CROSS-NETWORK GENOMIC DATA USER INTERFACE

• US 20200134136A1
• Filed: 10/24/2018
• Published: 04/30/2020
• Est. Priority Date: 10/24/2018
• Status: Active Grant

• Current Assignee: Helix, Inc.
• Original Assignee: Helix OpCo LLC
• Inventors: Dunaway, Keith, Merkoulovitch, Anna, Shinohara, Andrew, Walia, Anupreet
• Granted Patent: US 10,861,587 B2
• Time in Patent Office: Days
• CPC Class Codes: G06F 16/9535 Search customisation based on user profiles and personalisation
• CPC Class Codes: G06F 16/958 Organisation or management of web site content, e.g. publishing, maintaining pages or automatic linking
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• 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 50/30 Data warehousing; Computing architectures

Abstract

A genomic update system can generate a user interface from network pages based on variant data in one or more of the network pages matching user variant data. Some of the network pages may be in an elevated or trusted class and linking pages may link to those network pages. Content from the linking pages can be included with one or more visualizations in the user interface for interaction by a user via a user device, such as a handheld mobile device.

Claims

1. A method comprising:

receiving, from one or more select network servers, a plurality of network pages having variant values of genetic variations, each of the genetic variations being uniquely identified on the one or more select network servers by a variant identifier;

identifying, in a genetic variation structured data file of a user, user variant values based on variant identifiers in the received plurality of network pages;

determining that a portion of the user variant values in the genetic variation structured data file matches the variant values in at least one of the plurality of network pages;

generating a user interface displaying data from an additional network page that is linked to the at least one of the plurality of network pages having matching variant values; and

causing, on a client device, presentation of the user interface

2. The method of claim 1, further comprising:

identifying links to the plurality of network pages in a database storing genetic genome structured data.

3. The method of claim 2, wherein identifying the plurality of network pages comprises filtering one or more pages not hosted from the one or more pre-selected network servers.

4. The method of claim 2, wherein the database of genome structured data includes pages from a plurality of network servers, and the method further comprises:

receiving selections of one or more of the plurality of network servers;

storing the selections as the pre-selected network servers.

5. The method of claim 2, further comprising:

receiving an update to the database; and

responsive to the update, updating the user interface to include content of a page linked to a network page in the update to the database based on the network page having variant values that match another portion of the user variant values.

6. The method of claim 1, wherein the additional network page is a page from a network site that is not the one or more select network servers.

7. The method of claim 1, wherein the determining that the portion of the user variant values matches the variant values in one or more of the plurality of network pages comprises determining that the portion of the user variant values satisfy one or more thresholds of the variant values of the network of the plurality of pages.

8. The method of claim 7, wherein the one or more thresholds comprises a first statistical threshold and a second statistical threshold that is greater than the first statistical threshold;

and

wherein the user variant values satisfy at least one of;

the first statistical threshold or the second statistical threshold.

9. The method of claim 7, wherein the user interface includes a visualization that is associated with the one or more threshold values of the variant values, the visualization indicating at least one numerical likelihood of the user variant values expressing the genetic variation of the matching variant values of the plurality of networked pages.

10. The method of claim 1, wherein the user interface includes a genetic variation category selection element that is operable to include or exclude display of content of the additional network page.

11. The method of claim 1, further comprising:

determining that another portion of user variant values in the genetic variation structured data file does not match the variant values in one or more of the plurality of network pages.

12. The method of claim 11, wherein the user interface does not include content from the plurality of network pages that have variant values that do not match the user variant values.

13. The method of claim 1, further comprising:

identifying links in the plurality of network pages that link to the additional network pages; and

storing the data from the additional network pages for display in the user interface.

14. The method of claim 13, wherein the data from the additional network pages includes user interface content configured for display in the additional networked pages.

15. The method of claim 14, wherein the user interface content of the additional networked pages includes one or more of:

text data, image data, video data.

16. The method of claim 1, wherein the genetic variations comprise one of more of:

a single nucleotide polymorphism (SNP) variation or a multiple nucleotide variant (MNV).

17. The method of claim 16, wherein the variant identifier is a reference SNP identifier (RSID).

18. The method of claim 1, wherein the genetic variation structured data file is a variant call format (VCF) file.

19. A system comprising:

one or more processors of a client device; and

a memory storing instructions that, when executed by the one or more processors, cause the system to perform operations comprising;

receiving, from one or more select network servers, a plurality of network pages having variant values of genetic variations, each of the genetic variations being uniquely identified on the one or more select network servers by a variant identifier;

identifying, in a genetic variation structured data file of a user, user variant values based on variant identifiers in the received plurality of network pages;

determining that a portion of the user variant values in the genetic variation structured data file matches the variant values in at least one of the plurality of network pages;

generating a user interface displaying data from an additional network page that is linked to the at least one of the plurality of network pages having matching variant values; and

causing, on a client device, presentation of the user interface.

20. A machine-readable storage device embodying instructions that, when executed by a device, cause the device to perform operations comprising:

receiving, from one or more select network servers, a plurality of network pages having variant values of genetic variations, each of the genetic variations being uniquely identified on the one or more select network servers by a variant identifier;

identifying, in a genetic variation structured data file of a user, user variant values based on variant identifiers in the received plurality of network pages;

determining that a portion of the user variant values in the genetic variation structured data file matches the variant values in at least one of the plurality of network pages;

generating a user interface displaying data from an additional network page that is linked to the at least one of the plurality of network pages having matching variant values; and

causing, on a client device, presentation of the user interface.