Database techniques for storing biochemical data items

• US 20070112802A1
• Filed: 10/10/2006
• Published: 05/17/2007
• Est. Priority Date: 10/10/2005
• Status: Abandoned Application

• Current Assignee: Medicel OY
• Original Assignee: Medicel OY
• Inventors: Leppanen, Tero, Volanen, Jussi, Helttunen, Juha
• Application Number:
  US11/544,719
• Publication Number:
  US 20070112802A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/10 Ontologies; Annotations
• CPC Class Codes: G16B 50/20 Heterogeneous data integration
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: G16C 20/90 Programming languages; Computing architectures; Database systems; Data warehousing

Abstract

A database management system for storing a plurality of biochemical data items which originate from one or more external data sources. The database management system comprises a database which stores, for each biochemical data item, an objective identifier which comprises a set of attributes for characterizing measurable biochemical features of the biochemical data item; and a subjective identifier which comprises an identity value, an identity type value which has an association to the identity value and a reference to a data source, the reference being associated to the identity type value.

Claims

1. A database management system for storing a plurality of biochemical data items which originate from one or more external data sources, the database management system comprising a database operable to store, for each biochemical data item:

an objective identifier which comprises a set of attributes for characterizing measurable biochemical features of the biochemical data item; and

a subjective identifier which comprises;

an identity value;

an identity type value which has an association to the identity value; and

a reference to a data source, the reference being associated to the identity type value.

2. A database management system according to claim 1, further comprising an ETL logic for importing data items from at least one external data source into the database, wherein the ETL logic is operable to:

test if both the subjective identity and objective identity of the data item to be imported matches those of an existing data item;

use the data item to be imported for updating the existing data item if the result of the test is positive; and

to

insert the data item to be imported as a new record if the result of the test is negative.

3. A database management system according to claim 1, further comprising an ETL logic for importing data items from at least one external data source into the database, wherein the ETL logic is operable to:

test if either the subjective identity or objective identity of the data item to be imported matches those of an existing data item;

use the data item to be imported for updating the existing data item if the result of the test is positive; and

to

insert the data item to be imported as a new record if the result of the test is negative.

4. A database management system according to claim 1, further comprising a name generation function for ensuring unique constraints in cases wherein two or more external data sources use identical values.

5. A database management system according to claim 1, further comprising a namespace mapping function for mapping one or more identities from one namespace to another.

6. A database management system according to claim 1, further comprising a logic for identifying correspondence between entities originating from different data sources.

7. A database management system according to claim 1, further comprising a data version management logic, which comprises:

means for maintaining a plurality of projects and for logging in a user to a project in response to a successful login;

means for assigning one or more data sets to each of several projects such that data accessible to any project comprises one or more modifiable data sets assigned to the project in question and one or more tagged data sets assigned to other projects, wherein each tagged data set comprises a version number and is locked from modifications.

8. A database management system according to claim 7, wherein the data version management logic further comprises means for maintaining a one or more subprojects under at least one parent project and for assigning data generated by the one or more subprojects to the parent project.

9. A database management system according to claim 7, further comprising means for assigning a first table structure to modifiable data sets and a second table structure to tagged data sets.

10. A database management system according to claim 7, further comprising means for producing tagged data sets by streaming and for assigning a digital signature to a streamed data set.