/edin-data

Biomolecular events mined by Reach from PubMed Central

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License

Description

This repository contains "silver" biomolecular event mentions mined from the full text of a subset of PubMed Central publications using Reach (commit d6a84be099a155b2bedb69f2102493d5db9399fb). A portion of this data was used to supplement the training of edin.

Rules

rules.yml contains the Odin rules referenced in the event json data.

Events

File Event
ph_events.jsonl Phosphorylation
lo_events.jsonl Localization
ge_events.jsonl Gene Expression

Structure

Each .jsonl is a JSON lines file contains a list of JSON objects where each object represents an event mention in the schema defined in oas3-data-schema.yml. Click this link to render the schema in an editor.

Quick view

This command will pretty print the first gene expression event listed in ge_events.jsonl:

head -n 1 ge_events.jsonl | python -m json.tool