Information management system for biochemical information

• US 20050010373A1
• Filed: 07/02/2004
• Published: 01/13/2005
• Est. Priority Date: 07/04/2003
• Status: Abandoned Application

• Current Assignee: Medicel OY
• Original Assignee: Medicel OY
• Inventors: Varpela, Pertteli, Kolmer, Meelis
• Application Number:
  US10/883,047
• Publication Number:
  US 20050010373A1
• Time in Patent Office: Days
• US Class Current: 702/20
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics

Abstract

An information management system [=“IMS”] for managing biochemical information (200). The IMS comprises structured descriptions of biochemical pathways (700) that are formed of at least pathways (212), biochemical entities (218), connections (216) and interactions (222), such that each pathway (212) relates to one or more connections (216); each connection (216) joins one biochemical entity (218) and one interaction (222); and each pathway (212) relates to a specific location (214). The IMS also comprises means (220) for receiving genetic information from one or more sequence data bases, wherein the genetic information associations of an identifier of a gene and a coding area of the gene and a logic for automatically creating biochemical pathways from the genetic information.

Claims

1. An information management system [=“

IMS”

] for managing biochemical information, the IMS comprising;

a server and a database;

means for receiving genetic information from one or more sequence data bases, wherein the genetic information associations of an identifier of a gene and a coding area of the gene; and

a logic for automatically creating biochemical pathways from said genetic information.

2. An IMS according to claim 1, further comprising structured descriptions of biochemical pathways that are formed of at least pathways, biochemical entities, connections and interactions, wherein:

each pathway has a relation to one or more connections;

each connection joins one biochemical entity and one interaction; and

each pathway has a relation to a specific location indication.

3. An IMS according to claim 1, wherein said genetic information comprises genes and products, and the logic is operable to determine intermediate steps between the genes and products.

4. An IMS according to claim 3, wherein the logic is operable to receive a description of a pair of a gene and a protein, and wherein the intermediate steps comprise:

a transcript as a biochemical entity;

transcription interaction from the gene to the transcript;

translation interaction from the transcript to the protein.

5. An IMS according to claim 3, wherein the logic is operable to check, based on one or more amino acid sequences, if a similar protein has already been stored in the database.

6. An IMS according to claim 1, further comprising means for offering the automatically created biochemical pathways for completion by a user.

7. An IMS according to claim 3, wherein each interaction relates to one or more kinetic laws.

8. An IMS according to claim 3, further comprising means for associating one of several predetermines roles to each connection, wherein the role indicates the role of the biochemical entity in the interaction and the several predetermines roles comprise substrate, product, activator and inhibitor.

9. An IMS according to claim 3, further comprising means for associating a stoichiometric coefficient to each connection, wherein the stoichiometric coefficient indicates the number of molecules of the biochemical entity consumed or produced in the interaction.

10. An IMS according to claim 1, further comprising a user interface logic for showing visualizations of said structured descriptions of biochemical pathways.

11. An IMS according to claim 10, wherein the user interface logic comprises means for showing visualizations of measured or perturbated variables localized on the biochemical entities, interactions and/or connections of biochemical pathways.

12. An IMS according to claim 1, further comprising pathway connections for combining several pathways to complex pathways.

13. An IMS according to claim 1, wherein the biochemical information comprises variable data sets, wherein each variable data set comprises:

a variable value matrix containing variable values organized as rows and columns;

a row description list, in a variable description language, of the rows in the variable value matrix;

a column description list, in a variable description language, of the columns in the variable value matrix;

a fixed dimension description, in a variable description language, of one or more fixed dimensions that are common to all values in the variable value matrix.

14. An IMS according to claim 13, wherein:

the variable description language comprises variable descriptions, each variable description comprising one or more pairs of keyword and name; and

the IMS comprises a table of permissible keywords.

15. An IMS according to claim 14, further comprising a logic for performing a syntax check on variables expressed in said variable description language.

16. An IMS according to claim 14, wherein the IMS comprises compound variable expressions, each compound variable expression comprising two or more variable expressions separated by operators and/or functions.

17. An IMS according to claim 1, further comprising a user interface logic for showing data traces between inter-related variable data sets.

18. A method for storing biochemical information in a database, the method comprising:

receiving genetic information from one or more sequence data bases, wherein the genetic information associations of an identifier of a gene and a coding area of the gene; and

automatically creating biochemical pathways from said genetic information.