GEMDB»SEARCH

Description

• GEMDB contains user-provided microsatellite genotype data for cereals.
• Select GEMDB»SEARCH to search genotype information stored in GEMDB.
• Search results can be downloaded in 3 different formats, each of which can be customised.
• Search results can be marked for future use by "tagging". Tags can be used as a way of grouping samples or markers in GEMDB for future reference, to mark data that has to be deleted from GEMDB, or even as input for BINNER»MRT TAGS.
• For details on how to upload genotype data, please refer to the section on GEMDB»IMPORT.
• To browse the information available in GEMDB, please refer to the manual section on GEMDB»BROWSE.
• For details on how access to the data in GEMDB can be controlled, please refer to the manual sections on user groups.

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Search the GEMDB

• A GEMDB search involves three steps, illustrated on this screenshot of the GEMDB»SEARCH interface:
  1. Entering search parameters: In the top left-hand corner of the GEMDB»SEARCH interface, search parameters are entered and a search is launched.
  2. Choosing to display results from one or more searches: In the top right-hand corner, a "search history" table lists searches, their search parameters and number of "hits". A search's results can be viewed individually, or in combination with other search results. Searches can be combined with "AND", "OR" and "NOT"; operator precedence can be controlled with brackets.
  3. Viewing and managing search results: The actual search results are displayed on the lower half of the interface; these can also extend to extra results pagers. This results display can be customised. Results can be exported in their customised format and / or "tagged" for further use (e.g. for future reference, to delete data points or even to submit markers for binning).

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Entering search parameters

• Use the following search options either individually or in combination to search the genotype information in GEMDB.

Please note: For each search, search parameters are combined with "AND", i.e. only entries that meet all the criteria are selected. To combine search parameters with "OR" (meaning that entries are selected if they meet at least one of the search criteria), use the "COMBINE SEARCHES" option described further below.

• To launch a search, hit the SEARCH button.
• Searches are then listed in the "Search History" table on the top right-hand corner, where the number of "hits" for each search is listed alongside the search parameters used and the search number.
• Select to view the results for a search, or carry out other searches to combine with the first search. See the next section for details on how this is done.

Tag

This drop-down box gives you access to all the Sample and GEMDB tags you have previously created.

Group

Use the drop-down box to select data belonging to one or all of your user groups.

Project

Use the drop-down box to select data belonging to one or all of the projects. Only projects belonging to the selected user group(s) are listed.

Run

Use the drop-down box to select data belonging to one or all of the runs. Only runs belonging to the selected project(s) are listed.

Other

• Use the drop-down box to select a field you wish to search with a keyword.
• In the text box, enter a search string. As wildcards, use "%" (the percent symbol) to stand for any number of characters (including zero characters); use "_" (the underscore symbol) to stand for exactly one character.
• If more than one GEMDB field is to be searched, click on the [ADD] link next to the text box. This will save your first selection and open a new "Other" search option to enter another field-specific keyword search.

Marker

Use the drop-down box to select only data for one of the markers used in a project. Only markers belonging to the selected run(s) are displayed.

Allele

Use the drop-down box to specify if any allele entry is to be searched, or only alleles with a specific "allele number".

Range

Use the textboxes to select only data with specific allele values, by entering the allele size in base pairs. Enter only one allele value OR describe an allele range by entering the smallest and largest allele size in the range.

Not in Range

By ticking this box, only GEMDB entries falling outside the allele range specified for "Range" are selected.

Original Values

Tick this box to search allele values as they were imported for the values specified in "Range".

Converted Values

Tick this box to search allele values after their size has been calculated without the extra length introduced by the MRT tag and dye-drift effects. (Find out more about converted allele values...)

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Viewing results from one or more searches

• All searches are given a number and recorded in a "Search History" table, where the search number, hits, and search parameters are listed. (See the top right-hand corner of the GEMDB»SEARCH interface.)
• Click on the [REMOVE] link next to a search to delete it from the "Search History" table.
• Click on the [VIEW RESULTS] link next to a search to see the GEMDB entries for that search only.
• Use the "Combine Searches" option to combine and display results from more than one search:
  1. Enter the search numbers and how you wish to combine them in the "Combine Searches" textbox. Searches can be combined with the Boolean operators AND, OR, NOT; operator precedence can be controlled by using brackets.
     • AND: When searches are combined with AND, only GEMDB entries that meet the search criteria of all the combined searches are displayed ("intersection").
     • OR: By combining searches with OR, all the entries meeting the search criteria of any of the combined searches are displayed ("union").
     • NOT: By specifying e.g. "1 NOT 2", only entries selected by search "1" that are not also selected by search "2" are displayed ("exclusion").
     • Operator precedence:
       • Default operator precedence is "AND" before "OR". The entry: "1 AND 2 OR 3" would therefore be interpreted as meaning: "(1 AND 2) or 3" (i.e.: 'Display all the entries that searches "1" and "2" have in common, as well as all the entries from search "3".')
       • Use brackets to overwrite the default operator precedence, e.g. writing "1 AND (2 OR 3)" would be understood to mean: 'Display all the entries that search "1" has in common with either search "2" or search "3".'
  2. Hit the VIEW RESULTS button to combine searches and display results.

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Managing search results

• After search parameters have been entered and one or a combination of searches have been selected by hitting [VIEW RESULTS] next to a search or the "Combine Searches" textbox, GEMDB entries are displayed on the lower half of the GEMDB»SEARCH interface.
• 'GENica Marker Tools' allows a choice of display options that can be further customised. GEMDB search results can be exported in their customised format.
• Search results can be tagged for downstream purposes.

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Change the way GEMDB search results are displayed and exported

• A drop-down box at the top right-hand side of the GEMDB search results allows selecting different "views": The "SamplexMarker view", the "Table view" and the "Pager view".
• When search results are exported, the currently active display setting determines the export format and which fields are included in the downloaded file.

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The SAMPLExMARKER view

• The "SamplexMarker view" is the default view for search results. Marker names are arranged across the top of the table, sample names down the left-hand side.
• To prevent the creation of SamplexMarker tables that are too large to navigate conveniently in a web interface, only a limited preview of the data is shown to allow assessing a sample of the query results.
• To see the whole data set, the SamplexMarker table has to be exported by clicking on the [DOWNLOAD RESULTS] link.

Please note: If the SamplexMarker table has more than 256 columns, please also refer to the section on spreadsheet viewers without a 256-column limitation.

• Use 'GENica Marker Tools' OPTIONS to customise the SamplexMarker view:
  1. Change the number of alleles displayed for every marker.
  2. If genotyping data was created with multiplex-ready^TM markers, select if "MRT marker codes" (e.g. "hv0001") or published marker names are displayed.
  3. Select if "original" or "converted" allele values are displayed. ('GENica Marker Tools' performs allele size corrections to account for dye drift effects and for the size of the "MRT tag" (if applicable). See the section on GEMDB»IMPORT for details and for an import example.)

Please note: Search and display options are controlled separately, it is therefore possible e.g. to restrict a search to "converted allele values" (see section on entering search parameters), but to display the search results with their "original allele values".

• If all the search results are to be tagged for further use, select the [TAG ALL RESULTS] button and proceed as described in the section below on tagging. If you wish to tag individual GEMDB entries, switch to the "Table view" or the "Pager view" first.

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The TABLE view

• Switch to the "Table View" by selecting it from the drop-down box at the top right-hand side of the GEMDB search results table.
• All the GEMDB entries matching a query are listed. The information can extend over several results pagers. Use the [first], [prev], [next] and [last] buttons to move between pages, or type a page number into the "page" text box, then hit "enter".
• Click on a column header to sort the table by that column.
• Click on [SELECT COLUMNS] to open 'GENica Marker Tools' OPTIONS where the Table view can be customised:
  1. Select the columns to be displayed in the Table view by ticking / unticking the boxes under "GemDB Table View/Export Columns". All the fields from the original GEMDB import file are available, plus extra fields created within 'GENica Marker Tools' (e.g. "User Group", "Project", "Converted Allele").
  2. Change the number of lines displayed on each page.
  3. Change the number of alleles displayed for every marker.
  4. Select if "MRT marker codes" (e.g. "hv0001") or published marker names are displayed, if applicable.
  5. Select if "original" or "converted" allele values are displayed. ('GENica Marker Tools' performs allele size corrections to account for dye drift effects and for the size of the "MRT tag" (if applicable). See the section on GEMDB»IMPORT for details and for an import example.)

Please note: Search and display options are controlled separately, it is therefore possible e.g. to restrict a search to "converted allele values" (see section on entering search parameters), but to display the search results with their "original allele values".

• "Tag" search results for further use as described in the section on tagging.

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The PAGER view

• Switch to the "Pager View" by selecting it from the drop-down box at the top right-hand side of the GEMDB search results table.
• All the GEMDB entries matching your query are listed. The information can be displayed on several results pages. Use the [first], [prev], [next] and [last] buttons to move between pages, or type a page number into the "page" text box, then hit "enter".
• Click on a column header to sort the "Pager view" by that column.
• Use 'GENica Marker Tools' OPTIONS to customise the Pager view:
  1. Change the number of alleles displayed for every marker. If more alleles exist for a sample than you have specified, a warning ("More alleles exist past 'Max Alleles per Marker' setting") is displayed.
  2. Change the number of lines displayed on each page.
  3. Select if "MRT marker codes" (e.g. "hv0001") or published marker names are displayed, if applicable.
  4. Select if "original" or "converted" allele values are displayed. ('GENica Marker Tools' performs allele size corrections to account for dye drift effects and for the size of the "MRT tag" (if applicable). See the section on GEMDB»IMPORT for details and for an import example.)

Please note: Search and display options are controlled separately, it is therefore possible e.g. to restrict a search to "converted allele values" (see section on entering search parameters), but to display the search results with their "original allele values".

• "Tag" search results for further use as described in the section on tagging.

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Export GEMDB search results

• Select the [DOWNLOAD RESULTS] option to download data in its current format.
• The export file format is a delimited text file; choose from tab-delimited *.txt or comma-delimiated *.csv in 'GENica Marker Tools' OPTIONS.
• The downloaded results file can be opened with a text editor or a spreadsheet viewer. Please refer to the section below if a SamplexMarker table with more than 256 columns has been exported.

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TAG GEMDB search results

• "Tagging" a marker or a sample in 'GENica Marker Tools' is similar to adding a record to a "clipboard" or a "marked list" and saving this "clipboard" / "marked list" for future reference.
• Although a tagged entry remains e.g. in its "GEMDB project" or "marker set", it now also forms part of a tag. This allows grouping entries from different projects, marker sets, user groups, runs, etc., without having to save new "copies" of these entries in the database.
• Existing tags can be accessed and edited through the 'GENica Marker Tools' TAGS mode of function. Depending on the "type" of tag in question, choose TAGS»MARKERS, TAGS»GEMDB or TAGS»SAMPLE.

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"GEMDB Tags" versus "Sample Tags"

• When tagging GEMDB entries, select "GEMDB Sample Tags" to tag samples and "GEMDB Tags" to tag markers and the related allele values in a data set.
  • "GEMDB Sample Tags":
    • Tag GEMDB search results with a "GEMDB Sample Tag" to mark the samples selected by the search for future reference. This can be useful e.g. to quickly retrieve samples with a particular idiotype, once they have been selected by combining multiple searches in GEMDB»SEARCH.
    • Tag GEMDB search results with a "GEMDB Sample Tag" to delete the selected samples from a GEMDB dataset. This allows deleting one or more individual sample(s) from several runs, projects or even whole groups without having to go through every run's list of samples one at a time.
  • "GEMDB Tag":
    • Tag GEMDB search results with a "GEMDB Tag" to mark its markers for future reference. A GEMDB Tag can be opened within the MARKERS»SEARCH interface to access marker-specific information such as primer sequences, marker quality and a marker's origin. A GEMDB Tag can be opened within the GEMDB»SEARCH interface to access which samples were genotyped with the tagged markers and what allele values were recorded.
    • Tag GEMDB search results with a "GEMDB Tag" to bin its markers with BINNER»MRT TAGS, e.g. if errors noted in GEMDB require that genotyping is repeated in the lab for a couple of markers.
    • Tag GEMDB search results with a "GEMDB Tag" to delete its markers from a GEMDB dataset. This allows removing allele records for one or more marker(s) from individual samples or from all the samples in a particular run or even from all the samples assessed with the marker(s) in a whole project.

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TAG all search results

• Click on the [TAG ALL RESULTS] link to tag all the records selected by "view results". This will select all the hits for the selected search(es), regardless of whether results are displayed over several pagers or not actually visible in the "SamplexMarker" results preview.
• A "Tag Search Results" interface opens, where a new tag can be created or an existing tag can be selected. Be sure to select the correct "tag type" ("GEMDB Tag" or "GEMDB Sample Tag") for the tag's purpose.
• Click SAVE to begin tagging. After tagging is complete, the TAGS»GEMDB or the TAGS»GEMDB SAMPLE interface opens, depending on the chosen tag type, where a tag can be reviewed, edited or deleted.

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TAG individual records

• To tag individual records, switch to the "Table view" or the "Pager view" first.
• Check the boxes next to the records to be tagged.
• At the right-hand side above and below the GEMDB»SEARCH results pane is a TAG button next to a "Tag" drop-down box. Choose "New Tag" or the name of an existing tag from the drop-down box, as appropriate, and click on the TAG button.
• If creating a new tag, specify the tag name and tag type, making sure to select the tag type that is correct for your intended purpose.

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Spreadsheet options for data arrays with more than 256 columns

• Arrays downloaded from GENica Marker Tools can be wider than the 256 column limitation existing in Excel 2003 or earlier.

IMPORTANT: If Excel 2003 or earlier versions are used to open a file with more than 256 columns, extra columns are lost! These files can only be opened without losing data in one of the following applications:

• Excel 2007 (16,384 columns x 1,048,576 rows).
• "Corel Quattro Pro X3", available as part of the "Corel WordPerfect Office X3" package. Settings can be changed to allow up to 1,000,000 rows and 18,278 columns, see [1] for information and a trial version.
• "VisualStat" worksheet properties can be formatted to have up to 2,000,000,000 rows and up to 2,000,000,000 columns, see [2] for information and a trial version.
• A basic spreadsheet is available as part of Microsoft's Office Web Components (up to 18,278 columns and 262,144 rows, see [3] for information).
• "Gnumeric" can be compiled to have arrays with over 256 columns. Please refer to [4] for general information and to its FAQ site for advice on how to set maximum column and row numbers.

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Links to other user manual pages

I'd rather try the tutorial...

• Get started with the GMT Tutorial
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