BIDD TRMP Database

Category Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract The Therapeutically Relevant Multiple Pathways Database (TRMP) provides information about inter-related multiple pathways of a number of diseases and physiological processes.

This database provides information about known therapeutic targets within each network of multiple pathways, the corresponding drugs/ligands directed at each of these targets, the constituent individual pathways, and information about the proteins involved in these pathways.

Cross-links to other databases are introduced to facilitate the access of information about the constituent individual pathways and the function, sequence, nomenclature and related literature of each protein in the pathways.

The entries in this database are generated by using the information collected from a comprehensive search of related publications in MEDLINE (Wheeler et al., 2003).

The combination of three (3) keywords (disease name, target name and pathway) is used in searching the relevant publications.

The relevant information is derived primarily from review articles and pharmacology textbooks. Primary papers are also used for clarification purposes.

The extracted information is independently double checked against the referenced papers by different personnel. All the references used for generating the pathways are provided in the database.

Human data is used for human pathways and proteins. Likewise, the corresponding species data is used for bacterial or viral pathways and proteins.

TRMP is updated every six (6) months.

The manufacturer’s approach of linking human proteins to the human pathway constituents, with the exception of the viral- and bacterial- specific ones, is critically based on the assumption that all shown pathways happen in humans although this may Not have been experimentally verified.

The pathway model(s) in the review articles and textbooks are often based on the results of a patchwork of experimental systems involving genes and proteins of a different species origin.

Thus, caution is needed in interpreting the ‘molecular interactions’ and pathway constituents in TRMP.

Efforts are being made to promptly update newly reported results to the TRMP database.

The TRMP database currently contains 11 entries of multiple pathways that include 97 distinct individual pathways and 120 therapeutic targets covering 72 different disease conditions.

A total of 32 of the 97 distinct individual pathways are included in other pathway databases.

Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name.

Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable.

Cross-links to other databases are provided which include GeneCards (see G6G Abstract Number 20170), GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein.

The interactive maps of each pathway entry of TRMP are constructed by using Adobe Flash (previously called "Macromedia Flash").

The corresponding database architect associated with the pathway interactive maps was developed by using Active Server Pages (ASPs) with Oracle 9i support.

The database has three (3) layers. The top layer is the main graphical user interface with a querying tool for finding specific entries of multiple pathways.

The second layer is the graphical interface for the interactive maps of multiple pathways with a browser tool for retrieving additional information.

The browser tool can be used both for accessing information about the constituent individual pathways from other databases and for retrieving information about individual targets or non-target proteins and can also direct a retrieving request from TRMP.

The third layer is the graphic interface for entries of individual targets or non-target proteins with a browser tool for accessing additional information from other databases.

The database is searchable by selecting the name of a particular entry of multiple pathways.

It can also be accessed by the selection of the name of a disease or an individual pathway from the list provided in the corresponding selection field.

Searches involving any combination of these three (3) search or selection fields are also supported.

System Requirements

Contact manufacturer.


Manufacturer Web Site BIDD TRMP Database

Price Contact manufacturer.

G6G Abstract Number 20270

G6G Manufacturer Number 101832