Information Technology Projects Course

Professor Arthur Goldberg
Computer Science Department
NYU
Fall 2004
Project Proposal

First Genetic Trust

Company Description

As their web site states, this summarizes First Genetic Trust:

Genetic and genomic research is increasing the understanding of diseases and their treatments. As a consequence of this knowledge, medical science will produce new diagnostic techniques and safer, more effective medicines.
First Genetic Trust
is making possible the rapid development and deployment of diagnostics and therapeutics by providing highly secure and reliable genetic banking services. Our web-based enTRUST ® genetic bank system enables pharmaceutical and biotechnology companies, medical research centers, and government-sponsored research programs to efficiently collect, manage, and analyze genetic and medical data. For patients, First Genetic Trust promises a protected environment in which to maintain their privacy and the confidentiality of their genetic information while participating in genetic research.

Proposal: Tools For Building On-Line Medical Questionnaires

To achieve their goals First Genetic Trust (FGT) needs to computerize patient medical histories.  To be compatible with their suppliers and clients FGT must encode medical information in the standards employed by the rest of the world.  This effort is made more challenging by both the huge scope of medical information, and the overlapping--and sometimes conflicting or contentious--body of standardized medical classifications.

FGT helps its clients build computerized medical questionnaires--i.e., on-line case history forms.  The goal of this project is to streamline the process for building these forms while promoting the use of data standards for representing medical data.

The Clinical Data Interchange Standards Consortium (CDISC) (at http://www.cdisc.org/) is "a ... non-profit organization committed to the development of industry standards to support the electronic acquisition, exchange, submission and archiving of clinical trials data and metadata for medical and biopharmaceutical product development".  One of their standards is the Operational Data Model (ODM) which facilitates the exchange of data collected in medical questionnaires.  FGT uses the ODM to model online medical data collection forms. The building component of such forms is the Item, defined in Section 4. This element roughly corresponds to a single question. Questions are reusable across forms. As such, it is desirable to organize them centrally within a DBMS. Appropriate APIs can make the questions accessible to software tools for form-design. To ensure consistency across forms, modifications of questions within the DBMS need to be managed by version control software and processes. FGT has developed a first generation of tools for form-design and question management.

The National Cancer Institute (NCI) is the US government's leading center for cancer prevention and treatment research.  The NCI's Center for Bioinformatics (NCICB) "provides biomedical informatics support and integration capabilities to the cancer research community".  NCICB has a core infrastructure group, whose "main product is caCORE, the cancer Common Ontological Reference Environment. caCORE provides the open-source foundation upon which the NCI builds its research information management systems".  A key component of caCORE is caDSR, the cancer Data Standards Repository.  caDSR provides an implementation of an international standard (ISO/IEC 11179) developed to rationalize the definition and management of Common Data Elements (CDEs). At a very elementary level, CDEs can be thought of as a formally and semantically consistent way to represent questions that appear in online forms. caDSR provides a controlled software environment to manage CDEs.

The goal of this project is to integrate caDSR into the existing form-building tools used by FGT and to improve their overall functionality.  This project will have several deliverables:

The system will be implemented in Java and must be compliant with J2EE standards.

Students will need to sign an NDA to participate in this project.  Students that work for a FGT competitor are not eligible to participate.

Intern Address

First Genetic Trust, Inc.
201 Route 17 North, 9th Floor
Rutherford, NJ 07070

Public transportation:

Bus (all from Port Authority terminal)

Train

Authorizing manager

Aris Floratos, PhD, VP Bioinformatics & Computational Biology, (201)-842-0011 x10426, afloratos@firstgenetic.net

Project managers

Brian Cass, VP IT, (847)-317-9461, bcass@firstgenetic.net and
Aris

Meeting hours

TBD, per project needs.
They can arrange for meetings outside regular business hours.

Resources that will be made available to students


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