* BioCreative VI chemical-protein interaction (ChemProt) track *

/Held as part of BioCreative VI workshop -  2017, October18-20 11-14 2017, Bethesda, Maryland, USA/

Track URL: http://www.biocreative.org/tasks/biocreative-vi/track-5/

 
ChemProt track summary

A considerable number of approaches have been implemented to detect automatically mentions of chemical compounds and genes/proteins in running text, while far less attempts have been made to recognize automatically relations between them.
The aim of the CHEMPROT track is to promote the development of systems able to extract chemical-protein interactions of relevance for precision medicine, drug discovery as well as basic biomedical research.
For this track a large collection of PubMed abstracts was manually annotated with mentions of chemical compounds and of genes/proteins following the annotation guidelines that were originally used to prepare the CHEMDNER task corpora for BioCreative IV, V and V.5 [1-6].

For the CHEMPROT track a granular chemical-protein relation annotation was carried out, with the aim to cover most of the relations that are of importance from the point of view of biochemical and pharmacological / biomedical perspective.
To simplify the CHEMPROT track, and to focus mainly on a subset of key relevant relation types, all the annotated CHEMPROT relations (CPRs) were grouped into 10 semantically related classes that do share some underlying biological characteristics.

Those groups were labeled as [CPR:1, CPR:2, … CPR:10] ; and are detailed in the table below:


Group       Eval.        CHEMPROT relations belonging to this group

CPR:1      N               PART_OF

CPR:2      N               REGULATOR|DIRECT_REGULATOR|INDIRECT_REGULATOR

CPR:3      Y               UPREGULATOR|ACTIVATOR|INDIRECT_UPREGULATOR

CPR:4      Y               DOWNREGULATOR|INHIBITOR|INDIRECT_DOWNREGULATOR

CPR:5      Y               AGONIST|AGONIST-ACTIVATOR|AGONIST-INHIBITOR

CPR:6      Y               ANTAGONIST

CPR:7      N               MODULATOR|MODULATOR-ACTIVATOR|MODULATOR-INHIBITOR

CPR:8      N               COFACTOR

CPR:9      Y               SUBSTRATE|PRODUCT_OF|SUBSTRATE_PRODUCT_OF

CPR:10   N               NOT

For evaluation purposes only five groups labeled with ‘Y’ will be used, that is: CPR:3, CPR:4, CPR:5, CPR:6, CPR:9.

Additional details on the annotation process, task, format, evaluation and datasets are provided at the CHEMPROT track webpage, sample set and training set.

*Lab registration open at:
 
http://www.biocreative.org/events/biocreative-vi/team/


Note: In order to participate as a team, you need to register for Track 5.

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