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ntmirror

Local database mirroring NCBI taxonomy, kept up-to-date

https://github.com/ggonnella/ntmirror

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Local database mirroring NCBI taxonomy, kept up-to-date

Basic Info
  • Host: GitHub
  • Owner: ggonnella
  • License: other
  • Language: Python
  • Default Branch: main
  • Size: 35.2 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 4 years ago · Last pushed almost 4 years ago
Metadata Files
Readme Changelog License Citation Authors

README.md

NtMirror

NtMirror is a tool for creating and keeping up-to-date a local mirror of the NCBI Taxonomy database

Requirements

The software is distributed as a Python 3 package. The file requirements.txt lists the required pip modules (installable using pip -r requirements.txt).

A relational database management system (RDBMS) is required. NtMirror has been developed and tested using MariaDB as RDBMS. However, it can be probably used with any RDBMS supported by SqlAlchemy.

Optionally, on MariaDB, the database data loading is performed using the mysql library and not using SqlAlchemy, since the loading is faster.

Usage manual

For more information on the use of the software, see the user manual.

Owner

  • Name: Giorgio Gonnella
  • Login: ggonnella
  • Kind: user
  • Location: Goettingen, Germany
  • Company: Bioinformatics, University of Goettingen

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Gonnella"
  given-names: "Giorgio"
  orcid: "https://orcid.org/0000-0003-3900-5397"
title: "NtMirror: easily updatable local NCBI taxonomy database copy"
version: 1.0.0
date-released: 2022-04-22
url: "htts://github.com/ggonnella/ntmirror"

GitHub Events

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Last Year

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 35
  • Total Committers: 1
  • Avg Commits per committer: 35.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Giorgio Gonnella g****a@z****e 35
Committer Domains (Top 20 + Academic)
zbh.uni-hamburg.de: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Dependencies

setup.py pypi
  • loguru *
  • sqlalchemy *