Searching PFD
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Types Of Search
PFD has essentially two types of search, the standard search & the advanced search.
This article covers the standard search, for more indepth searching, please see our Advanced Search section.
Performing a Standard Search
Standard searches can be performed from the searchbox in the left menu.
The standard search searches across protein name, PDB, species name (both common & latin), SCOP Class, SCOP Family, mutation & mutant PDB fields.
You can enter a search term to search any of those fields for.
Search Term Examples
Search terms can be whole words:
"FKBP12" will return all entries of the protein "FKBP12".
"Human" or "Homo Sapien" will return all proteins from the "Human" species.
Search terms can also be partial words (this may return more results):
"Hu" will return all proteins from the "Human" species.
"Src" will return both "SrcSH2" & "SrcSH3".
Note: there is no need to enter the quotation marks in your search term.
The searchbox can also be left blank, this will return all wildtype protein data.
Search Keywords
As well as standard search words such as protein names, PDBs, species names, etc you can also use search keywords to expand & refine your search.
PFD's search currently supports the "+mutants" & "#<id>" keywords.
The "+mutants" keyword is used to indicate that you would also like to view mutant data amongst the wildtype proteins returned by a regular search.
Examples:
"FKBP12+mutants" will return all wildtype entries of the protein "FKBP12" plus it's mutants.
"CI2+mutants" will return all wildtype entries of the "CI2" plus it's mutants.
"+mutants" will return all wildtype entries plus their mutants.
The "#<id>" keyword can be used to indicate that you want to view a specific data entry.
Examples:
"#13" will return data for entry "13" (FKBP12).
"#21" will return data for entry "21" (Protein G).
You can find the data entry ID for a measurement beneath the protein image in the search results.
Search Keywords can also be combined:
"#13+mutants" will return data for entry "13" (FKBP12) plus the mutants for entry 13.
Note: there is no need to enter the quotation marks in your search term.
Search Results View
Once you have entered your search term, either click on the "Search" button, or hit the Enter/Return key.
This should search & you should then be presented with the search results view.
Ordering Results
By default all data in this view is ordered alphabetically by the Protein column, A being at the top of the results, Z being at the bottom.
You can reorder these results by clicking on the column headers along the top (Protein, Species, Family, etc).
When you order the data by a specific column, a little red arrow will appear, denoting which field the data is sorted on, and the direction of that sort (ascending or descending).
This image shows data sorted by Species column (ascending).
Clicking on a column again will reverse the direction of the sort.
Using "Field Select"
Field Select allows you to view more specific data about protein measurements by adding or removing data columns in the search results.
At the top of the search results view you should see a link entitled "Click here to open Field Select".
All the fields in the database, rather than being divided by the tables they appear in have been divided into a more logical & user friendly groupings.
The groupings are also colour coded to show which groups are related.
The colour codings are as follows:
Blue = General data about the protein. eg. name, species, PDB, sunids, etc.
Orange = Fields related to Equilibrium Methods, and data from that method. eg. pH, probe, ΔGD-N (m), etc.
Green = Fields related to Equilibrium Methods, and data from that method. eg. pH, probe, ku, kf, etc.
Grey = Mutant data. eg. mutation name, mutant PDB, ϕ values, etc.
Red = Other Measurement data. eg. ΔCp, Tm, ΔS Cal, etc.
Black = Extra optons. eg. Publications, Error values, etc.
Clicking on the link will open out the Field Select to show the various groupings.
Rows of groupings can then be expanded by clicking on the plus(+) icon on the left side of the row.
Rows can also be collapsed by clicking on the minus(-) icon, which appears instead of the plus icon when a row has been expanded.
You can then select or deselect fields from the expanded groups that you wish to add or remove in the search results view.
The "Select all" and "Deselect all" buttons make it easier to add or remove all fields in a grouping.
You may also have noticed the "Select all fields" & "Deselect all fields" in the white area at the top of the Field Select.
These buttons work similar to the buttons inside each grouping, they toggle the selection/deselection of fields, however rather than just do it for one grouping,
they do it across all groupings.
The "Restore to default fields" button is used for restoring the field selection to the default one returned by a standard search.
Ie. Protein, Species, Family, Class, Length, MW, Co (Rel.), ΔGD-N (m), mu, ku, kf.
After you have made your selection of fields to add and remove, you will need to click the either of the "Update Search Results View" buttons (located at the top & bottom of the Field Select) to update the results.
Here is a picture of the results of showing only fields in the "Construct related fields" group.
You can also reorder your data based on these newly added data columns.
Note: Method data columns cannot be ordered by.
Exporting Data
Once you have decided which fields you want to view & the order you want to view them in, you can then export the data into Comma Seperated Values (CSV) format.
The CSV format is supported by a wide range of spreadsheet applications such as Microsoft Office Excel, OpenOffice Calc & Gnumeric.
It is also supported by many online spreadsheet services like Google Docs & Spreadsheets & EditGrid.
Many database management systems & programming languages also support the importing of data from CSV format.
You can create a CSV file of the current search results view by clicking the "export this data to CSV" located at the top of the search results view.
Clicking the button should result in the page reloading & generating the CSV file.
Generation of a CSV file is usually fairly fast (under 5 seconds), however if you are exporting a lot of columns & a lot of data, this may take a bit longer, please be patient.
Once the CSV file has been generated the button should swap to a link to download the file.
As instructed by the link, you need to right-click (or control-click for mac users) and select the option the "Save Link As..." option (Note: This may be worded slightly differently depending on your browser).
Most modern web browsers are able to interpert CSV format, so left clicking may cause your browser to try to display the data as a page, rather than downloading the file, hence the need to right click.
The file should download to your download location as a file named "search_results_date_(time).csv", where date and time are the date & time that the server ran your query.
Safari users: Safari tends to add a ".txt" extension to the end of the file name, so it becomes "search_results_date_(time).csv.txt", you need to remove the ".txt" extension on the end of the file, so it ends in ".csv".
