The CarrotOmics homepage is divided into a few key areas to help facilitate navigation.

[A] A traditional pull-down menu bar in the header provides access to all of the site's functionality.

[B] A link to log in to CarrotOmics. This is only used by administrators for uploading new data and performing maintenance.

[C] The center region of the homepage contains a News and Events section which has news about CarrotOmics as well as from the community.

[D] Commonly used functions are provided in the Quick Start section of the home page for easy access.

[E] Funding and technical support information.

[F] You can return to the home page at any time by clicking on the CarrotOmics logo in the upper left corner of the current page.

The items under the Search and Tools menus are discussed in other tutorials, but here we want to highlight the Data, General and Help menus. Under the Data menu [G] you can see a data overview, learn how to submit data, information about the types of genetic markers in CarrotOmics, and transcript and expression data. A summary overview of all data in CarrotOmics which can be broken down by species and/or data type is found on the Data Overview page. Under Data Submission, there are details about submitting data to CarrotOmics. CarrotOmics 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.

On the Marker Types page, there is a table of the marker types that are in CarrotOmics. The markers have been generally grouped by the same technologies and we have provided a link to a reference that describes the marker technology.

The General menu [H] contains links to a variety of different items.

The Help menu [I] has a link to this CarrotOmics 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.

Search Functions

There are a number of functions in the Search pull-down menu.

There are three general types of searches available here: MegaSearch, BLAST, and Standard searches. Each of these are described on the following pages.

Taxonomy

Any type of data in CarrotOmics that references the taxonomy of a particular organism will have a corresponding organism page for that organism. These can be viewed either from the "Species" menu by selecting "Organism Summary", or from the home page Quick Start "Species List". The organisms listed in CarrotOmics have been derived from any of several sources:

• Germplasm accessions from various germplasm collections. See the Collection List for a list of these collections.
• Sequence metadata from the National Center for Biotechnology Information (NCBI)
• Publications containing sequence data or phylogenetic trees (example study).
• Publications containing lists of germplasm (example publication), or germplasm release notices (example publication).

Germplasm

Germplasm accessions can be viewed and searched through the "Search" menu "Germplasm Search" option, or from the home page Quick Start "Germplasm Search". Germplasm accessions can be searched by name, by keywords such as a trait or germplasm collection, by taxonomy, country of origin, and cultivar pedigree. Germplasm accessions will also in some case be found as cross-references on analysis or publication pages.

Biological Samples and Materials

CarrotOmics stores the information about biological samples from NCBI under a corresponding CarrotOmics Biological Sample page, for example SAMN17775433. These pages will link to CarrotOmics analyses and projects, and have references to corresponding NCBI entries. Information about other types of biological samples, such as a plant that has been evaluated for one or more phenotypes, is not represented by its own page, but will be found in the data files linked to the phenotyping project or analysis, for example 2013 Alternaria Resistance Evaluation

Phylogenetic Trees

A list of publications providing taxonomic trees can be accessed from the Trees page. All of the taxonomic trees within a given publication are collected under a single analysis that represents all trees in a publication, for example TreeBASE Study S15477. Each individual tree has a corresponding sub-analysis, listed in the Relationship field, which will ideally further describe analysis methods that were used to generate that tree, and each sub-analysis will have a link to the actual phylogenetic tree.

Phenotypic traits in CarrotOmics have been obtained from various sources, including the U.S. National Plant Germplasm System GRIN database, publications, and submissions from contributors.

Traits are classified as quantitative traits if the trait is measured numerically on a continuous scale. They are classified as qualitative traits if the trait is measured as discreet steps on a scale, for example scored from 1 to 5, or if the trait has discreet scoring terms, such as color of white, yellow, or orange.

There is a search page for each of these types of traits, the Quantitative Trait Search page, or the Qualitative Trait Search page, both of which are accessible under the top level "Search" menu.

If a trait has been placed on a genetic linkage map, it will have been categorized as a Quantitative Trait Locus (QTL) or as a Mendelian Trait Locus (MTL), and the page for that locus will have a corresponding MapViewer link to view that map. These types of trait markers can be found through the QTL or MTL Search under the Search menu. For example, the page for the MTL Y2 has links to several linkage maps, the map [A], when viewed, shows the Y2 locus at the end of linkage group CH7 [B]

Most markers in CarrotOmics are associated with one or more genetic linkage maps. The various types of markers known are listed on the CarrotOmics Marker Types page.

Desired markers can be found using the Marker Search page. There, markers can be subset by subspecies, marker type, mapping population, linkage group/chromosome, or a trait the marker is associated with.
In the example presented below, we will limit our search to SNP markers [A]
in one specific linkage map [B]
on one specific linkage group [C]
and then click on the Search button [D]

The results of the search are displayed at the bottom of the screen [E]

For markers with known genome locations, a link to the CarrotOmics JBrowse will appear [F]. Clicking on this link will take you to the genome location where the marker is located

Another useful function is to Search Nearby Markers, where a marker name can be used to identify markers within a user-defined genetic distance. In the following example, we will search for markers near GSSR-125 [G]
that are within 10 cM [H]

Nearby markers are listed in the Neighbors column [I]

Marker pages can also be accessed directly from the linkage map(s) they are contained in. For example, any of the marker names in column [J] of the map below can be clicked to lead you to the corresponding marker page.

CarrotOmics strives to have all published linkage maps for carrot available in the database. The maps are visualized using MapViewer.

MapViewer is a tool for viewing and comparing genetic maps using the Tripal MapViewer module version 2. Tripal MapViewer is a modern replacement for the cmap program which has not been updated since 2009.

The MapViewer Quick Start can be accessed from the Tools menu in the header, and on this page there are links to example maps and correspondence matrices. Maps can also be reached from the Map Search under the Search menu. Alternatively, from the Marker Search page, selected markers will display a link to any linkage map that they are present in. The Map Overview pages for each of the maps display summary graphics of all linkage groups, and clicking on a linkage group opens a more detailed view in MapViewer.

MapViewer displays the complete linkage group on the left, and the selected region on the right. 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. 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.

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

CarrotOmics has data download links associated with any content type which includes data files. You can search for downloadable files at the File Search page. A summary of some of the more "popular" downloads is available on the Data Download page.

In the following example we will search for a gene prediction analysis. Go to the home page, and on the Search menu select Project, Analysis, or Assay Search
In the Name box, enter DCAR V1.0 Gene Prediction and click on the Search button

The search results should provide a link to DCAR V1.0 Gene Prediction. If we click on this, we see that this analysis has links for downloading various files.
Select the first one [A] "DCARv2 V1.0 Gene Prediction JBrowse GFF3" by clicking on the link in the File column

This leads to the page for that file. Simply click on the link [B] in the Download File Name column to download the file. File size and an MD5 checksum are provided for most files stored at CarrotOmics.

Please check out the tutorial videos on the MainLab YouTube channel. The searches and tools use very similar frameworks across all of the MainLab databases.