IBD Integrated Database 

About us

The central goal of the Inflammatory Bowel Disease (IBD) Integrated Database is to advance IBD research at Mount Sinai by providing a secure platform for researchers to manage and share the complexity of study data. This goal is achieved through combining databases from many research projects at Mount Sinai, especially those containing patients affected by IBD. The integrated database provides effective sharing by adhering to each study’s consent permissions and standardizing language between studies. Integration of data from multiple projects allows for increased efficiencies in collaboration and research outcomes.

The contents collected for data include the following:

  1. EHR: structured database from the Mount Sinai Data Warehouse (MSDW) data mart
  2. Questionnaires: patient self-reported study specific questions
  3. Samples: types of samples collected from participants of the study include saliva, blood, serum and stool tissue
  4. Genetic assays: genotypes

Database Management

There are multiple studies and initiatives involved in the database. They include:

  1. RTP

A Mount Sinai IBD Initiative that encompasses multiple projects that individually and synergistically explore the concept of life before IBD. The goal of this study is to determine important events happening to the gastrointestinal tract before IBD is diagnosed. The program explores a better understanding for why relatives of patients with IBD are at higher risk for developing IBD.IBD Research more information

  1. Meconium

The Meconium study looks at the bacterial profiles of pregnant women with and without Inflammatory Bowel Disease (IBD) and their newborn babies. Genetic make-up, disease activity throughout pregnancy, medications and the clinical features on the bacterial composition of the baby are observed. In addition, breastfeeding versus formula and the associated behavior and antibiotic use and the potential modification of the microbiome from the usage are also explored. Meconium Study more information

  1. General Genetics

General Genetics encompasses multiple projects. One of them being the Cho Lab’s gastrointestinal genetics research. The Cho Lab studies the genetic and immunologic factors associated with Crohn’s Disease and Ulcerative Colitis, specifically to investigate the prevalence of IBD in the Ashkenazi Jewish population. This lab also studies the relationship between environmental factors and IBD by how human beings interact with our gut microbes in terms of susceptibility and pathogenesis. Cho Lab more information

  1. MSCCR

The goal of The Mount Sinai Crohn’s and Colitis Registry (MSCCR) is to create a database for clinical information and archive for samples for genetic, molecular and microbiological research to better understand IBD and develop new therapies. MSCCR more information

  1. BioMe

BioMe is an electronic medical record-linked biobank that allows researchers to conduct studies more efficiently due to the large collection of research specimens linked with medical information. It is non-selective in gender, race, ethnicity, age, medical condition or disease status. By doing so the database offers a wide variety for biomedical and genetic research.BioMe more information

Do not alter templates. The templates provided must be used. The templates can be used as a skeleton or foundation to build a study from but do not edit fields because they easily and automatically upload into our system to a certain configuration. We know that information changes over time therefore if options need to be altered, please contact Nicole Villaverde.

Nicole Villaverde

Data Collection

REDCap is a web supplication to facilitate building and managing online surveys and databases for research studies.

REDCap is used for Mount Sinai’s IBD research data collection. REDCap is a great tool to utilize because it is easy to understand with videos to show the user how to generate a survey or questionnaire along with all of the features of doing so. There are quick tasks where the user is able to create a questionnaire through the online designer. There it is also possible to look through the codebook in which different questions and answers within a survey are labeled with a code. Through the creation of a database where different studies are being inputted and integrated into one common language, this tool makes it easier to see what the fields are labeled and it makes it easier to compare studies with each other. There is a record status dashboard feature as well which shows how many participants there are in the study and how much of the study they have filled out.REDCap more information


The template for the IBD Integrative Database includes a Registration form, Consent, General Information, Medication, UC Baseline, and CD Baseline forms. It is important to use these for the data to be integrated with the rest of the studies. The questions from all of the studies and initiatives aforementioned have been analyzed to coincide with these templates for the database. It was necessary to find a common language throughout all of the studies so the database could have a unified language. The templates were reviewed and edited by physicians regarding what was most important to include content wise.

The registration form contains information regarding the participants contact information. The consent form looks for information about the capacities at which the specimen can and will be utilized. The general information form contains information about participant’s diagnosis of IBD and Jewish ancestry. The medication form explores which medications the participant has used previously or currently for IBD. UC and CD Baseline are specific to participant’s diagnosis and ask questions about the condition.


There is specific wording to be included in the protocol and in consents for studies.

Patient Health Information (PHI) and diagnosis related data is shared with the IBD integrated database. PHI, such as subject’s name, date of birth, and contact information, is used by the honest broker to assign unique identifiers in the integrated system. The mapping between PHI and ID number is stored separately from any data (phenotypic or genotypic) received. Data is stored on a password protected, secure server. Only de-identified or anonymized data is shared with research staff.

This is sharing language between the investigators in MSSM, the data and the specimen or sample. For the consent form, sentences that state that their specimen and info will be de-identified and shared with collaborators is important to specify. Also, that it can be used for future studies, related studies and for other unrelated studies.

This type of information is found under sections in the 503 protocol, part 5 – Study Design, subsection H – Data Management and Confidentiality

Descriptions and information about different projects, studies, or research tools and programs were taken and modified from the study’s website, lab’s website or research tool or program’s website.