System and method for integrating data for precision medicine
AssigneeOmics Data Automation, Inc.
InventorsGanapati Srinivasa, Melvin Lathara, Brian Hill, Jaclyn Smith, Nalini Ganapati, Hollis Wright
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Abstract
Methods and systems are provided for a platform and language agnostic method for generating inter-and intra-data type aggregations of heterogenous disparate data upon which various operations can be performed without altering the structure of the query or resulting distributed data set representation to account for which specific data sources are included in the query.
Claims20
Method for distributed compilation and joint analysis of data from multiple biomedical sources, the method being implemented by a computer system comprising one or more processors executing computer program instructions that, when executed, perform the method, the method comprising:
- receiving, at an integration server configured with a data integration specification and adapted to service requests from a client device, a query from the client device requesting analysis of one or more types of biomedical data;
- storing, in a memory of the computer system, a data integration schema and integrity constraints, wherein the integration server is part of the computing system;
- mapping the query with respect to the data integration schema and integrity constraints, wherein the data integration schema identifies sources of information usable for answering the query;
- storing, in the memory of the computer system, data source specific schema;
- retrieving a first instance of biomedical data from at least one data source based on a first data source specific schema of the stored data source specific schema;
- mapping the first instance of biomedical data from at least one data source to the data integration schema;
- generating a first data source object by attaching the retrieved first instance of biomedical data from at least one data source to a first distributed data object;
- retrieving a second instance of biomedical data from the at least one data source based on a second data source specific schema of the stored data source specific schema;
- mapping the second instance of biomedical data from the at least one data source to the data integration schema;
- generating a second data source object by attaching the retrieved second instance of biomedical data from the at least one data source to a second distributed data object;
- combining the first and second data source objects to form a data pool;
- processing an operation corresponding to the query on the data pool to generate a response to the query;
- and
- returning the response to the query to the client device.
A system for identifying cohorts of patients with related disease markers comprising:
- a processor;
- a storage device for storing a data integration specification and instructions executable by the processor to:
- receive queries from a client device and execute the queries, the client device comprising a computing device connected to an integration server via a network;
- store a data integration schema and integrity constraints comprising one or more data source specific schema for each of a plurality of data silos, wherein each data silo comprises biomedical data for a plurality of individuals;
- and
- extract one or more data sets from the plurality of data silos on the plurality of devices using the one or more data source specific schema,
- wherein the extracted one or more data sets are transformed into one or more data source objects, each of the one or more data source objects comprising a distributed data set with a particular data source-specific schema, and
- wherein the one or more data source objects are combined to form one or more data pools.
A system for identifying cohorts of patients with related disease markers comprising:
- an input device;
- a processor;
- and
- a storage device for storing a data integration specification and instructions executable by the processor to:
- receive queries from the input device;
- execute the queries;
- store a data integration schema and integrity constraints comprising one or more data source specific schema for each of a plurality of data silos, wherein each data silo comprises biomedical data for a plurality of individuals;
- and
- extract one or more data sets from the plurality of data silos using the one or more data source specific schema,
- wherein the extracted one or more data sets are transformed into one or more data source objects, each of the one or more data source objects comprising a distributed data set with a particular data source-specific schema;
- and
- wherein the one or more data source objects are combined to form one or more data pools.
Dependencies are inferred from the claim text.