The Automated pipeline for Consistent Outputs from Research Publications (Auto-CORPus) is a tool for the standardisation and conversion of publication HTML to three convenient machine-interpretable outputs (full-text, tables, abbreviations) in BioC-JSON formats to support biomedical text analytics.
Code repository for the creation and annotation of corpora in the CoDiet project providing scripts to generate Bronze and Silver annotated test datasets. It leverages multiple pipelines, including dictionary matching, MetaMap, enzyme annotation, PhenoBERT, MicrobELP, and BERN2.
microbELP is a text mining pipeline for automatic recognition and normalisation of microbiome-related entities in biomedical literature. It identifies microbial mentions (excluding viruses) in full-text scientific articles and links them to their NCBI Taxonomy identifiers.
