User Manual

This manual describes how to access data and use the tools on the Genome Database for Rosaceae (GDR).  Please use the sidebar on the left to navigate to different parts of the manual, or click on the section titles below. You can access the next page of the manual by clicking on the title of the next page below.

Homepage Overview

The GDR home page can be reached at www.rosaceae.org

For quick access to data, visit the SpeciesData or Search section in the navigation bar or click appropriate link from the Major Genera Quick Start or Tools Quick Start section.

 
1. GDR Logo
 
Users can return to the home page from any GDR page by clicking the logo.
 
2. Navigation bar
 
The dark green bar and white links found at the top of the page are navigational tools. The GDR provides the same navigation bar at the top of all of its pages to allow users to easily move between sections of the database. 
 
3. Log in
 
GDR users do not need an account to access public data. The breeders who need to access their private data needs to log in.
 
4. Search
 
Users can search the static content using this simple search form. For searching the genetic, genomic and breeding data, go to the appropriate site under 'Search' in the navigation bar.
 
5. Twitter
Follow GDR on Twitter and get all the latest news right away.
 
6. News and Events 
 
News items from GDR and the Rosaceae community
 
7. Major Genera Quick Start
 
By clicking on the icon for the genus of interest, go to the genus overview page where you can access all the data and tools available for the genus. If you are interested in a specific species, find a link to the species page from the dropdown menu of the 'Species' in the header bar.
 
8. Tools Quick Start
 
Quick links to common tools and data search interfaces.
 
If you have any questions/comments/feedback about the site overview, please let us know via the contact form. 
 

Species Overview Page

A species page is available for main species, genera and entire Rosaceae family so that users can easily access the data and tools for the species of interest. Species pages can be accessed under the 'species' pull-down menu in the main navigation bar. Please note that detailed textual descriptions for each member species are being developed by the US Roscaceae Executive Committee and will be availlable in November 2013.

The species pages have a resources bar on the left panel so that users can quickly access data and tools for the species. Depending on the species, more or less items will be displayed on the resource bar. Below are some items in the resource bars. 

1. Genome page

Where whole genome sequences are available, hyperlinks to each genome assembly page are shown on the resources bar.

2. GDR Cyc Pathways

Where PlantCyc databases are available for a species, hyperlinks to each PlantCyc page are shown on the resources bar. The predicted genes from the whole genome sequences were utilized in the construction of PlantCyc (metabolic pathway) databases using PathwayTools. Currently (September 2013), three PlantCyc databases, PeachCyc, AppleCyc and FragariaCyc, are available in GDR. 

3. Unigene page

Each species page has a hyperlink to the corresponding unigene page for the genus. Unigenes are constructed for the entire Rosaceae family and for each genus (PrunusMalusFragariaRosa, and Pyrus) using the publicly available Rosaceae ESTs downloaded from dbEST at NCBI. 

4. Maps

Each species page has hyperlink to dynamically generated list of the genetic maps that are available in GDR.

5. Whole Genome

A whole genome page provides summary information on the available whole genome data for the species. 

6. Links

The links subpage shows various useful links outside GDR for the species.

7. KEGG Analysis Reports

The predicted genes from whole genome sequences and EST unigenes are associated with KEGG pathway terms. The link in the resources bar leads to the KEGG analysis reports page where users can view a Venn diagram with GO terms and the number of associated sequences, browse the GO term heirarchy, choose a term and view/download all the associated sequences.

8. Germplasm

The germplasm page provides a list of germplasm that are stored in GDR.

9. GO Analysis Reports

The predicted genes from whole genome sequences and EST unigenes are associated with Gene Ontology terms. The link in the resources bar leads to the GO analysis reports page where users can view, seach and download the GO associated data.

If you have any questions/comments/feedback about the species site, please let us know via the contact form. 

 

Data Searches

To access the different data searches, click on 'search' in the menu header and then select the data type you would like to search. To learn more about each search interface, please see the links below the figure.
 
 

Search Genes and Transcripts

Search Genes and Transcripts is a page where users can search for genes and transcripts from various datasets available in GDR. Users can search for genes from various datasets: predicted genes from whole genome assemblies,a single non-redundant list of Rosaceae genes with gene symbols (GDR Gene Database), or gene and mRNA sequences parsed out from NCBI nucleotide database. These genes and mRNAs parsed out from NCBI sequences are aligned to the reference whole genome sequences when possible. When expert-contributed information is available, these gene names are associated directly with the predicted genes from whole genome assembly. Users can also search from transcripts from RefTrans sets, reference transcriptome sets built from all publicly available transcripts, or EST unigene contigs. For more detail, refer to 'Description of Gene and Transcript Dataset' page.

Please Note: All the search categories below, except the file upload, can be combined.

1. Genus/Species

Use these drop-down menus to limit results to genes from a specific genus or species. Once a genus is chosen, species for the genus are dynamically populated in the species dropdown. Major genera are listed on top of the Genus list under 'Common Selections' and the rest are listed as 'All options' in alphabetical order.

2. Dataset

Use this drop-down menu to limt the results to sequences from a specific dataset. Go to 'Description of Sequence Dataset in GDR' for more details. Multiple options can be selected by holding down the "Ctrl" key.

3. Genome Location

Users can limit their results of predicted genes by their genome location. When a genome assembly is chosen in the drop-down menu next to 'Dataset', the corresponding chromosome or scaffold names are dynamically displayed in the 'Genome Location' drop-down menu. Choose any option and then type in the position in bp in the text boxes.

4. Gene/Transcript Name

Users can search genes and transcripts by name for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu. The search is case-insensitive. Example gene names are MADS1, LFY2, or ppa027130m. Gene or transcript names in a file, separated by a new line, can be uploaded to do a batch search.

3. Keyword

Users can limit their result by associated funcitonal terms. Predicted genes from whole genome assembly and transcripts have been annotated with some of the followings: homology to genes of closely related or plant model species, InterPro protein domains, GO terms, KEGG pathway and ortholog terms. Users can enter any protein name (eg. polygalacturonase), KEGG term/EC number (eg. resistance, EC:1.4.1.3), GO term (eg. cell cycle, ATP binding), or InterPro term (eg. zinc finger) in the text box to limit the results with the entries that are associated with the functional annotation terms.

If you have any questions/comments/feedback about this search page, please let us know via the contact form. 

 

Search Genotype

Search SSR Genotype is a page where users can search the SSR genotype data by dataset name, marker name, germplasm name and/or species. Click the next tab to search for SNP Genotype. To search for SSR genotype data only for cultivars and breeding selections please visit the 'Search Genotyping Data' page in the Breeders Toolbox.

Please Note: All the search categories below can be combined.

1. Dataset

Users can search SSR genotype data by dataset from a dropdown list.

2. Marker Name

Users can search for SSR genotype data that used a specific marker by typing the marker name in the text box. Users can search for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu.

3. Germplasm Name

Users can search for SSR genotype data from a specific germplasm by choosing from the drop-down menu.

4. Species

Users can search for SSR genotype data from a specific species by choosing from the drop-down menu.

 

Search SNP Genotype is a page where users can search for the SNP genotyope dataset based on the germplasm and SNP markers used in the dataset. Click the next tab to search for SSR Genotype. To search for SNP genotype data only for cultivars and breeding selections please visit the 'Search Genotyping Data' page in the Breeders Toolbox.

Please Note: All the search categories below can be combined.

1. Dataset

Users can search SNP genotype data by dataset from a dropdown list.

2. Species

Users can search for SNP genotype dataset from a specific species by choosing from the drop-down menu.

3. Germplasm Name

Users can search for SNP genotype dataset from a specific germplasm by choosing from the drop-down menu.

4. SNP

Users can search for SNP genotype dataset that used a specific marker by typing the marker name in the text box. Users can search for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu.

5. Genome

Users can search SNP genotype data by the anchored position of SNPs in one of the whole genome sequences. Choose a genome in the drop-down menu next to 'Genome' then the corrposponding chromosome or scaffold names will by dynamically generated in the 'Chr/Scaffold' drop-down menu. Choose any option and then type in the position in bp in the text boxes. 

If you have any questions/comments/feedback about this page, please let us know via the contact form. 

 

Search Germplasm Images

Search Germplasm Images is a page where users can search for germplasm images available in GDR. The search can be restricted by genus, species, germplasm name and the legend of the image.

Please Note: All the search categories below can be combined.

1. Genus/Species

Use these drop-down menus to limit results to genes from a specific genus or species. Once a genus is chosen, species for the genus are dynamically populated in the species dropdown. Major genera are listed on top of the Genus list under 'Common Selections' and the rest are listed as 'All options' in alphabetical order.

2. Name

Users can search images by germplasm name for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu. The search is case-insensitive. 

3. Legend

Users can limit their result by associated legend of the image. Most images of Malus species have pedigree in their legends so users can search images by entering parent's name in the legend.

If you have any questions/comments/feedback about this search page, please let us know via the contact form.

 

Search Haplotype Block

Search Haplotype Block is a page where you can search for haplotype blocks, a genomic region which was identified to have a distinct combination of SNP genotype. The sesarch options include species, halotype block name or genome location to which the haplotype block is aligned. From the individual haplotype block page, you can view all the haplotype (alleles) identified along with the SNP genotypes that constitutes each genotype.


Please Note: All the search categories below can be combined.

1. Species

Use these drop-down menus to limit results to a specific species.

2. Name

Users can search by haplotype block name for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu. The search is case-insensitive. 

3. Genome 

Users can limit their results of haplotype blocks by their aligned genome location. When a genome assembly is chosen in the drop-down menu next to 'Genome', the corresponding chromosome or scaffold names are dynamically displayed in the 'Chr/scaffold' drop-down menu. Choose any option and then type in the position in bp in the text boxes.

If you have any questions/comments/feedback about this search page, please let us know via the contact form.

 

Search Maps

Search Maps is a page where users can find and view Maps by species.

1. Species

Users can search for Maps from a specific species by choosing from the drop-down menu.

If you have any questions/comments/feedback about the marker search sites, please let us know via the contact form. 

 

Search Publications

Search Publications is a page where users can search for publication using a combination of keywords (in the abstract or title), all or partial titles, authors, and other categories. Search results link to the publication detail pages that contain the abstract, citation, external link to the full article, and other details. The GDR houses information about publications on Rosaceae genomics, genetics, and breeding research. Details about publications were imported to the GDR from NCBI PubMed and the USDA National Agricultural Library using the query: (abstract: trait OR QTL OR gene OR genome OR map OR microsatellite OR annotation OR EST OR marker OR seqeuence) AND (abstract: rosaceae or prunus or pyrus or fragaria or malus or rubus). Additionally, details of publications from other journals not present in these databases are added.

1. Users can select a field in the drop-down menu (abstract, authors, citation, journal name, title or year) and the type in keywords in the textbox

2. Users can expand their query by choosing 'AND, OR, NOT' and add additional field.

3. Users can click the plus symbol to add additional field.

4. Users can type in years in xxxx format limit the results between certain years.

If you have any questions/comments/feedback about the publications site, please let us know via the contact form. 

 

Search QTL

Search QTL is a page where users can search for Quantatitive or Qualitative (Mendelian) Trait Loci in GDR.

Please Note: All the search categories below can be combined.

1. Type

Users can search trait loci by type, QTL or MTL.

2. Species

Users can search trait loci by species by choosing one of the options displayed in the drop-down menu. Users can choose multiple options by holding down the "Ctrl" key.

3. Trait Category

Trait loci are associated with one or more terms of eight trait categories (anatomy and morphology, biochemical, growth and development, quality, stature or vigor, sterility or fetility, stress and yield). Users can choose multiple options by holding down the "Ctrl" key. 

4. Trait Name

Trait loci are associated with trait names that belongs to the Rosaceae Trait Ontology. The Rosaceae Trait Ontology contains extra terms that are necessary for the description of Rosaceae traits in addition to the terms in Trait Ontology (developed with a focus on the traits of grass species). Examples include self-incompatibility, chilling requirement or fruit weight. Users can search these fields for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu. Users can also search by aliases. The search is case-insensitive.

5. Published Symbol

Published symbols can be used to search for trait loci. Examples include Pm1,Ls1, PPV-D or Skc. Users can search these fields for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu. 

6. QTL/MTL Label

Search by the QTL/MTL label given by the GDR team. 

An example QTL qSI.TE-ch5.1 indicates that:

qSI = a QTL for Self Incompatibility trait,
TE = this QTL has been mapped on the map drived by Texas x Earlygold population,
ch5 = this QTL is located on chromosome/linkage group 5 of the map, and
.2 = the self incompatibility trait has more than one locations on the chromosome, and this QTL is the second one in order of that along with the chromosome.
 
If you have any questions/comments/feedback about the trait loci site, please let us know via the contact form. 
 

Search Sequences

The Search Sequences page allows users to search for various sequences in the GDR database. These sequences include genes and transcripts from various sources, RosCOS unigene sets, RosaR80 v1.0. Please follow the link for more information on each source.

 

 
Please Note: All the search categories below, except the file upload, can be combined.
 
1. Species
 
Use this drop-down menu to limit results to sequences from a specific species. Multiple options can be selected by holding down the "Ctrl" key. 
 
2. Type
 
Use this drop-down menu to limit results to sequences of a specific type. Multiple options can be selected by holding down the "Ctrl" key. 
 
3. Dataset
 
Use this drop-down menu to limt the results to sequences from a specific source: genes and transcripts from various sources, RosCOS unigene sets, RosaR80 v1.0. Please follow the link for more information on each source. Multiple options can be selected by holding down the "Ctrl" key. 
 
3. Name
 
Users can search sequences by name for an exact match, contains, starts with or ends with the input, by selecting the desired option from the drop-down menu. The search is case-insensitive. 
 
4. File Upload
 
Users can obtain detailed information for a set of sequences by uploading a file with sequences names. Separate each name by a new line.
 
5. Location
 
Users can limit their results to those aligned to a specific genome assembly. In addition to the predicted genes and mRNAs from each assembly, NCBI Rosaceae genes and mRNA sequences are aligned to the reference whole genomes with criteria of >98% PID and >95% Aligned Length. When a genome assembly or 'NCBI Rosaceae genes and mRNA sequences' is selected in the drop-down menu next to 'Dataset', the corrposponding chromosome or scaffold names will be dynamically displayed in the 'Location' drop-down menu. Choose any option and then type in the position in bp in the text boxes. 

If you have any questions/comments/feedback about the trait loci site, please let us know via the contact form. 

 

Tools

To access the different Tools available on GDR, click on the 'tools' menu in the header and then select the tool you want to use. Many of the tools are also quickly accessed through links in the 'Tools Quick Start' section on the GDR homepage. To learn more about each search tool, please see the links below the figure.

 

GBrowse

JBrowse

GDR has an instance of the JBrowse genome browser for viewing genome data.  A list of the genomes available in GDR 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.

Sequence Retrieval

The Sequence Retrieval tool allows downloading of nucleotide and protein sequences including chromosomes, scaffolds, genes, mRNAs, transcript coding sequences, protein, reftrans contigs and unigene contigs. For the sequences aligned to larger sequences, such as genes, mRNAs and transcript coding sequences, a numeric value specifying the number of upstream bases and downstream bases can be typed in the text boxes. 

Below are currently available datasets for searching.

  • Fragaria ananassa GDR RefTrans V1
  • Fragaria Unigene v5.0
  • Fragaria vesca Whole Genome v1.0 (build 8) Assembly & Annotation
  • Fragaria vesca Whole Genome v1.1 Assembly & Annotation
  • Fragaria vesca Whole Genome v4.0.a1 Assembly & Annotation
  • Malus Unigene v5.0
  • Malus x domestica GDDH13 v1.1 Whole Genome Assembly & Annotation
  • Malus x domestica GDR RefTrans V1
  • Malus x domestica Whole Genome v1.0 Assembly & Annotation
  • Malus x domestica Whole Genome v1.0p Assembly & Annotation
  • Prunus avium GDR RefTrans V1
  • Prunus avium Whole Genome Assembly v1.0 & Annotation v1 (v1.0.a1)
  • Prunus persica GDR RefTrans V1
  • Prunus persica Whole Genome Assembly v2.0 & Annotation v2.1 (v2.0.a1)
  • Prunus persica Whole Genome v1.0 Assembly & Annotation
  • Prunus Unigene v5.0
  • Pyrus communis Genome v1.0 Draft Assembly & Annotation
  • Pyrus Unigene v5.0
  • Rosaceae Family Unigene v5.0
  • Rosa chinensis Whole Genome v1.0 Assembly & Annotation
  • Rosa Unigene v5.0
  • Rubus GDR RefTrans V1
  • Rubus GDR RefTrans V2
  • Rubus occidentalis Whole Genome Assembly v1.0 & Annotation v1
  • Rubus occidentalis Whole Genome Assembly v1.1
  • Rubus Unigene v5.0

1. Sequence Name

The names of the sequences to be retrieved can be typed in the text box. Each name should be separated with a new line or comma. Leave blank to retrieve all features matching other criteria.

2. Upstream and downstream bases

A numeric value specifying the number of upstream bases and downstream bases to include in the downloaded sequences can be typed in the text boxes. This only works if the feature is aligned to a larger sequence. 

If you have any questions/comments/feedback about the sequence retreival tool, please let us know via the contact form. 

 

Synteny Viewer

Synteny Viewer Help (Website)

 

GDR Video Tutorials

Breeding Information Management System (BIMS)

GDR 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 GDR 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 GDR.

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 GDR BIMS mailing list. The links below provide information on how to access GDR 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 GDR. 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 GDR without requiring an account on GDR.  Users can download public data from BIMS without an account, but will need their GDR user account to save the results. Access to private breeding data requires users to login with their GDR user account.  To create a breeding program, users need to create a GDR account and contact using the contact form for breeder privilege.

Figure 1.  How to access BIMS on GDR.

 

BIMS: Viewing Data

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

Figure 2.  Selecting the Crop and 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 crop and program, allows users to change crop or program, has a link to the GDR 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 crop and program have 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.  Cross details.

 

Figure 8.  Accession details.

Figure 9.  Trial details.

BIMS: Searching Data

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 Fruit Shape trait here is only for those accession from the parents 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 GDR 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

To start a new breeding program in BIMS, you must have a GDR account with the appropriate access level.  The first step in creating a new program is to select the appropriate crop.  To change crops, click the "Crop" button in the header (Fig. 18A).  Then select the crop from the list on the "Crop" tab (Fig. 18B).  When the new crop is selected, the "Manage Program" tab will open and then you can open the "Program Admin Menu" section (Fig.18C).  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 GDR 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

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

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

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. 32A).  On the "Manage Archive" tab, there is an "Archive Data" button (Fig. 32B).  When this button is clicked, an Excel file is generated that contains all the data in the current breeding program (Fig. 32C).

Figure 32.  Generating an archive file.

BIMS: FAQ and Troubleshooting

FAQ

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 chrome, on firefox, on internet explorer.