Computer graphical user interface with genomic workflow

Patent metadata

Field	Value
Publication number	US-11074993-B2
Application number	US-201916543002-A
Country	US
Kind code	B2
Filing date	Aug 16, 2019
Priority date	Mar 15, 2013
Publication date	Jul 27, 2021
Grant date	Jul 27, 2021

Abstract

Methods and computer apparatuses are disclosed for processing genomic data in at least partially automated workflows of modules. A method comprises: specifying a source from which nucleic acid sequence(s) are to be obtained; selecting module(s) for processing data, including at least one module for processing the one or more nucleic acid sequences; presenting, in a graphical user interface, graphical components representing the source and the module(s) as nodes within a workspace; receiving, via the graphical user interface, inputs arranging the source and the module(s) as a workflow comprising a series of nodes, the series indicating, for each particular module, that output from one of the source or another particular module is to be input into the particular module; generating an output for the workflow based upon the nucleic acid sequence(s) by processing each module in an order indicated by the series.

First claim

What is claimed is:

1. A method comprising:
presenting, in a graphical user interface, graphical components representing a series of nodes within a workspace;
generating a set of one or more items of genomic data that are based upon one or more nucleic acid sequences processed by the series of nodes;
generating a first data node, the first data node comprising the set of one or more items of genomic data;
receiving, via the graphical user interface, a first input that selects a subset of one or more items of genomic data from the set of one or more items of genomic data in the first data node; and
receiving, via the graphical user interface, a second input that moves the subset of one or more items of genomic data to a location on the graphical user interface not associated with the first data node;
wherein the method is performed by one or more computing devices.

2. The method of claim 1 , further comprising generating output that conforms to an ontology defining data structures that represent genomic data, the data structures representing at least all of: sequences, protein objects, alignment objects, annotations, and publications.

3. The method of claim 1 , further comprising:
receiving, via the graphical user interface, third input selecting a particular set of instructions to process the first data node;
adding the particular set of instructions to the end of the series of nodes; and
generating output for the workspace comprising a set of one or more items of genomic data, based upon the one or more nucleic acid sequences and the series of nodes.

4. The method of claim 1 , further comprising generating output, wherein the output comprises a set of one or more items of genomic data that are based upon the one or more nucleic acid sequences as processed by a set of instructions in an order indicated by the series of nodes.

5. The method of claim 1 , further comprising generating output for the workspace comprising a set of one or more items of genomic data by processing the one or more nucleic acid sequences by instructions received from at least one of an external web server or an external database server.

6. The method of claim 1 , further comprising:
saving workflow data describing the series;
causing the workflow data to be shared with multiple user computers;
subsequently reconstructing the series in a second graphical user interface based on the workflow data;
receiving third input, via the second graphical user interface, modifying the series to include one or more additional sets of instructions from at least one of the multiple user computers; and
generating output based upon the one or more nucleic acid sequences by processing the one or more additional sets of instructions, in an order indicated by the series.

7. The method of claim 1 , further comprising:
generating first output based upon the series;
merging the first output with a second output that is not in the series.

8. The method of claim 1 , further comprising:
presenting a first control, a second control and a third control for selecting one or more sets of instructions;
in response to input selecting a first set of instructions with the first control, causing searching for publications in an online database based on genomic data;
in response to input selecting a second set of instructions with the second control, outputting a sequence alignment for multiple sequences;
in response to input selecting a third set of instructions with the third control, automatically identifying protein families for a nucleic acid sequence.

9. The method of claim 1 , further comprising, in response to receiving the first input or second input, presenting visual feedback, while a first node is selected, indicating that genomic data output from the first node can be linked as input to a second node.

10. The method of claim 1 , further comprising:
automatically processing each node in the series without human intervention;
generating an output by concluding processing of a last node in the series.

11. One or more non-transitory computer-readable media storing instructions that, when executed by one or more computing devices, cause:
presenting, in a graphical user interface, graphical components representing a series of nodes within a workspace;
generating a set of one or more items of genomic data that are based upon one or more nucleic acid sequences processed by the series of nodes;
generating a first data node, the first data node comprising the set of one or more items of genomic data;
receiving, via the graphical user interface, a first input that selects a subset of one or more items of genomic data from the set of one or more items of genomic data in the first data node; and
receiving, via the graphical user interface, a second input that moves the subset of one or more items of genomic data to a location on the graphical user interface not associated with the first data node.

12. The one or more non-transitory computer-readable media of claim 11 , further comprising instructions that, when executed by one or more computing devices, cause generating output that conforms to an ontology defining data structures that represent genomic data, the data structures representing at least all of: sequences, protein objects, alignment objects, annotations, and publications.

13. The one or more non-transitory computer-readable media of claim 11 , further comprising instructions that, when executed by one or more computing devices, cause:
receiving, via the graphical user interface, third input selecting a particular set of instructions to process the first data node;
adding the particular set of instructions to the end of the series of nodes; and
generating output for the workspace comprising a set of one or more items of genomic data, based upon the one or more nucleic acid sequences and the series of nodes.

14. The one or more non-transitory computer-readable media of claim 11 , further comprising instructions that, when executed by one or more computing devices, cause generating output, wherein the output comprises a set of one or more items of genomic data that are based upon the one or more nucleic acid sequences as processed by a set of instructions in an order indicated by the series of nodes.

15. The one or more non-transitory computer-readable media of claim 11 , further comprising instructions that, when executed by one or more computing devices, cause generating output for the workspace comprising a set of one or more items of genomic data by processing the one or more nucleic acid sequences by instructions received from communicating with at least one of an external web server or an external database server.

16. The one or more non-transitory computer-readable media of claim 11 , further comprising instructions that, when executed by one or more computing devices, cause:
saving workflow data describing the series;
causing the workflow data to be shared with multiple user computers;
subsequently reconstructing the series in a second graphical user interface based on the workflow data;
receiving third input, via the second graphical user interface, modifying the series to include one or more additional sets of instructions from at least one of the multiple user computers; and
generating output based upon the one or more nucleic acid sequences by processing the one or more additional sets of instructions, in an order indicated by the series.

17. The one or more non-transitory computer-readable media of claim 11 , further comprising instructions that, when executed by one or

Assignees

• Palantir Technologies Inc

Inventors

• Wang Lekan
• Cho Hyunghoon
• Raja Abimanyu
• Caudill Elizabeth

Classifications

• G16B20/00 Primary

  ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations · CPC title

• G16B50/00

  ICT programming tools or database systems specially adapted for bioinformatics · CPC title

• G16B45/00 Primary

  ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks · CPC title

• G06F3/0482

  Interaction with lists of selectable items, e.g. menus · CPC title

• G06F16/951

  Indexing; Web crawling techniques · CPC title