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regulondb-datamarts

https://github.com/regulondbunam/regulondb-datamarts

Science Score: 44.0%

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
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    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: regulondbunam
  • License: other
  • Language: Python
  • Default Branch: master
  • Size: 4.18 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 11
Created over 5 years ago · Last pushed 10 months ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

RegulonDB Datamarts

Description

This software contains all needed to extract all data for RegulonDB Datamarts Collections. At this moment the collections that can be extracted are the next listed: - Gene - Regulon - Operon - Drawing Traces Tool (DTT) - Gene Coexpression - Sigmulon - SRNA - Regulatory Network

Motivation

With the reengineering of RegulonDB passing from relational model to an documental model that contains all data of collection named now as datamart, with this app can be possible to get data from RegulonDB Multigenomic model and build the datamarts for the GraphQL API Query Services.

System requirements

  • Python ^3.9.7
  • RegulonDB Multigenomic API Services
  • 8GB RAM
  • 50GB Space on Disk

Install

Clone this repo with git clone https://github.com/regulondbunam/RegulonDB-Datamarts

Quick start

First install RegulonDB Multigenomic API from its Repo in this link

Then you can use the following command to get all Datamarts Extraction files in JSON python3 __main__.py

The extraction might take a while, the results will be in lib/data

Project website

[NOT DEFINED]

License

Copyright 2023 RegulonDB

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Support contact information

[It should be clear where to go for support, for example a contact e-mail address]

Software quality checklist

Accessibility

  • [ ] Unique DOI identifier (Please update identifier and link)
  • [ ] Version control system

Documentation

  • [X] README file

Learnability

  • [X] Quick start

Buildability

  • [ ] INSTALL file

Identity

  • [ ] Website

Copyright & Licensing

  • [X] LICENSE file

Portability

  • [ ] Multiple platforms
  • [ ] Browsers

Supportability

  • [ ] E-mail address
  • [ ] Issue tracker
  • [ ] Slack
  • [ ] Gitter

Analysability

  • [ ] Source code structured
  • [ ] Sensible names
  • [ ] Coding standards - style guides

Changeability

  • [ ] CONTRIBUTING file
  • [ ] Code of Conduct file
  • [ ] Code changes, and their authorship, publicly visible

Reusability

  • [ ] Source code set up in a modular fashion

Security & Privacy

  • [ ] Passwords must never be stored in unhashed form

Owner

  • Name: regulondbunam
  • Login: regulondbunam
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.1.0
message: If you use this software, please cite it as below.
authors:
  - name: RegulonDB
    country: MX
    email: regulondb@ccg.unam.mx
    website: http://regulondb.ccg.unam.mx/
date-released: YYYY-MM-DD
doi: [example: 10.5281/zenodo.1003150]
identifiers: 
  - type: "other"
    value: "[example: mbiotools:RSAT_-_Retrieve_Sequence]"
license: [GPL-3.0-only | Apache-2.0 | MIT ]
repository-code: [URL example: https://github.com/regulondbunam/Components]
title: [example: Components]
url: [URL example: http://regulondbtools.ccg.unam.mx/Components]
version: X.X.X

GitHub Events

Total
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 1
  • Push event: 15
  • Pull request review event: 2
  • Pull request event: 7
  • Fork event: 1
  • Create event: 1
Last Year
  • Release event: 1
  • Delete event: 1
  • Issue comment event: 1
  • Push event: 15
  • Pull request review event: 2
  • Pull request event: 7
  • Fork event: 1
  • Create event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 7 minutes
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.33
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 7 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.33
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
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  • andresloal (5)
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enhancement (1)