DOI: 10.5281/zenodo.16845409
title: GutBrainIE 2025 – Gut Brain Interplay Information Extraction @ CLEF 2025

description: GutBrainIE 2025 – Gut Brain Interplay Information Extraction @ CLEF 2025

Dataset Description

Recent studies link the gut microbiota to mental health conditions and to neurodegenerative diseases such as Parkinson's and Alzheimer's. However, the rapid speed at which this research field is evolving presents a significant challenge for clinicians and researchers who have to keep pace with an ever-expanding volume of biomedical literature. In this context, automatic tools for extracting and structuring information from scientific texts are becoming essential to support the understanding of the gut-brain axis.

GutBrainIE promotes the development of Natural Language Processing (NLP) systems capable of extracting structured specialized knowledge from biomedical texts related to the gut-brain axis, aiming to accelerate biomedical discoveries through automated Information Extraction (IE).

Supported Tasks

GutBrainIE proposes four tasks of increasing complexity:



Named Entity Recognition (NER): systems have to identify and classify specific text spans (entity mentions) into one of the 13 predefined categories (e.g., bacteria, chemical, microbiota).

Binary Tag-based Relation Extraction (BT-RE): systems are provided with a set of predefined relation types, each defined by a combination of compatible head and tail entities (e.g., Chemical -> Microbiome via Impact or Produced by), and have asked to identify which entities are in relation within a document, without specifying the exact predicate or entity mentions involved. 

Ternary Tag-based Relation Extraction (TT-RE): this task extends BT-RE by requiring participants to predict the specific relation predicate connecting each head-tail entity pair. 

Ternary Mention-based Relation Extraction (TM-RE): this is the most challenging task, demanding to identify the exact entity mention involved in a relation and assign the correct relation predicate.  


 
description: Entity Types








Entity Label



URI



Definition







Anatomical Location



NCIT_C13717



Named locations of or within the body.

The categories "anatomic site" of NCIT and "organism subdivision" of UBERON can be used as references for this label.





Animal



NCIT_C14182



A non-human living organism that has membranous cell walls, requires oxygen and organic foods, and is capable of voluntary movement, as distinguished from a plant or mineral.

"Human" is a subordinate concept of "Animal", but for CLEF we distinguish only between humans and any other animal.





Statistical Technique



NCIT_C19044



A method of analyzing or representing statistical data; a procedure for calculating a statistic.





Biomedical Technique



NCIT_C15188



Research concerned with the application of biological and physiological principles to clinical medicine.

This category also includes the "assay" category, defined as a planned process with the objective of producing information about a material entity (the evaluant) by examining it. 





Bacteria



NCBITaxon_2



One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal.





Chemical



CHEBI_59999



A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types.

This category also includes "metabolites", which in biochemistry are the intermediate or end product of metabolism (more information here), and "neurotransmitters", which are endogenous compounds used to transmit information across the synapses.





Dietary Supplement



MESH_68019587



Products in capsule, tablet or liquid form that provide dietary ingredients, and that are intended to be taken by mouth to increase the intake of nutrients. Dietary supplements can include macronutrients, such as proteins, carbohydrates, and fats; and/or MICRONUTRIENTS, such as VITAMINS; MINERALS; and PHYTOCHEMICALS.





Disease, Disorder, or Finding (DDF)



NCIT_C7057



A condition that is relevant to human neoplasms and non-neoplastic disorders. This includes observations, test results, history, and other concepts relevant to the characterization of human pathologic conditions.





Drug



CHEBI_23888



Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances.





Food



NCIT_C62695



A group of solid, semi-solid, and liquid substances which are consumed by humans and animals.

Although we acknowledge that "dietary supplement" could conceptually fit within this category, we are considering these two as distinct.





Gene



SNOMEDCT_67261001



A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function.





Human



NCBITaxon_9606



Members of the species Homo sapiens.

This category includes all mentions of humans, even if they are not directly informative about biomedical processes or discoveries. For instance, mentions such as "psychiatrist", "clinicians", "medical personnel", and similar terms should also be annotated under this entity label.





Microbiome



OHMI_0000003



This term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eukaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions.





 
description: Relation Predicates








Head Entity



Tail Entity



Predicate







Anatomical Location



Human

Animal



located in





Bacteria



Bacteria 

Chemical

Drug



interact





Bacteria



Disease, Disorder, or Finding



Influence





Bacteria



Gene



change expression





Bacteria



Human

Animal



located in





Bacteria



Microbiome



part of





Chemical



Anatomical Location

Human

Animal



located in





Chemical



Chemical



interact

part of





Chemical



Microbiome



impact

produced by





Chemical

Dietary Supplement

Drug

Food



Bacteria

Microbiome



impact





Chemical

Dietary Supplement

Food



Disease, Disorder, or Finding



influence





Chemical

Dietary Supplement

Drug

Food



Gene



change expression





Chemical

Dietary Supplement

Drug

Food



Human

Animal



administered





Disease, Disorder, or Finding



Anatomical Location



strike





Disease, Disorder, or Finding



Bacteria

Microbiome



change abundance





Disease, Disorder, or Finding



Chemical



interact





Disease, Disorder, or Finding



Disease, Disorder, or Finding



affect

is a





Disease, Disorder, or Finding



Human

Animal



target





Drug



Chemical

Drug



interact





Drug



Disease, Disorder, or Finding



change effect





Human / Animal / Microbiome



Biomedical Technique



used by





Microbiome



Anatomical Location

Human

Animal



located in





Microbiome



Gene



change expression





Microbiome



Disease, Disorder, or Finding



is linked to





Microbiome



Microbiome



compared to





 
description: Website

Detailed information about the 2025 iteration of the GutBrainIE challenge can be found at the following website:

https://hereditary.dei.unipd.it/challenges/gutbrainie/2025/