Overview

This repository contains species related data from databases such as NCBI Blast and PubMed. This data is used to extract species information from the abstracts a given set of papers.

How to Run

The species_tagger.py file takes two positional arguments: the file path and output name + extension. This file is meant to be run on the PeTaL biomimicry data set format but can intake either JSON or CSV files and output them in either a CSV or JSON format.

Important Files

• common_names.txt

  • Text file consisting of a set of species common names.

• excluded_words.txt

  • Words to be ignored in abstracts when mining for species information.

• species_dict.json

  • Dictionary where keys are species scientific names and values are a list of the corresponding common names.

• ncbi_species.zip

  • Zipped JSON list of various formatted species information from NCBI Blast.

• species_tagger.py

  • Script responsible for ingesting a PeTaL document data set and returning a modified version with species and relevancy fields.