List widgets overview

There are several list widgets (widgets from now on) available on InterMine, and they are configured in Data and Widget Configuration.

There are three categories of widgets:

Category	Description
table	Displays the counts from the list for the collection specified
graph/chart	Displays a graph/chart based on a dataset you specify
enrichment	Displays the p-values of objects that appear in your list

To add a widget to your mine:

1. Add config to your webconfig-model.xml file
2. Re-release your webapp
3. View widget in a list analysis page

Below are the details on how to configure each widget type.

Configuration

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Please read the documentation carefully and check your config file for typos. Most attributes are case sensitive. When the webapp is released, the config is validated and any errors are displayed in the home page.

Table widgets

Table widgets display objects and the counts of related objects in your list.

An example table widget of Orthologues in FlyMine.

attribute	purpose	example
id	unique id used by JavaScript only. Spaces not allowed.	unique_id
pathStrings	which collection to use in the widget	Gene.homologues[type=orthologue].homologue.organism
exportField	which field from the objects in your list to export	primaryIdentifier
typeClass	types of lists that should display this widget. Use the simple class name	Gene

The following are optional attributes:

attribute	purpose	example
title	appears at the top of the widget	Orthologues
description	description of the widget	Counts of orthologues
displayFields	which fields from the objects in the collection (in the above example, Gene.proteins) to display, eg. primaryAccession	name
columnTitle	heading for the “count” column	Orthologues
externalLink	link displayed next to first column, identifier will be appended to the link
externalLinkLabel	label for external link
views	path fields display in the query running when the user clicks on the widget	symbol

Graph/Chart widgets

Graph widgets display datasets in graphical format.

attribute	purpose	example
id	unique id used by JavaScript only. Spaces not allowed.	unique_id
graphType	which type of chart to render	ColumnChart,``BarChart`` or PieChart
startClass	it’s the root class for all the paths specified in the configuration [1].	Gene
typeClass	type of lists that should display this widget. Use the simple class name.	Gene
categoryPath	Must be attribute. We can specify the subclass using the syntax path[subclass type]	mRNAExpressionResults.stageRange
seriesPath	the series path. This has to be an attribute. We can specify the subclass using the syntax path[subclass type]	mRNAExpressionResults.expressed
seriesValues	the values of different series. Case sensitive. You can specify Boolean values	true,false or Up,Down
seriesLabels	the labels displayed on the graphs to distinguish the different series inside a category	Expressed,Not Expressed or Up,Down
views	attributes paths displayed when the user clicks an area on the graph	name,organism.name

[1] All the paths set, will be built starting from that. Specify only the simple name (e.g. Gene). You can choose to set the bag type class or the root class associated to the category path.

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You can specify only one class in typeClass. If you need another type, you have to define a new widget.

The following are optional attributes:

attribute	purpose	example
title	appears at the top of the widget	BDGP expression patterns
description	description of the widget	Expression patterns
domainLabel	Label displayed on x-axis in the ColumnChart (on y-axis in the BarChart)	Stage
rangeLabel	Label displayed on y-axis in the ColumnChart (on x-axis in the a BarChart)	Gene count
filterLabel	label for filter form field	Organism
filters	the values for the filter, set in the dropdown [2].	All,KEGG pathways,Reactome data
listPath	the path used to build the bag constraint [3].	FlyAtlasResult.material
constraints	separated by comma, case sensitive, must be attributes, operator can be = or != [4]	organism.name=[Organism] [5]

[2] We can use static values or a grammar to specify the values contained in the list. The default value in general is the first value set in the ‘filters’ attribute or the first value returned by the query. With static values, you can add ‘All’ meaning no filter applied.

[3] Optional if the startClass contains the bag type class.

[4] For the values, we can use static values or the selected filter value using the syntax: path constraint = [filter identifier].

[5] organism’s name matching with the value selected in the filter with filterLabel ‘Organism’

Note The graphs use Google Visualitation API.

Enrichment widgets

Enrichment widgets calculate p-values representing the probability annotation occurred by chance. See List enrichment widgets statistics for more information on how the p-value is calculated.

attribute	purpose	example
id	unique id used by JavaScript only. Spaces not allowed.	unique_id
startClass	Root class for all the paths specified in the configuration. Use simple name (e.g. Gene)	Gene
startClassDisplay	Field displayed when user clicks on the widget on ‘Matches’ column	primaryIdentifier
typeClass	Type of lists that should display this widget. Use the simple class name.	Gene
enrich	Field to be enriched, displayed in the widget in the first column [6].	goAnnotation.ontologyTerm.parents.name
views	attributes paths displayed when the user clicks on View results button [6].	symbol,organism.name

[6] (1, 2) You have to specify only one field. Specify the subclass using the syntax path[subclass type].

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You can specify only one class in typeClass. If you need another type, you have to define a new widget.

The following are optional attributes:

attribute	purpose	example
title	appears at the top of the widget	Gene Ontology Enrichment
description	description of the widget	GO terms enriched.
label	heading for the column	GO Term
externalLink	link displayed next to first column	googie
filters	extra filters to add to the display [7]	organism.name=[list]
filterLabel	label for filter form field	Ontology
enrichIdentifier	identifier for the row displayed, if not specified, enrich field used [8].	goAnnotation.ontologyTerm.identifier
constraints	constraints separated by comma. The paths have to be attributes. The operator can be = or != [9].	organism.name=[list]
constraintsForView	constraints separated by comma used for building the query executed when the user clicks on the widget on ‘Matches’ column	results.expressed = true
correctionCoefficient	set to org.intermine.bio.web.widget.GeneLenghtCorrectionCoefficient to normalize by gene length

[7] Use static values or a grammar to specify the values contained in the list. The default value in general is the first value set in the ‘filters’ attribute or the first value returned by the query. With static values, you can add ‘All’ meaning no filter applied.

[8] Specify only one. This has to be an attribute. Used in the results table. Specify the subclass using the syntax path[subclass type].

[9] Case sensitive. For the values we can use: static values or the selected filter value using the syntax: path contraint = [filter identifier]. Only the value contained in the list.

Examples

See other mines' config files for more examples, eg:

• FlyMine's webconfig-model.xml
• HumanMine's webconfig-model.xml

Background population

In the enrichment widgets, you can change the reference population. The reference population is specific for widget, list and user. If you are logged on, you can save your preference selecting the checkbox 'Save your preference'. The background population selected should include all items contained in the list.

Gene length correction coefficient

Depending on the type of experiment your data comes from, it is sometimes necessary to normalize by gene length in order to get the correct p-values. If your data comes from a genome-wide binding experiment such as ChIP-seq or DamID, binding intervals are more likely to be associated with longer genes than shorter ones, and you should therefore normalize by gene length. This is not the case for experiments such as gene expression studies, where gene length does not play a role in the likelihood that a particular set of genes will be overrepresented in the list. If you want normalize by gene length, add the attribute correctionCoefficient, set to 'org.intermine.bio.web.widget.GeneLenghtCorrectionCoefficient'. The gene length correction coefficient is applicable only for lists containing genes with a length, so for a list of genes that do not have a length, the option is not shown. If a list contains some genes without a length those genes will be discarded.

Export Values

The exported file from enrichment widgets includes the enrichment identifier as the fourth column. It is contextual to the startClass attribute in the configuration. For example, an enrichment widget for publications would return the PubMedID field, whereas, a GO enrichment widget would return the GO Term field.