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Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.

BioCreative VII

BioCreative VII Workshop Information (Events) [2021-08-23]

The BioCreative VII workshop will be held on November 8-10, 2021. This event will be virtual and free.

We will use Zoom for main meeting presentation and YouTube channels for hosting posters and other presentations.

Registration


Registration is open to participants of the tracks and to anyone interested in learning/discussing about development of state-of-the-art text mining methods for real life applications. There is no fee. Registration is opened until November 5 or until full capacity is reached. However, track participants, speakers and poster presenters will be given priority. Register here

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Scientific Program


The scientific program includes the talks related to the individual tracks, a panel about mining adverse drug reactions, a keynote talk and a flash talks for selected posters. Detailed agenda is shown below

Monday, November 8, 2021

UTC (Universal)ESTSession
2:30-2:40 pm9:30-9:40 amOpening remarks
2:40-3:55 pm9:40-10:55 amNLM-Chem Track: Full text Chemical Identification and Indexing in PubMed articles (Track 2)
3:55-4:15 pm10:55-11:15 amBreak
4:15-5:00 pm11:15 am-12:00 pmKeynote: Dr. Joshua Denny, Chief Executive Officer of the All of Us Research Program, NIH
5:00-6:15 pm12:00-1:15 pmAutomatic extraction of medication names in tweets (Track 3)

Tuesday, November 9, 2021

UTC (Universal)ESTSession
2:30-2:40 pm9:30-9:40 amOpening remarks
2:40-3:55 pm9:40-10:55 amDrugProt:Text mining drug/chemical-protein interactions (Track 1)
3:55-4:15 pm10:55-11:15 amBreak
4:15-5:00 pm11:15 am-12:00 pmSelected poster flash talks
5:00-6:15 pm12:00-1:15 pmPanel: Challenges in mining adverse drug reactions

Wednesday, November 10, 2021

UTC (Universal)ESTSession
2:30-2:40 pm9:30-9:40 amOpening remarks
2:40-3:55 pm9:40-10:55 amLitCovid track Multi-label topic classification for COVID-19 literature annotation (Track 5)
3:55-4:15 pm10:55-11:15 amBreak
4:15-5:30 pm11:15 am-12:30 pmCOVID-19 text mining tool interactive demo (Track 4)
5:30-6:10 pm12:30-1:10 pmGeneral discussion
6:10-6:15 pm1:10-1:15 pmClosing remarks

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Poster session

BioCreative VII will host a poster session in the form of pre-recorded videos in a YouTube channel. We invite the larger community to submit abstracts on topics related to BioCreative VII.
Topics include chemical/drug name entity recognition, relation extraction involving chemicals/drugs, COVID-19 related text mining, and works about datasets and standards related to these topics.
A number of abstracts will be selected for the Flash talks poster session on November 9. All accepted abstracts are required to submit a 2 min recorded video presentation of the poster in mp4 format. Deadline for video submission for accepted abstracts is October 28, 2021. Details on how to submit these will be sent with acceptance email.


For more details on poster abstract submission see Work Submission section below.

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Work Submissions

BioCreative VII will accept two types of submissions:

  • Track paper submissions: Participants of BioCreative VII tracks should submit a paper per track describing corresponding systems/results.
    Specifications: Length up to 4 pages of text (not counting figures and references). Follow template with instructions here. Although template is a word document, the format for submission should be in PDF. It is mandatory to comply with format requested.
    Submission deadline: please follow the dates described in the track you are participating.
    Note that track submissions automatically qualify as posters if not selected for talk, you do not need to submit again under poster submissions.
  • Poster abstract submissions: Accept abstracts describing works related to BioCreative VII track's topics (chemical name entity recognition, relation extraction involving chemicals, COVID-19 related text mining, datasets and standards related to these)
    Specification: Length up to 500 words (excluding title and authors info), font Times New Roman , size 11. In addition, you can include up to two figures and 5 references (using numbers in parentheses in text).
    Submission deadline: October 18, 2021
    Acceptance message: October 22, 2021

To submit your work go to Easychair: https://easychair.org/conferences/?conf=bc7, and select the applicable option (a track or poster). Format for all submissions is PDF.

BioCreative VII proceedings will be published online and will be available at the time of the meeting.

We will invite selected track works for full publication in the Database Journal Special Issue for BioCreative.

Proceedings

BioCreative VII proceedings will be made available before the workshop.

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Key Dates

  • BioCreative VII workshop event: November 8-10, 2021
  • Posters:
    Abstract submission deadline: October 18, 2021
    Acceptance message: October 22, 2021
    Video submission deadline for accepted abstracts: October 30, 2021
  • Track papers
    Follow submission deadlines provided in individual Track pages

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BioCreative VII challenge and workshop (Events) [2020-01-22]

Note for Biocreative participants: For registration to a track please use the Google form.
Do not use the team "Team page" tab as it is non functional.

BioCreative VII Challenge and Workshop CFP

The workshop will take place on November 8-10, 2021. This workshop will be virtual.

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. We further offer Track 5, LitCovid Track on multi-label topic classification for COVID-19 literature annotation, calling for innovative text mining tools to support the curation of COVID-19 literature in LitCovid, a literature database of COVID-19-related papers in PubMed.

Here are more details about the tracks. Click on the Track number for accessing track specific pages:

  • Track 1- DrugProt:Text mining drug/chemical-protein interactions
    Organizers: Martin Krallinger, Alfonso Valencia
    DrugProt will explore recognition of chemical-protein entity relations from abstracts. The aim of the DrugProt track is to promote the development and evaluation of systems that are able to automatically detect relations between chemical compounds/drug and genes/proteins. We have therefore generated a manually annotated corpus, the DrugProt corpus, where domain experts have exhaustively labeled: (a) all chemical and gene mentions, and (b) all binary relationships between them corresponding to a specific set of biologically relevant relation types (DrugProt relation classes).

  • Track 2- NLM-Chem Track: Full text Chemical Identification and Indexing in PubMed articles
    Organizers: Rezarta Islamaj, Robert Leaman, and Zhiyong Lu, National Library of Medicine (NLM)
    Current chemical concept recognition tools have demonstrated significantly lower performance for in full-text articles than in abstracts. Improving automated full-text chemical concept recognition can substantially accelerate manual indexing and curation and advance downstream NLP tasks such as relevant article retrieval. The NLM-CHEM task will consist of two sub-tasks, focusing on (1) identifying chemicals in full-text articles (i.e. named entity recognition and normalization) and (2) ranking chemical concepts for full-text document indexing. The task will use the recently released NLM-CHEM corpus, consisting of 150 full-text articles, with ~5000 unique chemical names mapped to ~2,000 MeSH identifiers.

  • Track 3- Automatic extraction of medication names in tweets
    Organizers: Graciela Gonzalez-Hernandez, Davy Weissenbacher, Ivan Flores, Karen O’Connor
    The goal of this task is to extract the spans that mention a medication or dietary supplement in tweets. The dataset consists of all tweets posted by 212 Twitter users during their pregnancy. This data represents the natural and highly imbalanced distribution of drug mentions in Twitter, with only approximately 0.2% of the tweets mentioning a medication. Training and evaluating a sequence labeler on this data set will closely model the detection of drugs in tweets in practice. Click here for more information.

  • Track 4- COVID-19 text mining tool interactive demo
    Organizers: Cecilia Arighi, Andrew Chatr-Aryamontri, Lynette Hirschman, Martin Krallinger, Karen Ross, Tonia Korves
    The COVID-19 text mining tool interactive demo track is a demonstration task, and will focus on tools specifically developed to support COVID-19 research efforts. Similar to previous interactive tasks (e.g., PMID:27589961), tools will be reviewed by the research community, providing feedback on effectiveness and usability.
    The goal of this task is to foster the interaction between system developers and potential users to advance in the development of text mining tools that are useful for the research community. Participating teams will present a web-based system that can address some task(s) of their choice. Users will be recruited to review the system and provide feedback via a user questionnaire. More information here.

  • Track 5- LitCovid track Multi-label topic classification for COVID-19 literature annotation
    Organizers: Qingyu Chen, Alexis Allot, Rezarta Islamaj, Robert Leaman, and Zhiyong Lu, National Library of Medicine (NLM)
    The number of COVID-19-related articles in the literature is growing by about 10,000 articles per month. LitCovid, a literature database of COVID-19-related papers in PubMed, has accumulated more than 100,000 articles, with millions of accesses each month by users worldwide. LitCovid is updated daily, and this rapid growth significantly increases the burden of manual curation. In particular, annotating each article with up to eight possible topics, e.g., Treatment and Diagnosis, has been a bottleneck in the LitCovid curation pipeline. Increasing the accuracy of automated topic prediction in COVID-19-related literature would be a timely improvement beneficial to curators and researchers worldwide. The LitCovid track calls for a community effort to tackle automated topic annotation for COVID-19 literature. The task will use ~60K articles in LitCovid with manually reviewed topics.

    PUBLICATION

    The BioCreative VII Proceedings will host all the submissions from participating teams and it will be freely available by the time of the workshop.
    In addition, we are happy to announce that the journal Database will host the BioCreative VII special issue for work that has passed their peer-review process. Invitation to submit will be sent after the workshop.



    TEAM REGISTRATION

    Teams can participate in one or more of these tracks. Team registration will continue until final commitment is requested by the individual tracks.
    To register a team go to the Registration form. If you have restrictions accessing Google forms please send e-mail to BiocreativeChallenge@gmail.com.
    Note: The BioCreative site has a Team page link, please ignore it as it is non functional. Registration is done via Google forms this time.

    BIOCREATIVE ORGANIZING COMMITTEE

  • Cecilia Arighi, University of Delaware, USA
  • Andrew Chatr-Aryamontri, University of Montreal, Canada
  • Rezarta Dogan, National Center for Biotechnology Information (NCBI), NIH, USA
  • Graciela Gonzalez-Hernandez, University of Pennsylvania, USA
  • Lynette Hirschman, MITRE Corporation, USA
  • Martin Krallinger, Barcelona Supercomputing Center, Spain
  • Robert Leaman, National Center for Biotechnology Information (NCBI), NIH, USA
  • Zhiyong Lu, National Center for Biotechnology Information (NCBI), NIH, USA
  • Karen Ross, Georgetown University Medical School, USA
  • Alfonso Valencia, Barcelona Supercomputing Center, Spain
  • Davy Weissenbacher, University of Pennsylvania, USA
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    Corpora

    ChemProt corpus: BioCreative VI (Resources) [2017-11-21]

    Text mining chemical-protein interactions (CHEMPROT) corpus, including:
    • ChemProt sample set
    • ChemProt training set
    • ChemProt development set
    • ChemProt test set

    Downloads