[CN Trans test] v29 Germplasm Lists
关于 - About
通过种质清单管理器，您可以
The Germplasm List manager allows you to:
浏览种质清单- browse for germplasm lists导入现有种质清单- import a list of existing germplasm编辑列表元数据，锁定/解锁种质列表- edit list metadata, lock/unlock the germplasm list自定义列表视图- customize the list view批量导入列表更新- import list updates in batch重新排序条目- reorder entries删除条目- remove entries将特定列表中的条目添加到其他列表中- add entries from a specific list to a different list删除和克隆列表- delete and clone lists导出列表数据和标签- export list data and labels将列表移动到不同的文件夹- move a list to a different folder导出列表数据和标签- export list data and labels计算亲子关系系数- calculate Coefficient of Parentage
浏览种质清单 - Browse Germplasm Lists
点击浏览链接。您将看到列表树浏览器
Click on the Browse link. You will see the list tree browser
选择一个或多个种质清单
Select one or more germplasm lists
点击确定
Click OK
所选列表在不同的标签页中打开。
The lists selected are opened in different tabs.
选择条目 - Select Entries
打开列表后，您可以通过选中复选框来选择几个条目。如果需要选择列表中的所有条目，请单击复选框选择所有页面。
When a list is open, you can select a few entries by checking the boxes. If you need to select all entries in a list, click on the checkbox to select all pages.
搜索种质清单 - Search Germplasm Lists
您将看到系统中所有可用列表的分页表，其中包含相应信息（列表名称、父文件夹、描述、列表所有者、列表类型、条目数量、状态 - 锁定/解锁-、备注、列表日期）。
You will see a paginated table of all available lists in the system with the corresponding information (List Name, Parent folder, Description, List Owner, List type, #of Entries, Status -locked/unlocked-, Notes, List Date).
您可以使用相应的 “搜索条件 ”功能（默认情况下已添加列表名称过滤器），添加和组合任何这些列的过滤器。
You can add and combine filters using any of these columns using the corresponding "Search by" functionality (List Name filter added by default).
搜索方式 列表类型> 收获
Search by: List type> Harvest
应用过滤器
Apply the filter
使用 LIST BUILDER 选项创建列表 - Create a List using the LIST BUILDER option
您可以使用 LIST BUILDER 选项创建新列表。
You can use the LIST BUILDER option to create a new list.
点击 Show List Builder 按钮。
Click on the Show LIST BUILDER button.
打开列表 (s)，选择感兴趣的条目，然后将所选条目拖到 Build a new list 部分。
Open a list (s), select the entries of interest, and drag the chosen entries to the Build a new list section.
要保存列表，请单击 SAVE 页面上的 List Builder 按钮。选择或创建一个文件夹来存放新列表。命名 germplasm list 并保存。germplasm list 可从 germplasm list 或 Browse 选项中获取。
To SAVE the list, click the SAVE button on the List Builder page. Select or create a folder to house the new list. Name the germplasm list and Save. The germplasm list will be available from the germplasm list filter or the Browse options.
行动 - Actions
导入列表 - Import List
操作 > 导入列表
Actions > Import List
下载模板。该模板包含 Observation 和 Entry Details 表。
Download the template. This template has the Observation and Entry Details sheets.
Observation： 您应在文件中提供要列入列表的种质的 GID、GUID 或 DESIGNATION。如果您为一条记录提供多个值，系统将按照以下顺序进行检索： GUID、GID、DESIGNATION 进行检索。ENTRY_CODE 信息是可选的。
Observation: You should provide the file with either the GID, GUID, or the DESIGNATION of the germplasm to include in the list. If you provide multiple values for a record, the system will use the following order: GUID, GID, DESIGNATION for retrieval. The ENTRY_CODE information is optional.
Entry Details：包含作物可用条目详细信息（VARIABLE、ALIAS、DESCRIPTION、PROPERTY、SCALE、 METHOD、DATA TYPE、EXPECTED VALUES）。导入过程将验证为不同变量定义的值是否与为这些变量定义的标度相冲突。
Entry Details: contains the information about the available entry details for the crop (VARIABLE, ALIAS, DESCRIPTION, PROPERTY, SCALE, METHOD, DATA TYPE, EXPECTED VALUES). The import process validates that the values defined for the different variables do not conflict with the defined scale for such variables.
注：拥有相应权限的用户可通过本体管理器定义 “条目详情 ”变量类型（请参阅 https://ibplatform.atlassian.net/wiki/spaces/BMS/pages/3721511032/CN+Trans+test+v29+Manage+Ontologies#Add-%26-Edit-Variable ）。一旦用户创建了新的条目详细变量，它就会出现在列表导入的模板中，并可被添加到现有列表中 (https://ibplatform.atlassian.net/wiki/spaces/BMS/pages/3721505621/CN+Trans+test+v29+Germplasm+Lists#Add-and-Remove-Entry-Details )。
Note: Users with the corresponding permissions can define “Entry detail” variables type via Ontology Manager (see https://ibplatform.atlassian.net/wiki/spaces/BMS/pages/3721511032/CN+Trans+test+v29+Manage+Ontologies#Add-%26-Edit-Variable ). Once the user creates a new entry detail variable, it will be available in the template for the list importation and can be added to an existing list (https://ibplatform.atlassian.net/wiki/spaces/BMS/pages/3721505621/CN+Trans+test+v29+Germplasm+Lists#Add-and-Remove-Entry-Details )
浏览要导入的文件并点击 Next。
Browse for the file to be imported and click on Next.
示例 - Example:
导入列表过程可以通过变量名或别名读取分配给不同条目的变量。此外，导入还会验证为不同条目细节定义的值是否与定义的标度冲突，否则会阻止导入。
The import list process can read in the variables assigned to the different entries by variable name or alias. In addition, the import validates that the values defined for the different entry details do not conflict with the defined scale and prevents the import otherwise.
弹出 “变量 ”窗口，显示条目详情变量是存在于列表中（用于更新现有列表流程），还是新加入列表（也用于更新现有列表流程），还是在本体中找不到。
The Variables popup is displayed, indicating if the entry details variables exist in the list (for updating the existing list process), are new to the list (used in updating the existing list process too), or are not found in the ontology.
点击下一步 - Click Next
系统使用 GID 和/或 GUID 和/或 DESIGNATION 中提供的信息显示审查表，其中显示 1) 有单个匹配记录，2) 有多个匹配记录，3) 没有匹配记录。
The system uses the information provided in GID and/or GUID and/or DESIGNATION to show a review table showing which records 1) have a single match, 2) multiple matches, and 3) have no match.
您可以使用这些标准来筛选记录，然后点击 GID MATCHES，弹出相应种质的详细信息。
You can use these criteria to filter the records and click on GID MATCHES to get the details pop-up of the corresponding germplasm.
注意：您可以跳过有多个匹配项和/或无匹配项的条目
Note: You can skip the entries with multiple matches and/or entries without matches
点击下一步 - Click Next
如果有多个匹配项，则弹出 “选择匹配项 ”窗口。
For multiple matches, the Select match pop-up is displayed.
选择所需的匹配项，或点击 Omit 按钮省略条目
Select the match desired or omit the entry by clicking on the Omit button
点击下一步 - Click Next
当系统无法找到与一个或多个文件记录的标准相匹配的 germplasm 记录时，将显示 “选择匹配映射条目”。
When the system cannot find a germplasm record that matches the criteria for one or more file records, the Select match for mapping entries is displayed.
点击记录的映射操作。
Click on the mapping action for a record.
然后会弹出一个种质搜索弹窗，用户可以在此搜索整个种质数据库，找到要映射的种质（一个也是唯一一个）。
Then you will be prompted with a germplasm search popup where the user can search the entire germplasm database to find the germplasm (one and only one) to be mapped.
选择一个种质并点击 “选择”。系统将记录标记为匹配 (✓)
Select one germplasm and click on Select. The system marks the record as matched (✓)
系统会在表格中检索或显示匹配种质的 GID 和 DESIGNATION。
And the system retrieves or shows the GID and DESIGNATION of the matched germplasm in the table.
点击下一步 - Click Next
系统将显示一条确认信息，其中包含列表导入过程的摘要：
A confirmation message is displayed with a summary of the List importation process:
点击 Confirm - Click on Confirm
现在，您必须定义常用的列表元数据（名称、描述等）及其父文件夹。
Now you must define the usual list metadata (name, description, etc.) and its parent folder.
点击 Save - Click Save
系统将按照 Excel 文件的顺序自动清点 ENTRY_NO，然后列表将可供管理。
The system will auto-enumerate ENTRY_NO using the order of the Excel file, and the list will become available for management.
自定义列表视图 - Customize the list view
您可以自定义您的名单，让他们添加或删除任何 germplasm 信息。
You can customize your lists by enabling them to add and remove any germplasm information.
List 评选 - List Selection
Click on a list.
The system opens a new tab in the germplasm list section with the corresponding list entries having the following default columns (ENTRY_NO, GID, DESIGNATION, LOTS, AVAILABLE, UNIT).
If the list has associated Entry details variables, they are displayed in their corresponding field, and their values are populated in the list table.
You can also filter and sort some columns.
In the example displayed, GID, DESIGNATION, and LOTS are hyperlinks to the corresponding germplasm details.
Add and Remove Entry Details
Select an Entry detail variable and click on the remove link.
A confirmation message is displayed.
Confirm
The Entry detail variable and the values are not displayed anymore.
Click on Add button
Select an Entry detail from the variable dropdown
Save
You can add values manually for the Entry details variables
Click on a cell and add values. It could be typing a text, adding a number, selecting a categorical value, adding a date depending on the variable data type.
Add and Remove Columns
Using the Columns button you will be able to search, add and remove columns in the germplasm list table. NAMES, PASSPORT, and ATTRIBUTES are also included.
Open an F1CRT list type
Click on the Columns button
Select FEMALE PARENT NAME, MALE PARENT NAME, LOCATION NAME
Click on Apply button
The new columns added are populated with their corresponding values.
Note: The changes are saved automatically, if you close the list tab and re-open the list, you will see the changes applied previously.
For removing columns:
Click on the Columns button
Uncheck the column (s) desired
Click on the Apply button
The columns selected are not displayed anymore.
Define the level of the pedigree to consider for CROSS string
You can define the generation to be considered for the CROSS string (up to 10 levels).
Click on the Columns button
Add the Cross Column
Click on the Apply button
Click on the Cross expansion icon and specify the level desired.
Apply
Edit List Metadata
Click on the Edit List Metadata icon
The Edit list Metadata popup is displayed.
Edit the List Name, Description, and Notes
Save. A success message is displayed and the changes are applied.
Lock / Unlock a Germplasm List
You can unlock and lock the germplasm lists for restricting actions over the list. It can be done by clicking on the icon.
Note: When a list is locked the Edit List Metadata icon is not available. The Columns button is not displayed, and the options available under the Actions button are: i) Add entries to another list, ii) Clone list, and iii) Export list data and labels (See next section).
Create New List
You can create a new list from existing list (s) using the list builder option.
Click on the Show List Builder button.
Open germplasm list(s) and select entries of interest. You can select entries from multiple lists.
Drag the selected entries to the LIST BUILDER section.
To save the new list, Select the SAVE button at the bottom of the List Builder window.
Select or create a folder to house the new list. Name the germplasm list and Save. The germplasm list can be accessed from the Browse Lists or Search options.
To reset the list before saving, Select the Reset button at the bottom of the List Builder window.
Germplasm List Actions
Import list update
Using this action you will be able to update a germplasm list, update the ENTRY_CODE and ENTRY_DETAILS variables adding them, or edit the existing values. The action can be done for all entries or some of the germplasm list.
Open a germplasm list
Actions > Import list update
The Import list update popup is displayed.
You can download the template which has ENTRY_NO and ENTRY_CODE columns in the Observation sheet and a tab with the available entry details variables (VARIABLE, ALIAS, DESCRIPTION, PROPERTY, SCALE, METHOD, DATA TYPE, EXPECTED VALUES)
Download the germplasm list import update template
Specify the entry number you what to update under the ENTRY_NO column
Fill the file up with valid data
Browse for the file and click on Next
The import list process is able to read the variables assigned to the different entries by variable name or alias. In addition, the import validates that the values defined for different do not conflict with the defined scale and prevent the import otherwise.
Example:
The Variables popup is displayed, in a similar way that in the import list process, the status of the variable is indicated, if the variable imported already exists in the list, if the variable is new to the list, or not found in the ontology.
Click on Next
A confirmation message is displayed, click on Confirm.
The updates are displayed in the list table:
Note: For ENTRY_CODE you need to add the column using the Columns button and apply the change.
Reorder entries
Triggering this action, you will be able to manipulate the entry number order of the list entries under the condition that the sequential nature of the list (1 to N) is always preserved.
Open a list
Select one, or more than one entry. It could be from different pages.
Action> Reorder entries
The Reorder entries popup is displayed. There are three options for reordering the entries on a list: i) at the beginning of the list, ii) at the end of the list, and iii) select a specific position.
Choose the option: Select a specific position and type a valid value
Click on Reorder
A success message is displayed and the entries selected are reordered starting at position 10 in the example shown.
Remove entries
With this action, you are able to remove the selected entries (and corresponding entry detail values) from the list and re-enumerate ENTRY_NO.
Open a list
Select one or more than one entry. It could be done from different pages.
Actions> Remove entries
A confirmation message is displayed:
Confirm
A success message is displayed, the entries are removed from the list, and the ENTRY_NO is re-enumerated.
Add entries
The user can add additional entries to the list.
Open a list
Actions> Add entries
The Germplasm Search is opened permitting you to search and select the germplasm of interest using the existing filters.
Select one or many entries
Click on Select
A success message is displayed, “Germplasm entries added to list successfully!”
The system adds the selected germplasm as new entry/es at the bottom of the list, populating the corresponding configured columns and letting the user define the values for the corresponding entry details
Add entries to another list
This action enables you to add entries from one list to another list.
Open a list
Select one or more entries
Actions> Add entries to another list
The popup Add entries to the list is displayed. The system presents the list tree where the user can define the destination list of the selected germplasm.
Select the destination list
Click on Add button
A confirmation message is displayed.
Confirm
A success message is shown, “Germplasm entries added to list successfully!”
The system adds the selected germplasm as new entry/es at the bottom of the destination list, populating the corresponding configured columns and letting the user define the values for the corresponding entry details.
Delete list
Open the list you want to delete
Actions> Delete list
A confirmation message is displayed:
Confirm
A success message is shown, “Successfully deleted list.” And the list is not displayed anymore.
Clone list
When you trigger this action, the system permits you to clone a list. The BMS creates a new list with the specified name conserving the elements, enumeration (ENTRY_NO), germplasm columns, and entry details (variables and values) of the original list.
Open a list
Actions> Clone list
Then the system presents the list tree popup where the user can define the name and folder location of the new list.
Save
A success message is displayed, “Germplasm list cloned successfully!”.
The cloned list is opened in a new list tab
Export list data and labels
This component from the Germplasm List module has the same features that the other printing labels implemented into the BMS, the presets options, output formats, and the “specify labels stock” options for PDF format.
Export list XLS gives you the opportunity to export a view of the thing you want to modify and import it back as an entry details update file.
Additionally, the ability to print labels for the list will help you to physically identify the lines that they are preparing for shipping or study.
For germplasm lists, you can choose and drag fields from the Germplasm Details and Names and Attributes and Entry Details into the Left Side Fields and Right Side Fields (PDF), or Selected fields (XLS and CSV) to add them to your export file. For PDF you can only add 5 fields per side
Open a list
Actions> Export list data and labels
Select Excel Data output format
Include column headings in XLS export?: Yes
Select fields from Germplasm Details, Names, Attributes, Entry details and drag them to Selected fields
Add a preset name and Save preset
Export
The excel file is exported and populated properly with all fields included.
Coefficient of Parentage
You will be able to calculate the coefficient of parentage for a given set of germplasm. This coefficient in turn determines a measure of relatedness between germplasm by traversing their corresponding pedigree trees and recursively identifying the common ancestors.
btype parameter configuration
Go to Manage Crop Settings > Parameters tab
Notice btype field is editable. Configure the btype parameter according to your crop by choosing any of the following: 0=cross fertilizing, 1=self fertilizing, 2=self Fertilizing with unknown source but known parents.
Coefficient of parentage calculation
Go to Manage lists
Open the list you are interested in
Select entries
Actions > Coefficient of parentage (Beta)
You will see a confirmation message about the calculation progress.
When the Coefficient of parentage calculation finishes the results are displayed in a matrix.
In the Name Selector, GID and PREFERRED NAME options are always available, plus other common name types if available for all the GIDs selected.
Download the results in CSV format by clicking in the Download button.