Navigation and Searching in BovineMine

There are several ways for users to query BovineMine.

Quick Search

Quick Search allows users to search keywords from any of the BovineMine datasets. There is a Quick Search box on the BovineMine home page or a smaller search box in the upper right corner of all pages.

Quick Search Box on any page — Quick Search from any page

Quick Searches can be conducted with a number of identifiers including gene names, transcripts, pathways, gene identifiers or organisms. The wildcard character * can be used to retrieve all results that match a particular search query.

As an example, we will consider gene rpl24. Enter rpl24 in the search box and click Search. The results page is tabulated and shows a summary about your query, as shown below.

rpl24 search results — Search results for rpl24

Users can filter the results based on Category and Organism. The score column in the result table indicates the similarity of your query to each of the result fetched by BovineMine.

The results page can also be converted to a list. To enable this feature click on Gene in Hits by Category.

filtered rpl24 search results — Filtered search results for rpl24

This will filter the results for the feature type Gene and checkboxes will be available for users to select genes they would like to add to their list. Once the genes are selected, click on CREATE LIST.

Templates

Templates or predefined queries are another search method within BovineMine. Popular templates are displayed on the home page, grouped by category (e.g., Genes, Proteins, Variation) and the complete list can be seen by clicking the Templates menu tab.

Full template list — Full list of templates on Templates page

As an example, the Gene ⮕ Homologues template queries BovineMine to retrieves all homologues for a given gene. Here, we will do a search for the gene GSTM1.

The results page displays all of the homologues for that query gene. When logged in to BovineMine, users can save their results as a list for further analyses by clicking on the Save as List button above the results table then choosing columns to save in their list. See the lists section for more detail on creating and saving lists. Note the Trail: Query text at the upper left of the results table. Clicking on the Query link will bring you back to the query that generated the table to allow for edits without having to start with a new template.

Gene --> Homologues results — Example: Gene ⮕ Homologues template search results, identifier for Gene GSTM1

Generate query code

The code for each template query can be retrieved by clicking on the arrow next to Generate Python Code and choosing the desired language from the pull-down menu. The language options are Python, Perl, Java, Ruby, JavaScript, and XML.

Gene --> Generate code pull-down menu — Options for generating code from template query

Download results

The search results from a template query can be downloaded by clicking the Export button above the table and choosing the desired format from the pull-down menu to the right of the File name field. Available formats are tab-separated values, comma-separated values, XML, and JSON. When the results contain genomic features, they may also be downloaded in FASTA, GFF3, or BED format. Other options may be specified in the submenu to the left of the download box. By default, all rows and all columns are downloaded, but individual columns may be included or excluded by clicking on the toggles next to the column headers in the All Columns submenu. The number of rows and row offset are set in the All Rows submenu. Download the results as a compressed file by choosing GZIP or ZIP format in the Compression submenu (default is No Compression). Column headers are not added by default but may be included under the Column Headers submenu. Finally, the Preview submenu displays the first three rows of the file to be downloaded so that the desired format and options may be finalized before beginning the download. When ready, click the Download file button to download the results.

Customize output and manage columns

To customize the results table layout, click the Manage Columns button. This allows users to rearrange, remove or order columns. Filters can be edited or removed by clicking the Manage Filters button. To specify the entity relationships within the query and change the way the results are presented in the table, click Manage Relationships. Clicking on the Manage Relationships option bring also brings up a blue information panel (“What does this do?”) that provides more detailed information.

customize results table — Options for customizing the results of a template query.

To further manage column data, each column has a set of icons in its header. Mousing over any icon will reveal what it does. The sort icon resembles two triangles and allows you to sort a column in either direction (ascending/descending; a->z, z->a). To delete any column from your table, click on the “x” icon. Alternatively, the three dots “…” can be selected to “Toggle column visibility” and hide the column. Once hidden, the icon turns into a double arrow that can be selected to expand the column into its original form. The next icon resembling a funnel can be selected to edit or remove any currently active filters. A summary of the data within a column can be viewed by clicking on the icon that resembles a graph. The data within each summary can be selected for further filtering or downloading.

Optional filters

Some templates have optional filters that are disabled by default. For the Gene ⮕ Homologues query, there is an optional filter to specify the organism used in the query. To enable the filter, click ON below the Organism > Short Name label.

template query option — Using the optional organism filter in the Gene ⮕ Homologues query template.

QueryBuilder

The provided templates are suitable for many different types of searches, new queries may be built from scratch using the QueryBuilder. The possibilities of queries using the QueryBuilder are endless. The output may be formatted exactly as desired, and the query constraints may be chosen to perform complex search operations.

To begin, select a Data Type. For example, select Gene as a Data Type then click the Select button to be taken to the Model browser.

template query gene select — Selecting data type as **Gene** in QueryBuilder.

Model browser

After selecting a data type, the Model builder appears displaying the attributes for the chosen feature class Gene.

First lets select Gene as a Data Type in the QueryBuilder. Then click on Select. This will take you to a Model browser where you can select the attributes for the feature class ‘Gene’, which you would want to be shown in your results.

Model browser for query builder — Model browser with “Gene” selected as the data type.

QueryBuilder Examples

The following three examples provide details as to how to use the QueryBuilder using “Gene” as the selected data type.

Example 1: Querying for protein coding genes

In the Model browser, click Show next to Gene ID, Symbol, and Biotype, which will add these fields to the query. Notice that these two fields appear below the data type Gene in the Query Overview section.

Model browser eg1, step1 select — Model browser with “Gene” selected as the data type.

Example 1, Step 1: Select fields to be added to the query

Then click Constrain next to Biotype. The first drop-down menu defaults to = (equals sign). In the second drop-down menu, select protein_coding, then click the Add to query button. This adds a constraint to the query to search only for protein coding genes. Notice that the Query Overview section now shows “Biotype = protein_coding”. Also, two types of icons appear next to the attributes. Clicking on the red “X” icon next to an attribute will remove that field or constraint from the query. Clicking on the blue pencil icon next to a constraint brings up the constraint editing window where changes may be made to the query filters.

Query Builder for Gene showing attributes and constrained by status 'Protein Coding' — Example 1, Step 2 Adding a constraint to the query on Biotype.

Query Builder for Gene showing attributes with contraint 'Protein Coding' — Example 1, Step 2 Constraint has been added to the query on Biotype.

Lastly, click on Show Results above the Model Browser. The resulting table contains all protein coding genes in the database, with Gene ID, Gene Symbol and Gene Biotype as the table columns. Because the Biotypes should all be the same (protein coding), that column can be deleted by clicking the “x” above it. Alternatively, the three dots “…” can be selected to “Toggle column visibility” and hide the column. See the Customize output and manage columns section to review ways to manage column data.

Query Builder for Gene showing attributes results eg.1 — Example 1, Step 3 Display query results.

Example 2: Querying for protein coding genes on a particular chromosome

Users can customize the previously run query by adding another constraint for Chromosome. Note the “Trail: Query” text at the upper left of the results table. Clicking on the “Query” link will bring you back to the query that generated the table to allow for edits without having to build a new query. In the Model browser, click on the “+” (plus sign) next to the Chromosome feature class to display its attributes.

Adding an additional constraint for Chromosome name — Example 2, Step 1 View attributes of Chromosome feature class

Next click on the Chromosome ID attribute and in the text box of the pop-up window select “=” (equals). Enter NW_020192292.1 then click on Add to Query, which adds the additional constraint to the query.

Browser after adding an additional constraint for Chromosome name — Example 2, Step 2 Adding a constraint to the Chromosome ID

Click on Show results and the query will result in all protein-coding genes on the Chromosome with constrained ID. Note that the number of results has been reduced with the addition of the constraint.

Results after additional constraint for Chromosome name — Example 2, Step 3 Result table after constraining by Chromosome ID

Example 3: Querying for Protein Coding genes on a particular chromosome and their exons

This last example builds upon the previous queries to display all exons for each gene on a particular chromosome. Again, note the “Trail: Query” text at the upper left of the results table. Clicking on the “Query” link will bring you back to the query that generated the table to allow for edits without having to build a new query. Scroll down to Exon feature class and select the “+” (plus sign) next to Exons to display its attributes. Click Show next to DB Identifier and Length.

Results after additional constraint for exon — Example 3, Step 1 Expand exon attributes and add fields to the query

The Query Overview shows the query in progress with the selected fields. Also notice that a third type of icon, a blue square, appears next to some attributes. Clicking on a blue square icon brings up a window where the query Join Style may be modified. When adding a constraint, you can decide whether you want to show only those results with the information (genes with exons) or all results and the constrained feature if it exists (e.g., all genes and indicate exons if they exist). Click on the blue square icon next to Exon collection to bring up the Switch Join Style window. The default option is to show only Genes if they have a exon (inner join). Change this to Show all Genes and show Exons if they are present (outer join) then click Add to query.

Selecting join constraint for exon — Example 3, Step 2 Select join style for exons

Then click “Show results” to run the new query.

exon Join window results — Example 3, Step 3 Query results with exon constraint

The results table now lists a new column Gene Exons, which we added to the query. If we look at the first row in the table, it lists 3 exons. Click on the 3 exons link to expand that entry. That column now has additional rows containing the exon DB identifier and Length for each of the 3 exons.

exon expand results — Example 3, Step 4 Query results with exon column expanded

In changing the join style to an outer join, the exons have been grouped together by gene making it easier to determine how many exons are contained in each gene. If the same query is run with the default join (outer join) of Show only Genes if they have an Exon, the results table adds a new row for each new exon rather than grouping exons by gene.

exon default join results — Example 3, Step 5 Query results with default join style run for genes containing exons