Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
○DOI references
-
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (11.3%) to scientific vocabulary
Last synced: 9 months ago
·
JSON representation
Repository
Sequence ALignment ONtology (OWL)
Basic Info
- Host: GitHub
- Owner: benhid
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://w3id.org/salon/
- Size: 154 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Created over 5 years ago
· Last pushed over 3 years ago
https://github.com/benhid/SALON/blob/master/
# SALON - [Sequence ALignment ONtology](https://github.com/benhid/SALON) [](https://zenodo.org/badge/latestdoi/317975049) [](https://w3id.org/salon/) ### Ontology [SALON.owl](SALON.owl) was developed using Protg 5.5.0 (beta 5 SNAPSHOT). You can directly load the ontology in Protg using the provided URI: > https://w3id.org/salon/ ### Client **Note**: Unlike Virtuoso, [Stardog](https://www.stardog.com/) 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: ```shell $ 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: ```shell $ git clone git@github.com:benhid/SALON.git $ cd salon $ python setup.py install ``` Then, run ```shell $ saloncli --help ``` #### Settings Setup environmental variables as follows (using your own connection settings): ```shell $ 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 ```shell $ saloncli init -i SALON.owl ``` Transform sequence alignment from MACSIM/XML to Turtle ```shell $ saloncli parse -i examples/BB11001.xml -o examples/BB11001.ttl ``` Populates RDF repository ```shell $ saloncli load -i examples/BB11001.ttl ``` Enriches protein sequence given its URI ```shell $ saloncli enrich -x https://w3id.org/salon#BB11001_1aab_ ``` Generates UniprotKB FASTA header/description line for protein sequence given its URI ```shell $ saloncli header -x https://w3id.org/salon#BB11001_1aab_ ``` ### Documentation Documentation was generated with pyLODE 2.8.3: ```shell $ make docs ```— —
Designed & built by Khaos Research (University of Mlaga).
Owner
- Name: Antonio
- Login: benhid
- Kind: user
- Location: Málaga, Spain
- Company: University of Málaga
- Website: https://benhid.com/
- Repositories: 24
- Profile: https://github.com/benhid
Software / DevOps Engineer and Researcher @KhaosResearch
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: about 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
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Dependencies
setup.py
pypi
- Biopython *
- SPARQLWrapper *
- click *
- rdflib *
- requests *