https://github.com/audy/tree-of-life

:deciduous_tree: API for NCBI taxonomic lineages
https://github.com/audy/tree-of-life

bioinformatics phylogenetics

Last synced: about 1 month ago
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:deciduous_tree: API for NCBI taxonomic lineages

• Host: GitHub
• URL: https://github.com/audy/tree-of-life
• Owner: audy
• License: mit
• Created: 2012-09-17T20:59:36.000Z (about 12 years ago)
• Default Branch: master
• Last Pushed: 2023-03-16T05:37:46.000Z (over 1 year ago)
• Last Synced: 2024-10-03T17:41:38.450Z (about 2 months ago)
• Topics: bioinformatics, phylogenetics
• Language: Ruby
• Homepage:
• Size: 23.4 KB
• Stars: 3
• Watchers: 2
• Forks: 1
• Open Issues: 6
• Metadata Files:
  • Readme: readme.md
  • License: LICENSE

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README

        
# Tree of Life

A simple app for querying taxonomies based on NCBI taxonomy database. Capable of

handling many queries per second and is much simpler to use than the NCBI API.

Provides a web microservice that returns taxonomic descriptions when queried by

name (such as "Tyrannosaurus") or NCBI taxonomy id.

Returns taxonomy in JSON format.

### Example

```

$ curl http://localhost:9999/taxonomy/Tyrannosaurus%20rex

{"taxonomy":"cellular

organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Coelomata;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Tetrapoda;Amniota;Sauropsida;Sauria;Archosauria;Dinosauria;Saurischia;Theropoda;Coelurosauria;Tyrannosauridae;Tyrannosaurus;Tyrannosaurus

rex"}

```

## Requirements

- Tested on Ruby 1.9.3 w/ bundler

- SQLite 3

## Getting Started

```bash

bundle # installs dependencies

rake db:migrate # creates database.sqlite

# download and extract names.dmp and nodes.dmp from

# ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

# update database

rake update_database

# start webserver on port 9999

rackup

```

## LICENSE

(c) 2012-2016 Austin G. Davis-Richardson 

MIT. See `LICENSE` for details.