

   BioC/BEL task interaction:

                Would like to have BioC representation of BEL statements

                Exploring how to represent BEL in BioC

                RI has translated some BEL statements into BioC – will send draft

                Haven’t pursued normalization but:

                                BioGrid  – includes nonhuman; BEL – all human

                Could do mapping HGNC/UniProt

                Could easily incorporate both identifiers               in BioC format

  BEL Subtasks (down to 2 subtasks)

                Subtask 1: given evidence, generate BEL

                Subtask 2: given BEL, find evidence

                Selventa – will make more data available; which subset to use?



                Make available BEL documentation, mappings and list of name spaces

                Contact w OpenBEL consortium w documentation, supporting materials



Track 5 Interactive (CA) – not much to update, need to figure out UAG

                LH to follow up w Eric Wommac at U Delaware

re interest in text mining for metagenomis



UAG planning

                Primary need is for curators to judge interactive track entries

                                Maybe also bring in BioGrid, Metagenomics?

                Suggestion: have a Panel for curators – to bring in curators

                                And give them a voice

                                (Note: most tracks are now aligned with specific curation efforts)



Next meeting --  Jan 8, “usual time” (11-12 EST)






--
Cecilia Arighi, PhD
Research Associate Professor
Center for Bioinformatics & Computational Biology
Department of Computer and Information Sciences
University of Delaware
15 Innovation Way, Room 205
Newark, DE19711



--
Cecilia Arighi, PhD
Research Associate Professor
Center for Bioinformatics & Computational Biology
Department of Computer and Information Sciences
University of Delaware
15 Innovation Way, Room 205
Newark, DE19711
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