Biomedical annotation metaserver

Integrating independent resources for biomedical text annotation visualisation, prediction and benchmarking biomedical entity recognition between independent automatic prediction systems.

Biocreative & BeCalm Workshop: Conference Registration is Open. No registration fees.
February 24, 2017: CEMP and GPRO competition results are available now.
February 3, 2017: Reminder! TIPS phase 1 evaluation will start February, 6th and ​will​ end March, 31st.
January 18, 2017: TIPS task and the TIPS (Annotation server) tutorial have been updated
January 12, 2017: BeCalm final submission tutorial is available. Download it here
January 3, 2017: The test set patents of BioCreative V.5 have been released. Download it here
December 12, 2016:

Extended task deadlines. The final deadlines for the tasks are as follows:

  • CEMP/GPRO offline tasks:
    • tests set release January 3rd 2017
    • final submission January 15th 2017
  • TIPS online task:
    • servers alive January 31st 2017
    • server evaluation from February 1st till March 31st 2017

December 12, 2016: TIPS annotation server tutorial
December 05, 2016: NEW! BioCreative V.5 training set updated due to minor issues. BioCreative V.5 training set.zip
November 24, 2016: BeCalm metaserver will be unavailable from 6:00-18:00 Central European Time(UTC+01:00) on Monday, November 28, 2016.
November 24, 2016: TIPS evaluation metrics and phases (V.2) TIPS task.pdf
November 16, 2016: FAQ (Frequently Asked Questions) was published here
November 16, 2016: TIPS evaluation metrics and phases: TIPS task.pdf
November 7, 2016: BeCalm evaluation tutorial was published: BeCalm evaluation tutorial.pdf
October 13, 2016: GPRO and CEMP training patents and training annotations was published: BioCreative V.5 training set.zip
October 10, 2016: BeCalm NER resources webpage was published http://www.becalm.eu/NerResources
September 30, 2016: BioCreative V.5 CFP was launched.

Biomedical types supported by servers@BeCalm

  • Chemical
  • Protein
  • Disease
  • Organism
  • Anatomic component
  • Cell line and cell type
  • Mutation
  • Gene
  • Subcellular structure
  • Tissue and organ
  • MiRNA
  • Gene ontology
Annotation types

How It Works ?

A platform to visualise, predict and benchmark biomedical entity recognition between independent automatic prediction systems.

BeCalm multipropose

Biomedical Interest

This platform interconnects multiple annotation servers with various recognition abilities. The aim is to offer users information of practical biomedical use.

BeCalm  servers

Servers worldwide

The platform unites and standardised access to textual information extracted by various automatic systems interconnected worldwide.

BeCalm  Benchmarking

Benchmarking

Text miners may test the performance of their systems at the meta-server. The platform offers integrated access to high quality gold standards and state-of-the-art prediction systems.

Developed for text miners

Text miners can use the platform both for development purposes and to obtain annotations and classifications in a systematic and consistent way.

  • Text miners can run periodic comparative analyses of their predictions against the annotation servers and the gold/silver standards available in the platform.
  • System performance evaluation accounts for both recognition abilities and processing time. Precision, recall and F-score statistics are computed to understand and measure the relevance of the automatic annotations. The maximum and average latency times of the annotation servers are monitored continuously.
  • The web service API enables developers to integrate the platform data with their own applications. For example, to combine the results obtained by multiple annotation pipelines.
BeCalm laptop
BeCalm laptop

Developed for end-users

The development of a platform that can operate freely on the complete set of Medline abstracts has the potential of being of great advantage to the biomedical community.

  • Users may configure annotation projects according to their own purposes, including the set of documents to be processed, the annotation servers to be used and the biomedical annotations of interest.
  • The platform provides detailed information on the skills of the various annotation servers, the exhibited performance, and current status.
  • Results will be accessible via web browser and via web service API.

No installation required

The documents and annotations you want at any time and from anywhere. Without complications.

Public benchmark

Periodic report on annotation server performance.

REST API

Web interface and web services API provide access to the platform. New automatic systems are always welcome.

Technology independence

Annotation server implementation is totally independent of the platform. Developers only have to implement the methods specified in the REST API.

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About Us...

CNIO
OPENMINTED
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