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## This template may be useful for documenting use cases ## Developed in response to a hackathon request for formalized, detailed use cases |
## This template may be useful for documenting use cases ## Developed in response to a hackathon request for formalized, detailed use cases |
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|| '''Use Case Name''' : ... || || '''For Feature''' : ... || || '''Editors''': ... || ## EXAMPLE: |
||'''Use Case Name''' : ... || ||'''For Feature''' : ... || ||'''Editors''': ... || ## EXAMPLE: |
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We would like to be able to represent detailed sub-gene data in a second window after selecting a node from the parent graph. These below use cases apply to datasets where many different pieces of data (e.g. probesets or interaction partners) are available, that themselves can be represented as distinct nodes. Examples include individual probes or replicate spots from a microarray dataset, data from distinct time-point comparisons in a dataset polymorphism data from whole genome SNP experiments*, exon and exon-junction specific data*, ChIP on chip experiment data* and interaction partners for a node in the parent network*. Examples with an asterisk are illustrated below. |
We would like to be able to represent detailed sub-gene data in a second window after selecting a node from the parent graph. These below use cases apply to datasets where many different pieces of data (e.g. probesets or interaction partners) are available, that themselves can be represented as distinct nodes. Examples include individual probes or replicate spots from a microarray dataset, data from distinct time-point comparisons in a dataset polymorphism data from whole genome SNP experiments*, exon and exon-junction specific data*, ChIP on chip experiment data* and interaction partners for a node in the parent network*. Examples with an asterisk are illustrated below. |
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| '''Associating Data for Sub-Gene Views''' | |
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'''Associating Data for Sub-Gene Views''' 1. To view data with specialized sub-gene views (e.g. SNP view with annotations), first requires a relational database containing at a minimum, associations to genes or proteins. The GenMAPP group is currently designing a database that will support specific ID systems for microarray platforms that assay for specific sub-gene entities. This database will also have to accomidate new relationships appended to the database by the user for unsupported ID systems. For generic case, only those relationships need to connect individual array IDs (or other elements) to a gene are required. For more specialized cases, such as viewing SNP annotations associated with an array ID, these additional annotations must be stored in the relational database. 2. Once the user determines whether the primary ID from their data is supported in the gene database and a sub-gene view to select, the user will upload their data using a specialized interface, specify filters for node coloring and choose the sub-gene visualization methods. Prior to import the user must determine the sub-gene view of interest and determine whether there are sub-gene annotations for their data platform (e.g. Affymetrix SNP array). Requires a new interface for data input and selecting from specific options for compatible sub-gene views. Once required data is supplied for a specific sub-gene entity method (see above for built-in examples) or generic sub-gene objects (e.g. probesets) along with filters for node coloring supplied, values associated with specific 1. Choose "Form complex" from a context menu, main menu or toolbar 1. Automatically view collapsed view of complex with default label (editable) 1. Be able to expand complex as vertically stacked set of nodes by a very simple mechanism (e.g., click on a plus/minus icon) a. perhaps other restricted views of the children will be allowed: i. horizontal stack i. block (e.g., 2x2, 3x4) i. overlapping "clump" of nodes packed into a some defined circular area i. new network 1. Be able to destroy complex 1. Be able to expand-all or collapse-all complexes in a given network |
1. To view data with specialized sub-gene views (e.g. SNP view with annotations), first requires a relational database containing at a minimum, associations to genes or proteins. The GenMAPP group is currently designing a database that will support specific ID systems for microarray platforms that assay for specific sub-gene entities. This database will also have to accomidate new relationships appended to the database by the user for unsupported ID systems. For generic case, only those relationships need to connect individual array IDs (or other elements) to a gene are required. For more specialized cases, such as viewing SNP annotations associated with an array ID, these additional annotations must be stored in the relational database. 1. Once the user determines whether the primary ID from their data is supported in the gene database and a sub-gene view to select, the user will: a. upload their data using a specialized interface b. specify filters for node coloring c. choose the sub-gene visualization methods These options will stored along with the user raw data in a relational database. |
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'''Loading a Network with a Complex''' 1. Same as 3-6 above |
'''Selecting a Sub-Gene View''' |
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1. Open a network 1. Select the gene database used when loading the raw data from a context menu. 1. Select the user database with data and criterion from a context menu. 1. Select the sub-gene view of interest from a context menu. Once selected, by default the right click option will activate the sub-gene view. '''Visualizing Sub-Gene Data''' 1. Right click on a node in the network. This will open a new window (child network) containing the sub-gene view. 1. Select a node in the child network to view more detailed annotations provided from the gene database. |
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## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc) attachment:sub-gene-vis.jpg |
. attachment:sub-gene-vis.jpg |
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## Describe whether this use case is critical and how frequently users would come across it. Describe common work flows that might involve the use case (e.g., "this use case comes up regularly, on a weekly basis, whenever we want to analyze our protein superfamily networks"). |
This use case is necessary for any dataset with more than one piece of information linked to a single gene level node. Specific sub-gene views provide biological context and annotations for the original sub-gene identifiers loaded. |
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---- /!\ '''Edit conflict - your version:''' ---- Describe groupAPI/UseCase 3A here. ---- /!\ '''End of edit conflict''' ---- |
Use Case Name : ... |
For Feature : ... |
Editors: ... |
Summary
We would like to be able to represent detailed sub-gene data in a second window after selecting a node from the parent graph. These below use cases apply to datasets where many different pieces of data (e.g. probesets or interaction partners) are available, that themselves can be represented as distinct nodes. Examples include individual probes or replicate spots from a microarray dataset, data from distinct time-point comparisons in a dataset polymorphism data from whole genome SNP experiments*, exon and exon-junction specific data*, ChIP on chip experiment data* and interaction partners for a node in the parent network*. Examples with an asterisk are illustrated below.
Step-by-Step User Action
Associating Data for Sub-Gene Views
- To view data with specialized sub-gene views (e.g. SNP view with annotations), first requires a relational database containing at a minimum, associations to genes or proteins. The GenMAPP group is currently designing a database that will support specific ID systems for microarray platforms that assay for specific sub-gene entities. This database will also have to accomidate new relationships appended to the database by the user for unsupported ID systems. For generic case, only those relationships need to connect individual array IDs (or other elements) to a gene are required. For more specialized cases, such as viewing SNP annotations associated with an array ID, these additional annotations must be stored in the relational database.
- Once the user determines whether the primary ID from their data is supported in the gene database and a sub-gene view to select, the user will:
- upload their data using a specialized interface b. specify filters for node coloring c. choose the sub-gene visualization methods
Selecting a Sub-Gene View
- Open a network
- Select the gene database used when loading the raw data from a context menu.
- Select the user database with data and criterion from a context menu.
- Select the sub-gene view of interest from a context menu. Once selected, by default the right click option will activate the sub-gene view.
Visualizing Sub-Gene Data
- Right click on a node in the network. This will open a new window (child network) containing the sub-gene view.
- Select a node in the child network to view more detailed annotations provided from the gene database.
Visual Aides
- attachment:sub-gene-vis.jpg
Requirements for Cytoscape
Importance
This use case is necessary for any dataset with more than one piece of information linked to a single gene level node. Specific sub-gene views provide biological context and annotations for the original sub-gene identifiers loaded.
Other Examples