System, method and apparatus for assembling and mining life science data

• US 7,865,534 B2
• Filed: 08/20/2003
• Issued: 01/04/2011
• Est. Priority Date: 09/30/2002
• Status: Expired due to Fees

• Current Assignee: Selventa, Inc.
• Original Assignee: Selventa, Inc.
• Inventors: Slater, Ted M., Sun, Justin, Chandra, D. Navin, Elliston, Keith O., Pratt, Dexter R., Neumann, Eric K.
• Primary Examiner(s): Pham; Khanh B
• Application Number:
  US10/644,582
• Publication Number:
  US 20050038608A1
• Time in Patent Office: 2,694 Days
• Field of Search: 707100-102, 707/798, 707/803, 707/805, 702 19- 20, 702/27, 706/45
• US Class Current: 707/805
• CPC Class Codes: G05B 19/00 Programme-control systems
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/20 Heterogeneous data integration
• CPC Class Codes: G16H 50/70 for mining of medical data, e.g. analysing previous cases of other patients

Abstract

Method and system for managing and evaluating life science data. Life Science data is placed in a knowledge base, that may be used for a variety of analysis tasks. Creating a knowledge base from the life science data involves generating two or more nodes indicative of life science data, assigning to one or more pairs of nodes a representation descriptor that corresponds to a relationship between the nodes, and assembling the nodes and the relationship descriptor into a database, such that at least one of the nodes is joined to another node by a representation descriptor. In some embodiments, the representation descriptor includes a case frame that describes the relationships between elements of life science data.

Claims

1. A computer system for storing life science information in a database, the computer system comprising:

a processor;

an electronic database storage module for storing in the database a library of machine-readable symbolic representations into which life science knowledge is adapted to be encoded according to a life sciences ontology, each machine-readable symbolic representation comprising;

at least two unspecified object identifiers;

a relationship connector, wherein the relationship connector relates two of the at least two object identifiers to each other based on a casual relationship between the object identifiers; and

constraint information that defines which connections among the object identifiers are permitted so that life sciences knowledge encoded into the machine-readable symbolic representation is semantically rigorous and based on the life sciences ontology; and

a graphical user interface for managing addition of new life sciences data to a database, the graphical user interface comprising;

a display screen that receives an input selecting one of the machine-readable symbolic representations as a template to represent the new data based at least in part on the life science ontology;

the graphical user interface restricting input of any data element that does not conform to the constraint information associated with the selected machine-readable symbolic representation such that the semantically rigorous relationships for the life sciences ontology are maintained;

the graphical user interface receiving input of at least one data element that conforms to the constraint information to instantiate the machine-readable symbolic representation.

2. The computer system of claim 1, wherein a set of machine-readable symbolic representations define one of:

a biological function, and a chemical reaction.

3. The data processing computer system of claim 2, wherein the biological function comprises one of:

transport, and digestion of a biomolecule.

4. The computer system of claim 1, wherein at least one of the at least two object identifiers identifies one of:

a biomolecule, and a biological function.

5. The computer system of claim 1, wherein at least one of the at least two object identifiers identifies a relationship connector.

6. The computer system of claim 1, wherein at least one of the at least two object identifiers identifies an identity relationship.

7. The computer system of claim 1, wherein the relationship connector represents one of:

a product relationship, a substrate relationship, and an enzymatic relationship.

8. The computer system of claim 1 wherein the graphical user interface permits a user to query the database based on the relationship connector.

9. The computer system of claim 1 further comprising an access manager configured to restrict access to one or more portions of the electronic database.

10. The computer system of claim 1 further comprising an inference engine executed by the processor.

11. The computer system of claim 10 wherein the inference engine provides modifications to at least one machine-readable symbolic representation, wherein the modifications comprise one or more of the addition of new fields, the addition of new relationships, and the addition of metadata.

12. The computer system of claim 10 wherein the metadata comprises one or more sources of the new data, a date the new data was received, a time the new data was received, and one or more experimental conditions under which the new data was created.

13. The computer system of claim 1 further comprising a harmonization and transfer module executed by the processor to interface with multiple disparate sources of life science data.

14. The computer system of claim 13 wherein the harmonization and transfer module further translates given data into a data format compatible with at least one machine-readable symbolic representation.

15. The computer system of claim 1 wherein the graphical user interface displays pathways among the plurality of machine-readable symbolic representations, the pathways representing causal relationships among the machine-readable symbolic representations.

16. The computer system of claim 1 further comprising a managed account interface executed by the processor to attribute access restrictions to one or more machine-readable symbolic representations in the database, the access restrictions comprising one of:

public access rights, subscription-based access rights, and proprietary access rights.

17. The computer system as described in claim 1 wherein the database comprises machine-readable symbolic representations representing enzyme reactions, binding interactions, modifications of polymers, protein phosphorylation reactions, gene expressions, acetylation, peptide-bond cleavage, glycosylayion, lipidation, fatty-acylation, methylation, metallation, cross-linking, hydroxylation, sulfation, ADP-ribosylation, translocation and transcriptional activations.

18. The computer system of claim 1 wherein at least one machine-readable symbolic representation represents a protein phosphorylation reaction comprising a reactant, a product, and a catalyst.

19. The computer system of claim 1 wherein at least one machine-readable symbolic representation represents a gene expression comprising a gene and a gene product.

20. The computer system of claim 1 wherein at least one machine-readable symbolic representation represents a transcriptional activation comprising a gene expression, an activation, and a transcriptional activator.

21. The computer system as described in claim 1 wherein a machine-readable symbolic representation is XML or pseudocode.

22. The computer system as described in claim 1 wherein at least first and second machine-readable symbolic representations in the database comprise a knowledge base of semantically-rigorous life sciences representations against which one of more reasoning algorithms are applied.

23. The computer system as described in claim 22 wherein applying a reasoning algorithm generates one or more pathways associated with a query to the knowledge base.

24. The computer system as described in claim 23 wherein the one or more pathways are displayed in the graphical user interface.

25. The computer system as described in claim 1 wherein the graphical user interface receives attribution information identifying a source of the new life sciences data.