https://github.com/fnl/species

a modified version of the SPECIES tagger
https://github.com/fnl/species

Last synced: 22 days ago
JSON representation

a modified version of the SPECIES tagger

• Host: GitHub
• URL: https://github.com/fnl/species
• Owner: fnl
• Created: 2015-04-01T08:08:01.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2015-04-01T13:49:40.000Z (over 11 years ago)
• Last Synced: 2025-10-30T18:03:00.862Z (9 months ago)
• Language: C++
• Size: 59.3 MB
• Stars: 2
• Watchers: 1
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

          
SPECIES

=======

A standalone command line application capable of identifying taxonomic mentions in documents and mapping them to corresponding NCBI Taxonomy database entries.

Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, et al. **The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text.** (2013) [PLoS ONE 8(6): e65390](http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0065390)

This is a GitHub mirror of the SPECIES tagger with *modifications* of the tool. To get the original, unmodified code, please download it from its [homepage](http://species.jensenlab.org/).

The modified program parses a simpler input format (one citation per line, with PMID-title-abstract, tab-separated) and outputs the detected TaxIDs attached as an extra (fourth) field of comma-separated Taxonomy IDs for each input citation.

In addition, the added script `replace_tags.py` makes it possible to replace that list of TaxIDs in the output with the labels `TRUE`, `FALSE`, or `NULL`.