User Manual

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This manual describes how to access data and use the tools on the Citrus Genome Database (CGD).  Please use the sidebar on the left to navigate to different parts of the manual, or click on the "Outline" menu in the lower right. You can access the next page of the manual by clicking on the title of the next page below.

 

Homepage Overview

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The Citrus Genome Database (CGD) homepage is divided into a few key areas to help facilitate navigation.  The Species Quick Start (Fig. 1A), has icons for each species represented in CGD.  Clicking on the icon takes you to the Species Overview page (see Species Overview tutorial) which allows for quick access to all the data associated with that crop.  To the right of the Species Quick Start is the Tools Quick Start (Fig. 1B).  This area has links to common tools and data search interfaces.  The center region of the homepage contains a News and Events section (Fig. 1C) which has news about CGD as well as from the community.  The homepage also has the traditional pull-down menu bar in the header (Fig. 1D) which also provide access to the species overview pages, data, search pages, tools, and general information.

Figure 1.  CGD Homepage

The items under the Search and Tools menus are discussed in other tutorials, but we want to highlight the Data and General menus in this section of the tutorial.   Under the Data menu (Fig 2A), you can see a data overview, learn how to submit data, download data, view publication datasets and view information on CGD trait and marker type abbreviations.  A summary overview of all data on CGD which can be broken down by species and/or data type is found on the Overview page. Under Data Submission, there are details about submitting data to CGD.  CGD will accept published data and we highly recommend contacting us before starting to fill in the data templates.  There are two links to the contact form on this page. 

The Data Download page contains links to all the various data types in CGD.  The links redirect you to either a search page, analysis page, or a table where the information about the data and links to download files are located.  For the RefTrans, Unigene, and genome data, the links take you to the analysis page with details about the data and these pages have a link on the left for the download page.  For germplasm, markers, QTLs, transcripts and sequences, the links take you to the search page for that data.  On the search page, choose your parameters and click submit to retrieve data.  The resulting table can then be downloaded.  

The Trait Abbreviations page contains the QTL traits that are in CGD and the abbreviations that are used for the internal CGD database generated QTL ID.  We have tried to keep our abbreviations consistent with those used in the trait and crop ontologies.  On the Marker Types page, there is a table of the marker types that are in CGD.  The markers have been generally grouped by the same technologies and we have provided a link to a reference that describes the marker technology. 

Figure 2.  Data, General, and Help menu items.

The General menu (Fig. 2B) contains links to a variety of different items.  If you would like to subscribe to the CGD mailing list, please click on Mailing Lists and complete the web form.  The General menu also has links to past presentations about CGD, work that is in progress and completed, and how to reference CGD.  The Help menu (Fig. 2C) has a link to the CGD User Manual and video tutorials.  There is also a Contact Us link that opens a fillable web form.  We appreciate input on the website as well as reports of website bugs and data errors.  

Species Overview Page

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All the available data for each species is easily found through the Species Overview Page.  From the CGD homepage, the species overview pages are accessed either by clicking on the Species menu in the toolbar and selecting the species of interest (Fig. 3A) or clicking on the species under the Species Quick Start section (Fig. 3B).

Figure 3.  Accessing the Species Overview Pages from the homepage.

On the Species Overview Page, there are two main sections.  The left side toolbar is static and has a Data section and a Tools section (Fig. 4A).  Clicking on the links in these sections either changes the information to the right of the toolbar (Fig. 4B), or opens another tab with the linked information.  The Species Overview Page defaults to the Overview section for each species which contains basic information and a summary of the available data in CGD.

Figure 4.  CGD Species Overview Page

Many of the left toolbar links will dynamically change the content to the right of the toolbar (Fig. 5).   The Genomes link displays links for the available genomes.  On the Genomes pane, the genome name is linked to the analysis page which has detailed information and citations.  The second link opens JBrowse to visualize the data.  For Germplasm, clicking the link will display a list of germplasm in CGD.  Blue text indicates a hyperlink that will display more detailed information.  For Transcripts, a table with summary information for the RefTrans and Unigene assemblies is displayed along with links to more detailed information.  Under the tools section, the CMap link displays a table that has a list of maps for that species and the reference.  The map name has a hyperlink directly to the CMap drawing for that map.

Figure 5. Dynamic data

The rest of the left toolbar links open new tabs.  As an example, the Genetic Maps link opens a new tab that has a table of all the genetic maps for the species (Fig. 6).  Blue text on the table indicates links to detailed information.  The Markers, Publications, Sequences, and Trait Loci links open search interfaces for the selected data type.  Please see the separate tutorials for more information on how to use the different data searches and tools.

Figure 6.  Genetic Map page and example of detailed information available under hyperlink indicated by blue text.

Data Searches

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To access the different data searches, click on the Search menu in the header and then select the data type you would like to search (Fig. 7).  To learn more about each search interface, please see the Outline link below the figure.

Figure 7.  Search menu in header provides links to different searches.

 

Genes and Transcripts

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The Genes and Transcripts Search is located under the Search menu in the header.  The Genes and Transcripts Search allows you to search sequences that are available in CGD with several different parameters.  A few parameters can be used to return a broad range of results, or numerous parameters can be used to find very specific data.  Searches can be limited to a certain genus and species. Once a genus has been selected, the species list will be populated and then a species selection can be made (Fig. 8A).  Searches can also be limited to datasets, such as genome and RefTrans assemblies or NCBI genes.  For a genome assembly dataset, the search can be restricted to a chromosome or scaffold and further restricted to a region on that chromosome or scaffold (Fig. 8B).  Searches for a specific gene or transcript name, or a list of names that are uploaded as a text file, are also possible with this search interface.

Figure 8.  CGD Genes and Transcript Search interface.

All search results are returned as a table with hyperlinks to more info (Fig. 9).  The table can be downloaded and a Fasta file of the returned sequences can also be downloaded (Fig. 9A).  To do another search, click reset.

Figure 9. Gene and Transcript Search results table

Germplasm

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The Germplasm Search can be accessed through the Search menu in the header.  Information about germplasm linked to data in CGD can be searched by species (Fig. 10A) and/or name (Fig. 10B).  A list of germplasm names, in a text file, can also be uploaded to search for multiple germplasm at once.

Figure 10.  CGD Germplasm Search interface.

Results are returned in a table format that can be downloaded (Fig. 11A).  Blue text indicates hyperlinks to more detailed information (Fig. 11B).  Searches can be refined by editing the parameters or a new search can be initiated by clicking the reset button.

Figure 11.  Germplasm Search results

Markers

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To search the markers in CGD, click on the Search menu in the header and select Marker Search.  The Marker Search is useful for retreiving information about markers and can be a broad search or a very specific search depending on the number of parameters used.  Markers can be searched by typing in a marker name, or a text file of multiple marker names can be uploaded to search for multiple markers at once (Fig. 12).  The search can also be restricted by the marker type (Fig. 12A), the species the marker was developed in, or the species the marker was mapped in.  To find out more information about the marker types, click the question mark logo next to Marker Type.  For markers that have been mapped to a genetic map, the search can be restricted to a certain linkage group (Fig. 12B).  And the search can be even further restricted to a certain locations on the linkage group.

Figure 12.  CGD Marker Search interface

The search results are returned in a table format (Fig. 13).  There are hyperlinks within the table that take you to more details about the marker or where the marker is mapped.  This data table can be downloaded in a format that can be easily opened in applications such as Excel (Fig. 13A).  Clicking on the marker name (Fig. 13B), displays the marker page which has information such as alignments and map positions.  If you would like to change the search, either edit the parameters or click the reset button to start all over.

Figure 13.  Marker Search results

Publications

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To search publications on CGD, click on the Search menu and select Publication Search.  The Publication Search is like many common literature searches, but is limited to publications that have been added to CGD.  The publications can be searched by using keywords within different fields (Fig. 14A).  Multiple fields and keywords can be entered and more fields can be added by clicking the Add/Remove buttons (Fig. 14B).  A range of years can also be entered (Fig. 14C). 

Figure 14. CGD Publication Search interface

The search results table has information about each publication (Fig. 15A).  By clicking the publication title, more detailed information is displayed.  Most publications also have a link to the publisher website or PubMed record in their titles (Fig. 15B).

Figure 15.  Publication search results and detailed publication information

 

QTLs and MTLs

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Quantitative trait loci (QTLs) and Mendelian trait loci (MTLs) that are entered in CGD are searchable from the QTL Search option under the Search menu in the header.  The search can be restricted by QTL or MTL as well as by species (Fig. 16A).  A certain trait ontology category can be selected to limit the returned results to only that trait type.  If you are looking for a specific trait, you can do a keyword search of the trait names or search by the published name or the CGD assigned name (Fig. 16B).  Please see the CGD Trait Abbreviation Table for more information about the trait abbreviations used in CGD.

Figure 16.  CGD QTL Search interface

The results are returned in a table that has blue hyperlinks to more information about the QTL or MTL, the map it is located on, and the species it is from (Fig. 17).  The table can also be downloaded (Fig. 17A).  Clicking on the QTL label, opens the QTL information page which has a link to map positions (Fig. 17B).  From the map position table, the QTL can be viewed in MapViewer or CMap.

Figure 17.  CGD QTL Search results

Sequences

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To search sequences, click on the Search menu on the homepage header and select Sequence Search.  This search is useful for retrieving information about certain sequences from a larger dataset, or all the sequences from one or more datasets.  The Gene and Transcript Search page is for searching genes and transcripts only, whereas the Sequence Search page also includes other sequence types.  A few search parameters can be used to return a broad range of results, or more parameters can be selected to find very specific data.  This is not a BLAST search, BLAST is available under the Tools menu. 

Figure 18. CGD Sequence Search interface

Sequence searches can be limited by genus and species, or sequence type (Fig. 18A).   The search can also be restricted to a certain genome dataset and further restricted to a certain chromosome or scaffold location for within that assembly (Fig. 18B).  The sequences in CGD can also be searched by sequence name, and there is an option to upload a text file of sequence names (Fig. 18C).  

   

Figure 19.  Search results table

All search results are returned in a table with hyperlinks to more information (Fig. 19A).  The results table can be downloaded and a Fasta file of the sequences on the table can also be downloaded (Fig. 19B).  To do a different search, either edit the parameters and search again, or click the Reset button.

Tools

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To access the different Tools available on CGD, click on the Tools menu in the header and then select the tool you want to use (Fig. 20A).  Many of the tools are also quickly accessed through links in the Tools Quick Start (Fig. 20B). To learn more about each search tool, please see the links below the figure.

Figure 20.  Tools menu in header and Tools Quick Start on homepage

BLAST

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CGD offers BLAST with sequence databases from sweet orange, clementine, mandarin, and trifoliate orange.  Genome, unigene, and reference transcriptome assemblies for the citrus species are available along with complete genomes of Ca. Liberibacter and Liberibacter crescens.  The BLAST interface looks and functions like the interface available on NCBI and information on the different settings and how to use BLAST can be found in the BLAST Help manual.  The new Tripal BLAST module displays the results in a interactive interface (Fig. 21A) and for alignments to the genome scaffolds that are also in the CGD JBrowse, there is a link to view the BLAST hit in JBrowse (Fig. 21B).  Features that are in the CGDdatabase (CDS, peptides, unigenes, RefTrans), will have links to more information in CGD.

Figure 21.  BLAST results on CGD

JBrowse

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CGD has an instance of the JBrowse genome browser for viewing genome data.  A list of the genomes available in CGD can be accessed by clicking the JBrowse link in the Tools menu.  Please watch the JBrowse tutorial for more details about how to navigate and use JBrowse.

Figure 22.  JBrowse of C. clementina genome.

For the tracks of aligned reads (BAM files) in the C. clementina v1.0 genome, the table below describes what the read colors mean in JBrowse.

Aligned Read Color Meaning Color of Read
Forward Strand  
Reverse Strand  
Forward strand missing mate  
Reverse strand missing mate  
Forward strand not proper  
Reverse strand not proper  
Forward strand on different chromosome  
Reverse strand on different chromosome  

 

CitrusCyc

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CitrusCyc pathways were generated using Pathway Tools and are available under the CitrusCyc link in the Tools menu.  Pathway Tools allows users to view metabolic pathways that are in genomes.  Please see the manual for Pathway Tools for more information on use.

 

Figure 24.  Citrus clementina cellular overview in CitrusCyc on CGD

MapViewer

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MapViewer is a new tool for viewing genetic maps on CGD.  It can be accessed from the Tools menu in the header (Fig. 25A), the Species Overview page (Fig. 25B), or the Map Overview page.  The Map Overview page displays a summary graphic of all linkage groups (Fig. 25C) and clicking a linkage group opens a more detailed view in MapViewer.

Figure 25.  Different ways to open MapViewer.

MapViewer displays the complete linkage group on the left, and the selected region on the right (Fig. 26).  The selected region can be changed by dragging and resizing a window on the complete linkage group on the left side. There is a legend of the marker colors below the linkage group figure (Fig. 26A).  Information about the markers is displayed in the upper right corner when the pointer is over a marker name on the right side graph.  Clicking on the marker name on the rights side graph, opens the marker details page.

Figure 26.  MapViewer displays a static linkage group graph on the left and a dynamic graph on the right.

A different map or linkage group can be displayed using the controls at the bottom of the MapViewer page (Fig. 27A). The color of the markers and which markers are displayed can be changed with the controls (Fig. 27B).  The ruler and marker positions can also be toggled on or off (Fig. 27C).  After changing any of the four parameter sections, the Submit button must be pressed to display the changes.

Figure 27.  MapViewer control panel.

Pictures from MapViewer

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MapViewer allows users to export figures as a high-resolution PNG file that is suitable for publication.  Items that can exported have a clickable camera icon that will trigger a file download.  Users can export the map overview which has all the linkage groups (Fig. 1), a single linkage group (Fig. 2), a linkage group comparison (Fig. 3), a dot plot (Fig. 4) or a correspondence matrix (Fig. 5).

Figure 1.  How to download a map overview.

 

Figure 2.  How to download a linkage group figure.

 

Figure 3.  How to download a linkage group comparison figure.

 

Figure 4.  How to download a linkage group comparison dot plot.

 

Figure 5.  How to download a linkage group comparison correspondence matrix.

Synteny Viewer

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CGD uses the Tripal Synteny Viewer, developed by the Fei Bioinformatics Lab, to display the analysis results of Citrus and Liberibacter genomes that were compared using the program MCScanX.  Synteny Viewer is accessed under the "Tools" menu (Fig. 1A) or via a link on the Species Overview page.

Figure 1.  Accessing Synteny Viewer on CGD.

On the Synteny Viewer interface, there is some information about the tool and a pull-down menu to select the Organism Type (Fig. 2A) of "Plant" or "Bacteria" (Fig. 2B).  The "Plant" option allows for the comparison of Citrus sp. genomes and the "Bacteria" option is for comparing genomes of the Ca. Liberibacter sp. and Liberibacter sp.  If the block ID number is already known, the block ID value can be input directly to return just those results.

Figure 2.  Selecting plant or bacteria genome option.

Once the organism is selected, another pull-down menu becomes available to select the first genome for comparison (Fig. 3A).  After selecting the genome, the "Chromosome/Scaffold" menu will populate with the names of the appropriate scaffolds or chromosomes and one of the sequences can be selected (Fig. 3B).  The final option is to select one or more genomes for comparison (Fig. 3C), and then the "Search button" is clicked to start the search (Fig. 3D).

Figure 3.  Options for Synteny Viewer search.

When the search is complete, a new page opens with the results.  There is a summary of the input settings at the top of the page (Fig. 4A).  When multiple genomes are queried, there are tabs to switch between the results (Fig. 4B) and the circular graph (Fig. 4C) will change when a different genome is selected.  The syntenic regions are indicated on the circular graph by gray lines.  When the mouse hovers over the gray line, a summary is displayed (Fig. 4D).  Clicking on the gray lines, opens a page with more details (see below, Fig. 6).

Figure 4.  Synteny results and circular graphs.

Under the circular graph is a table listing the syntenic blocks that are displayed as gray lines in the circular graph.  Clicking on the block name (Fig. 5A) opens the same details page as clicking on the gray lines on the circular graph.

Figure 5. Synteny block list.

The syntenic block details page has an overview section at the top listing the details for each genome in the comparison (Fig. 6A), a side-by-side graphic of the syntenic block from each genome (Fig. 6B), and a table showing the genes in the syntenic block from each genome (Fig. 6C).  Clicking on the gene name in either the table or on the graphic will open the feature details page from the CGD database.

Figure 6.  Syntenic Block Details Page.

The side-by-side graph can be zoomed (Fig. 7) using the scroll wheel on the mouse and the view can be shifted up or down by click and dragging.

Figure 7.  Zoomed in view of graph.

CGD Video Tutorials

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CGD specific videos are in progress, but please check out the tutorial videos for our other databases on the Main Lab YouTube channel.  The searches use the same framework across all of our databases.

Breeding Information Management System (BIMS)

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CGD BIMS (Breeding Information Management System) is a Tripal module being developed by Mainlab Bioinformatics which allows users to explore the publically available breeding data in CGD while also providing a data management solution for private breeding programs.  BIMS is now open for breeders to create an account and start using it with current functionality. It is being continuously developed and once complete it will provide individual breeders with a secure and comprehensive online breeding management system that allows them to store, manage and analyze their private data, fully integrated with publicly available genomic, genetic and breeding data within Tripal databases such as CGD.

The BIMS tool now supports the use of Field Book, an Android app developed by the Poland Lab at Kansas State University for collecting phenotype data in the field.  Field Book is a free app that is available through the Google Play Store.  It provides easy and customizable interfaces for entering all types of biological data.  For more details about Field Book, please visit the developer's website to view the current manual and for more information. In the following sections we provide information on how to use the current version of BIMS, which will be updated as more functionilty becomes available. If you would like to be kept informed on progress please sign up for the CGD BIMS mailing list. The links below provide information on how to access CGD BIMS, View Data, Search Data, Create a Breeding Program, Import Data, Manage Data using Field Book and Archive Data. If you have any questions please contact using the contact form on CGD. We will be holding monthly "how to webinars" and are happy to provide individual program training and guidance and solicit input on further development. 

To access BIMS, simply click on the "Tools" menu (Fig. 1A) and then select "BIMS" (Fig. 1B).  The BIMS interface will then open.  Public data is available for all users of CGD without requiring an account on CDG.  Users can download public data from BIMS without an account, but will need their CGD user account to save the results. Access to private breeding data requires users to login with their CGD user account.  To create a breeding program, users need to create a CGD account and contact using the contact form for breeder privilege.

BIMS: Viewing Data

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To view data that has already been loaded into BIMS, you first need to choose the breeding program (Fig. 2A).  Once the selections have been made, the selected program names will appear in the upper left corner of the BIMS window  (Fig. 3A).  You can change the program by clicking on the buttons in the upper left corner.

Figure 2.  Selecting the Program in BIMS.

There are three main areas of the BIMS interface.  The first part is the header region (Fig. 3A) which displays the current program, allows users to change program, has a link to the CGD homepage (Site Home), and displays the user name.  The second part of the interface is the accordion menu on the left side (Fig. 3B).  This menu allows users to switch between different sections of the BIMS program.  The last region is the tab region (Fig. 3C) and this is where users primarily interact with BIMS.  Each tab in BIMS has an "Instructions" section that can be expanded by clicking on it.  The "Instructions" have information on how to use that tab.

Figure 3.  The main parts of the BIMS interface.

Once the program has been loaded, you can explore the data that have been loaded into BIMS by clicking on the "Manage Breeding" section of the accordion menu.  Under "Manage Breeding" there are links to view information about the Program, Trait, Location, Cross, Accession, and Trial.  To view information about a certain trait, click on "Trait" (Fig. 4A) and the "Manage Trait" tab will appear.  In that tab, click on the trait of interest (Fig. 4B).  Once a trait is selected, the "Trait Details" will be displayed (Fig. 4C).

Figure 4.  Selecting and viewing Trait Details.

If you are viewing data from a private breeding program, you can also edit the information for all the items under manage breeding.  Breeders with private breeding programs will also see an "Actions" section (Fig. 5A) on the details sections for the trait, cross, etc.  The "Actions" section allows breeders to edit the properties or delete the item.

Figure 5.  Editing abilities available to breeders with private programs.

You can also view information about the other data types under "Manage Breeding" by clicking on each type.  For "Location," information about each location can be displayed.  First select "Location" (Fig. 6A), then choose the location name (Fig. 6B), and then the details will appear (Fig. 6C).

Figure 6.  Location details.

For the "Cross" (Fig. 7), "Accession" (Fig. 8), and "Trial" (Fig. 9) data types, the data details are accessed the same way.  First select the data type under "Manage Breeding" (Fig. 7A-9A), then select the one of the names (Fig. 7B-9B), and then the details will appear (Fig. 7C-9C).  For these data types, in the "Details" section there is also a "View" button that opens another tab that displays further statistics/data.

Figure 7.  Accession details.

Figure 8.  Accession details.

Figure 9.  Trial details.

BIMS: Searching Data

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You can also search the data in a breeding program using BIMS.  Click on the "Search" section of the left side accordion menu and then click on "Accession" (Fig. 10A).  This will open the "Search Accession" tab (Fig. 10B). 

Figure 10.  Opening the Search tab.

The first step to start a search is to select a property or trait under the "Choose property" section (Fig. 11A).  In this example, we are choosing "Parent."  After the property is selected, the "Set filter" section will populate with options for that data type (Fig. 11B).  After selecting the options you want, click "Add."  The selected filter will then appear in the "Search results" section (Fig. 11).  If you want to reset the search, click the "Reset" button (Fig. 11C).

Figure 11.  Selecting a Property and setting a Filter in the Search Tab.

You can further filter the search results by adding another property or trait under the "Choose property" section.  In this example, we are further refining the search by adding the Fruit Shape trait (Fig. 12A).  The "Set filter" section will show the data that are relevant for the previous filter you chose. For example, the statistics shown for Asian Citrus Psyllid Adult Mean trait here is only for those accession from the trial you chose in the previous search. You can set the minimun and maximum value of this trait, and then click "Add" (Fig. 12B).  The new filter is added to the "Search results" section and the selected filters can be removed with the "Remove" button under "Search results" (Fig. 12C).  To view the search results, and to generate a file to export, click on "View" under "Search results" (Fig. 12C).

Figure 12.  Adding more filters to the search and viewing results.

When the "View" button is clicked (Fig. 12C), a new tab opens called "Search Results" (Fig. 13).  On this tab there is a "Column options" section (Fig. 13A) and a preview of the data table (Fig. 13B).

Figure 13.  Search Results tab.

Users can add more information to the table before exporting the data.  To do this, click on the "Column options" section to expand it (Fig. 14).  There are two sections, "Properties" (Fig. 14A) and "Traits" (Fig. 14B).  You can select additional items to display by clicking on the check boxes in these two sections.  Once all the selections have been made, click "Update" (Fig. 14C).

Figure 14. Adding more columns to search results table with Column Options section.

After selecting additional data to display on the table, you can preview the table on the "Search Results" tab (Fig. 15A) and see the original filters that were used to generate the initial table by clicking on "Descriptions" in the "Results" section (Fig. 15B).  To download the data table, click on the "Download" button in the "Save Results / Download Data" section (Fig. 15C).  If you do not see your browser start to downoad the file after clicking "Download," please make sure the pop-up was not blocked.

Figure 15.  Downloading data from the Search Results tab.

BIMS generates a CSV file of the search results table (Fig. 16).   This table is easily opened by Microsoft Excel and other programs.

Figure 16.  Example CSV file exported from BIMS.

If you have a CGD account, you can also save the search results to a list.  You will see a "Save" button with boxes for a list name and description (Fig. 17A).  This list will be saved to your program or to public program that you are in and accessed by clicking on "Search Results" in the "Search" section of the accordion menu (Fig. 17B).  You can also see details about the saved lists and delete, view, or edit them (Fig. 17C).

Figure 17.  Saving lists from searches to private breeding programs.

BIMS: Creating a New Breeding Program

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To start a new breeding program in BIMS, you must have a CGD account with the appropriate access level.  The first step in creating a new program is to select the Program Button (Fig. 18A). After selecting a program, the "Manage Program" tab will open and then you can open the "Program Admin Menu" section (Fig.18B).  Click "Create" to make a new program.

Figure 18.  Switching crops and opening the Manage Program tab.

After clicking the "Create" button, the "Add Program" tab opens (Fig. 19A).  Enter the new Program Name and make sure that the required column names are set to match your dataset (Fig. 19B).  The four columns are required columns in phenotype sheet of the data template and if you change the column names here the column names in the phenotype sheet of the template for download will automatically change. If you use Field Book App for phenotype collection, use these column names in the input files. After you have created the program, you will have the option to add other CGD users as members of the breeding program (Fig. 19C).  Once the program is created, data can be loaded to the program.

Figure 19.  Creating a new program and adding members.

BIMS: Importing Data

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To import data into BIMS, the data need to be in BIMS templates. Phenotype data can either needs to be files exported from Field Book or data entered into the BIMS templates.  To download the BIMS templates, click on the "Data Import" section of the left-hand accordion menu and then click on "Template List" (Fig. 20A).  You will then see the "Data Templates" tab that has information about each template and links to download the template (Fig. 20B).  You can also download all the templates as a single Excel file by clicking below (Fig. 20C).

Figure 20.  Downloading BIMS data templates. 

To upload data files, click on the "Upload data" link (Fig. 21A) under the "Data Import" section and the "Upload Data" tab will open.  Then, under the "Upload data by Excel template" section on the right side of the "Upload Data" tab, select the data file and click "Upload" (Fig. 21B).  Enter a file description if desired, and once the file has uploaded, click "Submit".  The file name will then appear in the "Uploaded Files" section (Fig. 21C).

Figure 21.  Upload Data tab in BIMS.

To view the progress of an upload job, click on the file name under "Uploaded files" (Fig. 22A).  Summary information about the file will appear below and then click the "View" button (Fig. 22B).  The "Upload Job" tab appears and will show the "Job Details" table (Fig. 22C).  On the table you can see the job progress.  If the job is still running, you can click the "Refresh" button to update the job progress.

Figure 22.  How to view upload job progress.

BIMS also provides links to log files on the "Upload Job" tab.  When a job successfully loads, there are three types of logs: New Data Logs, Warning Logs, and Duplicate Logs.  To view the logs, first expand the log type section you want to view and then click on "view" (Fig. 23A) to see the log messages (Fig. 23B).  New Data Logs describe the new data that was loaded.  Warning Logs indicate if any data was skipped due to incorrect column headers or typos, but this data was not critical for BIMS to load data so the job still completed.  It is recommended that you look at the Warning Logs to make sure data was not omitted accidently.  The Duplicate Logs display what data was a duplication of data already present in BIMS.

Figure 23.  BIMS upload job logs.

But what happens if there is an error in the data that causes the upload job to fail?  If an upload job fails, you will see "FAILED" under the job progress (Fig. 24A).   An Error Log section will also be available on the "Uploading Job" tab.  Expand the Error Log section and click on "view" (Fig. 24B) to see the error messages (Fig. 24C).  Use the Error Log information to correct the original file.

Figure 24.  Failed jobs and the Error Logs

To re-run a failed job, use the "Re-Run Job" section on the "Uploading Job" tab.  Select and upload the revised file (Fig. 25A) and then click the "Re-Run the Job" button (Fig. 25B).  To monitor the re-run progress, click on the "Refresh" button (Fig. 25C). If the error was something that you did online not in the template, for example you had a typo in the configuration setting, it is best not to use Re-Run Job, but go back and start the loading process again.

Figure 25.  Re-running a job.

BIMS: Field Book Management

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For breeders using the Field Book App, BIMS can help generate the trait and field input files to configure Field Book for data entry and BIMS can also import data in the trait and field files from Field Book.  For ongoing trials, BIMS can also help breeders sync data between different devices by loading the exported data from multiple devices into BIMS and generating an input file with combined information.  When breeders first create their programs, they have chosen the names for the four required columns. These columns should match the column names in Field Book Input file, and breeders make sure they match and change if needed. The configuration settings can be accessed either by clicking on "Configuration" under the "Field Book Management" section on the left-hand accordion menu (Fig. 26A) or by clicking on the icon in the header (Fig. 26B).  On the "Configuration" tab (Fig. 26C) there are two sections; "Field Book required columns" and "Field Book custom columns".  The first section is to set names for Accession and the three required columns in Field Book Input file, the second section is for users to choose the optional columns that they want to add in the Field Book Input file. When they generate Field Book Input file, these optional columns will show up for breeders to choose for each Field Book Input file that they generate.

Figure 26. Field Book configuration options.

Two different files types for input into Field Book can be generated using BIMS.  The first file type is the Trait (.trt) file when breeders want to add traits to Field Book using a file instead of creating one by one in Field Book App.  This file contains the details on the phenotypic traits being recorded.  To generate this file, click on "Trait" (Fig. 27A) and the "Trait" tab will open.  On the "Trait" tab, there will be a list of traits that have already been loaded into the program on BIMS (Fig. 27B).  Select the traits you want to export and then click the "Generate" button (Fig. 27C).  A .trt file will then download.

Figure 27.  Generating Trait file for Field Book.

The Field file (.csv) can also be generated for import into Field Book.  This file has the list of accessions and columns for the required columns (unique identifier, primary order, secondary order).  The Field file is generated by clicking on "Field" (Fig. 28A) to open the "Field" tab.  On the "Field" tab there are three options for generating the file (Fig. 28B).  The first option is to generate a "New Trial".  This can be used when breeders want to do another trail with accessions that are already in the database. If you have saved an accession list from a previous search (see Searching Data section), the option to use that list is available (Fig. 28C).  You can also select other accession properties to add to the file.  To generate the file, click the "Generate" button (Fig. 28D) and the file will download. In the generated file from this "New Trial" option, only the accession is provided and the three required colums (the unique identifier, primary order, and secondary order) will be empty since they depend on the planting design. The breeders should fill in those columns before importing into Field Book App.

Figure 28.  Generating a Field file for a New Trial.

Field files can also be generated from an Existing Trial.  Files from Existing Trials (Fig. 29A) contain the accessions from the existing trial that is selected as well as the custom columns the user chooses. This functionality is to provide a way to sync data from multiple devices that have Field Book App to check which individual has been phenotyped already. Breeders can first upload the data from multiple devices, then re-generate an input file from the existing trial with a trait value.

Cross option (Fig. 30) allows you to generate input file for a new cross. When users upload a file (Fig. 30A) with an information on the cross and the planting (eg. cross name, primary order, and progeny in each primary order) and type in prefix for the unique id (Fig. 30B), then BIMS generates a Field Book input file with new progeny names and three required columns automatically filled in (Fig. 30C). In the uploaded file (Fig. 30A), the order of the columns is important, not the colum head.

Figure 29.  Generating a Field file from an Existing Trial or Cross.

 

Figure 30.  Example input file and output file for Generating a Field file for a new Cross.

If you have already configured Field Book and would like to transfer the Trait and Field information to BIMS, that can be done by importing the Trait and Field files from Field Book.  To import a Trait file, use the "Upload trait file" option (Fig. 31A).  Select your file (Fig. 31B) and click "Upload."  Once the file has uploaded, click "Submit" (Fig. 31C) to start the import job.  The file then appears in the "Uploaded files" section (Fig. 31D).

Figure 31.  Importing Trait files from Field Book into BIMS.

Field files can also be imported into BIMS from Field Book.  Click on "Upload field file" (Fig. 32A) and then upload the field file and click "Inspect" (Fig. 31B).  After BIMS checks to see if the required columns are present in the Field file, the "Upload an exported field file" section appears (Fig. 31C) and the location and trial can be selected.  The file upload job is then initiated by clicking "Submit".

Figure 32.  Importing Field files from Field Book into BIMS.

 

BIMS: Archiving Data

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Creating an archive file of all the data in a breeding program is easily done using the "Archive" function in BIMS.  Open the "Archive" section in the left-hand accordion menu, and then click "Manage Archive" (Fig. 33A).  On the "Manage Archive" tab, there is an "Archive Data" button (Fig. 33B).  When this button is clicked, an Excel file is generated that contains all the data in the current breeding program (Fig. 33C).

Figure 33.  Generating an archive file.

 

BIMS: FAQ and Troubleshooting

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How do I search data?

How do I view/edit data in a program?

How do I import data?

How do I manage Field Book trait and field files with BIMS?

How do I create a new breeding program?

Troubleshooting

Section Problem Solution
General I have selected a crop and program, but do not see any options under Manage Breeding and other BIMS sections. Please refresh the page in your internet browser.
  I still have problems with viewing BIMS information, even after refreshing the page. Please clear the cached images/files, cookies, and hosted app data from your internet browser's history.  You will have to log back into BIMS and reopen your program.
Data Import/Field Book Management My data upload failed. Please make sure that the upload didn't fail due to data errors or typos first by looking at the error logs (see Importing Data section for more details).  If you need help, contact us.
  Even after I changed the max/min value of the trait descriptor in the template, BIMS still give an error saying that I have data outside the acceptable range. Once your descriptor has been loaded, you have to edit the the descriptor data in BIMS, not in template (go to Manage Breeding, Trait, choose the trait and click 'Edit' .)
 

What do the errors below mean?

The required column (unique_id) is missing
The required column (primary_order) is missing
The required column (secondary_order) is missing

BIMS allows you to change the column names in the template for 'accession_id', 'unique_id', 'primary_order', and 'secondary_order'. You get this type of error when the column names in your template do not match the ones in BIMS. Once you change it in BIMS, the templates downloaded from BIMS also changes. Please refer to Figure 26B in the manual.
  The output from Field Book Management - Generate input file (Field) - Cross option doesn't seem correct. Please check your file if it's in the order of cross name, row and the number of progeny for each row that you will plant. In this file, the order of the columns is important, not the column head. Please refer to Figure 30A in the manual.
Search I can't download my file. Please make sure that you allow pop-ups on your browser. Please refer to how to allow pop ups on chromeon firefoxon internet explorer.