Merging OpenLifeData with SADI services using Galaxy and Docker
نویسنده
چکیده
Semantic Web technologies have been widely applied in Life Sciences, for example by data providers like OpenLifeData and Web Services frameworks like SADI. The recent OpenLifeData2SADI project offers access to the OpenLifeData data store through SADI services. This paper shows how to merge data from OpenLifeData with other extant SADI services in the Galaxy bioinformatics analysis platform, making semantic data amenable to complex analyses, as a worked example demonstrates. The whole setting is reproducible through a Docker image that includes a pre-configured Galaxy server with data and workflows that constitute the worked example.
منابع مشابه
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker
BACKGROUND Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. FINDINGS This article describes how to merge data retrieved from OpenLifeData2SADI with o...
متن کاملAutomatically exposing OpenLifeData via SADI semantic Web Services
BACKGROUND Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data acc...
متن کاملExecuting SADI services in Galaxy
BACKGROUND In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy,...
متن کاملEcotoxicology Data Federation with SADI Semantic Web Services
Biologists and biotechnologists need to draw information from numerous distributed and heterogeneous resources, such as online biomedical databases, nomenclatures and specialised bioinformatics tools. These tasks can benefit significantly from semantic data federation with SADI Semantic Web services where multiple resources exposed through SADI services are accessed as a single virtual SPARQL-q...
متن کاملSADI for GMOD: Semantic Web Services for Model Organism Databases
Here we describe work-in-progress on the SADI for GMOD project (SADI: Semantic Automated Discovery and Integration; GMOD: Generic Model Organism Database), a distribution of ready-made Web services that will bring additional model organism data onto the Semantic Web. SADI is a lightweight standard for implementing Web services that natively consume and generate RDF, while GMOD is a widely-used ...
متن کامل