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CIDMS

Cardiac Integrated Database Management System

CIDMS Information Content:

Currently CIDMS covers genes, proteins, their interactions and pathways/networks that have been reported in the scientific literature to be involved in number of molecular, genetic and epigenetic events happening in the heart because of mutations, gene alterations, physiological and drug/chemical treatments, protein modifications etc.


The list of genes, proteins and pathways that are exclusively associated with  heart as shown by microarray, SAGE, EST, 2D-Mass Spectrometry and other biophysical/biochemical analysis are covered extensively and manually categorized. Quantitative information interms of reaction kinetics and computational/ mathematical models describing the mechanism of cardiac process are made available annotated with the qualitative information collected for their participating gene, protein and pathway members.


Apart from the above mentioned annotations which are obtained by manual curation process, annotation information that is available in various public databases is integrated with it. A complete comprehensive integrated information content about cardiac genes/proteins including function, structure, location, orthologs, disease relations, SNPs and expression profiles, molecular interactions, pathways, valuable quantitative information such as reaction equations, stochiometry, kinetic laws and parameters  used in a biochemical networks and models are provided. This information can be accessed systematically using gene ontology terms or CIDMS curated cardiology relevant categories.

Key features of CIDMS


Discover biological relevant information necessary for cardiac systems biology research and explore contents with minimum efforts by navigating systematically structured information, using intuitive browsers and search interface.


Easily retrieve cardiac genes/proteins categorically using CIDMS taxonomy (via CIDMS Annotation Browser). CIDMS taxonomy is manually curated list of ontological terms relevant to cardiology studies. It covers structural and functional aspects of the heart and associated systems. It allows for an intuitive means for information retrieval in a systematic hierarchical fashion. This enables cardiac researchers with an easy way to access accurate integrated information from multiple sources.

Get comprehensive and up-to-the-minute information with the help of cutting edge information technology directly from the primary sources through web services and from frequently updated data warehouse.


Provides a single point of access to highly relevant qualitative and quantitative information   from wide range of information sources including manually curated data from journal articles, public databases and web sites.

Cardiac Integrated Database Management System (CIDMS)


Abundant amount of biological data is currently available. However these data is heterogeneous and distributed, which renders it impossible for easy search and retrieval of all the relevant information. CIDMS integrates the heterogeneous -omic data (available from multitude of sources and in various formats such as publication and associated supplementary files, databases and web pages) that are generated at different biological levels.

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The goal of CIDMS is to make heart-related disease and physiological data, easily available to the scientific community. An special attempt is made to integrate the quantitative and modeling data for those working on modeling and simulation of biological process / whole organ. We hope that this will help scientists in their research using systems approach.

Cardiac 

Systems 

Biolgy


The Heart is a complex organ with numerous molecular participants in a dynamic network having myriad interactions, resulting in regulation of normal and pathological cardio physiology.

Systems Biology being an integrative approach has been successful in systematic management of the underlying biological complexities of cardiac system. Cardiac systems biology promotes integration of different biological levels from the bottom gene level to the top organ level.


Recent advances in high-throughput technologies and computational analysis have resulted in abundant amount of biological data at each of the different biological levels. A need for new integrative tools to support integrative analysis has become an absolute necessity in systems biological research. Cardiac Integrated Database Management System (CIDMS) is an effort to cater to such needs.

Gene Ontology

is a structured, hierarchical framework that describes the roles of genes and their products across all species. It aims to unify biological data by providing a standardized vocabulary, which facilitates consistent annotations and data sharing among researchers.

Gene Vs rotein

Proteins are essential macromolecules that play a critical role in virtually every biological process. They are synthesized based on the instructions encoded in genes, which are segments of DNA. Here's an overview of the relationship between genes and proteins:

1. Gene-to-Protein Process (Gene Expression):

Gene expression involves two main stages:

  • Transcription: The DNA sequence of a gene is transcribed into messenger RNA (mRNA) in the nucleus.
  • Translation: The mRNA is then translated into a protein by ribosomes in the cytoplasm, using transfer RNA (tRNA) to assemble amino acids into a polypeptide chain.


2. Structure of Proteins:

Proteins are polymers of amino acids and are characterized by:

  • Primary Structure: The specific sequence of amino acids.
  • Secondary Structure: Local folding patterns, such as alpha-helices and beta-sheets.
  • Tertiary Structure: The three-dimensional shape of a single polypeptide.
  • Quaternary Structure: The arrangement of multiple polypeptide subunits in a functional protein complex.

3. Function of Proteins:

Proteins are highly versatile and perform various functions:

  • Enzymatic Catalysis: Speeding up biochemical reactions (e.g., DNA polymerase).
  • Structural Support: Providing cellular and organismal structure (e.g., collagen, keratin).


  • Transport: Moving molecules (e.g., hemoglobin transports oxygen).
  • Signal Transduction: Relaying signals within and between cells (e.g., insulin).
  • Defense: Forming immune responses (e.g., antibodies).


4. Gene-Protein Relationship:

  • A gene contains the blueprint for one or more proteins (depending on alternative splicing).
  • Mutations in a gene can alter the encoded protein, potentially leading to loss of function, gain of function, or disease.


5. Post-Translational Modifications (PTMs):

After synthesis, proteins can undergo PTMs, such as phosphorylation, glycosylation, or acetylation, which regulate their activity, localization, and stability.


6. Applications in Research and Medicine:

  • Understanding gene-protein relationships helps in disease diagnosis (e.g., identifying genetic mutations) and drug development (e.g., targeting specific proteins with inhibitors or antibodies).
  • Proteomics, the study of proteins at a large scale, complements genomics in understanding cellular processes.
  • For more in-depth information, you can explore resources like the National Center for Biotechnology Information (NCBI) or UniProt.

Cardiac Disease

Cardiac disease refers to a broad range of conditions that affect the heart's structure, function, or blood vessels. It is one of the leading causes of morbidity and mortality worldwide.

A. Coronary Artery Disease (CAD):
  • Caused by the buildup of plaque in the arteries (atherosclerosis).
  • Reduces blood flow to the heart, potentially leading to angina or myocardial infarction (heart attack).
B. Heart Rhythm Disorders (Arrhythmias):
  • Includes atrial fibrillation, tachycardia, bradycardia, or ventricular fibrillation.
  • May cause palpitations, dizziness, or sudden cardiac arrest.
C. Heart Valve Diseases:
  • Dysfunction in heart valves (stenosis, regurgitation, or prolapse).
  • Common conditions include aortic stenosis and mitral valve prolapse.
D. Cardiomyopathy:
  • Affects the heart muscle's ability to pump blood effectively.
  • Types include dilated, hypertrophic, and restrictive cardiomyopathy.
E. Congenital Heart Diseases:
  • Structural heart defects present from birth, such as septal defects or Tetralogy of Fallot.
F. Heart Failure:
  • The heart's inability to pump blood effectively to meet the body's needs.
  • Can result from CAD, hypertension, or cardiomyopathy.