Tutorials

For a general description of SHAARE, the data it includes and its capabilities, please see the about page.

The following tutorials explain the basic functions of SHAARE, such as acccessing and handling SHAARE data, and provide a basic introduction to the query builder. If you have any questions that are not answered by the tutorials please contact us at support [AT] shaare.org.uk 

 

Tutorial 1. Quick Search

The Quick Search function provides a basic search facility for the data contained within SHAARE and provides a good way to browse the database. The Quick Search function can be found on the front page and on the main menu bar, which is present on all pages. You can search for an ID or description for most parts of the database. Wild cards (*) can be added to increase the range of a quick search.

Some example search terms:
For Genes use a gene symbol, genome project identifier, ensembl id, or NCBI Gene ID (e.g. zen*, MGI:107801, ENSMUSG00000025393 , 11947). If searching by gene symbol remember to use * to widen the search (i.e. zen*).
For OMIM use a OMIM identifier or description (e.g. 125700 or *diabetes*).
For Proteins use UniProt identifiers, primary accessions numbers or descriptions (e.g. CY1_BOVIN or P16909 or Cytochrome c1).
 
 
For example to search for gene Zen, the UniProt accession of 'zen*' would be entered into the search box and run by pressing the go button. A list of entries that match the search term are then displayed. Clicking on an entry will display its report page (described in the next tutorial). 
 
You can also search for template queries (these are common queries that you can alter to your needs) and lists. This is done by selecting either the templates tab or the lists tab on the main menu bar. Then use the specific search box at the top of the page (for lists click on view link first). 
 
To use Boolean terms such as AND, OR and NOT, be sure to include these in capitals. For example "Kinase AND human" will return records with Kinase and human in them. "Kinase and human" will look for all records with 'kinase', 'and' or 'human' in them.

 

Tutorial 2. Report page

Each entry within SHAARE has a report page. This page serves as a summary of all the information present within the database that relates to that entry and provides web links to external resources such as the MGI and ZFIN databases.

All report pages have the same basic structure: The top part provides basic information for the entry itself, whereas the lower part shows information from other data sources that are relevant to this particular entry. The 'Quick Links' bar across the middle moves the page to the different data source sections below. The 'External Links' section provides web links to external databases and the 'Lists' section shows any lists which have this entry including lists you have created yourself.

As an example the report page for gene 'MAPT' is shown below. The top section shows the different identifiers of the gene with a brief description. Below this is information from other data sources that are relevant (linked) to this particular gene. For example the summary section has the Gene Ontology annotation of the gene showing it is involved in neuron migration. The homology section show the same gene in other species (these can be clicked on to show the report page for that gene and so show any species specific experimental data). The expression section will show you any experimental evidence for expression for that gene for that species. The orange quick link bar below the top section can be used to take you directly to the corresponding data section.

To the right of the data tables is a 'Lists' section which shows if this gene is in any of your lists. If you have created any of your own lists (see tutorial 5) a button will appear that will allow you can add this particular entry to it here (as long as it is of the same type). Below this are the 'Links to other Mines'. These are sister databases to SHAARE and may contain additional information about the gene. The 'External Links' section contains web links to the relevant gene entry in the public databases where the data was originally taken from. 

 

 

 

Tutorial 3. Running a Query

SHAARE contains various prebuilt 'template queries' to make it easier to use the database. These queries are envisaged to be the most common queries required by a typical user and often span multiple data sources. Template queries can be run "as is" or can be further modified to meet particular requirements by using the query builder (see tutorial 7). 

Template queries can be found in two places:

1. Front Page. The most popular queries in SHAARE (based on usage) can be found in the middle of the front page, grouped by type.

2. Queries tab. This page is found on the main menu bar and contains a searchable list of all the queries in SHAARE including any queries you have created yourself (see tutorial 7).

 

Once you have selected a query, a screen similar to the screen shot below is presented. Before the query can be run, various constraints need to be added such as a search term (e.g. a gene ID), or an option needs to be selected from a drop down box. Wildcards (*) can be used to widen a search term ( e.g. zen* ). Some constraints have a yellow background in the box, and these automatically search for compatible terms as you type. For example in queries that search using GO annotation, to find a compatible search term just start typing a term, such as kinase, and it will automatically show a list of all the vaild options. Then just click on one of the options to set the constraint.

 

Using a list

Some template queries can also be run using compatible lists, such as lists of gene identifiers for gene queries (see tutorial 5 on how to create your own list). To use a list first tick the checkbox next to the 'constrained to be' and then select a compatible list from the dropdown box. Any compatible lists you have created yourself will be shown at the bottom of the dropdown. 

 

Once the constraints have been chosen the query can be run by clicking on "Show Results" button. The results page is discussed in the next tutorial. If the query does not exactly match your requirements it can be edited using the query builder by using the "Edit Query" button (see tutorial 7).

 

 

Tutorial 4. Results Page

The results of a query are displayed as a table. An example of the results page is shown below. Any entry in the table can be selected to bring up its report page. At the top right of each column title box is a small button that produces summary statistics for that column and allows sub-selections of the results. 

Above the table is a menu bar with various options which allows page navigation, the page size to be changed and further columns can be added.  

Entries can be saved to a new list or to an existing one using the 'Create / Add to List' button. Either select the entries individually, or tick the checkbox on the table header to select all. Then select the 'Create List' or 'Add to List' buttons on the results menu bar above the table. More information regarding lists and the My Account feature can be found in the following tutorial.

The Export results section allows the table to be exported in comma separated or tab separated format which is compatible with most spreadsheets including MS Excel. If proteins are in the results you can 'Export to Fasta' to export the sequences of the proteins in the table in FASTA format.

Tutorial 5. Uploading and analysing a list

Lists

All queries in SHAARE can be performed on lists of identifiers (such as Gene IDs) that you can create yourself. Lists can either be created from a results page (tutorial 4) or from uploading your own list into SHAARE. These lists can then be used as search terms in compatible template queries as well as in the Query Builder (tutorial 7). In addition various functions can be performed between lists such as union, intersect and subtraction, and all lists can be exported from SHAARE. 

 

How to upload your own list

Any gene identifiers that are compatible with SHAARE (Ensembl, MGI, ZFIN, HUGO, etc. ) can be uploaded as lists. 

There are two ways to upload lists in SHAARE. The first way is by using the quick list uploader on the front page if you want to upload gene identifiers. Just paste or type in your identifiers in the box. The identifiers should be separated by a comma, space, tab or new line. Then click the 'Upload List' button. 

The second way is using the advanced list uploader. This can be found either on the front page by clicking the advanced link at the bottom of the list uploader box or by going to the 'Lists' tab on the main menu bar. Here you can select different types of list you want to create from the dropdown box (not just gene as on the quick uploader). Optionally you can also set the organism for your list of identifiers - this is useful if you have, for example, gene symbols in your list, which may appear in more than one organism. A list of identifiers can then be typed, cut and pasted into the text box, or uploaded from a text file (Excel files are not supported). As before the identifiers should be separated by a comma, space, tab or new line. Then click "Create list". It is not possible to create a list containing different types of entry, such as proteins and genes, but it is possible to have a mix of types of identifier for the same type of entry (e.g. a list of genes may contain both Ensembl and MGI identifiers).

With either method when the list is uploaded all of the identifiers will be compared against the SHAARE database and identifiers with no match will be reported on the "Before we show you the results" page. If your identifier has more than one match in SHAARE (such as a gene symbol that is found in multiple species) you will also need to select the correct entry. 

 

Finally choose a name for your list and then click 'Save a list of...' button. This will produce a results table of your uploaded identifers. 

 

Widgets

For certain types of list 'widgets' will be shown under the results table. These widgets provide different types of analysis on the list such as:

  • The Gene Ontology widget shows annotation terms that are enriched in the list compared to a background population (this can take some time for very large lists so please be patient) 
  • The OMIM widget shows how many entries in the list are associated with specific human disorders.
  • The homology widget shows how many genes in the list have homologs in each of the species included in SHAARE.
  • The KEGG pathways widget shows all pathways from KEGG that are associated with proteins in the list, and how many genes are associated with each pathway.

 

Viewing uploaded lists

To view lists after they have been upoaded go to 'Lists' page on the main menu bar and select 'view'. Lists you have created yourself are shown at the top of the page. Alternatively lists that you have created yourself can be accessed through your My Account page (tutorial 8). Both pages contain a menu that allows lists to be copied and deleted as well as functions such as union, intersect and substraction to be performed between lists. 

 

Using a list

Once a list has been uploaded it can be used in all compatible queries as described in tutorial 3.

Tutorial 6. Build you own query using the Query Builder

 

SHAARE possesses a sophisticated integrated query builder that can produce queries that span many different sources of information. The query builder allows the both the modification of existing template queries and the creation of entirely new queries from scratch.
 
The easiest way to learn how to use the query builder is to pick an existing template query and click the edit template button on the right side of every query. 
 
This will show the query builder interface (shown below) and you can see how this the query was created. In the case of screen shot below, the gene table starting point is shown. To see an attribute (data field) in the results click the "show" button next to the attribute. Attributes from other linked tables can be shown by expanding the connections below by clicking "+". A description is available for many of the attributes and is viewable by moving the mouse cursor over the "i" at the end of the attribute name. 
 
 
To narrow the results of a query you can constrain attributes by clicking the "constrain" button next to "show". This allows the query to be restricted to include only a particular value or just whether the field has any value or not. Some attributes (with a yellow background in the box) will search for compliant terms as you type. Once the constraint has been selected click the "Add to query" button. 
 
 
You can also use a list as a constraint. To do this click the "constrain" button next to the title of the the table (e.g. Gene) and then click the check box next to "OR" and select a compatible list from the drop down box.  
 
 
More than one constrain can be added to a query. The "Constraint logic" section allows constraints to be used in an "and" or "or" context. In the example below, the gene query has been restricted to Human Protein Atlas - High expression AND must be Cardiovascular OR Blood immune system.
 
 
 
To change the order of the attributes in the results, the boxes in the "Columns to Display" section can be dragged and dropped to create the desired order. To sort the results table by the values of a particular attribute click the purple "sort" button. Buttons are also available within the boxes to remove an attribute from the results or change the description of the table header for that attribute. 
 
 
The newly created query can be saved to My Account where it can be run again or modified further (tutorial 9). Once a query has been created it can be run using the "Show results" button.
 
 
Instead of altering existing queries it is also possible to build a query from scratch. Go to the 'QueryBuilder' tab on the main menu bar and then select a data type to begin building using the interface. Query builder starting points can also be found on the data category pages (tutorial 6).
 
It is also possible to export and import queries in XML. This can be an easy way to share queries between users. An export XML button can be found at the bottom of every template query on the right hand side. To import an XML query select 'Import query from XML' on the 'QueryBuilder' page. Then simply copy and paste the XML into the box and click submit. 

Tutorial 7. My Account - Store lists and queries

All lists and your queries history will be saved temporarily in SHAARE for the current session. To save them permanently a 'My Account' account is required. An account also allows queries created in the query builder to be saved. It is also possible to export/import queries and templates as XML to share them with others. Your saved data is always private. To create an account no other information is required other than an email address and a password. To create an account or log in to an existing account use the "Login" button on the menu bar.

Tutorial 8: The SHAARE API

Advanced users may wish to write their own scripts to run queries in SHAARE directly, and SHAARE provides APIs to allow this. We currently have Perl, PythonJava and Ruby APIs available. Further documentation is available on the InterMine wiki. Should you wish to use the API without creating your own scripts, the bottom menu bar, which can be found on the Query Builder and Query pages, provides the code for the language of your choice.