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ACGT has a special application for Trial Management, called Ontology Based Trial Management for ACGT (in short OBTIMA). An overview of the application can be found here.

Please take a look at the ObTiMA's roles first in order to find out which of the following handbooks is closer to your needs. See registration and login sections to access the system.

• Handbook for ObTIMA Administrator
• Handbook for Trial Chairman
• Handbook for Clinicians

ACGT Knowledge Discovery/Data Mining Environment

The Data Mining Tools and additional resources are grouped and accessible in an integrated environment through the ACGT Portal.

• See ACGT Data Mining Overview first, for an overview of what ACGT has to offer bio-researchers and data mining researchers.
• See the Getting started and ACGT Passport sections to learn how to access the ACGT Environment.

Shortlist of main features:

• Importing data
• Storing data
• Retrieving data
• Browsing/registration of services
• Browsing/registration of data types
• Setting up workflows
• Analyzing data with R
• Working with the ACGT Ontology

The ACGT Programmer's Manual contains information for programmers (developers) who want to integrate new functionalities into the ACGT platform, in general any 3rd-party contributors. If you are only interested in using the ACGT platform, you can skip this section.

• Integrating R scripts
• Developing a new service
  • Web Service Wizard
• Developing a new Proxy Service
• ACGT Testbed Security Guide
• ACGT Bug Reporting - General Guidelines

This section covers examples of how to solve real-life problems in clinico-genomic research using the ACGT platform.

Scenarios using the ACGT environment

• ACGT End to End Scenario: From Trial Management to Data Mining Done
• Integrated demonstrators  Doing...

Real-life problem solving using the ACGT environment

• Multi-centric multi-platform data analysis Doing...

ACGT Tutorials

• ACGT Registration - The ACGT Knowledge Discovery/Data Mining Tools and additional resources are grouped and accessible in an integrated environment through the ACGT Portal. A single registration process described here is necessary to grant access to the ACGT environment. This tutorials shows the steps needed to get your ACGT Passport. Further information can be found here: HB:ACGT_Registration.
• ACGT Login - The ACGT Knowledge Discovery/Data Mining Tools and additional resources are grouped and accessible in an integrated environment through the ACGT Portal. This tutorials shows how to login using your ACGT Passport and how to create short-time Visas to login easier the next time or to login from other computers. Further information can be found here: HB:Logging_in_and_out.
• Querying clinical data - In the ACGT environment, data from different trials can be accessed "as if" it was stored in a single integrated repository. The ACGT Query Tool can be used to retrieve data from clinical registered trials by defining queries and testing them. You can register these queries in ACGT and use them to get clinical data in workflows.
• Register and access external databases - In addition to the databases that are connected statically and with a fixed ontology mapping, users of the ACGT environment can also connect SQL databases dynamically to the data mining tools. The Data Access area allows users to add new databases and to execute queries on previously added dynamic databases. These databases can then be used in more complex workflows as data pools.
• Register and use GridR services - You can add analytical components that use R programming language (R scripts) to ACGT in order to analyze data. This tutorial shows how to add GridR scripts as ACGT available services that can be used in workflows. The example in the tutorial can be used in workflows for the analysis of the association between a patient's treatment with a specific drug and tumor relapse.
• Create and use workflows - Workflows can be designed to use and reuse different data pools and knowledge discovery and analytical services for more complex research goals. In this example, a GridR service uses both clinical trial data (3 mediator queries created in the Query Tool) and data from an external database which is queried using SPARQL to plot the association between patient's treatment and tumor relapse.

• View the ACGT Master Ontology - The ACGT Ontology Viewer is a simple tool that allows you to browse or search the ACGT ontology and perform simple tasks on each concept in this ontology.

• Literature Mining Services (external) The literature mining services support discovery oriented searches of the scientific literature. Unlike PubMed where you specify a search term and get links to publications, these services allow you to explore correlations between concepts of interest. For example you may ask for the 10 most closely related genes to a particular disease or for the publication trends on any subject of interest.