printlogo
http://www.ethz.ch/index_EN
Welcome to the Center for Information Sciences and Databases
 
print
  

openBIS

 

openBIS_Logo_white_bg

The openBIS web page moved to the SIS web site. This page is only kept for reference.

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

 

openBIS Architecture
openBIS Architecture

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.

Relationship between openBIS Entities
Relationship between openBIS Entities

 

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.

openBIS Meta Data Model using Types and Properties
openBIS Meta Data Model using Types and Properties

 

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.

openBIS Filtering and Export of Results
openBIS Filtering and Export of Results

 

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.

openBIS Distributed Storage
openBIS Distributed Storage

 

 

Wichtiger Hinweis:
Diese Website wird in älteren Versionen von Netscape ohne graphische Elemente dargestellt. Die Funktionalität der Website ist aber trotzdem gewährleistet. Wenn Sie diese Website regelmässig benutzen, empfehlen wir Ihnen, auf Ihrem Computer einen aktuellen Browser zu installieren. Weitere Informationen finden Sie auf
folgender Seite.

Important Note:
The content in this site is accessible to any browser or Internet device, however, some graphics will display correctly only in the newer versions of Netscape. To get the most out of our site we suggest you upgrade to a newer browser.
More information

© 2016 ETH Zurich | Imprint | 18 January 2016
top