System, method and program product for management of life sciences data and related research

• US 20050149566A1
• Filed: 10/25/2004
• Published: 07/07/2005
• Est. Priority Date: 10/31/2003
• Status: Abandoned Application

• Current Assignee: International Business Machines Corporation
• Original Assignee: International Business Machines Corporation
• Inventors: Ewig, Carl Stephen, Baek, Ock Kee
• Application Number:
  US10/973,959
• Publication Number:
  US 20050149566A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: G06Q 10/06313 Resource planning in a project environment
• CPC Class Codes: G06Q 10/10 Office automation; Time management
• 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: G16B 50/30 Data warehousing; Computing architectures
• CPC Class Codes: G16B 50/40 Encryption of genetic data

Abstract

System, method and program product for managing data for researchers. A research data server receives and manages experimental data and research data and results from the researchers, and operates with a virtual storage device to maintain the experimental data and research data and results. A reference data access server receives and manages external reference data relating to the research and operating with the virtual storage device to maintain the external reference data. Computational resources allow researchers to capture, process and analyze experimental data to obtain results. A research data network connects the virtual storage device, research data server, reference data access server and the computational resources to allow transfer of data there between. Security management services authenticate and authorize access by the researchers to the system.

Claims

1. A system for managing data for researchers, said system comprising:

means for automatically receiving research data from laboratory instruments;

means for accessing a database containing established reference data;

means for automatically obtaining recently available reference data;

means for accessing a database containing experimental data;

a plurality of applications to process respective types of said data;

means, responsive to a request by a researcher to perform a data processing function, for invoking one or more of said processing applications and supplying to said one or more processing applications parameters to perform said data processing function; and

means, responsive to the invoking and supply of parameters, for said one or more processing applications to automatically access types of said data required to perform the respective data processing function.

2. A system as set forth in claim 1 wherein said invoking and supplying means determines which of said processing applications to invoke and which parameters to supply to said processing applications to be invoked, based on a type of function requested by said researcher.

3. A system as set forth in claim 1 wherein said invoking and supplying means determines identities of files containing said data required by said one or more applications, based on a type of function requested by said researcher.

4. A system as set forth in claim 1 further comprising an application to analyze patterns in respective types of said data, and wherein one of said one or more processing applications receives from the pattern analyzing application a pattern used to perform the requested data processing function.

5. A system as set forth in claim 1 further comprising means for determining if available data is valid, and

if not, not using said available data for said one or more processing applications;

if so, using said available data for said one or more processing applications.

6. A system as set forth in claim 1 further comprising means for formatting results of said one or more data processing applications to correspond to respective types of data processing requests.

7. A method for managing data for researchers, said method comprising the steps of:

automatically receiving research data from laboratory instruments;

maintaining a database containing established reference data;

automatically obtaining recently available reference data;

maintaining a database containing experimental data;

responsive to a request by a researcher to perform a data processing function, invoking one or more processing applications and supplying to said one or more processing applications parameters to perform said data processing function; and

in response to the invoking and supply of parameters, said one or more processing applications automatically access types of said data required to perform the respective data processing function.

8. A method as set forth in claim 7 wherein said invoking and supplying step determines which of said processing applications to invoke and which parameters to supply to said processing applications to be invoked, based on a type of function requested by said researcher.

9. A method as set forth in claim 7 wherein said invoking and supplying step determines identities of files containing said data required by said one or more applications, based on a type of function requested by said researcher.

10. A method as set forth in claim 7 further comprising the steps of analyzing patterns in respective types of said data, and providing results of said analyzing pattern step to one of said one or more processing applications to perform the requested data processing function.

11. A method as set forth in claim 7 further comprising the step of determining if available data is valid, and

if not, not using said available data for said one or more processing applications;

if so, using said available data for said one or more processing applications.

12. A method as set forth in claim 7 further comprising the step of formatting results of said one or more data processing applications to correspond to respective types of data processing requests.

13. A system for managing data for researchers, said system comprising:

a virtual storage device including online and near line storage, and having predefined policies for moving stored data between the online and near line storage;

a research data server for receiving and managing experimental data, research data and research results, and operating with the virtual storage device to maintain the experimental data, research data and research results;

a reference data access server receiving and managing external reference data relating to research of the researchers and operating with the virtual storage device to maintain the external reference data;

computational resources for the researchers to capture and process experimental data to generate the research results; and

a research data network connecting the virtual storage device, research data server, reference data access server and computational resources to allow transfer of data there between, the research data network further including security management services to authenticate and authorize access by the researchers.

14. The system of claim 13 further comprising a data import controller connected to the research data network and operable to retrieve external reference data from data sources external to the research data network according to one or more policies predefined by the researchers for retrieving external reference data.

15. The system of claim 14 wherein the data import controller processes retrieved reference data to determine if it is lower quality or redundant in view of reference data already stored in the virtual storage device.

16. The system of claim 15 wherein the data import controller filters out redundant or lower quality retrieved reference data from entry in the virtual storage device.

17. The system of claim 13 wherein the computational resources include a cluster of computing resources;

and the computational results further comprise a post processor, the post processor converts experimental data into useful forms which are relevant for the purpose and context of the research.

18. The system of claim 13 further comprising a laboratory information management system connected to the research data network and to one or more laboratory instruments, the laboratory information management system receiving experimental data from the laboratory instruments and providing that data to the research data server via the research data network.

19. The system of claim 18 further comprising a preprocessing server connected to the research data network, the laboratory information management server providing experimental data from the laboratory instruments to the preprocessing server which converts the experimental data into data which is useful and relevant for the research, the preprocessing server providing the converted data to the research data server via the research data network.

20. The system of claim 13 further including a knowledge management server connected to the research data network and operable to identify and provide a researcher with reference data and/or experimental data and results from the research data server and the reference data access server in accordance with queries made by the researcher.

21. The system of claim 20 wherein a researcher can create policies defining data types of interest to the researcher, and the knowledge management server, in accordance with the defined policy, identifies and provides reference data and experimental data and results of interest to the researcher.

22. The system of claim 13 further including a research application server connected to the research data network, the research application server providing at least one software application and/or tool required by researchers, the at least one application and/or tool operating on data stored in said virtual storage device in accordance with instructions from the researchers.

23. A method of managing research conducted by researchers, said method comprising the steps of:

creating a set of policies defining external reference information relevant to the research;

retrieving, at predefined intervals, external reference information in accordance with the policies;

comparing the retrieved information with reference data stored in a reference data server to determine if the retrieved information is redundant or of lower quality than data already stored in the reference data server and storing retrieved information which was determined to be non-redundant and/or of acceptable better quality in the reference data server;

storing experimental data from at least one laboratory instrument in a research data server; and

providing the researchers with access to the stored information in the reference data server and to experimental data in the research data server.

24. The method of claim 23, further comprising the step of the researchers defining a set of data storage policies for a virtual storage device including both online and near line storage capacity to store the data of the reference data server and the research data server, and moving the stored data between online storage capacity and near line storage capacity in accordance with the data storage policies.

25. The method of claim 23 further comprising the step of preprocessing the experimental data from the at least one laboratory instrument and storing the preprocessed experimental data in the research data server.

26. The method of claim 23 further comprising the step of publishing information to researchers by having the researchers identify to a knowledge management server information of interest to them and the knowledge management server examining the contents of the reference data server and the research data server to identify the information of interest to a researcher and the knowledge management server making the identified information available to the researcher.

27. The method of claim 23 further comprising the step of verifying the authenticity and authority of each researcher to access stored experimental data and stored reference data before providing that access.

28. A method of managing data for research, said method comprising the steps of:

providing a plurality of researchers with access to a research data network;

creating reference data policies defining for each of said researchers types of reference data that will be of use to the researcher, creating experimental data policies defining for each of said researchers types of experimental data and results that will be of use to the researcher and storing these policies on the research data network;

retrieving, at defined intervals, from data sources outside the research data network, external reference data as defined by the reference policies;

examining the retrieved reference data to determine if it is redundant in view of reference data already stored on the research data network or if it is of better quality than reference data already stored on the network and storing retrieved reference data on the research data network which has been determined to be non-redundant or of better quality than reference data already stored;

collecting experimental data from laboratory instruments through the research data network and storing the collected data on the research data network; and

publishing new reference data and experimental data to researchers according to the reference data policies and experimental data policies defined for the researchers.

29. The method of claim 28 wherein the reference data and the experimental data are stored in a virtual storage device on the research data network, the virtual storage device having both online and near line data storage capabilities and the research team having predefined a storage policy executed by the virtual storage device to transfer stored data between the online storage and the near line storage.

30. The method of claim 28 further comprising the step of at least one researcher processing published experimental data to obtain experimental results which are stored on the research data network, the stored experimental results also being subsequently published in the publishing step to researchers in accordance with experimental data policies of researchers.

31. A computer program product to manage data for research conducted by researchers, said computer program product comprising:

a computer readable medium;

first program instructions executable to provide the researchers with access to a research data network;

second program instructions to retrieve, at defined intervals, from data sources outside the research data network, external reference data as defined by reference policies created by said researchers;

third program instructions to examine the retrieved reference data to determine if it is redundant in view of reference data already stored on the research data network or if it is of better quality than reference data already stored on the network and to store retrieved reference data on the research data network which has been determined to be non-redundant or of better quality than reference data already stored;

fourth program instructions to store experimental data from at least one laboratory instrument in a research data server; and

fifth program instructions to provide the researchers with access to the stored information in the reference data server and to experimental data in the research data server; and

wherein

said first, second, third, fourth and fifth program instructions are recorded on said medium.

32. A computer program product according to claim 31, further including sixth program instructions to implement a set of data storage policies for a virtual storage device including both online and near line storage capacity to move the stored data between online storage capacity and near line storage capacity in accordance with the data storage policies;

and wherein said sixth program instructions are recorded on said medium.