{"id":20382754,"url":"https://github.com/bioinformatics-ua/scaleus","last_synced_at":"2025-04-12T08:54:16.639Z","repository":{"id":75794925,"uuid":"41923849","full_name":"bioinformatics-ua/scaleus","owner":"bioinformatics-ua","description":"Semantic Web Services Integration for Biomedical Applications ","archived":false,"fork":false,"pushed_at":"2017-07-11T11:00:04.000Z","size":2527,"stargazers_count":12,"open_issues_count":1,"forks_count":3,"subscribers_count":11,"default_branch":"master","last_synced_at":"2025-04-12T08:54:11.330Z","etag":null,"topics":["biomedical-applications","dataset","integration-tool","restfull-api","semantic-web","sparql"],"latest_commit_sha":null,"homepage":"http://bioinformatics-ua.github.io/scaleus/","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bioinformatics-ua.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-09-04T15:39:26.000Z","updated_at":"2023-11-27T20:54:11.000Z","dependencies_parsed_at":"2023-04-19T03:37:56.745Z","dependency_job_id":null,"html_url":"https://github.com/bioinformatics-ua/scaleus","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioinformatics-ua%2Fscaleus","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioinformatics-ua%2Fscaleus/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioinformatics-ua%2Fscaleus/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bioinformatics-ua%2Fscaleus/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bioinformatics-ua","download_url":"https://codeload.github.com/bioinformatics-ua/scaleus/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248543883,"owners_count":21121838,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["biomedical-applications","dataset","integration-tool","restfull-api","semantic-web","sparql"],"created_at":"2024-11-15T02:18:55.152Z","updated_at":"2025-04-12T08:54:16.622Z","avatar_url":"https://github.com/bioinformatics-ua.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SCALEUS\nSemantic Web Services Integration for Biomedical Applications\n\n![Dashboard](https://cloud.githubusercontent.com/assets/1446805/16911369/ff81f588-4cd5-11e6-9f35-ab60be43111a.png)\n\nScaleus 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.\n\n![Sparql](https://cloud.githubusercontent.com/assets/1446805/16911377/0ddccf68-4cd6-11e6-949d-01d135b47443.png)\n\n[AngularJS](https://angularjs.org/) + [Jetty Embedded](http://www.eclipse.org/jetty/) (RESTfull API) + [Apache Jena Framework](https://jena.apache.org/)\n\n### [Download](https://github.com/bioinformatics-ua/scaleus/releases)\n\n## Main Features:\n\n- Easy to deploy.\n- Simple RESTfull API for data management.\n- RDFS Inference support over SPARQL queries. Inference rules are also supported.\n- Multiple datasets support.\n- Spreedsheet import (.xlsx, .xls, .ods, etc.).\n\n## Documentation\n\n### Run \n\nSimple run the application at [http://localhost/scaleus/](http://localhost/scaleus/):\n```\njava -jar target/scaleus-1.0-jar-with-dependencies.jar\n```\n\nRun in another port:\n```\njava -jar target/scaleus-1.0-SNAPSHOT-jar-with-dependencies.jar -p {port}\n```\n\nRun and import data:\n```\njava -jar target/scaleus-1.0-SNAPSHOT-jar-with-dependencies.jar -d {dataset_name} -i {file_location}\n```\n\n### REST API\n\n**List all datasets available:**\n\n```\nGET /api/v1/dataset/ HTTP/1.1\nContent-Type: application/json\n```\n\n**Add dataset:**\n\n```\nPOST /api/v1/dataset/{dataset} HTTP/1.1\n```\n\n**Remove dataset:**\n\n```\nDELETE /api/v1/dataset/{dataset} HTTP/1.1\n```\n\n**SPARQL endpoint:**\n\n```\nGET /api/v1/sparqler/{dataset}/sparql?query={query}\u0026inference={inference}\u0026rules={rules}\u0026format={format} HTTP/1.1\nContent-Type: application/json\n\nSample parameters:\n\nquery = SELECT * { ?s ?p ?o } LIMIT 100\ninference = true | false\nrules = [rule1:  (?x rdfs:subClassOf ?y), (?a rdf:type ?x) -\u003e (?a rdf:type ?y)] [rule2: ... ]\nformat = json | rdf | ttl | rdf | text | csv\n\n```\n\n**Store triple:**\n\n```\nPOST /api/v1/store/{dataset} HTTP/1.1\nContent-Type: application/json\n\n{\n\t\"s\":\"http://bioinformatics.ua.pt\",\n\t\"p\":\"http://purl.org/dc/elements/1.1/title\",\n\t\"o\":\"University of Aveiro\"\n}\n```\n\n**Remove triple:**\n\n```\nDELETE /api/v1/store/{dataset} HTTP/1.1\nContent-Type: application/json\n\n{\n\t\"s\":\"http://bioinformatics.ua.pt\",\n\t\"p\":\"http://purl.org/dc/elements/1.1/title\",\n\t\"o\":\"University of Aveiro\"\n}\n```\n\n**Add namespace:**\n\n```\n\nPOST /api/v1/namespaces/{dataset} HTTP/1.1\nContent-Type: application/json\n\n{\n  \"prefix\": \"coeus\",\n  \"namespace\": \"http://bioinformatics.ua.pt/coeus/\"\n}\n```\n\n**Remove namespace:**\n\n```\n\nDELETE /api/v1/namespaces/{dataset}/{prefix} HTTP/1.1\nContent-Type: application/json\n\n```\n\n**Get namespaces:**\n\n```\nGET /api/v1/namespaces/{dataset} HTTP/1.1\nContent-Type: application/json\n```\n\n**Get resources matching:**\n\n```\nGET /api/v1/resources/{dataset}/{match} HTTP/1.1\nContent-Type: application/json\n```\n\n**Get properties matching:**\n\n```\nGET /api/v1/properties/{dataset}/{match} HTTP/1.1\nContent-Type: application/json\n```\n\n**Get TTL data:**\n\n```\nGET /api/v1/data/{dataset} HTTP/1.1\nContent-Type: text/plain\n```\n\n**Replace TTL data:**\n\n```\nPOST /api/v1/data/{dataset} HTTP/1.1\nContent-Type: application/x-www-form-urlencoded\n\n@prefix coeus: \u003chttp://bioinformatics.ua.pt/coeus/\u003e .\n@prefix dc:    \u003chttp://purl.org/dc/elements/1.1/\u003e .\n\ncoeus:ieeta dc:title \"University of Aveiro\" .\n```\n\n**Describe Resource:**\n\n```\nGET /api/v1/resource/{dataset}/{prefix}/{resource}/{format} HTTP/1.1\n\nSample parameters:\n\nformat = json | rdf | ttl | ld \n```\n\n## Python API\n\n[scaleus-python](https://github.com/bioinformatics-ua/scaleus-python)\n\n## Reference\n\nPlease use this reference when citing SCALEUS in your work:\n\n* DOI: [10.1007/s10916-017-0705-8](http://dx.doi.org/10.1007/s10916-017-0705-8)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioinformatics-ua%2Fscaleus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioinformatics-ua%2Fscaleus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioinformatics-ua%2Fscaleus/lists"}