Searching Data ############## Filtering Data =============== The Search section of the accordion menu allows users to search phenotype, genotype, and cross data depending on the data in the program.  Click on the "Search" section of the left side accordion menu and then click on "Phenotype".  This will open the "Search by Phenotype" tab. This guide explains only the **phenotype search**. A similar procedure is used for **genotype search**, but in genotype search, the genotypic file created can be downloaded from the **User Account Page**.   .. image:: images/SearchingData1.png :width: 800   The first step to start a search is to select a property or trait under the "Choose property" section.  In this example, we are choosing "Parent."  After the property is selected, the "Set filter" section will populate with options for that data type.  After selecting the options you want, click "Add."  The selected filter will then appear in the “Phenotype search results" section.  If you want to reset the search, click the "Reset" button.   .. image:: images/SearchingData2.png :width: 800   You can further filter the search results by adding another property or trait under the "Choose property" section.  In this example, we are further refining the search by adding the Fruit Shape trait.  The "Set filter" section will show the data that are relevant for the previous filter you chose. For example, the statistics shown for Fruit Shape trait here are only for those accessions from the parents you chose in the previous search. You can set the minimum and maximum value of this trait, and then click "Add".  The new filter is added to the “Phenotype search results" section and the selected filters can be removed with the "Remove" button under “Phenotype search results".  To view the search results, and to generate a file to export, click on "View" under “Phenotype search results".   .. image:: images/SearchingData3.png :width: 800 Viewing and Downloading Search Results =========================================   When the "View" button is clicked, a new tab opens called “Phenotype Search Results".  On this tab there is a "Column options" section for phenotype and genotype, respectively, and a preview of the data table.   .. image:: images/SearchingData4.png :width: 800   Users can add more information to the table before exporting the data.  To do this, click on the "Column options for phenotype” section to expand it.  There are three sections: “Accession Properties", “Sample Properties”, and "Traits".  You can select additional items to display by clicking on the check boxes in these sections.  Once all the selections have been made, click "Update".   .. image:: images/SearchingData5.png :width: 800 Adding Trait and Associated Data to Results Table ****************************************************   After selecting additional data to display on the table, you can preview the table on the “Phenotype Search Results" tab and see the original filters that were used to generate the initial table by clicking on "Descriptions" in the "Results" section.  To download the data table, click on the "Download" button in the "Download Data" section.  If you do not see your browser start to download the file after clicking "Download," please make sure the pop-up was not blocked.   .. image:: images/SearchingData6.png :width: 800   BIMS generates a CSV file of the search results table. This table is easily opened by Microsoft Excel and other programs. .. image:: images/SearchingData7.png :width: 800 Adding Statistical Values to Results Table ********************************************* If “Statistics” is selected before downloading, an additional section will be added to the first tab containing the number of data points, the maximum, the minimum, mean, standard deviation, and frequency for each selected trait. If “Include averages” is selected, additional tabs will be included in the download. “Ave-selected-samples” will include the average trait values for each of the selected samples and “Ave-all-samples” will include the average trait values of all samples for each accession.   .. image:: images/SearchingData8.png :width: 800 Saving Search Results ========================== If you have a GDR account, you can also save the search results to a list. Under “Save Search Results”, you will see a "Save" button with boxes for a list name and description. This list will be saved to your program or to the public program that you are in and accessed by clicking on "Saved Search" under “Search Results” in the "Search" section of the accordion menu. This saved list creates a list of the accessions (stocks) and samples associated with the filtered data. You can see details about the saved lists and delete, view, or edit them. For example, if you click ‘View’, you can view and download the data for the filtered samples.   .. image:: images/SearchingData9.png :width: 800 The list of the accessions, or stock, associated with the filtered data as well as the list of samples can be accessed in other parts of BIMS. Both the sample lists and the accession list can be used in the `Data Analysis section `_. The accession list, not the sample list, can be used to filter in further searches in the “Search” section of the accordion menu. To do so, select “Accession List” from the “Properties” section. Once you select “Accession List”, the names of your saved searches will appear under “Accession List”. Select the list you wish to filter with and click “Add”. This will add data for all the samples associated with the accessions in the stock list to the current filter. .. image:: images/SearchingData9b.png :width: 800 Accessions can also be added manually for filtering by selecting “Name”. Users can copy/paste the list of accessions in the textbox, or search through accessions using one of the options from the dropdown menu as follows: Start with, exactly, contains, not start with, not exactly, not contains. Type the corresponding information into the box below, making sure to only type one accession per line if listing multiple. Then select “Add”. The list of accessions aligning with the input data will be added to the filtered search. Next, select “View” to view the filtered data. .. image:: images/SearchingData10.png :width: 800 The “Phenotype Search Results” tab will open with the data from the filtered search. To save the list to your search results, select “Save Search Results”, provide a name for the list, and select “Save”. .. image:: images/SearchingData11.png :width: 800 Now, under the “Search” and “Phenotype” tab, you can search and filter using your saved accession list under the same “Accession List” selection from “Properties”. Your saved accession lists will appear under “Accession List”. Select the list you would like to use and click “Add”. The list will now be added as a filter to your search results. .. image:: images/SearchingData12.png :width: 800 Searching Image Data ===================== To search and view image data, first select ‘Search’ from the accordion menu and ‘Phenotype’. Select your photo trait from the selection of ‘Traits’. In this example, photos are stored under ‘t-photo’. In the ‘Set filter’ box, select ‘Photo’ and click ‘Add’. Once the photo selection has been made, the ‘T-photo’ filter will appear in the ‘Phenotype search results’ box. You can further filter the search results by adding another property or trait under the “Choose property” section. Click ‘View’ to view the search results. .. image:: images/SearchingImages1.png :width: 800 The ‘Phenotype search results’ tab will open with all accessions (or the accessions that you filtered with other properties) with image data listed at the bottom of the page. Click any accession with photos in the ‘Results’ table. .. image:: images/SearchingImages2.png :width: 800 Within the sample tab, you can view photos by clicking ‘View Photos’. This will open a gallery pop-up, allowing you to toggle through all images associated with the selected sample. .. image:: images/SearchingImages3.png :width: 800 On the same page, ‘Download’ can be selected to download all images associated with the selected sample. .. image:: images/SearchingImages4.png :width: 800 Downloading Photos ******************** Users can download all photo data for the filtered dataset under the ‘Phenotype Search Results’ tab by selecting ‘Photo Page’. Selecting this option will open another tab called ‘Photo’. Users can download a specific photo-format trait by selecting ‘Download’ next to the trait or all photo-format traits by selecting ‘Download All’ next to All Traits. Additionally, the zipped file can be saved to your account by selecting the check box next to “Save the zipped file in your account” before pressing ‘Download’. .. image:: images/SearchingImages5.png :width: 800