openBIS

 

Downloads

For downloading the current servers (Application server and Datastore server) please click here.

The source code can be found in the CISD Source Code Repository.

Documentation can be found here

 

openBIS is an open, distributed system for managing biological information. The main goal is to support biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for the following technologies:

 

- High Content Screening

- Proteomics

- Deep Sequencing

- Metabolomics

 

Data from HCS, mass spectrometry or deep sequencing are uploaded using dropboxes (via the web interface, file system or remote server). The ETL process extracts metadata, creates datasets with metadata in the database and adds datasets to the data store. The user can access openBIS to organize, search and share data and metadata. Data can be exported to Excel. Bulk export is possible via the web interface or command line. Integration with data analysis pipelines is realized via APIs.

 

Click here to run an openBIS demo (7:28)

Click here to access all openBIS screen casts.

Benefits

1. It enables researchers to safely and securely store and retrieve their data through implementation of a high-end data storage management system and controlled data access featuring robust authentication.

2. It allows data sharing and reusability through implementation of data standards.

3. It allows browsing, querying and downloading of datasets as well as searching of datasets by annotation or ontology by using a sophisticated graphical user interface.

4. It enables researchers to get answers to questions requiring data type integration across different research domains through implementation of data marts anchored to conformed dimensions and semantic web applications.

5. It allows researchers to integrate their software of choice into openBIS, through implementation of a plug-in architecture.

6. It provides systems biology researchers with a clean interface to all kind of data comprehensible by data generators as well as data users, such as data modelers and bioinformatic data analysts.

 

openBIS Schema

The openBIS schema models entities and relations that are familiar to scientists. In particular, Groups (of users), Spaces (assemblies of data), Projects, Experiments, Samples and Datasets.

 

Flexible Annotation Service

openBIS provides a generic mechanism for establishing metadata models that are often specific to an experimental venture. openBIS achieves this by allowing users to define Types of Experiment, Sample and Dataset which are in turn defined by a set of Properties. A Property can be regarded as a field definition where the value is constrained to be a type such as an integer, real-number, a free-text field, date or Controlled-Vocabulary (CV, a simple ontology). In turn, CVs can also be developed within the openBIS system.

 

Filtering and Export of Results Tables

Searching for datasets can be done by providing any kind of keyword or by refining the search criteria based on specific filters, such as:
- Dataset Code/ or Type
- Experiment Code/ or Type
- Sample Code/ or Type
- File Type
- Group Code
- Project Code
- Any property type in openBIS assigned to Dataset

The obtained search result in turn can be exported into Excel.

 

Support of Distributed Storage

A variety of mechanisms are available for the robust transfer of small and large Data Sets. These include the usage of the CISD applications :

• CIFEX
• DataMover

Two server processes make up the openBIS system. The Data Store Server (DSS) is responsible for the validation, transformation, loading and retrieval of Data Sets to and from the Data Store (DS). The DS is implemented as a directory hierarchy on the computer file system. The openBIS application server is the other server process that provides a rich graphical interface for browsing, searching and reporting of Data Sets and metadata.