SALON - Sequence ALignment ONtology

✨ Ontology

SALON.owl was developed using Protégé 5.5.0 (beta 5 SNAPSHOT).

You can directly load the ontology in Protégé using the provided URI:

https://w3id.org/salon/

🧰 Client

Note: Unlike Virtuoso, Stardog supports SWRL rules (which this ontology makes use of). Therefore, this tool requires a running Stardog server instance to unlock all features, albeit Virtuoso or any other triple store can be used. You can deploy Stardog on Docker with:

$ docker run -it -v ~/your/license/folder/:/var/opt/stardog -p 5820:5820 stardog/stardog

Installation

To download and install the SALON companion client just clone the Git repository hosted in GitHub:

$ git clone git@github.com:benhid/SALON.git
$ cd salon
$ python setup.py install

Then, run

$ saloncli --help

Settings

Setup environmental variables as follows (using your own connection settings):

$ export STARDOG_ENDPOINT=http://localhost:5820
$ export STARDOG_USERNAME=admin 
$ export STARDOG_PASSWORD=admin 
$ export STARDOG_DATABASE=salon

Alternatively, create a dotenv file in the current directory and append the former variables.

Usage

Creates database in RDF repository

$ saloncli init -i SALON.owl

Transform sequence alignment from MACSIM/XML to Turtle

$ saloncli parse -i examples/BB11001.xml -o examples/BB11001.ttl

Populates RDF repository

$ saloncli load -i examples/BB11001.ttl

Enriches protein sequence given its URI

$ saloncli enrich -x https://w3id.org/salon#BB11001_1aab_

Generates UniprotKB FASTA header/description line for protein sequence given its URI

$ saloncli header -x https://w3id.org/salon#BB11001_1aab_

📖 Documentation

Documentation was generated with pyLODE 2.8.3:

$ make docs

— ⭐️ —

Designed & built by Khaos Research (University of Málaga).

benhid / SALON