ArkMAP: ArkDB's Map Drawing Application

Contents

1. Introduction
2. Downloading, Installing and Launching the ArkMAP
3. Loading Maps
4. Configuring the Map Displays
5. Displaying Marker Details (and related Maps)
6. Loading User Maps
7. Saving Maps
8. Saving Images of Maps
9. Printing Images of Maps
10. Release Notes

The ArkMAP software is developed and owned by The Bioinformatics Group of The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, Scotland UK EH25 9RG as part of the ArkDB Project. Copyright (C) 2006-13 The Roslin Institute.

This application is free to use for academic and not-for-profit users only. The application and code libraries are available under the GNU General Public Licence (GPLv3) for use in free but not proprietary programs. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Licensing details for dependent third-party libraries are included in the licences directory of the JAR archive and listed here.

Please acknowledge use of this software.
Contact:roslin.bioinformatics@roslin.ed.ac.uk

 
 

1. Introduction

ArkMAP

ArkMAP is a desktop application that allows users to draw genetic maps. ArkMAP is downloaded as a Java WebStart application which installs on your desktop and automatically updates as new versions are released; alternate installers and downloads are available for Windows, Mac and platform-independent (Linux), which lack auto-updating.

Genetic Maps from ArkDB

Genetic maps of interest for many farmyard animals can be selected and downloaded from the ArkDB database using their ArkDB database accession number or by browsing the available maps by species, analysis, chromosome etc.

Genome Assembly Maps from Ensembl

Gene-annotated chromosome maps for every available species genome assembly may be downloaded via a direct link to Ensembl Datasources (from the Vertebrate, Invertebrate and Bacterial datasources). ArkMAP can download and display chromosomes from all available Ensembl releases, which can include successive assembly releases and patches.

Local Mapping Data

Local mapping data may also be loaded and displayed by the user.

Alignment of Maps

The markers located on adjacent maps can be linked by virtue of shared identity or name, allowing relationships between alternate genetic and physical maps to be drawn. ArkMAP can also link homologous genes between separate chromosomes, using the interspecies homology relationships stored in Ensembl. This allows regions of conserved synteny between species to be visualized.

Improvements to ArkMAP

The ArkMAP tool replicates and improves the functionality of our original applet used to draw maps within the ArkDB web application. ArkDB web services use a generic data format for exporting Genomic Mapping Data, defined by the GMD XML Schema, as described by Paterson and Law 2009. ArkDB web services are directly available, see the ArkDB web services home page.

The original version of the ArkMAP application used WebServices provided by Biomart to access the gene mapping data of the Ensembl Vertebrate genome builds. Recently we have initiated the JEnsembl project (Paterson & Law 2012) to provide a Java version of the Ensembl PERL API for data access. We have now adapted ArkMAP to make use of the JEnsembl API for datasource access in place of the Biomart access. Our new ArkMAP application provides access to both the Ensembl Vertebrate and Ensembl Genomes (Plant, Protist, Fungi, Metazoa and Bacterial) datasources.

2. Downloading, Installing and Launching ArkMAP

This Java application requires that you have the Java Virtual Machine version 1.6 (aka Java6) or higher installed on your machine. You can test which version of Java you are running here. If necessary you can download the JVM from Oracle (formerly Sun). (Note that Java 6 is only available for Mac OS X 10.5 upwards directly from Apple).

ArkMAP should preferably be downloaded using Java Web Start technology, which allows you to install the application and all of its dependencies via a simple single click in your web browser (Chrome, Firefox, Internet Explorer etc.) from our ArkMAP download page. Your web browser will need to be Java enabled to run WebStart. If it is not enabled you may be able to set this yourself using the Browser Options or Preferences panel.

Many modern computers use a 64-bit architecture and operating system and use of a 64-bit version of Java allows higher memory usage by ArkMAP. However, on Windows most web browsers are still 32-bit, and require a 32-bit Java plugin. These complexities and various possible solutions are discussed on our installation help page.

If you still have problems running WebStart through your Browser after installing and enabling JRE 1.6 it is possible that your System Administrator has zealously disabled automatic recognition of WebStart files, if this is the case you should ask them to re-associate '.jnlp' file types with javaws (a program bundled with the JRE).

Failing this, or if you don't use a browser, you can run the WebStart version of ArkMAP in a terminal/console as:

prompt>javaws http://www.thearkdb.org/webstart/arkmap-jensembl.jnlp

or

prompt>javaws http://www.thearkdb.org/webstart/arkmap-jensembl64.jnlp

[visit the javaws help page]

ArkMAP will also automatically download and launch when viewing maps within the ArkDB Web pages (when you click 'Draw Maps', for example).

During the download process, and whenever you run ArkMAP, you will be asked to accept our security certificate which is validated by Thawte (but may be reported as 'out of date'). Accepting this is necessary for full functionality of the application (see Figure 1).

Upon successful installation shortcuts for running ArkMAP will be installed on most users' computers (Figure 2).

However Windows shortcuts may be corrupted to point at the wrong Java version - if the shortcut doesn't work, right click the shortcut, select 'Properties', and ensure that the Target is specified as C:\Windows\System32\javaws.exe (or even more specifically C:\Program Files\Java\jre6\bin\javaws) NOT C:\Windows\SysWOW64\javaws.exe.


If this is not the case, or you do not use a desktop, you can start ArkMAP from the command line as above, or from the Java Control Panel application (which can be found as an executable in your Java installation 'bin' directory, called jcontrol or javacpl.exe and launched from the command line). (Figure 3).

[visit the Java Control Panel help page]

Alternatives to WebStart

As alternatives we provide Windows and Mac program installers and a failsafe platform-independent bundled JAR version of ArkMAP which can be run independently - with whatever memory footprint you desire.


Figure 1. Downloading ArkMAP

     
webstart download dialogue   Java security dialogue   Certificate Expired
 
When downloading, if WebStart is enabled, you can launch ArkMAP directly. Or you can save the 'JNLP' file to open later. You will be prompted to accept our security certificate, authenticated by Thawte, but now expired. Accepting security validation is necessary for download and full functionality of ArkMAP.  
 

Figure 2. Screenshots of ArkMAP Desktop Launch Icons

A: Windows

Windows Program Shortcuts
 

B: Mac

Mac Program Shortcuts
 
WebStart should install Program and Desktop shortcuts on Windows And Mac.
 

Figure 3. Launching ArkMAP from the Java Control Panel


A: Windows

Java Control Panel Java Control Panel - cache

Selecting Java Control Panel -> Temporary Internet Files -> View lists all your Web Start applications, which can be launched from here.

B: Mac

Mac Java Control Panel Mac Java Control Panel - cache

Click Applications -> Utilities -> Java Preferences -> Network -> View Cache Files to list all of your WebStart Applications, which can be launched from here.

 

2.1 Internet Connectivity

Web Start allows us to digitally sign ArkMAP, so that Java will allow it access to both the Internet (for data retrieval) and your own local directories (for data upload and saving). Some users' workplaces will be using an HTTP proxy to connect to the Internet, and upon launching ArkMAP attempts to configure the correct proxy settings (Figure 4), but if it cannot do this it will ask you to enter your proxy configuration details manually (Figure 5).
You may also run ArkMAP when 'offline', but will only be able to load local data files.


Figure 4. The ArkMAP Splash Screen


Splash Screen
 

Figure 5. Manually Setting your Proxy


Proxy Configuration
 
As it launches ArkMAP checks connectivity to relevant sites, and the world turns...   If connectivity problems are found, you will be prompted to manually configure your proxy. This window can also be accessed via the 'Options'/'Configure Proxy' menu item.
 

2.2 Updating ArkMAP - keeping track with Ensembl releases

Updating ArkMAP not only gives you access to the most fully featured version of ArkMAP but is essential for providing connectivity to the most recent release of Ensembl datasources. Ensembl is updated in regular 3 month cycles, which requires a reconfiguration of the JEnsembl API used by ArkMAP to connect to Ensembl.

Fortunately, using WebStart to launch ArkMAP provides automatic version updating.

The standalone versions of ArkMAP provides a warning when it detects that it is out of date with the server, requiring the user to manually download an up-to-date version.

The most recent release of Ensembl that ArkMAP is configured to recognize is reported when ArkMAP is launched, and can be confirmed by reading the Help -> About panel (example shown above).

2.3 The Main Menu


Download Maps
Opens a dialogue to download selected maps from any datasource (ArkDB, Ensembl or EnsemblGenomes) (see Section 3).
Open XML File
Opens a dialogue to open a locally available file of map data (in GMD XML format) (see Section 6).
Create New Map
Opens a dialogue for entering map data in simple text format (see Section 6).
Save XML
Opens a dialogue to save all the current maps in a GMD format file (see Section 7).
Save SVG
Opens a dialogue to save an SVG graphics format file of the current display (see Section 8).
Save PDF
Opens a dialogue to save a PDF output file of the current display (see Section 8).
Save PNG
Opens a dialogue to save an PNG graphics format file of the current display (see Section 8).
Page Set Up
Opens a dialogue to configure the page size (used for printing and the optional on-screen guides, see Section 9).
Print
Opens a print dialogue (see Section 9).
Exit

Configure Proxy
Opens a dialogue to allow the user to set local proxy configurations if these were not automatically discovered (see Section 2.1).
On-Screen Guides
Allows the user to choose whether the on-screen page size guides are displayed (see Section 9).
Link Markers by..
Allows the user to display whether markers are related between maps on the basis of database identity or merely by shared name (see Section 4.3)..
Colour Scheme
Displays the current colour scheme for the various types of inter-marker relationships (and any Genome Assembly Exceptions recorded in Ensembl). The colour scheme has been optimised to support colour-blind users and will be user configurable in future releases (see Section 4.3).
Globally Filter Relationships
Allows the user to control a threshold below which homology relationships are not drawn (applied globally to all maps, see Section 4.4).
List Current Filter Values
Displays the current filter thresholds set between maps relationships (including values set globally or pair-wise, see Section 4.4).

About
Opens 'About ArkMap' panel (example shown above).The information displayed includes the most recent release of Ensembl datasources that ArkMAP is configured to retrieve.
Online Help
Opens browser at ArkMAP help page (i.e. this help page).

3. Loading Maps

Please be aware that all of the information loaded into ArkMAP is retrieved by web service calls over the Internet, which may cause delays if the connection is slow, or the remote server is busy. Access to the Ensembl datasources is extremely reliable, but cannot be guaranteed.

3.1 ArkDB Maps

To load maps from the ArkDB web services, select the 'File'/'Download Maps' menu option, and then select the 'ArkDB Genetic Maps' option in the dialogue window ( Figure 6). You can then select how many maps you wish to load (the drop down list allows from one to twenty maps) (Figure 7). Next select which species for each map from the drop down list of available species in ArkDB (Figure 8).

The following window requires you to specify the named 'Mapping Analysis' for each map. The available Analyses for each selected species is presented in a drop down list divided into the available analysis types, for example: Linkage Maps, Radiation Hybrid Maps, Cytogenetic Maps, Composite Maps and ePCR mappings of Markers on Ensembl Sequence Assemblies. Select the desired Analysis by its Name, for example 'Consensus 2005 (A)' (There will usually only be one Cytogenetic Map, named 'Cytogenetic Map') (Figure 9).

The final dialogue step is to select each Map to display by Name; this Name generally corresponds to the Linkage Group or Chromosome Name (Figure 10). In Figure 11 you can see the resulting display loaded with the cytogenetic maps for Turkey and Chicken Chromosomes 1. Because the Turkey map includes mappings of some Chicken clones, these Markers are cross-linked between the maps - making it immediately apparent that these chromosomes exhibit gross scale conserved synteny between chicken and turkey.

Alternatively maps can be loaded directly using known ArkDB accession numbers, entered as a comma separated list of 14-digit identifiers (ARKXXX12345678) (see Figure 6).

Once ArkDB maps are downloaded they are displayed in the main drawing panel, which automatically expands as more maps are added. Each loaded map is listed in the right-hand upper panel, and when selected (by clicking either the map or the listed name) a map can be configured and rescaled etc. In Figure 11, map [1] is selected, and its configuration dialogues are shown in the right-hand lower panel. An active (selected) map can be deleted using the 'Dustbin' icon, or maps can be hidden by shutting the 'Eye' (map [3] is hidden here). The four (tabbed) configuration dialogues allow control of the Title displayed, the Fonts used, the Axis orientation, scale and range, and which Markers are shown on the map.

The controls vary slightly for different map types, and for all maps except Cytogenetic Maps the Axis configuration can also be accessed from the 'Axis Context Menu'. Maps can be repositioned on the drawing panel by dragging them with the mouse, and the scale can be stretched by dragging the bottom border of the map highlight.

Configuration of the maps is discussed in further detail below.

     

Figure 6. Connecting to ArkDB Web Services


Loading ArkDB Maps 1
 

Figure 7. Choosing How Many Maps to Display


Loading ArkDB Maps 2
 

Figure 8. Choosing the Species for Each Map


Loading ArkDB Maps 3
 

Figure 9. Choosing which Analysis for Each Map


Loading ArkDB Maps 4
 

Figure 10. Choosing Which Named Maps to Display


Loading ArkDB Maps 5
 
 
Generally the Map Name corresponds to the Linkage Group or Chromosome Name  
 

Figure 11. Displaying Turkey and Chicken Maps Exhibiting Conserved Synteny


Loading ArkDB Maps 6

'Identity' relationships between marker mappings are coloured red here.

3.2 Ensembl Maps

To load gene-annotated genome assembly maps from either the Ensembl(Vertebrate) or Ensembl(Other)Genomes datasources, select the 'File'/'Download Maps' menu option, and then select one of Ensembl options in the dialogue window (Figure 6). At this point it is possible to load 'ALL' releases available at the data source, or to restrict loading to a particular release version. Loading of 'ALL' releases may take several minutes, especially for the extensive bacterial resource. The list of available species is then retrieved from the datasource, together with the available Ensembl release data for each species (see Figure 12A). The most recent recognized version currently available at Ensembl will depend on the version of the JEnsembl API that ArkMAP incorporates. Gene annotations may vary between Ensembl releases, and the actual sequence assembly may be updated over time (see Figure 12B).

Following species and release/assembly selection, the user chooses which available chromosome or fragment to load (see Figure 12C). It is also possible to specify the zoom level for initial display (although the whole chromosome is downloaded together with its gene-annotations). Note that some immature genome assemblies may only include fragments or supercontigs, and even mature projects may include a number of unassembled regions. The Human project is special in that it also includes variant regions referred to as Assembly Exceptions - which include alternate haplotypes and inter-genome-build assembly corrections (patches). These variants are listed together with the available chromosomes, and are always highlighted as coloured regions on downloaded maps (see Section BOB).

As with ArkDB maps, the display of Ensembl maps can be configured via the tabs in the configuration panel and the 'Axis Context Menu'. Configuration of the maps is discussed in detail in Section 4.

     

Figure 12. Connecting to the Ensembl Databases through the JEnsembl API

A: Available Species

Loading Ensembl Maps 1

All of the species available in your chosen datasource are listed (with your recently chosen species listed as favourites, see C below).

 

B: Available Ensembl release version (and build) for selected Species

Loading Ensembl Maps 2

All of the available releases for your chosen species are listed (noting the genome build used by that Ensembl release). Note that the JEnsembl configuration may require updating for a new Ensembl release, and only those releases compatible with the current JEnsembl API will be shown. Updated JEnsembl code will be automatically downloaded by ArkMAP as it is released.

 

C: Search by name and resetting favourites

Loading Ensembl Maps 3

It is also possible to look up species using one of the many aliases used by Ensembl. ArkMAP remembers your recent choices as 'favourites' (see A above) and these may be manually picked using the 'Change Your Favourites' button'.

 

D: Selecting chromosome region (and zoom region) to display

Loading Ensembl Maps 4

At this stage you may limit the range of the chromosome to initially display - although all of the gene annotations will be retrieved and available. Various unassembled fragments and Assembly Exceptions may also be listed as 'Chromosomes' here.

 

4. Configuring the Map Displays

The format of each map displayed in the view pane is controlled independently. As the mouse enters each individual map in the main drawing panel, the border of the map panel is shown; clicking within here (or on the Map Name button in the top right panel) selects or activates this map, which both highlights the map and displays its configuration panel in the bottom right panel.

The whole map can be moved around by clicking and dragging in the main area of the map with the left mouse button; a map may be hidden or redisplayed by clicking on the 'Eye' icon on the Map Name button, or disposed of using the 'Dustbin' icon.

Maps may be resized (made longer or shorter) by using the left mouse button to drag the bottom of an active map panel up or down, or by using the Axis configuration panel.

On most computers the mouse pointer will change to an open hand when the map area is active for dragging, to a double arrow when active for resizing and to a cross-hair when selecting a region on the left hand side of the axis. (Problems with mouse behaviour should be reported to thearkdb.org).

4.1 Configure - The Map Drawing Options Dialogue

Selecting the 'Configure' button displays a multi-tabbed pane (see Figure 14) that allows you to configure:

Title Tab
change the Map's Title and whether it is displayed.

Font Tab
select which fonts and sizes are used for the Title, Marker labels and Axis scale.

Axis Tab
resize (stretch) the whole Map; select subsections of the map upon which to zoom in (or out); choose axis orientation: ascending or descending and with the markers drawn to the right or left of the axis. (Zooming also available from the 'Axis Context Menu').

Markers Tab
select which Markers to display on the Map. You may choose to Hide all Markers, Hide any Assembly Exceptions, show only a proportion of Markers or show only Markers linked by Relationships to other Maps.


Figure 14. Configuring a Map


Configuring Maps: Title Configuring Maps: Font Configuring Maps: Axis Configuring Maps: Markers
 

4.2 The Axis Context Menu

An alternative way to zoom a map is to access the map's 'Axis Context Menu'. A section of the map can be selected using the mouse: by pressing down left mouse button in the area to the left of the map axis and dragging the mouse to the desired range, then releasing, the 'Axis Context Menu' will be shown (the selected region remains highlighted in green). This menu allows the selected section of the map to be rescaled, or redrawn ('projected') as a new map.

Additional options are available for maps depending on their origin and type (see Figure 15):

All Maps

Zoom Location
Refines the coordinates displayed (zooms in or out).

Project Location on New Map
The map is copied, and the new map zoomed to the selected coordinates. (In Figure 16 the middle map has been projected from a selected region of the left map.)

Note that the coordinates selected by mouse can be manually edited.

ArkDB ePCR Maps

Import Ensembl Assembly
A gene-annotated chromosome for a selected species/Ensembl release is imported from Ensembl. In Figure 15B the ePCR mappings are copied from the ArkDB ePCR map onto the Ensembl chromosome map. (In Figure 16 the right-hand map is the imported region of the Ensembl assembly corresponding to the selected region of the middle map.)

Ensembl Assembly Maps

Import Ensembl dbSNP Map
Where available a map is drawn for the selected region displaying Ensembl's version of dbSNP records. The genes on this region are also displayed on the new map (see Figure 17).

 
Import Alternate Ensembl Assembly
Any available alternate release version can be displayed for the selected region (beware that coordinates can change between chromosome assembly releases). In Figure 18 the first 5MB of the bovine chromosome 20 in the most recent release (67) is compared with that of an earlier release (63). These releases use different assembles (UMD3.1 versus Btau_4.0) and clearly the first 3MB is inverted between the two assemblies.

Find Conserved Synteny
Each gene in the selected region is searched for homologues in the selected species. The chromosome regions containing the homologues are then displayed (i.e. potential regions of conserved synteny). Beware that searching for homologies and retrieving chromosome maps for large numbers of genes may take several minutes, particularly if the discovered homologues lie on many separate chromosomes. In Figure 18 searching for human homologues for the genes in the first 5MB of bovine chromosome 20 returns an extended region of conserved synteny, which is in agreement with the fragment orientation in the most recent bovine assembly, rather than the earlier build. If a user knows which target species chromosome they wish to search for homologous genes, they can pre-filter the homology search and improve the speed of data retrieval, alternately if multiple chromosome regions with homologous genes are discovered, the user can choose which chromosomes to draw (see Figure 18.2).

Filter Homology Relationships
If this map has homology relationships drawn with neighbouring maps, this selection will open a filter dialogue that allows pair-wise filter thresholds to be set. This allows the user fine control over the sensitivity of homology display between pairs of maps instead of using a global filter threshold (see Section BOB).

Figure 15. Context Menus

A: Context Menu on an ArkDB ePCR Map

Context Menu on ArkDB Map

B: Context Menu on an Ensembl Assembly Map

Context Menu on Ensembl Map
 

Figure 16. Projecting an ePCR Map

Projections on an ArkDB ePCR Map

The names of selected Markers are shown in red.
The red inter-marker relationship lines indicate marker 'Identity'.
The locations of the ArkDB ePCR mappings are projected onto the (right-hand) Ensembl gene map (Note that the correct release version of the Ensembl annotated pig assembly has been retrieved, matching the release used for the ePCR mappings).

Figure 17. Exploring SNP information on Ensembl Assemblies

Ensembl SNP map

A region of bovine chromosome 20 (left-hand map) is interrogated for dbSNP mapping records.
The names of selected genes are shown in red, and projected onto the retrieved dbSNP map (middle map).
The region surrounding each gene is projected onto enlarged sub-maps (right-hand).

Figure 18. Comparing Ensembl releases, and retrieving regions of conserved synteny

Resolving assembly errors using conserved synteny

Whilst the red inter-marker relationship lines indicate marker 'Identity', shades of blue/purple indicate various types of homology and orthology (see below).
Note that the homology relationships of bovine genes to human were retrieved from the same Ensembl release (63).
The apparent inversion of two blocks of conserved synteny may be the result of an assembly error in bovine assembly btau4.

Figure 18.2. Pre or Post filtering homology searches for regions of conserved synteny.

A: Selecting the source chromosome region, and the target species.

B: Message alerting the user to the possible delay.


C: Optional selection of a single target chromosome.

D: Filtering which resulting chromosome maps to draw.

E: Alignment of Zebrafish chromosome 4 with two Stickleback chromosomes showing extensive regions of conserved synteny.

4.3 Relationships between Markers

Relationships are only drawn between maps when the maps are moved adjacent (but not overlapping) to each other (for examples see Figures 16-18). It is possible to stack more than one map in a 'column' so that relationships can be drawn from one map to several others (see Figure 17).

Currently users can choose to display either Identical (shared ID) or Synonymous (shared Name) inter-marker relationships (using the 'Link Markers by..' menu option). 'Synonymous' markers are those that share a name as opposed to 'Identical' markers which 'are the same' marker with identical database accession IDs. Care should be taken when considering the significance of 'Synonymy' ('By Name') relationships. Just because two 'markers' share a name does not imply that they mark the same genetic object or use an identical detection technique. In ArkDB if markers on different maps have the same database accession ID, there is greater confidence that they represent the same detection protocol on each map (e.g. PCR detection with identical primers, the same hybridization probe etc.) One of the long term aims of ArkDB is utilize verifiable relationships between genetic objects, allowing us to represent various types of relationship, such as Identity, Synonymy, Homology, Sequence Similarity etc.

Colour-coded orthology relationships are drawn between genes on Ensembl chromosome maps where this information has been retrieved from the Ensembl datasources (i.e. after searching for regions of Conserved Synteny, see Figure 18). 'Orthologous' markers are Ensembl genes that have been annotated through the Ensembl Homology pipeline as true orthologues between Species (see Gene Orthology/Paralogy prediction method ).

The current types of possible relationships that are represented are colour-coded, with a default palette chosen for maximum resolution by colour blind users (see CUDO). The colours may be viewed by opening the the 'Options'/'Colour Scheme' menu item, where users may set their own preferred colour scheme (including the ability to hide relationships).

Relationship Colours

4.4 Filtering Homology Relationships.

The user can set thresholds below which homology relationships between genes on adjacent Ensembl chromosome maps are not drawn. Filter values can be set globally, to apply to all homology relationships (using the filtering dialogue available at Main menu -> Options -> Globally Filter Relationships) or between chosen pairs of maps (activating the filtering dialogue by selecting Filter Homology Relationships from the Axis Context Menu for an Ensembl map).

The user can chose to filter on either the Identity OR the Similarity score. The score value for a homology relationship reported by Ensembl is the sum of percentage identical (or similar) amino acids in target + source peptides (giving a maximum value of 200). The threshold is applied 'live' as the slider is moved up and down - allowing experimentation with suitable values. (For the case of very large datasets if the speed of redrawing becomes too slow and distracting it is possible to disconnect the live redrawing). In the case of the pair-wise filter dialogue - the user selects which adjacent map pairs that the filter is applied to.

Figure 18.3

Filter dialogue activated from Axis Context Menu of map 6. Maps 5 and 7 are identified as neighbouring paired maps for which it is possible to apply a filter. A filter with value of 164/200 has been applied to the relationships between maps 5 and 7, hiding one relationship with a score below this threshold. This filter value can be save, or reverted using 'Cancel'.

  The current filter values that have been set can be viewed at any time from the Main Menu -> Options -> List Current Filter Values. This table may be printed or saved in tab-delimited form.  

5. Displaying Marker Details, Homologies and Alternate Maps.

Hovering the mouse over a marker on a map highlights that marker and then displays a tool-tip box detailing the actual mapping coordinates(Figure 19A & B left panels). Where available, the orientation of gene transcription is given (e.g. for Ensembl Gene Maps in Figure 19B). Clicking a highlighted marker opens a new dialogue window displaying details the marker more fully (Figure 19 A & B middle panel). The contents and options for this window depend on the available information for this map and marker.

5.1 ArkDB Markers

The Marker Details window displayed for an ArkDB marker allows the user to search for all of the Maps available which include a mapping of this marker by clicking the 'Display All Maps' button. This action generates another dialogue window which allows the user to select alternate maps to retrieve from the database (Figure 19A). In this case the markers shared between the three loaded maps are all joined by the shared Identity Relationship (Figure 20).

Where possible ArkDB produces maps of ArkDB Markers placed on current ENSEMBL Assembly Sequences (by ePCR). These are currently available for the Pig, Cow, Chicken and Turkey assemblies. The map-axis context menu on these 'ePCR' maps allows the import of the gene-annotated Ensembl Assembly, (see Section 4.2), and the Marker Detail window for markers on these maps also allows the user to display this region of the genome in the Ensembl web-browser (see Figure 21). These ePCR maps are also published as GFF format files, which can be imported and displayed in the Ensembl's genome web-browser (see Figure 22). Instructions for loading GFF files are provided (see Figure 21b).

5.2 Ensembl Markers

The Ensembl assembly maps displayed in ArkMAP can show the mappings of Ensembl gene models, dbSNP locations obtained from Ensembl or ArkDB ePCR markers projected onto the assembly map. The Marker Details dialogue window displayed upon clicking an Ensembl gene marker provides the option to search for homologues for protein products of the gene. The full details of pair-wise homologies retrieved from the Ensembl Compara datasource (including orthology/paralogy classification and identity/similarity scores) are listed in a sortable, printable table (see Figure 23).The detail information in this table loads progressively.

In order to explore regions of 'Conserved Synteny' chromosome maps can be downloaded for orthologues of interest using the map-axis context menu (see above).


Figure 19. ArkDB Marker Details and Importing Related Maps A: ArkDB Maps


Marker Details: Coordinates Marker Details: Full Marker Details: Related Maps

Figure 19.B: Ensembl Maps


 
 

Figure 20. Three ArkDB Maps Linked by Common Markers


Maps Linked by Common Markers
'Identity' relationships between marker mappings are coloured red here.

Figure 21. Linking to the Ensembl Browser

A: Marker Details Window for an ArkDB ePCR Marker.

Marker Details for ArkDB ePCR maps

B: Instructions for Linking ArkDB GFF tracks to the Ensembl genome display

GFF instructions
 

Figure 22. Linking ArkDB GFF tracks to the Ensembl genome display.


GFF display
The Cow UMD3.1 ArkDB Markers track is added to the ENSEMBL browser display, showing the position of ArkDB markers as determined by ePCR.
Selecting a marker on the GFF track opens a description box.
 

Figure 23. Retrieving Orthologues for an Ensembl Gene)

A: Marker Details Dialogue

Marker Details : Find Orthology

B: Orthology Search Dialogue

Orthology Details
 

6. Loading User Maps

The user can load map data into ArkMAP either as GMD conformant XML data files, or by direct text entry.

Selecting the 'File'/'Create New Map' menu item launches a data entry dialogue, in which simple map data can easily be entered (Figure 24a). Maps can be given name and species identifiers, and both point and range mappings can be entered as described in the dialogue pane. Cut and paste functions are provided for desktop editing, and it is also possible to upload the contents of a text file to the editor pane. Typically user-entered Markers will not have a relevant database ID, but if ArkMAP is configured to show 'Link by Name' (synonymy) relationships (see above) user-entered maps can be linked to other maps from ArkDB or Ensembl (e.g. Figure 24b). In the atypical case that database identifiers are known they may be entered by the user.

The 'File'/'Open XML File' menu item allows the user to load mapping data files which are formatted in the GMD data format (see Paterson and Law 2009). Roslin ArkDB has developed the GMD format as a generic XML Schema for describing Genomic Mapping Data, and the ArkDB web services export data in this format, as does ArkMAP itself (see below).

Figure 24. Displaying User Map Data: and Linking to Datasource Maps.

A: Simple data Entry Dialogue.

User Map Wizard

B: Alignment of an ad hoc User Map with ArkDB and Ensembl Maps by Synonymy of Markers.

User Map Display
  'Synonymy' relationships between marker mappings are coloured grey here.

7. Saving Maps

By selecting the 'File'/'Save XML' menu item all of the currently loaded maps are saved to a single GMD format data file. By default this file is given the suffix '.ark' and a second '.config' file is also produced which simply lists the maps present in data file. These data files can be re-opened in ArkMAP at a later date using the 'File'/'Open XML File' menu item.

Note: saving data is file system dependent and may be slow or occasionally fail. Ensembl chromosome maps will not be saved. Maps from ArkDB may be slow to save as any missing data is downloaded from the server.

8. Saving Images of Maps

By selecting the 'File'/'Save SVG' menu item all the currently loaded maps are saved to a single SVG graphics file. This can be displayed in a good browser and manipulated in various graphics packages (for example the excellent free open source Inkscape program).

By selecting the 'File'/'Save PNG' menu item all the currently loaded maps are saved to a single PNG graphics file.

By selecting the 'File'/'Save PDF' menu item all the currently loaded maps are saved to a single PDF document file.

Note: in each case any colour-highlighting of the maps and marker labels is removed from the saved image.

9. Printing Images of Maps

The workspace has orange guide-lines showing the current page margins for printing. These can be turned on or off using the 'Options'/'On-Screen Guides' menu item. The page size and orientation can be configured via the 'File'/'Page Setup' menu item (see Figure 25). This allows the user to optimally position page breaks to fit maps on pages. Additionally the maps can be dragged around the workspace and rescaled to suit.

The workspace can then be printed via the 'File'/'Print' menu item.

Figure 25. Print Page Setup via Guide-lines

Printing
 

10. Release Notes

Current Release: 2.17.71.2

Configured to retrieve data from most recent Ensembl Version release: 71 (Ensembl Genomes release 18).

(Using JEnsembl API version 1.17 /config 1.71).

Data available for Ensembl release versions: 50 - 71 (Ensembl Genomes 1 - 18).

Added Licence information for all third-party libraries.

Added further download options: Windows installer and Mac Disk Image.

These Notes

Updated for release 2.17.71.2

However, only Figures 18 & 19 have been updated to show that gene orientation arrows are now displayed on Ensembl Gene Maps.