/biocreativeVIII_Track1

Apache License 2.0Apache-2.0

BioRED track lasigeBioTM submission: Relation extraction using Domain Ontologies with BioRED

The present repository contains the data used for our participation at the BioCreative VIII Track 1 Biored in both sub-tasks.

The paper describing our participation (team lasigeBioTM) will be available here.

Data availability

Tools

Knowledge Bases

NER

RE

Sub-task 1 Results

Official Runs

RUN 1 P R F
Entity pair: 0.1942 0.9914 0.3248
Entity pair+Relation type: 0.0435 0.2218 0.0727
Entity pair+Novelty: 0.0770 0.3963 0.1290
Entity pair+Relation type+Novelty: 0.0177 0.0908 0.0296

Unofficial Runs

RUN 1 RUN 2 RUN 3
P R F P R F P R F
Entity pair: 0.1942 0.9914 0.3248 0.1942 0.9914 0.3248 0.1942 0.9914 0.3248
Entity pair+Relation type: 0.0825 0.4214 0.1381 0.0801 0.4091 0.1340 0.0435 0.2218 0.0727
Entity pair+Novelty: 0.0770 0.3963 0.1290 0.0770 0.3963 0.1290 0.0770 0.3963 0.1290
Entity pair+Relation type+Novelty: 0.0329 0.1695 0.0552 0.0309 0.1592 0.0518 0.0177 0.0908 0.0296

Sub-task 2 Results

Official Runs

RUN 1 P R F
NER: 0.0003 0.0001 0.0001
Normalization: 0.4477 0.0710 0.1226
Entity pair: 0.0563 0.0219 0.0315
Entity pair+Relation type: 0.0128 0.0050 0.0072
Entity pair+Novelty: 0.0187 0.0073 0.0105
Entity pair+Relation type+Novelty: 0.0047 0.0018 0.0026

Unofficial Runs

RUN 1 RUN 2
P R F P R F
NER: 0.7703 0.6411 0.6998 0.7703 0.6411 0.6998
Normalization: 0.4212 0.2280 0.2958 0.4212 0.2280 0.2958
Entity pair: 0.0427 0.0633 0.0510 0.0427 0.0633 0.0510
Entity pair+Relation type: 0.0110 0.0163 0.0131 0.0084 0.0125 0.0100
Entity pair+Novelty: 0.0207 0.0307 0.0247 0.0207 0.0307 0.0247
Entity pair+Relation type+Novelty: 0.0058 0.0086 0.0069 0.0040 0.0060 0.0048