Computer graphical user interface with genomic workflow

Patent metadata

Field	Value
Publication number	US-9501202-B2
Application number	US-201313831791-A
Country	US
Kind code	B2
Filing date	Mar 15, 2013
Priority date	Mar 15, 2013
Publication date	Nov 22, 2016
Grant date	Nov 22, 2016

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:
receiving a first input specifying a source from which one or more nucleic acid sequences are to be obtained, the one or more nucleic acid sequences being converted by a data conversion component into converted data in a data structure defined by an ontology associated with a workflow;
receiving one or more second inputs selecting one or more modules for processing data, including at least one module for processing the converted data, and when the at least one module processes the converted data by sending at least a portion of the converted data to one or more external tools, the one or more external tools processing the portion of the converted data and returning processed data, the processed data being converted by the data conversion component to the data structure defined by the ontology;
presenting, in a graphical user interface, graphical components representing the source and the one or more modules as nodes within a workspace;
receiving, via the graphical user interface, one or more third inputs arranging the source and the one or more modules as the workflow comprising a series of nodes, the series indicating, for each particular module of the selected modules, 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, 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 that are processed by each module of the one or more modules in an order indicated by the series;
generating a first data node from the output, the first data node comprising the set of one or more items of genomic data, the first data node linked to a last module in the series;
receiving, via the graphical user interface, fourth 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;
receiving, via the graphical user interface, fifth 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;
generating a second data node comprising the subset of one or more items of genomic data, wherein the output for the workflow is reconfigured to generate multiple data nodes, one corresponding to the first data node comprising the set of one or more items of genomic data other than the subset of one or more items of genomic data, and another corresponding to the second data node comprising, the subset of one or more items of genomic data;
wherein the method is performed by one or more computing devices.

2. The method of claim 1 , wherein each module of the one or more modules generates output that conforms to an ontology defining data structures that represent genomic data, the data structures including at least sequences, protein objects, alignment objects, annotations, and publications.

3. The method of claim 1 , further comprising:
receiving, via the graphical user interface, sixth input selecting a particular module to process the first data node;
adding the particular module to the end of the series;
generating third output for the workflow based upon the one or more nucleic acid sequences by processing each module in the series, including the particular module, in the order indicated by the series.

4. The method of claim 1 , wherein the one or more modules include a plurality of modules, wherein generating the output for the workflow comprises using output from the source as input to a first module, and using output from the first module as input to a second module.

5. The method of claim 1 , wherein the at least one module is configured to process the one or more nucleic acid sequences by communicating with 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 users;
subsequently reconstructing the series in a second graphical user interface based on the workflow data;
receiving sixth input, via the second graphical user interface, modifying the series to include one or more additional modules;
generating second output based upon the one or more nucleic acid sequences by processing each module in the series, including the one or more additional modules, in an order indicated by the series.

7. The method of claim 1 , wherein the one or more modules include a first module that generates first output based upon the source, and a second module that merges the first output with second output from a third module that is not in the series, wherein the source, first module, second module, and third module are all nodes within a workflow.

8. The method of claim 1 , further comprising presenting controls for selecting the one or more modules, wherein the controls include at least: a first control for selecting a first module that searches for publications in an online database based on genomic data, a second control for selecting a second module that outputs a sequence alignment for multiple sequences, and a third control for selecting a third module that identifies protein families for a nucleic acid sequence.

9. The method of claim 1 ,
wherein receiving the one or more third inputs comprises presenting visual feedback while a first node is selected that indicates that genomic data output from the first node can be linked as input to a second node.

10. The method of claim 1 , wherein the one or more modules include at least two modules, wherein processing each module of the one or more modules in an order indicated by the series comprises automatically processing each module, without human intervention between beginning processing of a first module in the series and generating the output by concluding processing of a last module in the series.

11. One or more non-transitory computer-readable media storing instructions that, when executed by one or more computing devices, cause:
receiving a first input specifying a source from which one or more nucleic acid sequences are to be obtained, the one or more nucleic acid sequences being converted by a data conversion component into converted data in a data structure defined by an ontology associated with a workflow;
receiving one or more second inputs selecting one or more modules for processing data, including at least one module for processing the converted data, and when the at least one module processes the converted data by sending at least a portion of the converted data to one or more external tools, the one or more external tools processing the portion of the converted data and returning processed data, the processed data being converted by the data conversion component to the data structure defined by the ontology;
presenting, in a graphical user interface, graphical components representing the source and the one or more modules as nodes within a workspace;
receiving, via the graphical user interface, one or more third inputs arranging the source and the one or more modules as the workflow comprising a series of nodes, the series indicating, for each particular module of the selected modules, 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, 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 that are processed by each module of the one or more modules in an order indicated by the series
generating a first data node from the output, the first data node com

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

• G06Q10/10

  Office automation; Time management · CPC title

• G16B45/00 Primary

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

• G16B50/00

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

• G06F3/0482

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