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https://github.com/bioinformatics-ua/scaleus
Semantic Web Services Integration for Biomedical Applications
https://github.com/bioinformatics-ua/scaleus
biomedical-applications dataset integration-tool restfull-api semantic-web sparql
Last synced: about 2 months ago
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Semantic Web Services Integration for Biomedical Applications
- Host: GitHub
- URL: https://github.com/bioinformatics-ua/scaleus
- Owner: bioinformatics-ua
- License: mit
- Created: 2015-09-04T15:39:26.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2017-07-11T11:00:04.000Z (over 7 years ago)
- Last Synced: 2024-04-16T20:00:15.413Z (9 months ago)
- Topics: biomedical-applications, dataset, integration-tool, restfull-api, semantic-web, sparql
- Language: JavaScript
- Homepage: http://bioinformatics-ua.github.io/scaleus/
- Size: 2.41 MB
- Stars: 12
- Watchers: 12
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# SCALEUS
Semantic Web Services Integration for Biomedical Applications
Scaleus is a semantic web migration tool designed to be simple to deploy and use. The solution is tailored to help users in the creation of new semantic web applications from scratch. In a single package, we include a high-perfomance triplestore supporting multiple independent datasets, simplified API and services for data integration and management, and a SPARQL query engine, supporting real-time inference mechanisms and optimized text searches over the knowledge base.
[AngularJS](https://angularjs.org/) + [Jetty Embedded](http://www.eclipse.org/jetty/) (RESTfull API) + [Apache Jena Framework](https://jena.apache.org/)
### [Download](https://github.com/bioinformatics-ua/scaleus/releases)
## Main Features:
- Easy to deploy.
- Simple RESTfull API for data management.
- RDFS Inference support over SPARQL queries. Inference rules are also supported.
- Multiple datasets support.
- Spreedsheet import (.xlsx, .xls, .ods, etc.).
## Documentation
### Run
Simple run the application at [http://localhost/scaleus/](http://localhost/scaleus/):
```
java -jar target/scaleus-1.0-jar-with-dependencies.jar
```
Run in another port:
```
java -jar target/scaleus-1.0-SNAPSHOT-jar-with-dependencies.jar -p {port}
```
Run and import data:
```
java -jar target/scaleus-1.0-SNAPSHOT-jar-with-dependencies.jar -d {dataset_name} -i {file_location}
```
### REST API
**List all datasets available:**
```
GET /api/v1/dataset/ HTTP/1.1
Content-Type: application/json
```
**Add dataset:**
```
POST /api/v1/dataset/{dataset} HTTP/1.1
```
**Remove dataset:**
```
DELETE /api/v1/dataset/{dataset} HTTP/1.1
```
**SPARQL endpoint:**
```
GET /api/v1/sparqler/{dataset}/sparql?query={query}&inference={inference}&rules={rules}&format={format} HTTP/1.1
Content-Type: application/json
Sample parameters:
query = SELECT * { ?s ?p ?o } LIMIT 100
inference = true | false
rules = [rule1: (?x rdfs:subClassOf ?y), (?a rdf:type ?x) -> (?a rdf:type ?y)] [rule2: ... ]
format = json | rdf | ttl | rdf | text | csv
```
**Store triple:**
```
POST /api/v1/store/{dataset} HTTP/1.1
Content-Type: application/json
{
"s":"http://bioinformatics.ua.pt",
"p":"http://purl.org/dc/elements/1.1/title",
"o":"University of Aveiro"
}
```
**Remove triple:**
```
DELETE /api/v1/store/{dataset} HTTP/1.1
Content-Type: application/json
{
"s":"http://bioinformatics.ua.pt",
"p":"http://purl.org/dc/elements/1.1/title",
"o":"University of Aveiro"
}
```
**Add namespace:**
```
POST /api/v1/namespaces/{dataset} HTTP/1.1
Content-Type: application/json
{
"prefix": "coeus",
"namespace": "http://bioinformatics.ua.pt/coeus/"
}
```
**Remove namespace:**
```
DELETE /api/v1/namespaces/{dataset}/{prefix} HTTP/1.1
Content-Type: application/json
```
**Get namespaces:**
```
GET /api/v1/namespaces/{dataset} HTTP/1.1
Content-Type: application/json
```
**Get resources matching:**
```
GET /api/v1/resources/{dataset}/{match} HTTP/1.1
Content-Type: application/json
```
**Get properties matching:**
```
GET /api/v1/properties/{dataset}/{match} HTTP/1.1
Content-Type: application/json
```
**Get TTL data:**
```
GET /api/v1/data/{dataset} HTTP/1.1
Content-Type: text/plain
```
**Replace TTL data:**
```
POST /api/v1/data/{dataset} HTTP/1.1
Content-Type: application/x-www-form-urlencoded
@prefix coeus: .
@prefix dc: .
coeus:ieeta dc:title "University of Aveiro" .
```
**Describe Resource:**
```
GET /api/v1/resource/{dataset}/{prefix}/{resource}/{format} HTTP/1.1
Sample parameters:
format = json | rdf | ttl | ld
```
## Python API
[scaleus-python](https://github.com/bioinformatics-ua/scaleus-python)
## Reference
Please use this reference when citing SCALEUS in your work:
* DOI: [10.1007/s10916-017-0705-8](http://dx.doi.org/10.1007/s10916-017-0705-8)