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102 Welcome to the Breedbase manual!
104 This manual is intended for database users.\\
105 If you are a developer looking for software implementation details, please visit the developer wiki instead: \url{https://github.com/solgenomics/sgn/wiki}
114 \subsection{Verifying first that you do not already have an account}\label{verifying-first-that-you-do-not-already-have-an-account}}
116 Before creating an account, please verify first that you don't already have an account. You can use ``Search'' menu to check if you already registered as a user.
118 In the ``Search'' menu, selecting the ``People'' tab and search your name. If nothing is found, proceed with the instructions below. Otherwise, clicking the ``Login'' button. If you have forgotten your password, you can retrieve it by clicking the ``Forgot your password?'' link on the login page.
123 On the right of the toolbar, clicking on ``Login.'' It will take you to the login page. On the login page, clicking on the link ``sign up for an account.'' It will take you to the page below:
127 Filling in all of the information, then clicking ``Create Account.''
129 After you submit the information, an email will be sent to the provided email address. Checking your email and clicking on the link to activate your account.
137 To login, clicking the ``Login'' link in the toolbar on any page and enter your username and password.
139 If you have forgotten your password, you can retrieve it by clicking the ``Forgot your password?'' link on the login page.
146 Account settings can be edited by clicking on the ``my profile'' link displayed as your user name, on the right of the toolbar. You must login, in order to access and change account settings.
150 You can add personal information to your account using the ``View or update personal information'' link.
152 To change your password, username, or your contact email, clicking on ``Update account information'' link. You must provide your old password before you can make any changes.
157 \subsection{Changing Your Account Status: From ``User'' to ``Submitter''}\label{changing-your-account-status-from-user-to-submitter}}
159 After you create an account, your account has a ``user'' status. This account has limited privileges.
161 Accounts with ``user'' status are able to:
164 \tightlist
165 \item
166 Change personal information
167 \item
168 Post comments on pages
169 \item
170 Post to the forum
173 To upgrade your account status to ``submitter,'' contact the database curators using the ``contact'' link provided at the footer of each page. Submitter accounts can add data, such as new plots, accessions, phenotype data and images.
176 \subsection{Submitting Feedback on an SGN Database}\label{submitting-feedback-on-an-sgn-database}}
178 We appreciate your feedback! Feel free to submit any questions or suggestions by using the ``Feedback'' link provided at the footer of each page.
183 SGN Database websites have a toolbar on the top of each page with a number of menus for convenient access of major functions. The menus, as pictured below, are ``search,'' ``manage,'' ``analyze,'' and ``maps.'' The toolbar also provides a quick search, a ``log in'' button, and a ``new user'' button.
194 In the Search menu, the options are:
201 Tab
203 Description
206 \endhead
208 \endlastfoot
209 Wizard & Search different accessions and plots by location, year, trial, and trait data. Can also be used to create lists of different types. \\
210 Accession and plots & Search accessions and plots using a variety of criteria \\
211 Trials & Search trials by name, description, breeding program, year, location, and trial type. \\
212 Markers & Search different markers \\
213 Images & Search images contained in the SGN database \\
214 People & Search database users \\
221 In the Manage menu, the options are:
228 Tab
230 Description
233 \endhead
235 \endlastfoot
236 Breeding Programs & View, add and delete breeding programs \\
237 Locations & View, add and delete locations \\
238 Accessions & Manage and search different accessions \\
239 Seedlots & Manage and search different seedlots \\
240 Crosses & Create new crosses in the database \\
241 Field Trials & Manage field trials. Create trials using different field layouts. \\
243 Phenotyping & Upload phenotyping files from the Tablet Field Book application \\
244 Field Book App & Manage the field book app data (download files to tablet) \\
245 Barcodes & Refers to the old barcode system, mainly historical \\
246 Download & Download information in the database based on lists \\
254 In the Analyze menu, the options are:
261 Tab
263 Description
266 \endhead
268 \endlastfoot
270 Breeder Home & Access breeding functionalities. Lists important and helpful links. \\
271 Barcode Tools & Manage, create, and download barcodes. Also access barcode tools. \\
272 Genomic Selection & Can search for traits, start building a GS model, and predict values based on genotypes \\
274 BLAST & Sequence homology search \\
276 Ontology Browser & Browse all recorded ontologies \\
282 Lists are collections of identifiers that are stored in the database. Lists can be composed of accessions, plots, traits, locations, and trials. Lists are attached to the individual user's account, and can only be created and seen by the user while logged in. SGN databases make heavy use of lists in a number of tools on the website. For example, trials are created using lists of accessions.
287 Lists can be generated in various ways:
289 One way to create a list is by clicking on the ``Lists'' link located on the toolbar.
291 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_start} \end{center}
293 To create a new list, enter the name of your new list and then clicking on the ``New List'' button. The name of the list can be anything, but should be unique and should be something to help you easily identify.
295 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_new_list} \end{center}
297 You can find the list that you entered on the ``Your Lists'' page. To add items to your list, click on the ``View'' icon to open ``List Contents'' page.
299 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_view_list} \end{center}
301 On the ``List Contents'' page, enter items that you want to add to the list, then click on ``Add'' button.
303 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_add_items} \end{center}
305 The page will be updated and will display your items in a table at the bottom of the page. It is possible to sort the list if you need.
307 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_added_items} \end{center}
309 Select the type of items in your list. To verify that the items that you added to your list are already stored in the database and that you selected a correct type for the items, click on the ``Validate'' button.
311 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/list_manager_list_types} \end{center}
313 If those items are already in the database, a message will indicate that ``This list passed validation''
317 Note that a list cannot contain duplicate elements. If a duplicate item is entered, the list manager will inform the user that the element is already in the list and will not add it again.
319 Another easy way to create a list is to use \ref{search-wizard}, which can be accessed from the Search menu.
324 Lists can be viewed and edited using the ``Lists'' link on the toolbar. Clicking on the link will open a window that displays all of your lists, as well as an option to create new lists.
328 This page shows all lists that have been created, including those created by using the Search Wizard. You can view and edit your lists by using ``Actions'' buttons.
332 \item
333 Clicking on the ``view'' icon will open a new window called ``List Contents'' that allows you to change the list name, the type of the list, add new items, or delete existing items.
334 \item
335 Clicking on the ``delete'' icon will delete your list. \textbf{Caution: this action cannot be undone}.
336 \item
337 Clicking on the ``download'' icon will download the contents of your list to your computer.
338 \item
339 Clicking on the ``make public'' icon will make your list available for other users to view and use your list.
347 Breedbase accounts are assigned one or more of four different roles to determine the level of access they have within the database. The possible roles are \textbf{User}, \textbf{Submitter}, \textbf{Sequencer}, and \textbf{Curator}. Each role grants specific permissions, and careful management of them helps prevent data from being altered or deleted in error.
351 Accounts are also assigned Breeding Program role(s) to grant access to the specfic breeding program(s) they work with.
354 \tightlist
355 \item
356 The \textbf{User} role gives an account permission to view and download data throughout the database.
357 \item
358 The \textbf{Submitter} role gives an account permission to design field experiments and to upload and edit data using the tools in the ``Manage'' section. In order to submit and manage breeding data within a given breeding program, a submitter also must have a matching Breeding Program role.
359 \item
360 The \textbf{Sequencer} role gives an account permission to design genotyping experiments and submit plates to a genotyping service.
361 \item
362 The \textbf{Curator} role gives an account permission to do all of the above, as well as to delete data within the database. The Curator role also enables the addition or deletion of roles for all database accounts in the `Manage User Roles' tool.
368 You can search for information on the database by using the following search options: Wizard, which uses combined criteria specified by users; Accessions and Plots; Trials; Markers; Images; People; FAQ.
375 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/wizard_interface} \end{center}
380 The search wizard presents a number of select boxes, which are initially empty. You start searching by picking a category of data from the dropdown above the left-most select box.
382 Once a category has been picked, the database will retrieve all the options within this category and display them within the first select box. You then select one or more options from the first select box, which activates the second dropdown.
384 You can then select a category from the second dropdown, and repeat this same search process through all four dropdowns and select boxes.
386 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/wizard_interface_selections} \end{center}
389 \item
390 In the example above, the ``locations'' category was chosen in the first dropdown. The first select box then displayed all the possible locations in the database. The option Ibadan was selected.
391 \item
392 This activated the second dropdown. The category ``years'' was chosen in the second dropdown. The second select box then displayed all the years that are linked in the database to the location Ibadan. From that list, the options 2011 and 2012 were selected.
393 \item
394 This activated the third dropdown. A final category, ``accessions'', was chosen in the third dropdown. The third select box was then populated with the 3847 accessions in the database that are linked with the location Ibadan in the years 2011 or 2012.
397 In addition to the basic search operations demonstrated above, users can take advantage of two more features:
401 \begin{center}\includegraphics[width=0.25\linewidth]{assets/images/wizard_select_list} \end{center}
404 \tightlist
405 \item
406 Instead of picking a category in the first dropdown, users can instead populate the first selectbox from a list by scrolling down in the first dropdown to the ``Load Selection from List'' subheading and selecting a list. This is useful for starting queries with a list of plots, as this category is not among the options in the first dropdown.
411 \begin{center}\includegraphics[width=0.25\linewidth]{assets/images/wizard_any_min_all_toggle} \end{center}
414 \item
415 By default, the search wizard combines options within a category using an OR query. In the example above, in the third panel the wizard retrieved accessions associated with the location `Ibadan' in \textbf{ANY} of the years ``2011 \textbf{OR} 2012''
416 \item
417 If the user clicked the toggle below the second select box to change it to \textbf{ALL} before choosing accessions in the third dropdown, the wizard would instead retrieve accessions associated with the location `Ibadan' in the years ``2011 \textbf{AND} 2012''. This will be a smaller set of accessions, because any accessions used only in 2011, or only in 2012 will be excluded.
418 \item
419 A more advanced search could use the \textbf{MIN} toggle option. This allows the user to make a query in between an ANY or ALL query, where a minimum number of matches from the selected column will be used as a filter for the next column. The minimum can be provided as either a percentage (\%) or an actual count of items (\#). In the example above, if the years 2011, 2012, and 2013 were selected in the second column, the user could enter `2' in as the minimum and select `\#' as the minimum match type. This would select accessions in the third column that were used in 2 or more of the selected years.
422 \begin{center}\includegraphics[width=0.25\linewidth]{assets/images/wizard_any_min_all_toggle_min_details} \end{center}
431 Any option in the wizard select boxes (except for years) can be clicked to open a page with more details. The new page is opened in a new tab.
437 You can store the highlighted items in any selected box to lists. This is done using the inputs and buttons directly below the select box. \textbf{Don't forget, you must be logged in to work with lists!}
442 \item
443 To \textbf{add items to an existing list}, first pick an existing list using the ``Add to List\ldots{}'' dropdown on the left. Then click the ``Add'' button. A popup window will confirm the action, and display the number of items added to your existing list.
444 \item
445 To \textbf{store items to a new list}, first type a new list name in the ``Create New List\ldots{}'' text input on the left. Then click on the ``Create'' button. A popup window will confirm the action, and display the number of items added to your new list.
452 You can download trial metadata, phenotypes and genotypes associated with the highlighted items in the wizard select boxes. This is done using the buttons in the download section at the bottom of the page. \textbf{Don't forget, you must be logged in to download data!}
454 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/wizard_download_options} \end{center}
460 Trial metadata can be downloaded by selecting a subset of trials from the database or based on your search categories. To download, click on ``Related Trial Metadata'', a dialog will appear. Select download format and click the ``Metadata'' button to complete your download.
462 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/wizard_related_metadata_download} \end{center}
468 The phenotypes download is quite flexible, and can download a subset of all the trial data in the database based on whichever categories and options you currently have selected. Simply click on the ``Related Trial Phenotypes'' link, review the options, changing or adding any additional parameters you like, then click `Download Phenotypes'.
470 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/wizard_related_phenotypes_download} \end{center}
476 The genotype download is more stringent. It requires a minimum of one accession and one genotyping protocol to be selected in the wizard select boxes. The text box in the download section of the page will help track what has been selected. Once clicked, the ``Download Genotypes'' button will download a genotype file for the selected accessions.
482 As discussed above, the selections of the individual select boxes in the wizard can be saved separately to a list. The lists can be used as inputs in other tools on the site. However, sometimes creating a selection is quite time consuming and restoring the selections from four different lists would be cumbersome too. Therefore, the selections can be saved together in a dataset, and named for later retrieval. This is done in the section ``Load/Create Datasets'' that is below the first two wizard select boxes. To select an existing dataset, one uses the ``Load Dataset'' dropdown. A particular dataset can be chosen, and the ``Load'' button can be clicked to retrieve and display the dataset in the wizard. To create a new dataset using items that are selected in the wizard, one can enter the name of the new dataset in the ``Create New Dataset'' text box. Once the dataset has been given a name, clicking the ``Create'' button will save the new dataset.
484 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/wizard_load_create_dataset} \end{center}
489 The search wizard uses a copy of the database, or a cache, to return results quickly. If data appears to be missing, it usually means that the cache needs to be updated. Users with submitter privileges or above can do this using the `Update Wizard' button. One can also use the `Refresh Lists' button to update the available lists.
491 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/wizard_update_list_refresh} \end{center}
493 This will take just a few seconds in small databases, but may take a few hours to complete in larger databases.
498 Accessions and their related materials (cross, plant, plot, population, tissue\_sample, training population) can be searched by using ``Search Accessions and Plots'' page. On this page, ``accession'' is the default stock type; however, you can change stock type by selecting an option from the drop-down list. From this page you can construct detailed queries for stock types. For example, by using the ``Usage'' section, the ``Properties'' section, and the ``Phenotypes'' section you could search for accessions which were diploids used in a specific year and location and were also phenotyped for height. You can also search for accessions based on genetic properties, such as the location of an introgression on a specific chromosome.
500 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_accessions} \end{center}
502 It is possible to query over any of the available properties, such as ``ploidy\_level'', ``country of origin'', ``introgression\_chromosome'', etc.
504 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_accessions_properties_search} \end{center}
506 In the search result table it is possible to select any of the available properties to view.
508 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_accessions_properties_view} \end{center}
510 At the bottom of the accession search there is a phenotype graphical filtering tool. Here you can filter down accessions based on combinations of trait performance. The filtered down accessions are then able to be saved to a list.
512 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_accessions_graphical_filtering} \end{center}
514 For information on adding Accessions please see the Managing Accessions help. For information on how field trial plots, plants, tissue samples, and subplots are added to the database, please see the Managing Field Trials help.
519 Trials on the database can be searched based on trial name, description, breeding program, year, location, trial type, design, planting date, and harvest date.
526 On the Trait Search page (menu item \texttt{Search\ \textgreater{}\ Traits}), traits in the database can be searched by ID, name, or descripiton. Optionally, a starting list of traits can be selected to filter down results.
528 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trait-search-default} \end{center}
530 Selecting traits in the results of the search allows one to add the selected results to a trait list, or create a new trait list from the select results.
537 A more advanced tool for searching for Traits is the ontology browser, available by clicking on Analyze and Ontology Browser. From here you can search ontologies and see the various classifications of terms in a tree display.
539 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/ontology_browser} \end{center}
541 The terms which appear in the Trait Search in 2.4 are only variable terms. The ontology browser shows these variables as different from their grouping terms by indicating VARIABLE\_OF like in the following screenshot.
543 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/ontology_browser_variable} \end{center}
548 Seedlots are different from Accessions in that they represent the physical seed being evaluated in an experiment. Seedlots have things like physical storage locations and seed quantities, which accessions do not. To search for available seedlots you go to Manage and then click Seed Lots. By clicking Search Seedlots, you can specify query information. The results from your search will be in the table below the search form.
550 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_seedlots} \end{center}
552 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlots} \end{center}
557 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_user_roles_page} \end{center}
562 Every user account in Breedbase has one or more associated ``roles'' that determine the authorizations (what the user is allowed to do) in the database. There are three fundamental roles, ``curator'', ``submitter'', and ``user'', which determine basic read/write levels. The ``curator'' status can read and write everything in the database. The ``submitter'' status can add information and edit or delete previously submitted information. The ``user'' type can only read data. Additional roles represent the breeding programs, and are sometimes used to fine-tune write and edit capabilities, as it necessary for multiple users in a breeding program to edit each other's data.
567 In the ``Manage'' menu, select the item ``User Roles''. This will show the current users in the database with their associated roles. If you are logged in as a curator, the table will show system roles as well as breeding program roles; if you are logged in as a submitter or user, it will show breeding program membership.
569 If logged in as a ``curator'', the roles can be added or deleted.
572 \tightlist
573 \item
574 To delete a role, click on the X in the role name. A confirm dialog will be displayed to prevent accidental deletion.
575 \item
576 To add a role, click on the plus sign next to the roles. A dialog will pop up with a list of roles. Select the desired role and click ``Submit''.
577 \item
578 The new role should be displayed next to the user immediately.
579 \item
580 Role deletions and additions will be effective immediately.
583 It is recommended that few users be given the ``curator'' privileges to avoid confusion over data ownership and accidental data overwriting and deletion.
585 @ref(managing\_user\_roles)
590 New breeding programs can be added by using ``Add New Program'' button on the ``Manage Breeding Programs'' page.
594 Clicking on the ``Add New Program'' button will generate a blank form for you to fill out the name and description of the breeding program that you want to add. After completing the form, click on ``Add Breeding Program'' button to finish the process.
601 Field locations can be managed using the ``\textbf{Manage Locations}'' page. On this page, locations in the database are organized based on their breeding programs. Each location has a link to trials conducted in that location. To add a new location, click on the ``Add Location'' button that links to the ``Add New Location'' form.
605 On the ``Add New Location'' form, fill out the location name that you want to add. Latitude, longitude, and altitude are optional. Submit the new location by clicking on the ``Add Location'' button at the bottom right of the form.
612 The ``Manage Accession'' page provides links for adding new accessions. You can choose to add accessions into the database by either using a List you have created or by uploading XLS or XLSX file. Both options will be detailed below. To begin click on the ``Add Accessions or Upload Accession Info'' link.
614 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_link} \end{center}
616 This will open a dialog allowing you to select either ``Using Lists'' or ``Uploading a File''.
621 First we will show how to add accessions ``Using Lists''.
623 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_using_lists} \end{center}
625 Here you select an accession list which you have previously made. If you need to create or edit your list you can do so now by clicking ``Manage Lists''. Once you have selected your list you can click ``Continue''.
627 The first dialog which can appear will show the accessions which already exist in the database.
629 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_found} \end{center}
631 Click ``Continue''. The next dialog which can appear will show accessions which have very similar matches to the accession names you are adding. In the example below, there are two accession names that are very similar to accession names already in the database. `TME0419' is very similar to `TME419', and actually is probably a mistake that should not be added to the database.
633 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_fuzzy} \end{center}
635 To avoid situations in adding a mistaken duplicate accession, the database gives you options for moving forward with these very similar looking accession names. You can either ``continue saving the name in your list'', ``replace name in your list with selected existing name'', ``remove name in your list and ignore'', or ``add name in your list as a synonym to selected existing name''.
637 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_fuzzy_options} \end{center}
639 Clicking ``Download Fuzzy Matches'' will return a tabular result of the ``fuzzy'' accession name results shown. Click ``Make changes and continue'' to move on.
641 The final dialog shows the accessions that will be added. Here you need to assign the species of these accessions. You can optionally group the accessions into a population and/or add an organization for the accessions.
643 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_complete_using_list} \end{center}
645 Once you click ``Add Accessions'', the new accessions will be created in the database and you will see the following confirmation dialog, which includes links to the newly created accessions.
647 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_saved} \end{center}
650 \section{Uploading Accessions and Accession's Info From A File}\label{uploading-accessions-and-accessions-info-from-a-file}}
652 The process to upload accessions is very similar to using a list, but enables you to add a variety of properties, such as synonyms, to the accessions in bulk.
654 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_using_file} \end{center}
656 Clicking on ``Spreadsheet format'' will show the following dialog. Here it shows that the file must be XLS or XLSX format and can contain a number of header columns as attributes. It is important that you use exactly the same header column names as listed here. In columns that indicate that many attribute values can be passed at once using (s), such as synonym(s), you can pass a comma separated list of values, such as `synonym1,synonym2'.
658 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_spreadsheet_info} \end{center}
660 Once you have selected your XLS or XLSX file for upload, click ``Continue''.
662 The following process is the same way as with lists:
664 The first dialog which can appear will show accession names which are already in the database.
666 Click ``Continue'' and the next dialog that can appear will show ``fuzzy'' matches for the accession names you are trying to upload. Here you can choose to prevent adding accession names which look very similar to each other as wrongly duplicated accessions.
668 Click ``Continue'' and the final dialog that will appear will show the information to be added into the database. Here it is divided into accession names that are new and accession names that already exist in the database; however, for the accession names that already exist it will show additional attributes that originated from your file that will be added to these accessions.
670 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_accessions_add_accessions_complete_using_file} \end{center}
672 Once you click ``Add Accessions'', the new accessions and information will be created in the database and you will see the following confirmation dialog, which includes links to the created and updated accessions.
674 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/manage_accessions_add_accessions_saved} \end{center}
679 When uploading accessions from a file, you have the option to receive email notifications about the status and results of your upload by clicking the ``Email Alert'' checkbox. By default, the system will use the email address associated with your account, but you have the option to enter a different email address if you prefer. After submitting, the upload process runs in the background, allowing you to continue using the interface without interruptions. Once the process completes, you will receive an email with the upload results, including any warnings or errors that may have occurred during the upload.
681 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/accession_upload_using_email} \end{center}
684 \section{Add Parentage (Pedigree) Information to Accessions}\label{add-parentage-pedigree-information-to-accessions}}
686 Pedigree data can be uploaded from your computer by clicking on ``Upload Pedigree File''
690 \textbf{\emph{IMPORTANT!} Please use only tab-delimited text file format (.xls or .xlsx formats are NOT supported).}
692 You can find detailed information on how to prepare pedigree file by clicking on ``File format information''
694 The currently supported format has four tab separated columns:
696 progeny name female parent accession male parent accession type
698 Type can be biparental, self, backcross, sib, polycross, reselected, or open. In the case of the open type, the male parent accession field can remain blank. For all other types, both columns should be filled, even if they contain the same information as another column (such as self).
702 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/pedigree_upload_format} \end{center}
707 Grafts are plants that are composed of a rootstock and a scion, which are genetically different and fused together, usually at the stem level.
709 To work with grafts, the grafts interface needs to be activated by adding a configuration parameter in the sgn\_local.conf file. The parameter is show\_grafting\_interface. It should be set to 1 in sgn\_local.conf, the default is 0 (in sgn.conf).
711 Grafts to be created need to be specified using an Excel file (xlsx format) with two columns. The first column should have the header ``scion accession'' and should list accession names that will be scions. The second column should have the header ``rootstock accession'' and should list accession names that will be rootstocks.
713 In the database, the graft accessions will created as single accessions. The graft accession will have two relationships, one to the scion accession (scion\_of relationship) andone to the rootstock (rootstock\_of relationship). These relationships are displayed on the pedigree viewer. The graft accession name is created from the scion accession name and the rootstock accession name, separated by the graft separator character. By default, the graft separator character is the plus sign `+'. The graft separator character can be changed in the sgn\_local.conf file, using the parameter graft\_separator\_string. The graft separator string should not occur in any other accession names that are not grafts.
715 When the grafting interface is activated, a new button will be shown on the manage accessions page, called ``Upload Grafts''.
717 Clicking the button brings up the upload grafts dialog.
719 Select the Excel file containing the grafting information. The system will validate the file, for example, check whether the accessions are in the database, and if the headers are correct.
721 The validation result will be presented, and if problems are found, they will be listed. In addition, if there are problems, the Upload button will be grayed out and upload will not be possible. Conversely, if there are no problems, the Upload button will be activated and can be clicked to upload the data.
723 If the upload completes, a completion message is displayed with a summary what was uploaded.
725 Grafted accessions can be used like any other accession, for example, they can be used on field layouts. If you create a list of graft accessions, use the list type `accessions'.
727 Note that you shouldn't create new grafts based on other grafts. The scion accession and the rootstock accession have to be different, otherwise they will not be created.
732 Accessions can be renamed in bulk using the rename accessions feature. To rename accessions, prepare a tab delimited file with two columns: the first column should have the header ``old name'' and contain the accession names that need to be changed. The second column should have the header ``new name'' and contain the names that the accessions in column 1 should be renamed to.
734 The accession renaming feature is available from the Manage-\textgreater Accessions page. Click on the ``Rename Accessions'' button. The first step is the upload of the file with a verification step. The verification step checks whether all the accession names in column 1 exist in the database, and whether all the accession names given in column 2 do NOT exist in the database. Only if both conditions are met, will the ``rename'' button become active, otherwise an error message is displayed listing the offending accession names.
736 Optionally, the old name can be automatically added as a synonym to the renamed accession, using the checkbox on the submit form. This option is clicked by default. Unclick the checkbox to NOT save any old names as synonyms.
738 Note that accession renaming should not be undertaken lightly. This feature is intended for special use cases, such as where accessions are created in a nursery with a name that is different from the accession name in the downstream breeding program.
740 It can also be used to rename accessions in bulk that have spelling mistakes and other issues. Please note however, that the tool does not make any attempt to change the names of associated elements, such a plots, that may have been constructed using accession names.
742 Because of the many implications of accession renaming, the feature is limited to accounts with the curator role.
747 Seedlots are different from Accessions in that they represent the physical seed being evaluated in an experiment. Seedlots have things like physical storage locations and seed quantities, which accessions do not. The seed in seedlots can be from crosses or can be named accessions. Seedlots from crosses would represent seed harvested. Click Manage and then Seed Lots to begin.
749 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlots} \end{center}
754 To add a single new seedlot, click on ``Add Seedlot''. This will bring up the following dialog where you enter information about where the seedlot exists, what accession or cross is contained in it, and how many seeds there are. A seedlot must contain either an accession or a cross, and not both. A seedlot must have a weight in grams or a seed count or both of these.
756 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlot_add_seedlot} \end{center}
758 In the case where you have many seedlots to add to the database, you can upload an excel XLS or XLSX file instead. Click ``Upload Seedlots'' to see the following dialog.
760 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlot_upload_seedlots} \end{center}
765 Seedlots are capable of tracking where seeds came from, such as from crosses, and to where seeds go, such as to plots in the field. If you navigate to a seedlot detail page you will see the following.
767 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/seedlot_detail_page} \end{center}
769 On this page you see and can edit information regarding a single seedlot, such as its name and location. You will also see a table indicating all t he transactions that a seedlot has been involved in, such as if it was planted in a plot in the field. Transactions to field plots are created when adding or uploading a new trial or from a trial's detail page. Clicking on ``Add New Transaction'' let you add a transaction from between this seedlot and another seedlot. This kind of transaction is useful for representing if you have distributed seed to different locations.
771 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/seedlot_add_new_transaction} \end{center}
776 To inventory your seed: 1) Make sure your seedlots are in the database. Use ``Add New Seedlot'' to add a single seedlot or ``Upload New Seedlots'' to add many. 2) Make sure your seedlots are barcoded. You can print these barcodes from the database. 3) Use the ``Inventory'' Android Application to scan seedlot barcodes and record weight. Then use ``Upload Inventory'' to upload this info into database. If you prefer you can create your own CSV file and upload that, if you do not want to use the Inventory Application. For more info about the ``Inventory'' Android Application go to Inventory.
778 Clicking the ``Upload Inventory'' button will bring the following dialog:
780 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlot_upload_inventory} \end{center}
782 The CSV file that should contain your inventory should meet these Template requirements. The Seed Inventory Android Application exports this exact file.
784 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlot_upload_inventory_template} \end{center}
789 A convenient tool for searching available seedlots for a list of accessions is available in the list tool. First open up your list of accessions. For help opening a list of accessions please see the List section help. There is a button called ``See Available Seedlots''.
791 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/manage_seedlot_accession_list_search} \end{center}
793 Once you click this, you will see the following table in a dialog. From here you can create a list of seedlots using the checkboxes and the input at the bottom.
795 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlot_list_available_seedlots} \end{center}
798 \section{Create a seedlot for an Accession or Cross}\label{create-a-seedlot-for-an-accession-or-cross}}
800 Complementary to what we saw above for creating seedlots from the ``Manage Seedlots'' page, it is possible to create a new seedlot from an accession's detail page or from the cross detail page. On the accession detail page, this is visible in the ``Related Stocks'' section as seen below. The cross detail page has an identical section. Notice the link for creating a new seedlot, which streamlines adding the seedlot.
802 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlot_accession_detail} \end{center}
807 Quality information can be added to a seedlot in the quality field. This is also available as a column in the file upload format. It is recommended to use a controlled vocabulary, defined by the user, for the quality field. For example, good quality seed should be labelled ``ok'', whereas other quality descriptors could be ``moldy'', ``insect damage'', or ``low sprouting'', etc.
812 For some crops, such as sugar kelp, a ``seedlot'' requires routine maintenance for the successful long-term storage of the seedlot. (For example, a Seedlot Maintenance Event for sugar kelp would be the routine change of the water that gametophytes are kept it). Breedbase can now store a record of these Seedlot Maintenance Events associated directly with existing Seedlots. Maintenance Events can be uploaded using a simple Excel template or recorded directly on the website.
817 Each Breedbase instance needs to be configured to support the storage of Seedlot Maintenance Events since each crop will have their own distinct set of maintenance events for their seedlots. To check if your Breedbase instance supports this feature, go to the Manage menu and select the Seed Lots page. Make sure you are logged in and look for the \textbf{Seedlot Maintenance} button near the top, next to the \textbf{Create Seedlot(s)} and \textbf{Upload Inventory} buttons. If you don't see this button, contact the developer(s) supporting your Breedbase instance and ask if they can setup this feature.
819 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_seedlots_seedlot_maintenance} \end{center}
821 \emph{The location of the Seedlot Maintenance button on the Manage \textgreater{} Seed Lots page}
826 Seedlot Maintenance Events can be added using two methods: 1) Uploading an Excel template or 2) Recording events directly on the website
829 \subsubsection*{Uploading Events with Excel Template}\label{uploading-events-with-excel-template}}
832 To bulk-upload a file of Seedlot Maintenance Events, first create an Excel (.xls or .xlsx) file with the following headers:
835 \tightlist
836 \item
837 \textbf{seedlot} - the name of the Seedlot to associate the event with (must exactly match an existing Seedlot in the database)
838 \item
839 \textbf{type} - the name of the Seedlot Maintenance Event type (these vary between Breedbase instances, a list of supported event types is displayed on the upload page)
840 \item
841 \textbf{value} - the value of the Seedlot Maintenance Event (these may be different for each event type and vary between Breedbase instances, a list of supported event values is displayed on the upload page)
842 \item
844 \item
846 \item
850 Once you have an Excel file with the events filled out, follow these steps to upload the events to the database:
854 \tightlist
855 \item
856 Make sure you are logged in to your Breedbase instance
857 \item
859 \item
861 \item
863 \item
864 Choose your Excel (.xls or .xlsx) file to upload
865 \item
869 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/seedlot_maintenance_upload} \end{center}
871 \emph{The Seedlot Maintenance upload dialog, showing the supported event types and values (for sugar kelp)}
877 To add individual Seedlot Maintenance Events to the database in real time, as they're being recorded, use the \textbf{Record Maintenance} page. Follow these steps to record Seedlot Maintenance Events:
881 \tightlist
882 \item
883 Make sure you are logged in to your Breedbase instance
884 \item
886 \item
888 \item
890 \item
891 Enter the \textbf{Seedlot Name} or scan a barcode that has the Seedlot Name encoded. Once entered, the box at the top of the page will display basic information about the Seedlot as well its recently recorded events.
892 \item
893 Select or Enter the values of individual events
894 \item
895 Optionally, notes button next to each event to add additional notes/comments about that specific event
896 \item
897 Make sure the operator/username and timestamp are correct
898 \item
899 Select the \textbf{Submit} button to add the recorded events to the database. NOTE: any events that remain selected as ``Not Recorded'' will not be submitted to the database.
902 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/seedlot_maintenance_record} \end{center}
909 Recently recorded Seedlot Maintenance Events are displayed in a table from the main Seedlot Maintenance page, as well as the detail page for individual Seedlots.
911 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/seedlot_maintenance_events_unfiltered} \end{center}
915 The events displayed in these tables are sorted by timestamp, with the most recently recorded events displayed first. The displayed events can be filtered using any number of supported filter criteria, such as: - seedlot names (as entered on the page or using an existing seedlot list), - dates (on, on or before, before, on or after, and/or after the entered dates) - event types - event type values - operator/username
917 Select the properties of the filter(s) you want to apply, then select the \textbf{Add} button next to the button to add the filter to the list of applied filters. Once you're done adding filters, select the \textbf{Filter} button to search the database for the filtered events.
919 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/seedlot_maintenance_events_filtered} \end{center}
923 The filtered events can be downloaded directly from the table using the \textbf{Excel} or \textbf{CSV} buttons at the top of the table. Or Seedlot Maintenance Events can be bulk-downloaded (this includes all events for a Seedlot) using a list of Seedlots from the main downloads page (see below).
928 To bulk-download all events for a specific subset of Seedlots:
932 \tightlist
933 \item
934 Create a list containing the Seelots you are interested in.
935 \item
937 \item
939 \item
940 Select your list of Seedlots
941 \item
945 The downloaded file will follow the same format as the upload template and will contain all recorded Seedlot Maintenance Events for each Seedlot in the list.
950 Seedlots can be deleted on the Manage Seedlots page (/breeders/seedlots) by search the seedlot and then clicking the X to delete one seedlot at a time. To delete a seedlot, the logged in user needs the required delete privileges on the seedlot. The seedlot also should not have any transactions associated with it (except for the initial transaction).
952 To delete seedlots in bulk, generate a list of type seedlot, for example, using the wizard. Open the section ``Delete seedlots using a list'' on the Manage Seedlots page and select the list. Seedlot deletion using a list is only available to user with curator status.
957 Populations are modeled as groups of accessions. This grouping can be useful in downstream analyses. To manage these populations go to Manage Accessions and scroll tp the bottom.
959 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_populations} \end{center}
961 To add a new population click ``Create Population''. The following dialog will appear where you choose a list of accessions and give a name to the new population. Please note it is also possible to create a population when you are uploading new accessions into the database.
963 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/manage_populations_add_population} \end{center}
965 Click on the plus (+) button next to Populations to see all the available populations. Click on a population name to see the accessions in the population.
967 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_populations_expand_table} \end{center}
969 From here you can delete accessions from a population as well as add new accessions to the population.
971 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_populations_table} \end{center}
976 Information for crosses can be managed using the ``Crosses'' option in the Manage menu.
983 Different crosses in the same trial/nursery/project are grouped via ``\textbf{crossing experiment}''. Crossing experiments are organized based on their breeding programs. To find a crossing experiment, you can either type the crossing experiment name in the ``Search'' box, or look for the crossing experiment directly in its breeding program by clicking on the ``\textbf{+}'' icon. In each breeding program, crossing experiments can be placed directly in the breeding program, or organized in folders. The ``\textbf{Folders}'' section allows you to place crossing experiments in folders, move a crossing experiment in a folder to another folder, or rearrange your folders within a breeding program.
985 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_crosses1} \end{center}
987 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_crosses2} \end{center}
992 To add a new crossing experiment, click on ``Add Crossing Experiment'' link.
994 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_crosses_crossingtrial} \end{center}
996 Required Information:
998 • ``\textbf{Crossing Experiment Name}'': enter a name for the crossing experiment. The crossing experiment name must not already exist in the database.
1000 • ``\textbf{Breeding program}'': select a breeding program that is available in the database. New breeding programs can be added on the ``Breeding program'' page, accessible from the ``Manage'' menu. \emph{Breeding Program Page}
1002 • ``\textbf{Location}'': select a location for the crossing experiment. New locations can be entered on the ``\textbf{Locations}'' page, accessible from the ``\textbf{Manage}'' menu. \emph{Location Page}
1008 After filling in the information, click ``\textbf{Submit}'' to generate the crossing experiment.
1010 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/add_crossingtrial} \end{center}
1019 \subsubsection*{Add a cross by using the ``Add New Cross'' dialog}\label{add-a-cross-by-using-the-add-new-cross-dialog}}
1022 To add a single new cross, click on ``Add Cross'' link.
1024 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_crosses_addcross} \end{center}
1026 Enter cross information in the popup dialog.
1030 Required Information:
1036 • ``\textbf{Cross name}'': enter a name for the cross. The cross name must not already exist in the database.
1038 • ``\textbf{Cross type}'': the options for cross types are: biparental, self, open pollinated, bulk, bulk selfed, bulk and open pollinated, double haploid, polycross, reciprocal and multicross.
1040 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/new_cross_dialog_type} \end{center}
1042 • The ``\textbf{Female Parent''} and ``\textbf{Male Parent''} field are auto-complete fields for accessions that are already in the database. The parents specified will be entered in the pedigree of the new accessions generated by this cross.
1044 Optional Information:
1046 • ``\textbf{Female Plot and/or Male Plot}'': In addition to the accession names, specific plots used in the cross can also be added to the database. To retrieve plot names associated with each female/male accession, enter your trial name, then click ``\textbf{Search Plots}''. Plot names of each parental accession in that field trial will be shown in the drop-down list, you can then select the plot used in the cross.
1048 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/new_cross_dialog2} \end{center}
1050 Additional crossing experimental information such as pollination date, number of flowers, number of fruits, number of seeds can be specified during adding new cross. Alternatively, this information can be updated or edited directly on the ``\textbf{Cross Details}'' page.
1052 If you know the number of accessions that are generated from the cross, they can be instantiated immediately in the database by clicking the ``\textbf{Add accessions for progeny}'' checkbox and specifying the number.
1054 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/add_cross_info} \end{center}
1056 Click ``Submit'' to generate the cross.
1062 To upload new crosses from an Excel file (.xls or .xlsx), click on ``Upload Crosses'' link.
1064 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_crosses_upload} \end{center}
1066 Select a crossing experiment and a location available in the database from drop-down lists and choose a file that you want to upload, then click ``\textbf{Upload File}''.
1068 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/upload_crosses} \end{center}
1070 Please check spreadsheet format carefully. The file must be an Excel file (.xls or .xlsx).
1072 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_upload_format} \end{center}
1077 To upload progenies and/or experimental info of crosses already in the database, go to ``\textbf{Manage-Upload}'' page.
1079 In the ``\textbf{Crosses}'' section, there are links for uploading progenies and experimental info.
1081 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_upload_page} \end{center}
1083 Please check spreadsheet format in each link carefully. The file must be an Excel file (.xls or .xlsx).
1085 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/progenies_upload_spreadsheet} \end{center}
1087 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/crossinfo_upload_spreadsheet} \end{center}
1089 Note: crossing experimental information is customized based on the need for each crop. As a result, column headers for experimental info in your database may be different from the information shown in this manual.
1094 An Android ODK application is being developed to record cross information on a mobile device in the field. To link this mobile application with the database, the Cross Wishlist can be used to create a plan for which crosses to perform.
1096 This tool is available on the Manage Cross page. It is currently only available on certain databases, so when you click this link you may see an alert mentioning that the cross wishlist is not available on your database.
1098 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_cross_click_cross_wishlist} \end{center}
1104 \subsubsection*{Step 1. Select the accessions to be crossed in your trial}\label{step-1.-select-the-accessions-to-be-crossed-in-your-trial}}
1107 There are two interfaces for this step, either ``Not Using Lists'' or ``Using Lists''. Depending on if you already have a list of female and male accessions to use, you can decide on which interface to use. The end result of using either interface is the same.
1109 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_wishlist_initial_dialog} \end{center}
1111 We will start by showing ``Not Using Lists''. First select the trial in which the crosses are to be performed. This will populate a select box with all the accessions used in that trial. From here, one or many accessions can be selected as the female accession.
1113 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_wishlist_not_using_list_01} \end{center}
1115 Once the female accessions are selected, a table is populated. Each row in this table begins with the female accession that was selected, followed by a select box with all the accessions used in the trial. From here, one or many accessions can be selected as the male to use in the cross.
1117 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_wishlist_not_using_list_02} \end{center}
1119 Once the male accessions are selected to cross with each female accession, a table indicating priorities appears. Priority is meant to indicate an order in which to attempt the cross; first the highest priority male will be considered, but if this cross is not possible then subsequent males will be considered. An equal priority can be given and this will not indicate a specific order to follow.
1121 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_wishlist_not_using_list_03} \end{center}
1123 Alternatively, we could have used the ``Using List'' interface instead. Here we select the trial in which the crosses will be performed and we provide a list of accessions to consider for the females and the males to be crossed.
1125 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_wishlist_using_list_01} \end{center}
1128 \subsubsection*{Step 2. Select the female plots to be considered in the crosses}\label{step-2.-select-the-female-plots-to-be-considered-in-the-crosses}}
1131 After selecting your lists, the table below is populated. The first column has all the female accessions specified and the header row has all the male accessions specified. The males to consider crossing with each female are indicated with priority.
1133 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_wishlist_using_list_02} \end{center}
1135 After female and male accessions are selected to cross, either by the ``Nor Using List'' or ``Using List'' interface, click Next. The next dialog will allow selection of specific female plots to use for the cross. Sections for each female accession selected will appear with the field layout displayed. Selecting all plots in which the female is present indicates that the cross should be performed on all plots where that female accession is present.
1137 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_wishlist_not_using_list_04} \end{center}
1140 \subsubsection*{Step 3. Transfer the cross wishlist to your mobile crossing application}\label{step-3.-transfer-the-cross-wishlist-to-your-mobile-crossing-application}}
1143 Clicking ``Push Cross Wishlst for ODK Use'' will send the cross wishlist plan to the ONA server for use by the mobile ODK application. Crosses can then be performed and recorded in the field using the mobile application. Afterwards, the crosses are sent back to our database and stored.
1148 Information for crosses in the same crossing experiment is compiled in the crossing experiment detail page.
1150 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/crossingtrial_1} \end{center}
1152 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/crossingtrial_2} \end{center}
1154 Each cross name, female parent, male parent, female plot and male plot has a link to its own detail page, which contains information specific to each one. Note: crossing experimental information is customized based on the need for each crop. As a result, the details of the information in your database may be different from the information shown in this manual.
1159 Information of each cross can also be viewed in its detail page.
1165 This page allows you to update or edit crossing experimental information and add progenies related to that cross. Note: crossing experimental information is customized based on the need for each crop. As a result, the details of the information in your database may be different from the information shown in this manual.
1167 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/edit_cross_info} \end{center}
1169 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/cross_add_progenies} \end{center}
1174 To view trial details on the database, click on the ``Field Trials'' link under the ``manage'' menu on the toolbar.
1178 Clicking on the ``Field Trials'' link will bring you to the ``Manage Trials'' page. On this page, trials are organized according to their breeding programs. To access trial details, click on the + icon next to your breeding program.
1182 Trials can be placed directly in their breeding program. Alternatively, they can be organized by using folders within each breeding program. Clicking on trial name will take you directly to the trial details page.
1189 Trial detail page displays important information about individual trial including breeding program, location, year, description of the trial, design, and any files associated with that trial.
1191 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_start} \end{center}
1193 The ``Navigator'' section on the trial detail page allows easy access to all aspects of your trial. This section contains subsections for printing labels for your plots or plants, recording phenotypes, viewing your trial layout or design, viewing phenotypes for this trial, or conducting analyses.
1195 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_navigator} \end{center}
1197 The ``transplanting date'' field feature will only be shown if it has a value. To add a transplanting date after creating a trial, change the show\_transplanting\_date parameter from 0 to 1 in the SGN config file. As a result, you will be able to add a date under the transplanting date field by clicking the ``Edit Trial Details'' on the trial detail page.
1199 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/add_transplanting_date} \end{center}
1204 Only users with the account status of ``submitter'' may create trials. To learn how to change your account status from ``user'' to ``submitter'' visit the \ref{managing-your-account} page.
1210 \item
1211 To add a trial, all of your accessions should already exist in the database before you begin to design a trial. If you have accessions that are not in the database, see the instructions for adding accessions .
1212 \item
1213 Breeding program and location for your trial should also exist in the database. If you need to add breeding program and/or location to the database, see instructions for adding breeding program and location in the ``Managing Breeding Programs'' and ``Managing locations'' respectively.
1216 On the ``Manage Trials'' page, there are three alternative methods for you to add new trials: by using ``Add Trial'' form, ``Upload Trial'' form, or ``Add Multi-location Trial'' form.
1218 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_manage_trials} \end{center}
1221 \subsection{Adding a trial by using ``Add Trial'' form}\label{adding-a-trial-by-using-add-trial-form}}
1224 \subsubsection*{Step 1. Begin the ``Design new trial'' workflow}\label{step-1.-begin-the-design-new-trial-workflow}}
1227 Click on ``Design New Trial'' to begin.
1229 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_open_form} \end{center}
1231 The first step in this workflow is an introduction that looks like:
1233 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_1} \end{center}
1235 Here it gives information about what is required for a trial, including that to create a new trial, you need to create a list of the accessions that you would like to use in the trial. Lists can be viewed, created, and modified with the ``\textbf{lists}'' tool at the upper right of the screen. For more information on lists, click \protect\hyperlink{working-with-lists}{\emph{here}}.
1241 On this screen you need to enter basic information about the trial, such as breeding program and location(s). You must also select a design type, such as Complete Block Design. The design is important because it influences how your genotypes are distributed and randomized over the trial. You must first click validate before proceeding to the next step.
1243 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_2} \end{center}
1249 On this screen you need to specify a list of accessions to use in the experiment. This list must be a valid list of accessions. You must also specify all required design information, such as number of blocks in this case.
1251 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_3} \end{center}
1254 \subsubsection*{Step 4. Enter ``Field Map Information'' (Optional)}\label{step-4.-enter-field-map-information-optional}}
1257 On this screen you can specify how the row and column numbers will be generated for the plots in the trial. The row and column number represent a relative position of the plot in the field. If you are not exactly sure of how you will plant the plots in the field or you have an irregular (non-rectangular) layout, you can skip this step for now. This information can be added on the Trial Detail Page once the trial is saved in the database in order to reflect exactly how the plots were planted in the field.
1259 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_4} \end{center}
1262 \subsubsection*{Step 5. Custom Plot Naming (Optional)}\label{step-5.-custom-plot-naming-optional}}
1265 On this screen it is possible to change the format in which plot names will be generated for your trial. It is recommended to skip this step and just use the format generated by the database by default.
1267 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_5} \end{center}
1273 On this screen you can review the trial that the database has generated.
1275 You will see a graphical representation of the trial. The numbers on the squares represent the plot\_number of each plot and on mouse hover you can see further information about the plot.
1277 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_6_top} \end{center}
1279 You will also see a table representation of all the plots and their information. If you want to redo the randomization, you can click the ``Redo Randomization'' button.
1281 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_6_middle} \end{center}
1283 At the bottom there is a brief summary of the trial followed by two buttons.
1285 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_6_bottom} \end{center}
1288 \subsubsection*{Step 7. Add Field Management Factors to your design (Optional)}\label{step-7.-add-field-management-factors-to-your-design-optional}}
1291 You can add Field Management Factors by clicking ``Add Field Management Factor(s) to Design''. Clicking this opens a dialog to name your factor. You can name this to account for fertilizer or watering regime or inoculation or anything else. This is optional and can be added from the trial detail page afterwards.
1293 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/add_management_factor_name_dialog} \end{center}
1295 Click ``Continue'' and a dialog will appear where you can specify plots for which the factor was applied. There is a select all button also.
1297 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/add_management_factor_dialog} \end{center}
1300 \subsubsection*{Step 8. Saving new trial in the database}\label{step-8.-saving-new-trial-in-the-database}}
1303 Once you are done reviewing the trial you can click ``Confirm'' to save the generated trial into the database. Once the trial has saved you will see the final completion screen:
1305 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_create_form_7} \end{center}
1310 If you already have trial design layout in a spreadsheet, you can add your trial into the database by using ``Upload Trial'' form. To access ``Upload Trial'' form, click on ``Upload Existing Trial(s)'' button on the ``Manage Trials'' page.
1314 When you click ``Upload Existing Trial(s)'' you will see the following workflow. Notice that there are 5 numbered sections to the workflow.
1320 The first step is to understand what the format of the trial upload is. It is important to understand that the field layout represents plots in the experiment. Each plot has a globally unique plot\_name, a sequential plot\_number that is unique in the trial (but not globally unique. e.g.~101, 102, 103 for three separate plots), an accession\_name representing what genotype is planted in that plot, and a block\_number representing design replication. Each plot can be thought of as having a row\_number and a column\_number representing the relative position of the plot in a grid (e.g.~the top left plot is row 1 column 1 following by row 1 column 2). Each plot can be planted with an amount of seed from a seedlot, where the seedlot\_name represents the specific seed packet that was used, and num\_seed\_per\_plot and weight\_gram\_seed\_per\_plot represent amount that were transferred from the seedlot\_name to the plot\_name. Treatments (management factors) can be applied onto plots using additional column names in your file, where a 1 represents if the factor was applied to the plot and an empty cell means it was not applied.
1322 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_upload_trial_1} \end{center}
1324 This information and more can be found by clicking ``Information about file format'', which shows the following:
1326 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_upload_trial_template} \end{center}
1333 \item
1334 All accession names in the file must exist in the database. See adding accessions for more information.
1335 \item
1336 The uploaded file should be XLS or XLSX file format (NOT CSV).
1337 \item
1338 The first row (header) must contain the column names: plot\_name accession\_name plot\_number block\_number is\_a\_control rep\_number range\_number row\_number col\_number seedlot\_name num\_seed\_per\_plot weight\_gram\_seed\_per\_plot
1341 Minimal Example:
1383 \endhead
1385 \endlastfoot
1397 \tightlist
1398 \item
1399 In case of errors in the uploaded file such as missing or invalid data, a window will appear listing the specific errors in the file that must be corrected before a successful upload.
1403 \paragraph*{Uploading a trial with Field Management Factors}\label{uploading-a-trial-with-field-management-factors}}
1407 \tightlist
1408 \item
1409 You can upload a trial with field management factor(s) by adding additional column(s). The column header will be the factor e.g.~fertilizer, watering regime, inoculation, etc. and the values in these columns will be either 1 or empty, indicating that the factor was applied to the plot or not.
1416 Once you feel that your experiment field layout is in the right format, click on to the Next Step. You will see the following form which must be filled in completely:
1418 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_upload_trial_2} \end{center}
1420 The trial name must be globally unique in the database. Please try to follow standard naming conventions for your group.
1422 First you need to validate the form, and then you can click ``Upload Trial''.
1428 In the case where you have uploaded an experiment using accession\_names that are not already present in the database, you will be taken to this screen. If the accession\_names in your file are all already in the database, this step will be skipped. The reason it is necessary for your accessions to be in the database before you can add a trial using them is that a single accession can be used among many trials and therefore must exist as a separate entity in the database; because of this it is also very important to be careful about adding wrongly duplicated accession\_names into the database. From this screen it is possible to make a new list with the missing accession\_names and then click ``Add Accessions to the database'' to immediately resolve the issue. Once all your accessions are in the database, click to move to the Next Step.
1430 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_upload_trial_3} \end{center}
1436 In the case where you have uploaded an experiment using seedlot\_names that are not already present in the database, you will be taken to this screen. If the seedlots in your file are all already in teh database, this step will be skipped. The reason it is necessary for your seedlots to be in the database before you can add a trial using them is that a ginel seedlot can be used among many trials and therefore must exist as a separate entity in the database. From this screen it is possible to add the missing seedlots; you can either upload an XLS or XLSX file to add many at once or you can add them one by one. Once all your seedlots are in the database, click to move to the Next Step.
1438 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_upload_trial_4} \end{center}
1444 If there are any other errors with your file, such as if the plot\_names are not globally unique in the database or your plot\_numbers are not unique in your trial or row\_number is not an integer or any other error, you will see the errors listed in the red box. It is up to you to correct these errors in your file. Simply open up the file you selected earlier in Excel and correct the issues and then save the file. Then you can click ``Submit Trial'' and it will resubmit it for you. You can continue to edit your file here and submit as many times as you need until it is accepted.
1446 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_upload_trial_5} \end{center}
1452 Whether you were lucky enough to submit your trial successfully on Step 2 or if you tried many times on Step 5, once your trial has been saved in the database you will see the following screen:
1454 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_upload_trial_6} \end{center}
1459 To add multi-location trials, simply select the multiple locations while using the `Add Trial' form.
1461 This will create a separate trial for each selected location, but they will share the same design and will be grouped in a single folder.
1463 By default each trial design will have a fresh randomization, but if desired you may check the ``Use same randomization for all locations'' option.
1466 \subsection{Email alert for multiple trial design upload}\label{email-alert-for-multiple-trial-design-upload}}
1468 When uploading multiple trials from a file, you have the option to receive email notifications by clicking the ``Email Alert'' checkbox. By default, the system will use the email address associated with your account, but you have the option to enter a different email address if you prefer. After submitting, the upload process runs in the background, allowing you to continue using the interface without interruptions. Once the process completes, you will receive an email with the upload results.
1470 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/multiple_trial_upload_with_email} \end{center}
1473 \subsection{Viewing Plot Layout and Trait HeatMap}\label{viewing-plot-layout-and-trait-heatmap}}
1478 In the ``Field Layout Tools and Phenotype Heatmap'' section of a Trial Detail page, the trial physical layout is displayed by default. The relative position of the plots will be displayed based on the row and column positions given to the plots during the trial creation or upload steps. The plots are color-coded based on the plot's rep and block numbers and whether or not it is used as a check. Hover the mouse over the plot to see details about a specific plot.
1480 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/fieldmap_trial_layout} \end{center}
1482 If there is more than one trial grown in the same physical field, the trial layouts of all of the trials can be shown together if the trials share these properties:
1484 Each trial has the same year
1486 Each trial has the same location
1488 The location type of the trials' location is set to Field
1490 The row and column positions of all of the plots (across the related trials) don't overlap. For example, trial \#1 starts at row 1 and trial \#2 starts at row 10.
1492 When these conditions are met and you check the ``Select Trials in Same Field'' checkbox, the plots from all of the related trials will be displayed on the same field layout. The plots will be color-coded by trial. The planting order and harvest order downloads will include the plots from all of the displayed trials in the order in which the plots occur in the field.
1494 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/fieldmap_multi_trial_layout} \end{center}
1497 \subsubsection{Viewing plot layout for multiple trials}\label{viewing-plot-layout-for-multiple-trials}}
1503 Plot images can be seen on fieldMap if a plot is associated to any image.
1505 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/fieldmap_plot_image} \end{center}
1507 To view plot image(s), click on a plot, a dialog will appear.
1509 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/fieldmap_view_plot_image} \end{center}
1511 On the appeared dialog, click on View plot images. To see more images if a plot has more that 2 images, click on See more images\ldots{} Medium size of an image can be viewed by clicking on an image.
1513 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/fieldmap_display_plot_image} \end{center}
1519 Phenotype heatmap can be viewed by selecting a specific assayed trait from the selectbox drop-down. Mousing over the plots, highlights the plot in green and also displays the plot's field information including the selected trait's phenotype value.
1521 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/heatmap_assayed_trait_view} \end{center}
1527 Clicking on a plot on the heatmap would display a dialog that has a button for suppressing a plot phenotype value for a given trait. A suppressed plot value can be excluded during trial analysis and phenotype download.
1529 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_suppress_phenotype} \end{center}
1532 \subsection{Adding additional information in the ``Trial Detail'' page}\label{adding-additional-information-in-the-trial-detail-page}}
1534 After you added a new trial to the database, you can edit trial details or add more information for that trial through the``Trial Detail'' page.
1540 You can upload physical trial layout by clicking on the ``Upload trial coordinates'' button on the ``Trial Detail'' page.
1544 Please check file format carefully. You can find file format information by clicking on the ``Spreadsheet format'' on the ``Upload trial coordinates'' window.
1548 Spreadsheet format:
1553 \subsubsection*{Physical Trial Layout File requirements}\label{physical-trial-layout-file-requirements}}
1557 \item
1558 All plot names in the file must exist in the database.
1559 \item
1560 The uploaded file should be tab delimited (txt).
1561 \item
1562 The first row (header) must contain the column names
1565 Example:
1571 \endhead
1573 \endlastfoot
1579 Select the trial layout coordinates file that you want to upload for this trial, then click ``OK'' button to upload the file.
1583 The following message is displayed after the coordinates are uploaded.
1587 The field layout can be viewed by clicking on the ``Trial Heatmap Section'' to see a drop-down of the field map.
1589 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/heatmap_default_display} \end{center}
1595 Field map spreadsheet can be downloaded if the trial has field coordinate (row and column numbers) uploaded for it plots. To download, click on the Download FieldMap Layout link on the Trial Heatmap section.
1597 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/field_map_download_link} \end{center}
1599 A dialog will appear, click on the submit button to download.
1601 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/field_map_download_dialog} \end{center}
1603 Click to view downloaded spreadsheet.
1605 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/field_map_download_spreadsheet} \end{center}
1611 ``Usage Help'' link contains information on how to edit physical trial layout.
1619 There are three different options for editing trial layout:
1622 \item
1623 Replacing plot accession by clicking on the plot in the layout.
1624 \item
1625 Replacing trial accession by using ``Edit Field Map'' link.
1626 \item
1627 Substituting plot accessions by using ``Edit Field Map'' link.
1630 When you move a cursor over a plot on the trial layout, information for that plot appears.
1634 To edit a specific plot, clicking on that plot. Entering new accession on the ``Replace Plot Accession'' form, then clicking on ``Replace Plot Accession'' button.
1638 To replace an accession (in every plot/plant of that accession), clicking on ``Edit Field Map'' button.
1642 On the ``Edit Field Map'' window, clicking on ``Replace Accession'' button.
1646 Selecting any accession that you want to replace and entering your new accession, then clicking ``Replace Trial Accession'' button.
1650 You can switch plot accessions between any two plots by clicking on ``Substitute Accession'' button.
1654 On the ``Substitute Plot Accession'' form, selecting the two plots that you want to switch, then clicking on the ``Substitute Plot Accession'' button.
1659 \subsection{Downloading the Trial Layout from the ``Trial Detail'' page}\label{downloading-the-trial-layout-from-the-trial-detail-page}}
1661 Click on ``Download Layout'' on the Trial Detail page.
1665 The trial layout includes all information regarding the observation units in the experiment. The observation units can be plots, plants, or subplots. The trial layout can include trial design information such as the block\_number and rep\_number. It can also include physical map information such as the row\_number and col\_number, if that information is available for the trial. The trial layout also includes information regarding treatments that have been applied in the field. Optionally, the layout can give information regarding accession's global performance for a list of traits.
1672 After you added a new trial to the database you can choose to add plant entries to your trial. Adding plant entries enables plant level phenotyping. It is generally better to enter data at the plant level into the database because it is always possible to calculate plot level phenotypes from the individual plant data.
1674 Plant entries can be added to your trial in two ways: 1) Automatically generated by the database. The only input required is the number of plants per plot. 2) Uploaded in an XLS or XLSX file. This allows you to specifically name your plant entries.
1676 These two options are available in the ``Plant Entries'' section on the Trial Detail Page, as shown in the screen shot below.
1678 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_add_plant_entries} \end{center}
1681 \subsubsection*{Automatically Generate Plant Entries}\label{automatically-generate-plant-entries}}
1684 Clicking on ``Add plant entries'' opens the following dialog box. The only input required is the number of plants per plot. This will create plant entries that are named as a concatenation of the plot\_name and the plant's index number e.g.~plot\_name\_plant\_1
1686 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_add_plant_entries_autogenerated} \end{center}
1692 Alternatively, you can choose to upload an XLS or XLSX file that contains the names of the plant entries. Clicking on ``Upload plant entries'' opens the following dialog box.
1694 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_add_plant_entries_upload} \end{center}
1696 Clicking on ``Spreadsheet format'' will give you information about the XLS or XLSX file to upload. Clicking this will open the following dialog box.
1698 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_add_plant_entries_upload_info} \end{center}
1700 This shows you that the files requires the header to contain ``plot\_name'' and ``plant\_name''. The plot\_name must exist in the database already and the plant\_name must be unique in the database.
1702 Along with the file, you must specify ``number of plants per plot''. This is intended to be the total number of plants that were plants. If the file you upload shows three plants in one plot and four plants in another plot, that is fine.
1705 \subsection{Adding Tissue Sample Entries To Your Trial}\label{adding-tissue-sample-entries-to-your-trial}}
1707 Some trials require tissue samples to be collected from plants in a field trial. The database will generate these tissue sample identifiers for you and will maintain all relationships with the plant, plot, accession, etc. To begin, go to the Design section of a trial's detail page and open the ``tissue sample entries'' section. Please note that tissue samples are directly related to plants, therefore your trial requires plants before you can add tissue samples.
1709 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_tissue_sample_default} \end{center}
1711 When you click on ``Add tissue sample entries'' you will see a dialog where you specify the number of tissue samples you require per plant. Once you have specified how many tissues samples, you can give specific words to distinguish samples, such as ``root'' or ``stem'', as seen below.
1713 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_tissue_sample_create} \end{center}
1715 Once you have added tissue sample entries they will appear in the design section of the trial as seen below.
1717 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_tissue_samples} \end{center}
1719 Each tissue sample has a detail page where you can add information about the sample, such as if it is in transit or in storage somewhere.
1721 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_tissue_sample_detail} \end{center}
1723 The related stocks section near the bottom of this detail page displays the relationships between all stocks, including tissue samples.
1725 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_trials_tissue_sample_related_stock} \end{center}
1730 You can upload GPS coordinates for the plots in your trial. There is a link on the Trial Detail Page as shown below.
1732 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_add_plot_gps} \end{center}
1734 Clicking on this link will bring up the following dialog.
1736 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_add_plot_gps_dialog} \end{center}
1738 Here you can upload an XLS or XLSX file. To see information on the format of the file that should be uploaded, click on ``Spreadsheet format''. This will bring up the following dialog.
1740 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_add_plot_gps_upload_info} \end{center}
1742 This dialog tells you that the file must be XLS or XLSX and must contain: plot\_name WGS84\_bottom\_left\_x WGS84\_bottom\_left\_y WGS84\_bottom\_right\_x WGS84\_bottom\_right\_y WGS84\_top\_right\_x WGS84\_top\_right\_y WGS84\_top\_left\_x WGS84\_top\_left\_y The GPS coordinates should be WGS84 format and specify a four-pointed polygon around the plot.
1747 It may be of interest to you to upload additional documents, images, or recordings to your trial. To do this, scroll down to the ``Uploaded Additional File'' section on the trial detail page. From here you can view and download any of these additional files.
1749 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_upload_additional_file} \end{center}
1751 To upload an additional file, click on the ``Upload Additional Files'' link. A dialog will appear where you simply select your desired file. For information, you can click ``Upload information'' to see the following message.
1753 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_upload_additional_file_info} \end{center}
1758 To delete a trial data, click on the ``Delete trial data'' section. There are links to delete traits, layout and trial entry data.
1760 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_delete_trait1} \end{center}
1762 To delete assayed trait data, click on ``Delete trait data'' link. On the appeared dialog, confirm deletion by clicking on the ``Select Traits For Deletion'' button, then select one or more traits to delete from the trial.
1764 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_delete_trait2} \end{center}
1766 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_detail_page_delete_trait3} \end{center}
1768 To delete trial layout data, click on the ``Delete layout data'' link. Confirm deletion on the appeared dialog.
1770 To Delete trial entry, click on ``Delete trial entry'' link. Confirm deletion on the appeared dialog.
1775 Genotyping Plates represent the content of a genotyping plate sent to a genotyping facility (e.g.~samples in specific wells). To streamline this process, it is possible to upload this information or let the database create a plate for you. Once the genotyping plate is saved in the database it is then possible to export the information directly to genotyping facilities that are BrAPI compliant. The genotyping facility can then provide status information to us via BrAPI.
1777 To begin go to Manage-\textgreater Genotyping Plates.
1779 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_trials} \end{center}
1781 Here the genotyping plates are divided by Breeding Program. These sections can be expanded by clicking on one.
1783 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_trials_expand} \end{center}
1788 To begin, click on ``Add Genotyping Plate''. Notice that this form is split into three sections: ``Plate Information'', ``Well Information'', and ``Confirm''. The first section is for defining information about the genotyping plate, such as a Plate identifier, plate format (96 well), etc. The second section is for defining the samples in the wells, such as sample names, sample concentrations, well position, etc. The final section is for Submitting the info.
1790 All fields in the Plate Information section are required.
1792 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_trials_add_trial} \end{center}
1794 In the Well Information section you can choose to either 1) Upload an XLS or XLSX spreadsheet with your sample layout or 2) let the database create the sample layout.
1796 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_trials_add_trial_wells} \end{center}
1798 If you choose to upload an XLS or XLSX spreadsheet, the Spreadsheet Template info requires the following:
1800 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_trials_upload_template} \end{center}
1802 In either case, the sample identifier is generally a concatenation of Plate name and well position, e.g.~MyGenotypingTrial1\_A01. In either case, you need to provide a ``source\_observation\_unit\_name'' for each sample. This can be a tissue sample name, a plant name, a plot name, or an accession name; however, in any case, the identifier must already exist in the database. This allows us to link the sample in the well to specific field trial plots, or, plants, or tissue\_samples. If you only know which accession is in the well, you can use the accession name.
1804 In the final Confirm section you can decide whether to submit this information to the genotyping facility you selected. This requires that the genotyping facility is BrAPI compliant to work.
1806 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_trials_add_trial_confirm} \end{center}
1811 If you open a specific genotyping plate, it will take you to the detail page. Here you can see the Accessions used in the plate (if you created the trial and the source\_observation\_unit\_names you used were plots, this will still work because we know the accession of the plot or plant or tissue sample).
1813 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_trials_detail_info} \end{center}
1815 Further down you can see a graphical representation of your plate with well positions. This can be 96 well or 384 well depending on your plate format.
1817 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_trials_detail_table} \end{center}
1824 SGN databases support the Android Field Book App for collecting phenotypic data in the field with tablet computers. The app is available here:
1826 \href{https://play.google.com/store/apps/details?id=com.fieldbook.tracker}{\emph{https://play.google.com/store/apps/details?id=com.fieldbook.tracker}}
1829 \item
1830 The app can also be downloaded directly from the Google Play store. There is no charge for the app.
1831 \item
1832 Field Book App requires two files for collecting data: Field layout file and trait file.
1833 \item
1834 SGN databases can generate the field layout file and trait file, which can be downloaded onto your computer, then transferred to an Android tablet device.
1842 \item
1843 Creating a \protect\hyperlink{creating-layout-files}{\emph{field layout file}} based on the design of field trial
1844 \item
1846 \item
1847 Downloading the field layout file and trait file from the database to your computer
1848 \item
1849 Downloading the field layout file and trait file to the tablet (where the Field Book App is installed)
1850 \item
1851 Collecting phenotypes
1852 \item
1853 Exporting phenotypes from Field Book App to your computer
1854 \item
1855 \protect\hyperlink{uploading-pheno-files}{\emph{Uploading the exported phenotype file}} from your computer to the database
1861 There are two alternative methods for creating ``Field Layout Files''.
1865 \item
1866 Using ``Field Book Tools'' page
1867 \item
1868 Using ``Trial Detail'' page.
1872 \subsection{Creating ``Field Layout Files'' by using ``Field Book Tools'' page.}\label{creating-field-layout-files-by-using-field-book-tools-page.}}
1874 To access ``Field Book Tools'' page, clicking on ``Field Book App'' in the ``Manage'' menu.
1878 On the ``Field Book Tools'' page, clicking on ``New''
1882 On the ``Download Fieldbook'' window, selecting trial name and data level (plots or plants), then clicking on ``Submit'' button. A treatment can be selected, which allows you to record phenotypes based on treatment application. A list of traits can be selected, which provides a summary of an accession's global performance for those traits in the Fieldbook.
1886 If the field book layout file was successfully created, a pop-up window will indicate that the field book layout file was saved successfully. Clicking on the file name will immediately download the file onto your computer. The file is also available to download on the ``Field Book Tools'' page, if you need to re-download it.
1890 To download field layout file to your computer, clicking on ``Download File'', the file can then be transferred to your tablet. If you no longer want to keep the field layout file, clicking on ``Delete Layout File''.
1895 \subsection{Creating ``Field Layout Files'' by using ``Trial Detail'' page.}\label{creating-field-layout-files-by-using-trial-detail-page.}}
1897 To create ``Field Layout Files'', go to the ``Trial Detail'' page of the trial that you want to create the file. On the ``Trial Detail'' page, scrolling down to the bottom of the page to find ``Android Field Book Layout'' in the ``Files'' section, then clicking on the ``Create Field Book'' link.
1901 Clicking on the ``Create Field Book'' link will open a new window showing the name of the trial that you selected, as well as data level (plots or plants). A treatment can be selected, which allows you to record phenotypes based on treatment application. A list of traits can be selected, which provides a summary of an accession's global performance for those traits in the Fieldbook. To proceed, clicking on ``Submit'' button.
1905 If the field book layout file was successfully created, a pop-up window will indicate that the field book layout file was saved successfully. Clicking on the file name will immediately download the file onto your computer. The file is also available to download on the ``Field Book Tools'' page, if you need to re-download it.
1909 To download field layout file to your computer, clicking on ``Download File'', the file can then be transferred to your tablet. If you no longer want to keep the field layout file, clicking on ``Delete Layout File''.
1916 Steps to Create a Trait File:
1921 After you logged in, lists can be created and managed using the Search Wizard or the ``Lists'' link. For more information on how to create lists, click \protect\hyperlink{working-with-lists}{\emph{here}}.
1928 After you have your trait list, clicking on the ``\textbf{Field Book App}'' link found under the ``\textbf{Manage}'' menu tab. This will take you to the ``Field Book Tools'' page.
1932 To create a new trait file, finding the heading ``Trait Files'', then clicking on the ``New'' link.
1936 Clicking on the ``New'' link will open a dialogue box titled ``Create Trait File''. Please enter your ``Trait file name'' and select ``List of traits to include'' from drop-down list that you previously created. You can only use traits included in the list. Check the box titled ``Include Notes Trait'' if you would also like to record and upload general plot notes in the field. Click ``OK'' to submit.
1940 If your trait file was successfully created, a new window will indicate that the trait file was saved, then clicking on ``Close''.
1944 After the trait file was saved, you will see your file listed in the ``Field Book Tools'' page. Clicking on ``Download'' link to download the trait file to your computer.
1948 After downloading the trait file to your computer, the file can be transferred to an Android Tablet. You need the Android Field Book App to open the file. The Android Field Book App can be downloaded at: \emph{\url{http://www.wheatgenetics.org/bioinformatics/22-android-field-book}}
1951 \section{Transferring Files from Your Computer to Android Tablet}\label{transferring-files-from-your-computer-to-android-tablet}}
1956 After downloading, Field Layout files and Trait files can be found in the ``Downloads'' folder of your computer. Field Layout files on your computer will have a prefix ``fieldbook\_layout\_'' added to the beginning of the file name. For example: \textbf{``2014-01-28\_19:14:34\_Trial Demo\_location 6767.xls''} on the the database website will be saved as \textbf{``field\_book\_layout\_2014-01-28\_19:14:34\_Trial Demo\_location 6767.xls''} on your computer.
1960 The files can be transferred to Android tablet by copying the files into the tablet's Internal Storage File.
1965 To transfer Field Layout file and Trait file to your Android tablet, connecting an Android tablet to your computer, then clicking on tablet icon on your computer. Clicking on the tablet icon will open a window showing an ``Internal Storage'' file.
1969 After you installed the Android Field Book App, all files for the app are stored in the ``fieldBook'' folder within the ``Internal storage'' folder.
1973 Within the ``fieldBook'' folder, there are five sub-folders:
1976 \item
1977 field\_export
1978 \item
1979 field\_import
1980 \item
1981 plot\_data
1982 \item
1983 resources
1984 \item
1985 trait
1996 You can either drag and drop, or copy the Field Layout file and the Trait file from your computer to the folders in your Android tablet.
1999 \section{Setting up ``Field Book App'' for data collection}\label{setting-up-field-book-app-for-data-collection}}
2001 After you transferred the Field Layout file and Trait file from your computer to Android tablet, you still need to set up ``Field Book App'' on your tablet for data collection.
2003 To set up the Field Book App:
2007 \tightlist
2008 \item
2009 \textbf{To open the Field Book App in the Android Tablet, clicking on the Field Book App icon, which is a green rectangle.}
2017 \tightlist
2018 \item
2019 \textbf{To import Field Layout files, clicking on the ``Fields'' section of the main menu of the Field Book App.}
2024 Clicking on the ``Fields'' tab will open a new dialogue that will let you select the file that you want to import.
2028 Choosing a Field File will generate a new dialogue that will ask you to choose between an Excel or CSV format. Since the data from the database is in Excel format, choose the Excel option.
2032 After submitting the file format, a final dialogue box will appear. Please provide information about the file that you want to import. Please ensure that ``plot\_name'' is set as the unique identifier. To finalize the process, clicking ``OK'' button.
2039 \tightlist
2040 \item
2041 \textbf{To import Trait Files, clicking on the ``Traits'' tab on the main menu of the Field Book App.}
2046 Then, clicking on the three dots symbol found on the upper right corner of the Field Book screen. This will open a drop down menu with the choices ``Import'' and ``Export''. Clicking on ``Import''
2050 Clicking on ``import'' will open a new dialogue that displays a list of trait files that you can select to import to the Field Book App.
2054 The trait file is now imported into the Field Book App. The traits page will show all trait files and available traits.
2061 Data that were collected on the Field Book App can be exported back to your tablet folder, which can then be transferred to your computer.
2063 To export files containing data from the Field Book App to your tablet, clicking on the ``Export'' link on the main menu page of the Field Book App.
2067 Clicking on the ``Export'' link will open a new dialogue window. To ensure that data are exported in a correct format for the database, checking the ``Database Format'' box, then clicking on ``OK'' button.
2071 The exported file can then be found in the ``field\_export'' sub-folder within the ``fieldBook'' folder on your tablet. Once you connect your tablet to your computer, you can directly transfer the file to your computer.
2080 To upload phenotype files to the database, clicking on ``Field Book App'' in the ``Manage'' menu.
2084 On the ``Field Book Tools'' page, clicking on ``Upload'' link in the ``Uploaded Phenotype Files'' section.
2088 Clicking on the ``Upload'' link will open a new dialogue asking you to choose a file that you want to upload to the database website. Please ensure that ``plot\_name'' is the first column of the file to be uploaded. To make sure that the file has the correct format for uploading, click on the ``Verify'' button. After the file format has been verified, click on the ``Store'' button.
2092 The list of uploaded phenotype files can be found on the Field Book Tools page
2096 The uploaded files will also be seen in the corresponding ``Trial Detail'' page.
2103 To facilitate uploading process for phenotypic data, ``Manage Phenotypic Data'' page provides two options for uploading: Field Book Phenotype file in database format and phenotype file in Excel (.xls or .xlsx) file format. To access ``Manage Phenotypic Data'' page, clicking on ``Phenotyping'' in the ``Manage'' menu.
2113 The database upload of Field Book phenotype data relies on the ``Database'' format from the Field Book. Please make sure to export the ``Database'' format from the Field Book if you intend to upload the data using the Field Book Upload we describe below. If you prefer to use the ``Table'' format that the Field Book exports, you can modify this format to work with the Speadsheet Upload we describe below.
2118 To upload a Field Book Phenotype file in a database format, click the ``Upload Fieldbook'' link
2122 The ``Upload Fieldbook'' link on this page and ``Upload'' link on the ``Field Book Tools'' page open the same dialogue. Please follow instructions for uploading phenotypic files on the \ref{using-fieldbook-app} page.
2129 To upload a phenotype file in an Excel (.xls or .xlsx) file format, click the ``Upload Spreadsheet'' link.
2133 Please specify ``Data Level'' (Plots or Plants) and select the Excel file that you want to upload.
2140 You can find more file format information by clicking on ``Spreadsheet Format'' link. Clicking on ``Spreadsheet Format'' will open the following dialog.
2142 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/phenotype_spreadsheet_upload_help_dialog} \end{center}
2144 Clicking on ``Create Phenotyping Spreadsheet'' will bring up a dialog where you can indicate the trial(s) you are interested in and the trait list you are interested in. Clicking ``Submit'' will download the xlsx file onto your computer, where you can then fill in the phenotypes.
2146 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/create_phenotype_spreadsheet_dialog} \end{center}
2151 To ensure that the file has a correct format for uploading, click on the ``Verify'' button. This will check the contents of the file and also perform quality checks on the values in the file. These checks include checking the trait definition for categorical values, minimum and maximum values, and data type checking. It will also check if there are already values uploaded for the given observation units and traits. If there are, there is an option to overwrite the existing values with the new values in your file. If the file is valid, only then can you click ``Store'' to store the information in the database.
2153 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/phenotype_spreadsheet_upload_dialog} \end{center}
2158 SGN databases provide tools for generating barcodes for stock identification. To access ``Barcode Tools'' page, clicking on ``Barcodes'' in the ``Manage'' menu.
2162 ``Barcode Tools'' page provides four options for generating barcodes:
2165 \item
2166 Single barcode
2167 \item
2168 Multiple barcodes
2169 \item
2170 Plot phenotyping barcodes
2171 \item
2172 Trial barcodes
2175 To generate single barcode, clicking on ``Generate Barcode'' link on the ``Barcode Tools'' page.
2179 In the ``Generate Barcode'' section, specify the name of the barcode, size of the barcode, then clicking on ``Generate Barcode''
2183 The database will generate a barcode for your stock. The barcode can be printed for your stock identification. It also appears on its corresponding stock page.
2187 If you have a list of stocks that you want to generate barcodes, you can use ``Download Stock Barcodes'' section. You have three options for entering stock names:
2191 \item
2192 Typing in stock names, or copy and paste from other file into the box (1)
2193 \item
2194 Choosing a list of stocks from your ``Lists'' (2), and transferring the list into the box (1) by clicking on ``paste'' button.
2195 \item
2196 Uploading a ``Tab-delimited Text File'' with stock names.
2197 \item
2198 Select an optional printing format from the available formats.
2201 You can select printer settings that you prefer in the ``Printer Settings'' section. After you enter stock names and specify printer settings, clicking on ``Download Barcodes'' button at the bottom of the page.
2205 If you have a list of plots that you want to generate phenotyping barcodes, you can use ``Download Plot Phenotyping Barcodes'' section. You have three options for entering plot names:
2209 \item
2210 Typing in plot names, or copy and paste from other file into the box (1)
2211 \item
2212 Choosing a list of plots from your ``Lists'' (2), and transferring the list into the box (1) by clicking on ``paste'' button.
2213 \item
2214 Uploading a ``Tab-delimited Text File'' with plot names.
2217 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/plot_pheno_barcode} \end{center}
2219 If you have a list of trials that you want to generate barcodes, you can use ``Download Trial Barcodes'' section. You have three options for entering trial names:
2223 \item
2224 Typing in trial names, or copy and paste from other file into the box (1)
2225 \item
2226 Choosing a list of trial from your ``Lists'' (2), and transferring the list into the box (1) by clicking on ``paste'' button.
2227 \item
2228 Uploading a ``Tab-delimited Text File'' with trial names.
2236 Breedbase provides an interactive design tool for creating custom labels. To access the Label Desginer, click on ``Label Designer'' in the ``Manage'' menu. The following sections explain your many options as you advance through each step of the design workflow.
2241 The first step is to select a data source. Since the label designer can generate labels for different data types, you can optionally filter the source selection by the data type you're interested in. Then, select a field, genotyping, or crossing trial to populate your labels with the trial design information. Or select a list to populate your label with the list contents. For data sources with multiple levels of information you will also be asked to pick a level (plot, plant, etc.) before proceeding. To generate plot-level labels for more than one trial at once, select a list of trials as the source and plot as the level.
2248 Now choose whether to create a new design or load a saved design. If you choose new, you will be prompted to select a page size and label size. If you do not see your page or label size as an option, then select Custom and enter your desired dimensions in pixels, or 1/72nds of an inch. If you choose saved, you will be prompted to select a saved design then will be taken directly to the design step with the saved design elements preloaded.
2255 Below is a draw area where you can begin adding elements to your label. First select a type, then field, size, and font, then click `Add' You can add text to an exisiting field or create a completely custom field by clicking `Create Custom Field' Once added, you can drag and drop elements, or delete them by clicking on the red box in their upper left corners. Barcodes can also be resized by dragging on the green box in their lower right corners. If you are creating labels for a trial it is highly recommended to include a barcode encoding your plot, plant, or tissue sample names. These are your unique identifiers that will need to included with any phenotypic or genotypic measurements loaded into the database. When you are satisfied with your design, click next!
2262 Last step! Here you can tweak your formatting and page layout, save your design, or download your labels. The additional settings dialog will allow you to fine tune the print margins and margins between labels. The units are pixels or 1/72nds of an inch. It's not recommended to change these until you've already done a test print. You can also set the \# of copies per label, filter by rep, or download just the first page for test purposes. To save you're design just type a unique name and hit save. This will save your design to your list manager where you can set it to public to share it with others. Finally if you are ready just hit download to generate and download your labels!
2269 You can download phenotype, trial meta-data, pedigree, GBS genotype and GBS genotype QC files from the database to your computer by using ``Lists''. To download, clicking on ``Download'' in the ``Manage'' menu.
2273 For each category, you can select a list of accessions from your ``Lists'' to download their phenotypes, pedigree, GBS genotype, GBS genotype QC. In the case of downloading trial meta-data, you would provide a list of trials, while for downloading phenotype and GBS genotype QC, you can also use a list of trials or traits.
2275 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/trial_meta_data_download} \end{center}
2284 To access this page go to Manage and then ODK Data Collection. ODK is used for remotely collecting data on Android and IOS devices. We currently are working to support two ODK service providers, namely ONA and SMAP. We are using ONA to collect crossing information, including all lab activities following seed production. We are using SMAP for phenotypic data collection.
2292 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/odk_ona_management} \end{center}
2294 To begin collecting data using the ONA ODK form you must first have a crossing plan in the form of a Cross Wishlist. To do this from this page, click the ``Export Cross Wishlist to ONA'' button. Please refer to the ``Create Cross Wihlist'' help section for more information. It is possible to view the current available cross wishlists by clicking the ``Export Cross Wishlist to ONA'' button and then clicking ``Available Cross Wishlists''.
2296 Once your cross wishlist is available, you can use your mobile ODK application to record crosses being done realtime. You can also record all laboratory activities following seed extraction up to greenhouse plantlet hardening.
2298 As you collect data using your mobile ODK application, your responses will be synchronized with our database. The ``Schedule Import for Selected Form'' section gives you options to perform the import daily or more frequently. It is also possible to initiate a data import from ONA at anytime by clicking ``Import Crossing Data from Selected Form on ONA''.
2303 The mobile ODK application has options to collect information about the status of plants in the field, such as if they are flowering. Images for each plant can also be recorded. The database will report this information here in a summary table that looks like the following. Notice that images are also transferred to the database.
2305 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/odk_ona_cross_status} \end{center}
2308 \subsection{Graphical Summary For Performed Crosses}\label{graphical-summary-for-performed-crosses}}
2310 There is a section to summarize activities done for each cross. In this table each row represents a single cross performed. All the activities that have been performed will be shown here, such as ``first pollination'' and ``embryo rescue''. The scatter plot shown tracks seed numbers generated on the Y axis and date of activity on the X axis.
2312 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/odk_ona_cross_progress_graph} \end{center}
2315 \subsection{Summary Information For Performed Crosses}\label{summary-information-for-performed-crosses}}
2317 There is a secondary section to summarize what has been done across the entire Cross Wishlist. This tree structure shows all activities performed for a cross and shows how these crosses relate to the Cross Wishlist.
2319 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/odk_ona_cross_progress_tree} \end{center}
2324 To access this page go to Manage and then Tissue Samples.
2329 A field trial contains plots planted with a specific accession. Each plot can contain many plants, which in turn can contain many tissue samples. On the manage tissue sample page we can see the field trials that contain tissue samples already. We can choose to download the tissue sample layout as seen in the below picture.
2331 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_field_trial_download} \end{center}
2333 If the field trial you want to collect tissue samples from is not in the above table, you can click the button highlighted below.
2335 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_field_trial_button} \end{center}
2337 Once you have clicked this button, you will enter a workflow that begins with the following introduction.
2339 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_field_trial_intro} \end{center}
2341 Once you click next, you will need to select your trial.
2343 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_field_trial_select} \end{center}
2345 Next, if your trial currently only has plot entries saved, you will be asked to enter how many plants are in each plot.
2347 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_field_trial_num_plants} \end{center}
2349 Finally you will be asked how many tissue samples you want for each plant. You can specify a string to include in the tissue sample name, such as leaf or root.
2351 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_field_trial_num_tissues} \end{center}
2353 Afterwards you should see the following success message, indicating that the tissue samples are saved.
2355 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_field_trial_submit} \end{center}
2358 \section{Genotyping Plate Tissue Samples (96 or 384 well plates)}\label{genotyping-plate-tissue-samples-96-or-384-well-plates}}
2360 A genotyping plate represents a 96 or 384 well plate. You can use the Coordinate Android application to create your plate layout, or you can upload your own Excel plate layout, or you can use the database to generate a plate layout. Ideally, you will use tissue sample names originating from a field trial as the ``source'' for each well tissue sample, but you can also use plant names, plot names, or accession names.
2362 From the manage tissue samples page, you can see the genotyping plates saved in the database. You can also download the layouts as shown below.
2364 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_genotyping_trial_download} \end{center}
2366 If you need to create a new genotyping plate, you can click the button shown below. This will guide you through a workflow for uploading or creating the new plate layout.
2368 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_tissue_samples_create_tissues_genotyping_trial_button} \end{center}
2370 Genotyping vendors require you to send a plate layout during submission. You can download the plate layout as shown above, or you can go to a genotyping plate detail page to download the Intertek formatted file.
2372 In the future you will be able to directly export your genotyping plate plate layout to vendors.
2378 \section{Managing Observation Variables with Traits, Methods, and Scales}\label{managing-observation-variables-with-traits-methods-and-scales}}
2380 Observation variables are the identifiers used when collecting phenotypic data. An observation variable is composed of a trait, a method, and a scale. The trait describes the attribute being measured e.g.~`Plant Height'. The method defines the protocol in which the trait was observed e.g.~`Using a one meter long measuring stick'. The scale defines the units or dimensions for which the measurement was taken e.g.~`Meters'.
2382 Generally, observation variables are defined in ontologies that are predefined. We often use ontologies from cropontology.org. In this case, you will not be able to define your own observation variables directly; instead, you will need to contact us and we will add the observation variable for you.
2384 For databases where the user has greater control, we have an interface to allow addition of observation variables, along with traits, methods, and scales. To begin, go to the Search-\textgreater Traits page.
2386 If the database you are on allows you to directly add observation variables, you will see the following button at the bottom of the page.
2388 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_observation_variables_start_button} \end{center}
2390 When you click the button, the following workflow will appear. You should be logged in or else it will not allow addition of the observation variable. The workflow begins with an introduction.
2392 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_observation_variables_workflow_intro} \end{center}
2394 On the next workflow step, you select the ontology that you want to insert the new observation variable into. You must also give a name and a definition for the new observation variable.
2396 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_observation_variables_workflow_observation_variable} \end{center}
2398 On the next workflow step, you select the trait ontology to use. Once you select a trait ontology, a select containing all the terms in the selected ontology will appear. You can either select a trait or if it does not exist in the select, you can create a new one by giving a name and a definition for the new trait.
2400 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_observation_variables_workflow_trait} \end{center}
2402 On the next workflow step, you select the method ontology to use. Once you select a method ontology, a select containing all the terms in the selected ontology will appear. You can either select a method or if it does not exist in the select, you can create a new one by giving a name and a definition for the new method.
2404 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_observation_variables_workflow_method} \end{center}
2406 On the next workflow step, you select the scale ontology to use. Once you select a scale ontology, a select containing all the terms in the selected ontology will appear. You can either select a scale or if it does not exist in the select, you can create a new one by giving a name and a definition for the new scale. You can also define a format, minimum, maximum, categories, and default value for the new scale.
2408 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_observation_variables_workflow_scale} \end{center}
2410 On the last page of the workflow, you confirm the submission.
2412 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_observation_variables_workflow_submit} \end{center}
2414 Afterwards, you can use the newly created observation variable ontology term in your phenotyping.
2424 \tightlist
2425 \item
2426 Upload raw image-captures in a compressed file (.zip) for orthophotomosaic assembly or upload previously stitched orthophotomosaic raster (.PNG, .JPG) imagery.
2427 \item
2428 Dashboard shows all field trials and uploaded imaging events in collapsible sections.
2429 \item
2430 Follow standard processes to manually create templates for assignment of plot-polygon images to the field experiment design.
2431 \item
2432 All imagery is shown with the spectral category within collapsible sections. Figure shows NIR imagery.
2433 \item
2434 Apply Fourier transform filtering, thresholding, and vegetation index masking. Plot-polygon images for all image processes are shown.
2435 \item
2436 Extract and export phenotypic values from plot-polygon images for analyses and model training.
2442 Clicking ``Upload Imagery'' will open the following dialog.
2444 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_upload_intro} \end{center}
2446 Raw-captures can be uploaded in a compressed (.zip) file so that they can be assembled into an orthophotomosaic. If orthophotomosaic assembly is not required, raster images (.PNG, .JPG) can be uploaded. Example data is given for raw Micasense RedEdge 5-band multispectral captures and for stitched orthophotomosaics.
2448 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_upload_field_trial} \end{center}
2450 To begin uploading images, a field trial must be selected. The field trial must already be saved in the database. For information about adding a field trial, please read the Field Trial documentation.
2452 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_upload_drone_run} \end{center}
2454 The image data is added to an imaging (drone run) event. Here you can select a previously saved imaging event or you can create a new one by defining a name, description, and date.
2456 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_upload_image_info_1} \end{center}
2458 The uploaded data can be raw image-captures or complete raster images. Here you can select whether orthophotomosaic stitching is required.
2460 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_upload_image_info_2} \end{center}
2462 In the case that orthophotomosaic stitching is required, select `yes'. On the next step you will see the following: Upload a zipfile with the raw-captures. When uploading Micasense RedEdge raw-captures, provide images of the Micasense calibration panels in a zipfile as well.
2464 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_upload_images_zipfile} \end{center}
2466 In the case that orthophotomosaic assembly is not required, simple upload the raster images. Select the number of image bands that will be uploaded e.g.~for a five band multispectral camera, select 5.
2468 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_upload_image_info_3} \end{center}
2470 In the caes that orthophotomosaic stitching is not required, select `no'. On the next step you will see the following:
2472 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_upload_images_rasters} \end{center}
2474 Upload an image at each band with a unique name, description, and spectral type.
2479 Once imagery is uploaded, it will appear on the dashboard under the field trial. Clicking the ``Run Standard Process'' button will begin extracting plot-polygon phenotypes from the imagery.
2481 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_button} \end{center}
2483 Clicking the button will open the following dialog.
2485 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_intro} \end{center}
2487 Select a drone run band to use in this process. In the case of the Micasense 5 band multispectral camera there will be 5 bands shown here; select the NIR channel in this case because it has the highest contrast. In the case of standard color images, there will only be the RGB Color Image option here.
2489 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_drone_run_band} \end{center}
2491 Rotate the image so that there the plots are oriented in a grid fashion. There can be a skew in the field layout, as seen in the following example.
2493 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_rotate} \end{center}
2495 Perform a rough cropping of the image by clicking on the four corners of the field. Cropping is important to remove any extraneous parts of the image.
2497 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_cropping} \end{center}
2499 This step shows a histogram of the cropped image. The standard process will magnitude threshold the top and low ends of the distribution.
2501 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_threshold_hist} \end{center}
2503 In this step, the template for the plot polygons in the experimental field design are associated to the image. First, defined the number of rows and columns in the field experiment. Then click the four corners of the image, in respect to the top right, top left, botton left, and bottom right positions. Next click on ``Draw Plot Polygon Template''. Review the template and clear/repeat the process until the template matches well. It is possible to ``copy/paste'' templates in the case where there are large breaks in the field design. Next, scroll down to the ``assign Plot Polygons to Field Trial Entities'' section. Select the location of Plot Number 1 as either ``top left'' or ``top right'' and whether the field design is serpentine or zigzag. Click on ``Generate Assignments'' and review that the names of the plots appear correctly in the overlay on the image. Finally, click ``Finish and Save Polygons to Plots'' when you have have confirmed the assignments.
2505 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_plot_polygon} \end{center}
2507 Next, the dialog shows you that the standard process will be repeated for all uploaded image bands.
2509 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_apply} \end{center}
2511 Next, choose which vegetation indices to apply.
2513 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_vegetation_index} \end{center}
2515 Next, choose the phenotypic values to extract. You must define the time point for which the phenotype is; if the field trial has a planting date, the time point will automatically be populated as image date minus the planting date.
2517 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_image_phenotyping_standard_process_phenotypes} \end{center}
2519 After completing the standard process, the job will continue in the background until it completes. You can check the status of the job from the dashboard.
2524 Ground control points can be saved after an imaging event has undergone the standard process on orhomosaics. Ground control points can then be used across imaging events on the same field experiment in order to automate the entire standard process.
2532 Genotyping data in VCF can be loaded from the web-interface. Breedbase can store any genotypic variants from a VCF, allowing for polyploids, structural variants, etc. without problems.
2534 To begin go to Manage-\textgreater Genotyping Plates and click the button seen below: Note that you do not need to have genotyping plates uploaded to upload VCF data; you may upload genotyping data to accessions or you can upload genotyping data for tissue samples in genotyping plates.
2536 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_data_upload_button} \end{center}
2538 The workflow begins with an intro:
2540 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_data_upload_dialog_intro} \end{center}
2542 On the following step in the workflow, a genotyping project is defined or selected. A genotyping project is a high-level entity for grouping several genotyping events. It is defined with a name, description, name, breeding program, and genotyping facility (IGD, Intertek, etc.).
2544 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_data_upload_dialog_project} \end{center}
2546 The following step is to define or select a genotyping protocol. A genotyping protocol represents the set of markers being called against a specific reference genome. A genotyping protocol is defined with a name, description, reference genome name, species name, and a location of data generation. Note in the picture that you can select whether the samples in your file are accessions or tissue samples in the database; tissue samples are for when a genotyping plate is stored in the database. There is an option to parse the sample names for appended sequencing numbers from IGD, where the sample names are like ``accession:igdnumber''.
2548 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_data_upload_dialog_protocol} \end{center}
2550 The final step is to select the VCF from your computer and upload it. The web interface can be used to upload files arbitrarily large; it is a NGINX configuration to set this size.
2552 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_data_upload_dialog_vcf} \end{center}
2557 The Search Wizard is the primary means of querying data in the database. Go to Search-\textgreater Wizard to begin.
2559 Once genotyping protocols are stored, select Genotyping Protocols from the first dropdown menu. Then if you select one or more and select Accessions from the second dropdown menu, you will see the accessions for which genotypes were stored. As seen in the following picture, there is a section for filtering genotypes by chromosome, start position, and end position. Genotypes can be downloaded in VCF or DosageMatrix formats.
2561 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_data_wizard_download_prot} \end{center}
2563 Using the ``Default genotyping protocol'' which is configured in a system, you can query over field phenotypic evaluations before downloading genotypes and phenotypes.
2565 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_genotyping_data_wizard_trial} \end{center}
2570 Genotyping protocols can be search by going to Search-\textgreater Genotyping Protocols. To download genotypes accessions must be selected, though any combination of search criteria can be used to filter and select those accessions. If a genotyping protocol is not selected, then the default genotyping protocol set in the configuration will be used. Genotyping protocols can also be selected in the wizard.
2572 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_wizard_genotyping_protocols_download_main} \end{center}
2574 The genotyping download menu on the Search Wizard presents options for filtering by chromosome, start position, and end position. Genotypes can be downloaded in VCF of Dosage Matrix formats. The genomic relationship matrix (GRM) can be downloaded for the selected accessions in a tab-delimited matrix format or in a three-column format that is useful in Asreml. Genotypes can be computed from the parents in the pedigree if those parents are genotyped by clicking on the ``compute from parents'' checkbox. Additionally, the GRM can be computed using genotypes of parents in the pedigree if the ``compute from parents'' checkbox is selected.
2576 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/search_wizard_genotyping_protocols_download_genotypes} \end{center}
2578 As is described elsewhere, the Search Wizard presents a way to filter phenotypic values by minimum and maximum values, and allow for download in CSV and Excel formats.
2580 \begin{center}\includegraphics[width=0.75\linewidth]{assets/images/search_wizard_genotyping_protocols_download_phenotypes} \end{center}
2585 The genotyping protocol detail page will show all information about the protocol such as the reference genome used, the header information lines in the uploaded VCF file, the markers involved, and the samples genotyped.
2587 The markers section will show all markers used and their annotations, such as position, chromosome, alternate allele, reference allele, marker format, etc.
2589 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/genotyping_protocol_detail_page_markers} \end{center}
2591 The samples section will show all samples genotyped. Notice the Download links in the table which can be used to easily get the VCF file results for each genotyped samples with all markers in the genotyping protocol. For getting mulitple samples at once, use the Search Wizard as discussed above.
2593 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/genotyping_protocol_detail_page_samples} \end{center}
2595 The genotyping protocol and all associated genotyping data can be deleted from the genotyping protocol page.
2597 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/genotyping_protocol_detail_page_delete} \end{center}
2602 Breedbase has implemented a flexible spectral data storage protocol that handles spectral data irrespective of the source spectrometer. Spectral data storage and analysis in Breedbase makes use of the R package \emph{waves} for outlier identification, plotting, sample aggregation, and prediction model training.
2604 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/waves_breedbase_schema} \end{center}
2611 Spectral data can be added as a CSV file that includes metadata in the leftmost columns followed by one column per spectral measurement to the right. Rows represent a single scan or sample, each with a unique ID that must match to a Breedbase observationUnitName. Future data transfer using \href{https://brapi.org}{BrAPI} will allow for interoperability with data collection software.
2613 To upload a spectral dataset, navigate to the `Manage NIRS Data' page by selecting `NIRS' in the `Manage' menu and click the blue `Upload NIRS' button. This will open an upload workflow. A link to the required file format and an example .csv file can be found by clicking in the light blue info box in this workflow. Another example of the file format is shown below.
2616 \tightlist
2617 \item
2619 \item
2621 \item
2623 \item
2624 \textbf{observationunit\_name}: Required field that matches existing data in the database. It can be the plot name, subplots, plant name, or tissue sample, depending how your trial is designed.
2625 \item
2627 \item
2628 \textbf{device\_type}: Required field. It is possible upload data for a single device type. They can be: SCiO, QST, Foss6500, BunchiN500, or LinkSquare.
2629 \item
2630 \textbf{comments}: Optional field for general comments. All other columns are required wavelengths. You can add how many columns you want upload -- there is no limit.
2633 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_NIRS_main_display} \end{center}
2635 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/upload_NIRS_example_format} \end{center}
2640 Spectral calibration models can be heavily affected by the presence of outliers, whether they come from spectrometer spectral artifacts or user errors. Mahalanobis distance (Mahalanobis, 1936) is a measure of the distance between a single observation and a larger distribution and is commonly used in the identification of outliers in a multivariate space (Des Maesschalck et al, 2000). The \emph{FilterSpectra()} function in the R package \href{https://CRAN.R-project.org/package=waves}{\emph{waves}} calculates the Mahalanobis distance of each observation in a given spectral matrix using the \emph{stats::mahalanobis()} function. Observations are identified as outliers if the squared distance is greater than the 95th percentile of a \(\chi\)\textsuperscript{2}-distribution with \emph{p} degrees of freedom, where \emph{p} is the number of columns (wavelengths) in the spectral matrix (Johnson and Wichern, 2007). In Breedbase, this procedure is applied on a per-dataset basis on upload and outliers are given binary tags ``Outlier.''
2645 After outlier identification, a plot is generated using the \emph{PlotSpectra()} function in \href{https://CRAN.R-project.org/package=waves}{\emph{waves}}. This function uses the filtered spectra and \emph{ggplot2::ggplot()} to create a line plot with outliers highlighted by color. A list of rows identified as outliers are shown beneath the plot. Plots are saved as .png files and linked to the original input datasets. Plot image files can be downloaded via the ``Download Plot'' button in the upload workflow.
2647 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/upload_NIRS_plot_example} \end{center}
2652 To obtain a stable and reliable spectral profile, most spectrometer manufacturers recommend that multiple spectral scans are captured for each sample. While some spectrometers aggregate these scans internally, many do not, requiring the user to do so before analysis can take place. Breedbase handles these cases upon data upload following filtering steps by calling the \emph{AggregateSpectra()} function from \href{https://CRAN.R-project.org/package=waves}{\emph{waves}}, saving the aggregated scans for future access through the search wizard feature. Scans are aggregated by sample mean (e.g.~plot-level basis) according to the provided observationUnitName field. After aggregation, the user exits the upload workflow and the raw data file is saved in the upload archive.
2658 \tightlist
2659 \item
2660 De Maesschalck, R., Jouan-Rimbaud, D., and Massart, D. L. (2000). The Mahalanobis distance. Chemom. Intell. Lab. Syst. 50(1): 1-18.
2661 \item
2662 Johnson, R. A. \& Wichern, D. W. (2007). Applied Multivariate Statistical Analysis (6th Edition). p 773.
2663 \item
2664 Mahalanobis, P. C. (1936). On the generalized distance in statistics. National Institute of Science of India.
2672 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/sequence_metadata_manage} \end{center}
2677 Sequence Metadata is a feature that allows for the efficient storage and retrieval of sequence annotations for a specific region along a reference genome. The annotation data can contain a primary ``score'' value and any number of secondary key/value attribute data. For example, Sequence Metatadata can store MNase open chromatin scores for every 10 basepairs along the reference genome as well as genome-wide association study (GWAS) statistics, including the trait information associated with the result. This data can then be filtered by position and/or scores/attribute values and even cross-referenced with markers stored in the database.
2682 Sequence Metadata can be loaded into the database using a gff3-formatted file. The following columns are used to load the data:
2685 \tightlist
2686 \item
2687 \textbf{\#1 / seqid:} The name of the database feature (ie chromosome) the metadata is associated with (The feature name must already exist as a feature in the database)
2688 \item
2690 \item
2692 \item
2694 \item
2695 \textbf{\#9 / attributes:} (optional) Secondary key//value attributes to be saved with the score. These should be formatted using the gff3 standard (key1=value1;key2=value2). The attribute key cannot be either score, start, or end.
2698 To upload the gff3 file:
2702 \tightlist
2703 \item
2705 \item
2707 \item
2708 On Step 2 of the Wizard, select the Type of data to be uploaded
2711 \tightlist
2712 \item
2713 This groups similar datasets together in the same Data Type category
2715 \item
2716 On Step 3 of the Wizard, select an existing Protocol or create a new one
2719 \tightlist
2720 \item
2721 The Protocol is used to describe how the data was generated and define the score value and any secondary attributes. Adding the attributes (and their descriptions) to the Protocol will allow the Sequence Metadata queries to filter the data based on the value of one or more of these attributes. Attributes not defined in the Protocol will still be stored and displayed on retrieval, but will not be able to be used in a search filter.
2723 \item
2724 Finally, select and upload your gff3 file to the database. The database will verify the format of the file before its contents are stored.
2730 To retrieve stored Sequence Metadata, go to the \textbf{Search \textgreater{} Sequence Metadata} page.
2735 The basic Sequence Metadata search options include selecting the reference genome and species, the chromosome, and (optionally) the start and/or end position(s) along the reference genome. In addition, one or more specific protocols can be selected to limit the results.
2737 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/sequence_metadata_search_basic} \end{center}
2739 The Sequence Metadata search results are returned as a table, including the chromosome and start/stop positions of the annotation, along with the primary score value and any additional key/value attributes. The markers column will include a list of marker names of any stored markers that are found within the start/stop positions of the Sequence Metadata. The data can be downloaded as a table in an Excel or CSV file or a machine-readable (code-friendly) JSON file. If the Sequence Metadata JBrowse configuration is set, the filtered results can be displayed as a dynamic JBrowse track.
2741 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/sequence_metadata_search_results} \end{center}
2746 Any number of advanced search filters can be applied to the query. The advanced filters can limit the search results by the value of the primary score and/or any of the secondary attribute values.
2748 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/sequence_metadata_search_advanced} \end{center}
2753 A table of Sequence Metadata annotations are embedded on the Marker/Variant detail page. The table will include any annotations that span the poisiton of the marker (for data of the same reference genome and species).
2758 A publicly accessible RESTful API (Application Programming Interface) is available to query the database for Sequence Metadata directly from your programming environment (R, python, etc) to be used in analysis. The data is returned in a JSON format. Documentation for the API can be found on the \textbf{Manage \textgreater{} Sequence Metadata} page
2764 \section{What is Outliers Functionality in Dataset ?}\label{what-is-outliers-functionality-in-dataset}}
2766 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/outliers_dataset_icon} \end{center}
2770 The dataset incorporates a feature to identify outlier points, which we may choose to exclude from a specific dataset. It's important to note that these exclusions only apply at the dataset level, and no data is permanently removed from the database. Additionally, outlier categorization can be modified at any time, and these changes are visible to all other functionalities within the system.
2772 Each dataset stores a wholly unique set of outlier points, completely independent of any other dataset in the database. Outliers are specifically designated for traits within datasets, exclusively encompassing phenotype data. If a particular dataset lacks traits as a part of wizard selection, this functionality is not available.
2774 Each trait has its own set of defined outliers.
2779 Once you've selected a specific trait, the web application provides access to a visualization of the data points associated with that trait.
2781 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/outliers_dataset_basic_panel} \end{center}
2786 Once you've selected a specific trait, the web application provides access to a visualization of the data points associated with that trait.
2789 \tightlist
2790 \item
2791 \textbf{Green Points}: As per the legend, represent values for the selected trait that fall below the cut-off point set by the slider. (non-outliers)
2792 \item
2793 \textbf{Black Outlined Points}: These data points are outlined with black borders, indicating that they are currently designated as outliers in the database.
2794 \item
2795 \textbf{Red Points}: The red data points denote the cut-off points established by the slider for the allowable deviation value.
2798 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/outliers_dataset_full_visualisation} \end{center}
2803 You have two fundamental options for setting cut-off points:
2806 \tightlist
2807 \item
2808 \textbf{Median with MAD}: This option involves using the median (middle value) along with the Mean Absolute Deviation (MAD) as a reference point for determining cut-off values.
2809 \item
2810 \textbf{Mean with Standard Deviation}: Alternatively, you can choose to use the mean (average) in conjunction with the Standard Deviation to set cut-off points.
2816 The slider allows you to specify the deviation multiplier from a central point, which influences the cut-off values.
2821 Beneath the graph, you'll find four buttons, each serving a distinct function:
2824 \tightlist
2825 \item
2826 \textbf{Add selection to outliers}: This button enables you to save the current cut-off points to the database for future reference.
2827 \item
2828 \textbf{Reset outliers for current trait}: You can use this option to reset outliers for the selected trait.
2829 \item
2831 \item
2832 \textbf{Download Phenotype Table without outliers}: You can download the phenotype data table in a comma-separated value format file, using this feature, with outliers excluded for selected dataset.
2835 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/outliers_dataset_actions} \end{center}
2837 These tools and functions are designed to provide you with control and insights when working with data visualization and outliers.
2842 SGN databases provides several tools for phenotype data analysis, marker-assisted selection, sequence and expression analyses, as well as ontology browser. These tools can be found in the ``Analyze'' menu.
2849 To determine rankings of accessions based on more than one desirable trait, SGN databases provide a ``Selection Index'' tool that allows you to specify a weighting on each trait. To access the tool, clicking on ``Selection Index'' in the ``Analyze'' menu.
2853 On the Selection Index page, selecting a trial that you want to analyze.
2857 After you selected a trial, you can find traits that were assayed in that trial in the ``Trait'' box.
2861 Selecting a trait that you want to include in the analysis will open a new dialogue showing the selected trait and a box that you can assign a ``Weight'' of that trait. After you are done, you can continue by selecting another trait by clicking on ``Add another trait'' link.
2865 After you selected another trait, this page will automatically update information for you by showing all of the traits that you selected for the analysis.
2869 You also have options to choose a reference accession, choose to include accessions with missing phenotypes, scaling values to a reference accession. After you complete your setting, clicking on ``Calculate Rankings''
2873 The Selection Index tool will generate rankings of accessions based on the information that you specified. You can copy the results to your system clipboard, convert the table data to CSV format, or print the data.
2877 Clicking on ``Raw Average'' will display average values of the phenotypes of those ranked accessions.
2881 Selection Index tool also allows you to save top ranked accessions directly to ``Lists''. You can retrieve top ranked accessions by selecting a number or a percent.
2888 The prediction of breeding values for a trait is a one step or two steps process, depending on what stage in your breeding cycle you are. The first step is to build a prediction model for a trait using a training population of clones with phenotype and genotype data. If you have yet to select parents for crossing for your first cycle of selection you can use the breeding values of the training population. If you are at later stages of your selection program, you need to do the second step which is applying the prediction model on your selection population. All clones in your training and selection populations must exist in the database.
2890 To use the genomic selection tool, on \href{http://cassavabase.org/}{\emph{cassavabase.org}}, select `Genomic Selection' from the `analyze' pull-down menu.
2894 There are three ways to build a model for a trait.
2899 One way to build a model is, using a trait name, to search for trials in which the trait was phenotyped and use a trial or a combination of trials to build a model for the trait. For example, if you search for 'mosaic disease severity, you will get a list of trials you can use as training populations.
2903 You will get a list of trials (as shown below) in which the trait of your interested was phenotyped. From the list, you can use a single trial as a training population or combine several trails to form a training population for the prediction model of the trait. Let's say, you want to create a training population using individuals from trials `cassava ibadan 2001/02' and `cassava ibadan 02/03' and build a model for `cassava mosaic disease severity' using all clones from the training population.
2907 Select the trials to combine (the same coloured), click `done selecting', click the `combine trials and build model' button, and you will get a model and its output for the trait. On the model detail page, you can view the description of input data used in the model, output from the model and search interface for selection populations the model you can apply to predict their breeding values. The description of the input data for the model includes the number of phenotyped clones, and the number of markers, scatter and frequency distribution plots for the phenotype data, relationship between the phenotype data and GEBVs, population structure. The model output includes model parameters, heritability of the trait , prediction accuracy, GEBVs of the individuals from the training population and marker effects.
2911 Expand each section to see detailed information.
2913 If you expand the `Trait phenotype data' section, you will find plots to explore the phenotype data used in the model. You can assess the phenotype data using a scatter and histogram plots and the descriptive statistics.
2919 A regression line between observed phenotypes and GEBVs shows the relationship between the two.
2923 You can also explore if there is any sub-clustering in the training population using PCA.
2927 To check the model accuracy, a 10-fold cross-validation test, expand the `model accuracy' section.
2931 Marker effects are also available for download. To do so, expanad the `Marker Effects' section and click the `Download all marker effects' link and you will get a tab delimited output to save on your computer.
2935 The breeding values of the individuals used in the training population are displayed graphically. Mousing over each data point displays the clone and its breeding value. To examine better, you can zoom in into the plot by selecting an area on the plot. You can download them also by following the `Download all GEBVs' link.
2940 \subsubsection*{Estimating breeding values in a selection population}\label{estimating-breeding-values-in-a-selection-population}}
2943 If you already have a selection population (in the database), from the same model page, you can apply the model to the selection population and estimate breeding values for all the clones in the population. You can search for a selection population of clones in the database using the search interface or you can make a custom list of clones using the \protect\hyperlink{working-with-lists}{\emph{list interface}}. If you click the `search for all relevant selection populations', you will see all relevant selection populations for that model. However, this option takes long time decause of the large set of populations in the database and the filtering. Therefore, the fastest way is to search for each of your selection populations by name. If you are logged in to the website you will also see a list of your custom set of genotyped clones.
2947 To apply the model to a selection population, simply click your population name or `Predict Now' and you will get the predicted breeding values. When you see a name of (or acronym{]}) of the trait, follow the link and you will see an interactive plot of the breeding values and a link to download the breeding values of your selection population.
2954 Another way to build a model is by selecting a trial, instead of selecting and searching for a specific trait. This approach is useful when you know a particular trial that is relevant to the environment you are targeting to breed material for. This method allows you to build models and predict genomic estimated breeding values (GEBVs) for several traits within a single trial at once. You can also calculate selection index for your clones when GEBVs are estimated for multiple traits.
2956 To do this select the ``Genomic Selection'' link found under the ``analyze'' menu. This will take you to the same home page as used with Method 1. However, instead of entering information to search for in ``Search for a trait'', click on ``Use a trait as a trial population''. This will expand a new menu that will show all available trials.
2964 To begin creating the model, select the existing trial that you would like to use. In this example I will be using the trial and trait data from ``Cassava Ibadan 2002/03'' trial. Clicking on a trial will take you to a page where you can find information such as number of markers and number of phenotypes clones.
2968 In addition to the number of phenotype clones and number of markers, the main page for the trial selected also has information and graphs on phenotypic correlation for all of the traits. By moving your cursor over the graph you can read the different values for correlation between two traits. A key with all of the trait names of the acronyms used can be found in the tab below the graph.
2972 Below the ``Training population summary'' there is a tab for ``Traits''. Clicking on this tab will show all available traits for the specific trial. You can create a model by choosing one or multiple traits in the trial and clicking ``Build Model''. In this example, the traits for ``cassava bacterial blight severity'' and ``cassava mosaic disease severity'' have been selected.
2976 Clicking on `Build Model' will take you to a new page with the models outputs for the traits. Under the ``Genomic Selection Model Output'' tab you can view the model output and the model accuracy. Clicking on any of the traits will take you to a page with information about the model output on that individual trait within the trial. There you can view all of the trait information that was seen in more detail in \protect\hyperlink{method-1}{\emph{Method 1}}.
2980 You can apply the models to simultaneously predict GEBVs for respective traits in a selection population by clicking on ``Predict Now'' or the name of the selection population. You can also apply the models to any set of genotyped clones that you can create using the `lists' feature. For more information on lists, click \protect\hyperlink{working-with-lists}{\emph{here}}. Follow the link to the trait name to view and download the predicted GEBVs for the trait in a selection population.
2984 To compare clones based on their performance on multiple traits, you can calculate selection indices using the form below. Choose from the pulldown menu the population with predicted GEBVs for the traits and assign relative weights for each trait. The relative weight of each trait must be between 0 - 1. 0 being of least weight and importance, not wanting to consider that particular trait in selecting a genotype and 1 being a trait that you give highest importance.
2986 In this example we will be using the ``Cassava Ibadan 2002/03'' population and assigning values to each of the traits. Remember that there is a list of acronyms and trait names at the bottom of the page for reference. After entering whatever values you would like for each trait click on the ``Calculate'' button to generate results. This will create a list of the top 10 genotypes that most closely match the criteria that you entered. The list will be displayed right below the ``selection index'' tab. This information can also be downloaded onto your computer by clicking on the ``Download selection indices'' link underneath the listed genotypes and selection indices.
2993 In addition to creating a model by searching for pre-existing traits or by preexisting trial name, models can also be created by using your own list of clones. This creates a model by using or creating a training population.
2995 The page to use the third Method for creating a population model is the same as for the other two models. Select ``Genomic Selection'' from under the ``analyze'' menu of the main toolbar. This will take you to the Genomic Selection homepage and show you all three available methods to create a model. To see and use Method 3 scroll down and click on the tab labeled ``Create a Training Population''. This will open a set of tools that will allow you to use pre-existing lists or to create a new list.
2999 Once the ``Create a Training Population'' tab is opened you have the option to use a pre-existing list or create new one. To learn how to create a list, click \protect\hyperlink{working-with-lists}{\emph{here}}. The ``Make a new list of plots'' link will take you directly to the Search Wizard that is usually used to create lists.
3001 Please note: the only lists that can be used in Method 3 to create a model are lists of plots and trials. If the pre-existing list is not of plots or trials (for example, traits, or locations) it will not show up and cannot be used as a training population. When you create you use a list of trials, the trials data will be combined to create a training data set.
3003 To use your custom list of plots or trials as a training population, select the list and click ``Go''. This will take you to a detail page for the training population.
3007 From here on you can build models and predict breeding values as described in \protect\hyperlink{method-2}{\emph{Method 2}}\textbf{.}
3012 There are two ways to evaluate genotype information within the browser, from an accession detail page or a trial detail page.
3017 If you are interested in browsing genotype information for a single accession, for example `BAHKYEHEMAA', navigate to the accession detail page.
3021 Near the bottom of the detail page is a collapsible section called ``Accession Jbrowse''.
3025 This section will contain a link to the accession jbrowse page if the necessary genotype data is available. Clicking the link should take you to a page that looks like this, a which point you can browsre the genotype data in the form of a vcf track aligned to the latest build of the genome.
3032 If you are interested in browsing genotype information for the accessions within a given trial, navigate to the trial detail page.
3036 Halfway down the page is a collapsible section called ``Trial Jbrowse''. This section will contain a link to the trial jbrowse page if the necessary genotype data for at least two accessions planted in the trial is available.
3040 Clicking the link should take you to a page that looks like this, a which point you can browse the genotype data in the form of vcf tracks aligned to the latest build of the genome.
3047 Principal component analysis helps estimate and visualize if there is sub-grouping of individuals within a dataset based on a number of variables. Currently, you can use marker data to run PCA on datasets.
3049 You can run PCA from multiple places on the website. To do PCA on
3053 \item
3054 individuals from a trial, go to the trial detail page and find the PCA tool under the `Analysis tools' section.
3055 \item
3056 individuals from a training population you used in a GS modeling, do your modeling and find the PCA tool in the model output page.
3057 \item
3058 individuals in a training population and selection population you applied the training model, do your modeling, apply the model on the selection population and find the PCA tool on the selection population prediction output page.
3059 \item
3060 individuals in a list of accessions you created, for example using the search wizard, go to the `Analyze' menu and select the `Population Structure', select your list of individuals and run PCA.
3061 \item
3062 individuals from multiple trials, create a list of the trials using the search wizard, go to the `Analyze' menu and select the `Population Structure', select your list of trials and run PCA.
3065 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/pca_iita_naccri_trials} \end{center}
3067 With all the options, you will get a interactive plot of the two PCs (shown below) that explain the largest variance. Point the cursor at any data point and you will see the individual name with its corresponding PCs scores. By clicking the `Download all PCs', you can also download the 10 PCs scores in the text format.
3072 Currently, ANOVA is implemented for a single trial (single year and single location). You can do ANOVA for RCBD, CRD, Alpha and Augmented trial designs. ANOVA is done using linear mixed effects model, where the genotypes is fixed effect and the replications and blocks are random effects. Fixed effect significance level is computed using `lmer' from `lmeTest' R package.
3074 You can do ANOVA from two places: trial detail and training population detail. In both cases, if the phenotype data was from the supported trial designs,
3076 -- Go to the ANOVA section down in the trial or training population page
3078 -- Select the trait of you want to perform ANOVA
3080 -- Click the `Run ANOVA' and wait for the result
3087 The K-Means method allows you to partition a dataset into groups (K number). The hierarchical clustering, agglomerative, allows you to explore underlying similarity and visualize in a tree structure (dendrogram) the different levels of similarities (clusters) among samples. You can do clustering based on marker data, phenotype data and GEBVs. When you use phenotype data, first clone averages for each trait are calculated. Both methods use Euclidean distance as a measure of similarity. For the hierachical clustering, the complete-linkage (farthest neighbour) method is used to link up clusters.
3089 There are three pathways to using this tool.
3093 \tightlist
3094 \item
3095 When you have data in the form of a list or dataset from the search wizard:
3100 \item
3101 -- go to the `Analyze' menu and select the clustering option
3102 \item
3103 -- make sure you are logged in
3104 \item
3105 -- Select the relevant genotyping protocol, if you are clustering using genotype data
3106 \item
3107 -- select your list or dataset, click `Go'
3108 \item
3109 -- select clustering type
3110 \item
3111 -- select the data type to use
3112 \item
3113 -- If you are running K-Means clustering, provide the number of partitions (K). If left blank it will partition the data set into optimal numbers for the dataset.
3114 \item
3115 -- click the `Run Cluster' and wait for the analysis to finish or queue the request and wait for an email with the analysis result.
3116 \item
3117 -- You can download the outputs following the download links.
3123 \tightlist
3124 \item
3125 From the trial detail page:
3130 \item
3131 -- Go to the `Analysis Tools' section
3132 \item
3133 -- Follow steps D to G in (1)
3139 \tightlist
3140 \item
3141 In the solGS pipeline:
3146 \tightlist
3147 \item
3148 -- Once you you are in a model output put page, you will see a section where you can do clustering in the same way as above (option 2).
3151 K-Means clustering:
3153 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/k-means-cluster} \end{center}
3155 Hierarchical clustering:
3162 You can check for genetic gain by comparing the the GEBVs of a training and a selection population. You can do this in the solGS pipepline once you build a model and apply the model to predict the GEBVs of a selection population. Once at that stage, you will see a section `Check Genetic Gain'. Select a selection population to compare with the training population and click the `Check Genetic Gain' button. The genetic gain will be visualized in boxplots. You can download the boxplot(s) as well as the GEBVs data used for the plot(s).
3169 This tool allows you to estimate genetic relatedness between a pair of individuals (kinship), homozygousity across loci in an individual (inbreeding coefficient), and genetic similarity of an individual relative to the rest of the population (averge kinship).
3171 There are three pathways to using this tool.
3173 (1) When you have a list or dataset clones, created from the search wizard:
3177 \item
3178 -- go to the `Analyze' menu and select the kinship and inbreeding
3179 \item
3180 -- make sure you are logged in
3181 \item
3182 -- Select the genotypic protocol for the marker data
3183 \item
3184 -- select your list or dataset of clones, click `Go'
3185 \item
3186 -- click the `Run Kinship' and wait for the analysis to finish, depending on the data size this may take minutes. You can choose to submit the analysis and wait for an email notice to view the results or wait for it to complete.
3187 \item
3188 -- You can download the output following the download links.
3191 (2) From the trial detail page:
3195 \item
3196 -- Go to the `Analysis Tools' section
3197 \item
3198 -- Follow steps C to G in (1)
3201 (3) In the solGS pipeline:
3205 \tightlist
3206 \item
3207 -- Once you you are in a model output put page, scroll down to the `Kinship and Inbreeding' section and run kinship.
3210 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/kinship-inbreeding} \end{center}
3215 If you calculate selection index based on GEBVs of multiple traits, and you want to select a certain proportion of the indexed individuals (e.g.~top 10\%, or bottom 10\%) and then you want to partition the selected individuals into a number of groups based on their genotypes, you can use the k-means clustering method.
3217 The procedure is:
3221 \item
3222 predict GEBVs for 2 or more traits
3223 \item
3224 In the models output page, calculate selection indices. Note the name of the selection index data.
3225 \item
3226 Go to the clustering section,
3229 -- select the selection index data,
3231 -- select `K-means',
3233 -- select `Genotype',
3235 -- in the K-numbers textbox, fill in the number of groups you want to create,
3237 -- in the selection proportion textbox, fill in the proportion of the indexed individuals you want to select, e.g.~for the top 15 percent, 15. if you wish to select bottom performing, prefix the number with minus sign (e.g.~-15)
3239 -- then run cluster and wait for the result.
3241 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/selection_proportion_clustering} \end{center}
3244 \section{Search Wizard Genomic Relationship Matrix (GRM) Download}\label{search-wizard-genomic-relationship-matrix-grm-download}}
3246 The genomic relationship matrix (GRM) is useful for understanding underlying structure in your population. Breedbase can compute the GRM using rrBLUP. First, select accessions in the search wizard and optionally select a genotyping protocol. If no genotyping protocol is selected, the default genotyping protocol in your system is used (as defined in sgn\_local.conf). Specify the minor allele frequency, missing marker data, and missing individuals data filters to apply. The GRM can be returned in a matrix format (.tsv) which shows all pairwise relationships between the selected accessions and is useful for visualization; alternatively, the GRM can be returned in a three-column format (.tsv) which is useful for programs like ASReml outside of Breedbase. The GRM can also be returned as a simple correlation heatmap image (.pdf). The GRM can be computed from parents of the selected accessions granted the parents were genotyped, by clicking the checkbox ``compute from parents''; this is useful for programs where parental lines are genotyped and then hybrids are created and evaluated in the field.
3248 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_wizard_genotype_analyses_grm} \end{center}
3251 \section{Search Wizard Genome Wide Association Study (GWAS)}\label{search-wizard-genome-wide-association-study-gwas}}
3253 Performing a genome wide association study (GWAS) can determine genotypic markers which are significantly correlated to phenotypic traits. Breedbase can compute GWAS using rrBLUP. First, select accessions and trait(s) in the search wizard, and optionally select a genotyping protocol. If no genotyping protocol is selected, the default genotyping protocol in your system is used (as defined in sgn\_local.conf). Several traits can be selected in the search wizard; if the traits are not to be treated as repeated measurements then select `no' in the select box and this will tell Breedbase to return GWAS results independently for the selected traits. If the selected traits are indeed all repeated measurements then select `yes' in the select box and Breedbase will return as single GWAS analysis across all the phenotypic records. Specify the minor allele frequency, missing marker data, and missing individuals data filters to apply. GWAS results can be returned in a tabular format (.tsv) where the -log10(p-values) for the selected traits are returned; alternatively, the GWAS results can be returned as Manhattan and QQ plots for the selected traits. The GWAS can be computed from parents of the selected accessions granted the parents were genotyped, by clicking the checkbox ``compute from parents''; this is useful for programs where parental lines are genotyped and then hybrids are created and evaluated in the field.
3255 The GWAS will filter the data by the input MAF and missing data filters provided. After filtering the data is imputed using an `EM' method in rrBLUP. The Kinship matrix (GRM) is computed from the imputed genotypic data and used in the GWAS model. The GWAS uses fixed effects for different field trials and replicates in the phenotypic data.
3257 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_wizard_genotype_analyses_gwas} \end{center}
3259 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_wizard_genotype_analyses_manhattan_plot} \end{center}
3261 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/search_wizard_genotype_analyses_qq_plot} \end{center}
3266 Visible and near-infrared spectroscopy (vis-NIRS) can be related to reference phenotypes through statistical models to produce accurate phenotypic predictions for unobserved samples, increasing phenotyping throughput. This technique is commonly used for predicting traits such as total starch, protein, carotenoid, and water content in many plant breeding programs. Breedbase implements the R package \href{https://CRAN.R-project.org/package=waves}{\emph{waves}} to offer training, evaluation, storage, and use of vis-NIRS prediction models for a wide range of spectrometers and phenotypes.
3268 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/waves_breedbase_schema} \end{center}
3273 In order to initiate an analysis, the user must select one or more datasets using \ref{search-wizard}. A dataset in Breedbase can contain observationUnit-level (plot-, plant-, or sample-level) trial metadata and phenotypic data from one or more trials. After navigating to the ``NIRS'' webpage under the ``Manage'' tab in Breedbase, the user can initiate an analysis and select one of these datasets as input for model training. An optional test dataset can be selected in the second step of the workflow.
3275 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_NIRS_prediction_workflow_intro} \end{center}
3277 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_NIRS_prediction_workflow_dataset} \end{center}
3282 Five cross-validation schemes that represent scenarios common in plant breeding are available for this analysis. These include CV1, CV2, CV0, and CV00 as outlined below and described in depth by Jarquín et al.~(2017) as well as random and stratified random sampling with a 70\% training and 30\% validation split. For those schemes from Jarquín et al.~(2017), specific input datasets must be chosen based on genotype and environment relatedness. Cross-validation choices: * \textbf{Random sampling} (70\% training / 30\% validation) * \textbf{Stratified random sampling}, stratified based on phenotype (70\% training / 30\% validation) * \textbf{CV1}, untested lines in tested environments * \textbf{CV2}, tested lines in tested environments * \textbf{CV0}, tested lines in untested environments * \textbf{CV00}, untested lines in untested environments
3284 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_NIRS_cv} \end{center}
3289 Preprocessing, also known as pretreatment, is often used to increase the signal to noise ratio in vis-NIR datasets. The \emph{waves} function \emph{DoPreprocessing()} applies functions from the \emph{stats} and \emph{prospectr} packages for common spectral preprocessing methods with the following options: * Raw data (default) * First derivative * Second derivative * Gap segment derivative * Standard normal variate (SNV; Barnes et al., 1989) * Savitzky-Golay polynomial smoothing (Savitzky and Golay, 1964)
3291 For more information on preprocessing methods and implementation, see the \href{https://CRAN.R-project.org/package=waves}{\emph{waves}} manual, available through CRAN: \href{https://cran.r-project.org/web/packages/waves/waves.pdf}{waves.pdf}
3293 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_NIRS_snv} \end{center}
3298 Several algorithms are available for calibration model development in Breedbase via the \href{https://CRAN.R-project.org/package=waves}{\emph{waves}} package. The \emph{TrainSpectralModel()} function in waves performs hyperparameter tuning as applicable using these algorithms in combination with cross validation and train functions from the package \emph{caret}. Currently, only regression algorithms are available, but classification algorithms such as PLS-DA and SVM clasification are under development. * \textbf{Partial least squares regression} (PLSR; Wold et al., 1982; Wold et al., 1984) is a popular method for spectral calibrations, as it can handle datasets with high levels of collinearity, reducing the dimensionality of these data into orthogonal latent variables (components) that are then related to the response variable through a linear model (reviewed in Wold et al., 2001). To avoid overfitting, the number of these components included in the final model must be tuned for each use case. The PLSR algorithm from the \emph{pls} package is implemented by waves. * \textbf{Random Forest regression} (RF; Ho, 1995) is a machine learning algorithm based on a series of decision trees. The number of trees and decisions at each junction are hyperparameters that must be tuned for each model. Another feature of this algorithm is the ability to extract variable importance measures from a fitted model (Breiman, 2001). In Breedbase, this option is made available through implementation of the RF algorithm from the package randomForest in the waves function TrainSpectralModel(). This function outputs both model performance statistics and a downloadable table of importance values for each wavelength. It is worth noting that this algorithm is computationally intensive, so the user should not be alarmed if results do not come right away. Breedbase will continue to work in the background and will display results when the analysis is finished. * \textbf{Support vector machine regression} (SVM; Vapnik, 2000) is another useful algorithm for working with high-dimension datasets consisting of non-linear data, with applications in both classification and regression. The package waves implements SVM with both linear and radial basis function kernels using the kernlab package.
3301 \subsection{Output: common model summary statistics}\label{output-common-model-summary-statistics}}
3303 After training, model performance statistics are both displayed on a results webpage and made available for download in .csv format. These statistics are calculated by the \emph{TrainSpectralModel()} function in \href{https://CRAN.R-project.org/package=waves}{\emph{waves}} using the \emph{caret} and \emph{spectacles} packages. Reported statistics include: * Tuned parameters depending on the model algoritm * \textbf{Best.n.comp}, the best number of components to be included in a PLSR model * \textbf{Best.ntree}, the best number of trees in an RF model * \textbf{Best.mtry}, the best number of variables to include at every decision point in an RF model * \textbf{RMSECV}, the root mean squared error of cross-validation * \textbf{R2cv}, the coefficient of multiple determination of cross-validation for PLSR models * \textbf{RMSEP}, the root mean squared error of prediction * \textbf{R2p}, the squared Pearson's correlation between predicted and observed test set values * \textbf{RPD}, the ratio of standard deviation of observed test set values to RMSEP * \textbf{RPIQ}, the ratio of performance to interquartile distance * \textbf{CCC}, the concordance correlation coefficient * \textbf{Bias}, the average difference between the predicted and observed values * \textbf{SEP}, the standard error of prediction * \textbf{R2sp}, the squared Spearman's rank correlation between predicted and observed test set values
3308 Once a model has been trained, it can be stored for later use. This action calls the \emph{SaveModel()} function from \href{https://CRAN.R-project.org/package=waves}{\emph{waves}}. Metadata regarding the training dataset and other parameters specified by the user upon training initialization are stored alongside the model object itself in the database.
3310 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_NIRS_export_model} \end{center}
3313 \subsection{Predict phenotypes from an exported model (routine use)}\label{predict-phenotypes-from-an-exported-model-routine-use}}
3315 For phenotype predictions, users select a dataset and can then choose from models in the database that were trained using the same spectrometer type as the spectral data in the chosen dataset. Predicted phenotypes are stored as such in the database and are tagged with an ontology term specifying that they are predicted and not directly measured. Metadata regarding the model used for prediction is stored alongside the predicted value in the database. Predicted phenotypes can then be used as normal in other Breedbase analysis tools such as the Selection Index and GWAS.
3317 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_NIRS_select_model} \end{center}
3319 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/manage_NIRS_prediction_results} \end{center}
3324 The Breedbase Spectral Analysis Tool does not allow for prediction models involving data from multiple spectrometer types at once.
3326 References * Barnes, R.J., M.S. Dhanoa, and S.J. Lister. 1989. Standard normal variate transformation and de-trending of near-infrared diffuse reflectance spectra. Appl. Spectrosc. 43(5): 772-777. doi: 10.1366/0003702894202201. * Breiman, L. 2001. Random forests. Mach. Learn. 45: 5-32. doi: 10.1201/9780429469275-8. * Ho, T.K. 1995. Random decision forests. Proc. Int. Conf. Doc. Anal. Recognition, ICDAR 1: 278-282. doi: 10.1109/ICDAR.1995.598994. * Jarquín, D., C. Lemes da Silva, R.C. Gaynor, J. Poland, A. Fritz, et al.~2017. Increasing Genomic-Enabled Prediction Accuracy by Modeling Genotype x Environment Interactions in Kansas Wheat. Plant Genome 10(2): plantgenome2016.12.0130. doi: 10.3835/plantgenome2016.12.0130. * Johnson, R.A., and D.W. Wichern. 2007. Applied Multivariate Statistical Analysis (6th Edition). De Maesschalck, R., D. Jouan-Rimbaud, and D.L. Massart. 2000. The Mahalanobis distance. Chemom. Intell. Lab. Syst. 50(1): 1-18. doi: 10.1016/S0169-7439(99)00047-7. * Mahalanobis, P.C. 1936. On the generalized distance in statistics. Natl. Inst. Sci. India. * Savitzky, A., and M.J.E. Golay. 1964. Smoothing and Differentiation of Data by Simplified Least Squares Procedures. Anal. Chem. 36(8): 1627-1639. doi: 10.1021/ac60214a047. * Shrestha, R., L. Matteis, M. Skofic, A. Portugal, G. McLaren, et al.~2012. Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice. Front. Physiol. 3 AUG(August): 1-10. doi: 10.3389/fphys.2012.00326. * Vapnik, V.N. 2000. The Nature of Statistical Learning Theory. Springer New York, New York, NY. * Wold, S., A. Ruhe, H. Wold, and W.J. Dunn, III. 1984. The Collinearity Problem in Linear Regression. The Partial Least Squares (PLS) Approach to Generalized Inverses. SIAM J. Sci. Stat. Comput. 5(3): 735-743. doi: 10.1137/0905052. * Wold, S., M. Sjöström, and L. Eriksson. 2001. PLS-regression: a basic tool of chemometrics. Chemom. Intell. Lab. Syst. 58(2): 109-130. doi: 10.1016/S0169-7439(01)00155-1.
3331 The general mixed model tool is available at /tools/mixedmodels and a link is provided from the Analyze menu.
3333 To use the mixed model tool, first create dataset using the Wizard containing the data that you would like to analyze.
3335 Select the Mixed Model tool from the Analyze menu.
3337 You are presented with a workflow. On the first step of the workflow, select the dataset that you wish to analyze, click on ``Choose dataset'' to continue.
3339 The second part of the workflow presents you with the traits in the dataset; you can select one or more traits from the lists using the select buttons. If you selected one trait, a bargraph of the trait distribution will be shown. Click the ``Next step'' button to move to the next screen.
3341 \begin{center}\includegraphics[width=0.95\linewidth]{assets/images/mixedmodel_tool_model_build_step} \end{center}
3343 On the model build screen, all the factors are displayed that are contained within the dataset. The factors are presented as a list of blue buttons that can be dragged using the mouse to areas on the screen which build a mixed model equation. The areas correspond to fixed factors, random factors, and optionally to more complex factors, such as fixed factors with interaction and fixe factors with vriable slope/intersects. Drag the available factors to the corresponding area. To calculate BLUPs for germplasm, drag the germplasmName button to the ``Random factors'' area. To calculate BLUEs, drag it to the ``Fixed factors'' area. The factors need to have different levels contained within them, for example, if there is only one trial in the dataset, it cannot be used as one of the factors. Click on ``Run analysis and got to next step'' to run the mixed model and display the results.
3345 The result view contains two tabs, one with the raw data, either BLUPS or BLUEs, and the other the adjusted means from the raw data.
3347 The results can be stored in the database as an analysis, by clicking the button provided on the top of the data.
3350 \section{Genomic Prediction of Cross Performance (GCPC)}\label{genomic-prediction-of-cross-performance-gcpc}}
3352 The GCPC tool is available at /tools/gcpc and a link is provided from the Analyze menu. The GCPC tool implements genomic prediction with additive and directional dominance in the linear mixed model to predict for cross performance.
3354 Before using the tool, first create a dataset using the Wizard containing the data that you would like to analyze. (The dataset should have genotyping\_protocols). Second, create Selection Indices for your traits using Selection Index in Analyze Menu.
3356 To use the tool, Select the GCPC tool from the Analyze menu.
3358 Then, select the dataset with genotyping\_protocols that you wish to analyze, click on ``Proceed to Factor Selection'' to load available factors that can be included in the model.
3360 Select the factors you wish to include in the model either as Fixed or Random. Click ``None'' for factors that you don't want to include in the model. Note that the ``germplasmName'' is factored as Random by default.
3362 The next step is to select the selection index for your traits on the dropdown menu.
3364 Once you are through, click ``Run GCPC'' to run the model. The output will be presented in form of a table with ``ID'', ``Parent1'', ``Parent2'' and their cross prediction merit organized in descending order. The results will also have sex information based on whether the dataset has plant sexes available in the database.