With the Item overview function you can get an overview of all bioassays, extracts, samples, annotations, raw data sets, etc. that are related to a given item. In the overview you can also validate the data to find possibly missing or incorrect information.
You can access the overview for an item by navigating to the single-item view of the item you are interested in. Then, switch to the Overview tab that is present on that page. Here is an example of what is displayed:
The page is divided into three sections:
To the left is a tree displaying items that are related to the current item. The tree is loaded gradually when you click your way through the sublevels. The only exception is after a validation has been done, in this case the whole tree is loaded through the validation-process.
The lower right shows a list of warnings and error messages that was found when validating the data. This section is empty if no validation has been done. Click on the Temperature protocol parameter for one of the samples.button to validate the data and load errors and warnings. In the example you can see that we have failed to specify a value for the
The upper right shows information about the currently selected item in the tree. This part will also contain more information about errors or warnings for this item, but only if a validation has been done. It may also present you with one or more suggestions about how to fix the problem and with a link that takes you to the most probable location where you can fix the error or warning.
Click on the Validation options dialog.button in the toolbar to open the
The validation procedure is highly configurable and you can select what you want to ignore, and what should be displayed as an error or warning.
The list contains predefined and user defined validation options. Use thebutton to save the current options as a user defined preset. The button is used to remove the currently selected preset. Predefined presets cannot be deleted.
The options in this section are used to check if your experiment uses the same values as set by the project default values of the currently active project (see Section 6.2, “Projects”). If no project is active these options are ignored. The validation is only performed if the project has at least one item with a matching type. For example, if no default array design has been added to the project, all array designs are allowed. For items that can have a subtype, the subtype is also considered. For example, if only a default sampling protocol has been selected, no warnings are generated for extraction protocols.
The options in this section are used to check if you have specified values for optional items. For example, there is an option that warns you if you have not specified a protocol. For items that can have a subtype, the rule here is to use the information about related subtypes before reporting a missing item. For example, the labeled extract subtype is related to the label subtype and if a label is missing it is reported as a warning. If there is no related subtype no warning is generated.
The options in this section are used to check that related items have a subtype that matches the subtype of the main item. For example, if we have an extract which is a labeled extract subtype the subtype for the related tag should be label, but if the extract is a library the subtype of the tag should be barcode.
The options in this section are used to check problems related to annotations. The most important ones are listed here:
The options in this section are related to the validity of data files that can be attached to some items, for example, raw bioassays and array designs. The data files are usually validated immediately when they are used and the result is saved to the database. The options in this dialog can be used to find (or ignore) problems with data files.
The options in this section are used to check if you do not have access (read permission) to an item in the experiment hierarchy. If this happens the validation cannot proceed in that branch. This might mask other validation problems.
The options in this section are used to check that links between (multiple) items are consistent with each other. The most important options are:
This section collects options that does not fit into any of the other sections. The most important options are:
Click on thebutton to use the current settings. The display will automatically refresh itself.
The overview includes a function that allows you to quickly fix most of the problems found during the validation. The easiest way to use the function is:
|If you do not have permission to fix a problem the links will be inactive and you'll have to talk to someone with more powers.|