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LinkAtlas - links between strains and taxonomy#

release: 0.1.0 MIT LICENSE Documentation Status

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A collection of libraries for gathering possible links between strains and taxonomy from different sources like literature and sequence databases.

Installation - Development#

Prerequisites#

  • GNU/Linux
  • Docker (optional)
  • Docker Compose (optional)
  • Dev Container CLI (optional)

Steps#

  1. Clone the repository: 
    git clone https://github.com/LeibnizDSMZ/cafi.git
cd cafi

Docker#

  1. If using Docker, start the development container manually or use VSCode: 

    devcontainer up --workspace-folder .
devcontainer exec --workspace-folder . bash

  2. Create and activate a virtual environment (inside docker the container): 

    make dev
make runAct

Contributors#

  • Isabel Schober

BDLINK - strains in BacDive#

Search BacDive and create a database for all detected culture collection numbers.

CATLINK - strains in catalogs#

Search catalog websites and create a database for all detected culture collection numbers.

PUBLINK - strains in literature#

Search publications and create a database for all detected culture collection numbers.

SEQLINK - strains in sequences#

Search sequence providers and create a database for all detected culture collection numbers.

SILINK - strains in StrainInfo#

Search StrainInfo and create a database for all detected culture collection numbers.

TAXALINK - strains in taxonomy#

Search taxonomy data and create a database for all detected culture collection numbers flagged as type strains.

UTILSLINK - shared library#

A shared library for linkatlas packages.