Retrieve and Relate Wiki

List View

List View

Once you have applied all the filters of your interest, you can see your results in the List View page.

The benefit of this page is having a scrollable list of records that describe the sequences in a customizable tabular format.

This enables more specific selection and filtration.

List_view_wiki

The new panel added to this view contains the buttons “Fields”, “Download” and “No Filter”. At the far right is the total number of data records displayed on your screen. As you can already see, this page provides annotation information related to protein structures and genes ontology for all the records.

You can choose to display more or less columns of information by clicking on the “Fields” button, which has a list of attributes you can customize according to your needs. It looks like this:

Large GIF (1716x934)

This pop-up window allows you to choose among the following attributes:

  1. Score: An internal rubric to measure ‘importance’ of sequence

  2. Sequence ID: In the format “Original database”:”unique ID in that database”

  3. Description: The annotation information that best describes this sequence

  4. Data Source: Database which contains this information

  5. Sequence Type: Either of DNA/RNA/AA

  6. Gene ontology definition: Annotate functionality of gene and/or gene product

  7. High level ontologies: General definition of what aspects this sequence affects in the organism [biological process/molecular function/cellular component]

1For example, you can unselect “Data Source” to not see that column anymore!

You can view more details about a particular record by clicking on it. The dialog box will show:

4-333988b7-c6b6-4477-8b13-1da95b4928a6

This displays the name of this record followed by a description of the cellular component it belongs to, the sequence type and the sequence itself. You can copy the entire sequence by clicking “Copy Sequence” link. You can see the original database linked to this record by clicking “Open externally”.

You can also download the entire table of search results as a (.csv) file by clicking on the “Download” button.

Towards the far right, you can see the “No Filters” button. This is a useful tool to selectively view just a portion of your data by filtering out the subdomains in every domain.

List view GIF

The options available to filter the data more specifically include: 

  1. CATH topology (if available for certain records)

  2. Data Source

  3. GO Ontology (PFC categories)

  4. Taxonomy

  5. GO Definition

  6. Top Concepts (contains unique words from all the records’ descriptions)

  7. Sequence Type

  8. High-Level Ontology.

1For example, you may choose to filter out all “unknown” fields in “High Level Ontology”.
2The name of this button will then change to “Filters(n)” where (n) represents the number of domains you changed.