Call For Participation: BioCreative VII Challenge and Workshop

11 views
Skip to first unread message

Robert Leaman

unread,
Feb 24, 2021, 4:35:05 PMFeb 24
to Robert Leaman
[Apologies for cross-posting]

Call For Participation

BioCreative VII Challenge and Workshop

November 2021

BioCreative: Critical Assessment of Information Extraction in Biology is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. BioCreative has been an invaluable source for advancing state-of-the-art text mining methods by providing reference datasets and a collegial environment to develop and evaluate these methods in both shared and interactive modes. 

 

The sudden spread of COVID-19 has triggered an unexpected pressure on the biomedical community to quickly identify potential treatments by repurposing existing drugs or identifying new chemicals with anti-Sars-CoV-2 activity. Thus, BioCreative VII will focus around detection of chemicals, drugs and related substances with three tracks: Track 1 (DrugProt) focuses on the detection of interactions between chemicals/drugs/substances and genes/proteins in abstracts, Track 2: (NLM Chem track) focuses on detecting chemical names and their MeSH encoding in full-length articles and Track 3: Medications in Tweets focuses on extracting medication mentions from social media. In addition, COVID-19 has triggered the development of multiple text mining tools to support ongoing research efforts that await community feedback. Thus, we are offering an interactive track, Track 4, to provide an environment for tools to be reviewed by users and get their feedback on utility and usability. 

 

The workshop will take place sometime during the first two weeks in November 2021 (exact dates still to be determined) and will have a virtual component. Teams can participate in one or more of the tracks. We will ask teams to prepare a system description paper for the workshop Proceedings and the BioCreative special issue in a peer-reviewed journal. Those selected will have an opportunity to present at the workshop. As usual, we will have a special issue in a peer-reviewed journal.


Team registration starts on February 25, 2021 and will continue until the testing data is released. To register a team go to https://forms.gle/cJtHdRfJhUiaLbb58

If you have restricted access to Google forms, please contact Biocreativ...@gmail.com


General information: http://www.biocreative.org

 

Tracks:

Track 1- DrugProt: Text mining drug/chemical-protein interactions

Organizers: Martin Krallinger, Alfonso Valencia

URL: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-1/

 

Track 2- NLM-Chem Track: Full text Chemical Identification and Indexing in PubMed articles

Organizers: Rezarta Islamaj, Robert Leaman, and Zhiyong Lu

URL: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-2/

 

Track 3- Automatic extraction of medication names in tweets

Organizers: Graciela Gonzalez-Hernandez, Davy Weissenbacher, Ivan Flores, Karen O’Connor

URL: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-3/

 

Track 4- COVID-19 text mining tool interactive demo (more info available soon)

Organizers: Cecilia Arighi, Andrew Chatr-Aryamontri, Lynette Hirschman, Martin Krallinger, Karen Ross, Tonia Korves

 

Important Dates 

February 2021: Registration starts

March 2021: Release training data 

June-July 2021: Release of testing data (consult individual track)

September 2021: System description papers due.

October 2021: Organizers publish final rankings and invite speakers to the workshop

November 2021: BioCreative Workshop

Reply all
Reply to author
Forward
0 new messages