Wiki Navigation

Index

I. General FAQ about FlyMine

Q. How can I query FlyMine?

FlyMine provides three web-based ways to query the integrated data: A QuickSearch, predefined template queries and a QueryBuilder. The FlyMine tour (accessible from the homepage) shows a very brief overview of how to use FlyMine.

QuickSearch: Allows you to browse the database, starting from a particular name or identifier. This is very useful if you do not have a particular query you want to run and want to browse all the information or specific information about a particular entry in the database. A QuickSearch box is available on the FlyMine homepage and in the top menu bar on every FlyMine page.

Template queries: These predefined queries provide quick and easy access to the data. A template query basically consists of a form, in which you fill in the boxes to define your query. Template queries range from fairly simple queries to complex queries covering two or more datasets.

The QueryBuilder: Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create their own template queries. Access the FlyMine QueryBuilder via the FlyMine homepage, the QueryBuilder tab in the top menu bar on every FlyMine page, or choose a query starting point on a data category page.

Q. Can I do a search for a set of genes all at once, instead of one at the time?

It depends on the type of search you want to do. The QuickSearch box does not accept more than one entry yet, but the template queries and the QueryBuilder do. To do so, you need to create a list of all the genes you're interested in and constrain your search to the genes in your list.

Q. How can I create a FlyMine account?

Click on the 'Log in' link on the top right of every FlyMine page or on the MyMine page. If you have never logged in before, go to '..or create an account'. Enter your email address, choose a password and confirm it and click on 'Create account'. You can then log in. Your username is the email address for which you chose a password. If you forgot your password, click on 'forgotten password'. You will be asked to enter your email address. Click on 'Request password' and your password will then be sent to you again.

Q. Help! My question hasn't been answered!

Please contact us! Email us at info[at]flymine.org with any questions you may have. We're always glad to hear from InterMine users!

II. Data

Q. How can I find out what data are in FlyMine?

The data in FlyMine are divided into data categories for easy navigation. Each data category is displayed on the home page. Clicking on a data category will display a page that provides:

More detailed information about the actual data loaded.
Access to bulk download for this data.
A set of template queries related to this type of query (some spanning data from other data categories).
A set of starting points for using the QueryBuilder.

For a summary table of all data available in FlyMine, click on the data tab in the top menu bar on any FlyMine page.

Q. How can I find out where the results of my query originally come from?

If you have run a template query, there will be one or more columns in the results table which will show the original dataset or the publication that the result originated from.

If you are building your own query using the QueryBuilder, to find the dataset you need to constrain the evidence class to 'Dataset' and choose fields from this class to show in your results. For many types of data there will also be a 'publication' class available. This is often more useful than the dataset class as the dataset class shows where we got the information from (eg Intact for protein interaction data) rather than the original publication of the data.

We are currently working on trying to make it more clear what the orginal dataset is (including which version).

III. Report Pages

Q. How can I find a report page?

Report pages can be accessed using the QuickSearch box on the FlyMine homepage or on the top menu bar of every FlyMine page, or from result tables or lists by clicking on an object that provides a link. If you are using the QuickSearch box, you may be taken to a report page directly if only one object in the database matches your search.

IV. Lists

Q. What is a list?

A list is any set of objects of the same type. Eg a list of genes or a list of proteins.

Q. What is a public list?

Public lists are lists that we have made for you. They are mostly sets of interesting genes from published results. Public lists can be identified as they always begin PL xxxx.

Q. What can I do with lists?

Lists can be used in three different ways: to constrain a query (either a template query or a query constructed using the QueryBuilder), to save query results within FlyMine and to perform logical operations.

Any variable (box) in a template query can be constrained to a list (or 'not in' a list) rather than to a single value, provided you have a list of the correct type saved in MyMine. For example, if you want to run a particular query for a list of genes rather than a single gene, you can create a list of genes and run a template query using this list. To constrain a query to a list, select the checkbox underneath the variable box and choose the list from the drop-down list.

Lists of data can be used to constrain queries in the QueryBuilder. If you have lists of saved data under MyMine you will automatically be able to use these from within the QueryBuilder to constrain a query. When a field is selected for constraining a query using the QueryBuilder the constraint options in the right hand constraint panel will ask you to either 'Filter query results on this field having a specific value' or 'Filter query results on the contents of your list'. This latter option will only appear if you have lists of the correct type saved in MyMine. To add a list constraint, click on 'Filter query results on this field having a specific value' and chose your list from the drop down list. Note there is also the option to change 'IN' list to 'NOT IN' list.

Results from queries can also be saved into a list. To save your data to a list select the required data on a results page and either add it to an existing list or save it to a new list, using the boxes displayed underneath the results. Selecting the check boxes next to the column headings will select the entire column for saving. Alternatively, individual items can be saved by selecting check boxes next to the items. Currently, a list can only contain one column. However, if you have multiple columns for the same item (eg a column for gene identifier and one for gene symbol), you will notice that all related columns become highlighted when you select the checkbox next to one. This is because you are saving the actual item (eg the gene) to a list, not just the identifier.

The logical operations, union, intersect and subtract, can be performed on lists of data. These operations are available both on the lists page and on the lists tab of your MyMine page. Use the check-boxes next to your saved lists and/or public lists to select lists for these operations and enter a name for the new list.

Q. How do I make a new list myself?

There are two ways of making a new list:

(1) you can make a list from an external source via the Upload option on the Lists page,

(2) you can create a list from data displayed in a result table.

Both options are described in more detail below.

Q. How do I make a list from an external source?

Go to the Upload option on the Lists page. Here you can type or past in a list of identifiers, or upload a file containing the list:

Type of list: To make a list you must first select the type of list you want to make (for example a list of genes). At the moment, it is not possible to make mixed lists.
Constrain by organism (optional): You can optionally set the organism for your list of items. This is useful if, for example, you have a list of gene symbols, as the same symbol may be present in more than one organism.
Type/Paste in identifiers: Either type or paste in your list or:
Upload identifiers from a file: click on 'Browse' to find your file for upload.
Create list: Click on 'Create list' to upload your list.

A new page will appear saying: Confirm list creation. The list that you upload is checked against the FlyMine database to ensure that everything in your list can be found in FlyMine. Any discrepancies are reported as follows:

Low quality matches: These are items in your list that do not match a key (main) identifier in FlyMine but were found as synonyms. This may mean you have a secondary (old) identifier or are using a gene symbol that is not the official symbol for that gene. If you are happy that the item identified is the correct one, you can add it to your list by clicking on 'Add' in the last column.
Converted types: These are items in your list that matched something in FlyMine, but not of the type you selected. (For example, if you selected type=gene, but had a protein identifier in your list). FlyMine can convert these into the type you selected so that you can add the item to your list - click on 'Add' in the last column.
Unresolved identifiers: These are items in your list that were either not found in FlyMine, could not be converted to the type you selected or matched objects from an organism other than the one you selected.

Now save your list: Give your list a name and click on 'Save list'. This will take you to a List analysis page.

Q. Can I upload a list from an excel file?

At the moment, that is not possible yet. One can only upload plain text files that are tab, comma or newline delimeted.

Q. How can I make a list from a results table?

To save your data from a results page to a list, select the required data and either add it to an existing list or save it to a new list, using the boxes displayed underneath the results. Selecting the check boxes next to the column headings will select the entire column for saving. Alternatively, individual items can be saved by selecting check boxes next to the items. Currently, a list can only contain one column. However, if you have multiple columns for the same item (eg a column for gene identifier and one for gene symbol), you will notice that all related columns become highlighted when you select the checkbox next to one. This is because you are saving the actual item (eg the gene) to a list, not just the identifier.

Q. When I save data from my results table to a list, I end up with much less rows than in the results table, why is that?

Duplicate objects are not saved in the list. Lists only contain unique values.

Q. How can I find out more about my list?

Every list (your own lists and public lists) have a list analysis page. This can be displayed by clicking on the list name (either from the lists page or your MyMine page). Lists analysis pages are automatically displayed when you create a new list.

Q. How can I search my list?

At the moment a small list can be searched best by browsing it after displaying it as a result page. For bigger lists, you can do a QuickSearch for the item you're looking for: At the bottom of the corresponding report page, it says 'Lists in which this can be found: ' where you can check for your list of interest.

We are working on a more efficient way to edit and search lists.

Q. How can I delete one or more items from my list?

Unfortunately, that is not possible yet. At the moment, you need to make a new list: display your current list as a result table, select all items exept the ones you want to delete and save them in a new list.

We are working on a more efficient way to edit and search lists.

Q How can I add one or more items to an existing list?

You can add data from a result page to an existing list using the boxes displayed underneath the results. Selecting the check boxes next to the column headings will select the entire column for saving. Alternatively, individual items can be saved by selecting check boxes next to the items. Note: If the existing list and the selected results are of a different type, you won't be able to add the results to that list.

At the bottom of a report page, there is the option to add that object to an existing list by clicking the GO button next to 'Add this object to existing list'. Note: If the existing list and the new object are of a different type, you won't be able to add it to that list.

It is currently not possible to add more items to an existing list via the list upload page, but that will hopefully be possible soon.

We are working on a more efficient way to edit and search lists.

Q. How can I export the content of a list?

To export the contents of a list, click on the list name. This will display the contents of the list on a list analysis page. On that page, click on 'View all xx records' below the table which will display the contents of the list as a results page - with the export options available at the bottom of the page. Data can be exported from the results page in various formats - currently Excel (or open office) format, comma separated values, tab separated values, or for objects with sequences, FASTA format. Currently, either the entire results table or specific columns can be exported. If nothing is selected, the entire data set will be exported. If you do not wish to export certain columns these can be hidden using the small double arrow in the column header.

Q. How does a union of lists work?

A union of lists will combine all objects from the lists you selected, and store these objects in a new list. The objects that are found in more than one list will only be stored once in the new list. To perform a union: selects all lists you want to unite, give a name for the new list and click 'Union'.

Q. How does an intersection of lists work?

An intersection of lists will search for objects that are found in each list that you selected, and store these objects in a new list. To perform a intersection: selects all lists in which you want to find the common objects, give a name for the new list and click 'Intersect'.

Q. How does a subtraction of lists work?

An subtraction of lists will search for objects that are not found in each list that you selected, and store these objects in a new list. To perform a subtraction: selects all lists in which you want to find objects that are not common to all of them, give a name for the new list and click 'Subtract'.

Q. Can I do an operation on more than two lists at once?

Yes, you can. All three operations (Subtract, Intersect, Union) can be done on two or more lists at once.

V. Templates

Q. How do I run a template query?

To access the template query form, click on the name of the template query. When you have entered the values you wish to run the template query with, click on 'Show results' to get the results of your query. If you are on a report page and want to run a listed template query with a different value, you need to click on the blue-circled T to access the template form (from report pages, clicking on the template name will show the results for that template for the object you are viewing).

Q. How can I find a template query / How do I access template queries?

Template queries can be accessed in three main ways:

From the templates page - accessible from the FlyMine home page or from the templates tab in the menu bar on every FlyMine page. On this page, all templates will be displayed by default. You can search for a particular template using keywords, filter for your favourite templates or just your own templates, or filter the templates according to a data category.

From each data category page - each data category page lists templates relevant to that type of data.

From the report pages and list analysis pages - both report pages and list analysis pages have sets of template queries that have been pre-run on the object or list of objects you are viewing.

In addition, if you have made your own templates queries, these can be accessed and managed from your MyMine page.

Q. How can I change the output of a template query?

A column can be moved to the right or to the left by clicking on the appropriate arrow on top of the column. Clicking on the smaller double arrow on top of a column will hide the column. The types of columns and their initial order are determined by the underlying QueryBuilder. To change the output, click on 'Query' in the trail at the top of the result page. If the results originated from a template, the template page will be displayed. Clicking on 'Edit Query' will display the query in the QueryBuilder. If the results originated from a query, the query will be directly displayed in the QueryBuilder.

Q. How are the data in the results table sorted?

The results table displays the results in alphabetic order, based on the content in the first column. To sort the results based on a column different from the first one, you need to put that column first using the QueryBuilder (changing the order on the result page using the arrows will currently not re-sort the results).

Q. How can I export the data in the results table?

Data can be exported from the results page in various formats - currently Excel (or open office) format, comma separated values, tab separated values, or for objects with sequences, FASTA format. Currently, either the entire results table or specific columns can be exported. If nothing is selected, the entire data set will be exported. If you do not wish to export certain columns these can be hidden using the small double arrow in the column header.

If the results table contains a column with objects that have a nucleotide or amino acid sequence, it is possible to export all sequences from that column in FASTA format. Currently, the FASTA export option will export the sequences belonging to objects in the first visible (i.e. not hidden) column only. Therefore, if that column does not contain any sequence-linked objects, the FASTA export option will not be activated. Columns can be moved to the first position by using the arrows in the header. If objects appear more than once in the column, the sequence will only be exported once.

VI. Importing and exporting queries and templates

Q. How can I import a query?

To import a query, you need to be logged-in. Once logged-in, click on the 'Import query from XML' link at the bottom of the MyMine page. Enter query in XML format in the space provided and press 'Submit'. The imported queries will be stored under 'Saved Queries'. Queries with names identical to existing queries will get an automatic extension to make it unique, e.g. dmel-proteins-1, dmel-proteins-2.

Q. How can I export a query?

Queries can be exported as XML or IQL from the QueryBuilder page ('Actions - Export this query as XML or IQL'). A query can also be exported from your Query History page. Select queries using the check-boxes (or click on the check-box on top of the column to select all at once) and click the 'Export' button at the bottom of the MyMine page. Alternatively, one query can also be exported by clicking on 'Export' in the 'Actions' column. Saved queries can also be exported as XML from your Saved Queries on your MyMine page, in a similar way. Exporting a query will not delete it from your account.

Q. How can I import a template query?

In order to import a template, you need to be logged-in into FlyMine. Go to Saved Templates on your MyMine page and click on 'Import template queries...'. Enter template in XML format and press 'Submit' to save the template to your account. The imported templates will be stored under 'Saved Templates'. Template queries with names identical to existing templates will get an automatic extension to make it unique, e.g. dmel-proteins-1, dmel-proteins-2.

Q. How can I export a template query?

Template queries can be exported as XML from your Saved Templates on your MyMine page. Select templates using the check-boxes (or click on the check-box on top of the column to select all at once) and click the 'Export' button at the bottom of the page. Alternatively, one template query can also be exported by clicking on 'Export' in the 'Actions' column. Exporting a template will not delete it from your account.

VII. QueryBuilder

VIII. Specific query questions

Q. How can I find out if my favourite gene has any orthologues in other species?

The easiest way is to go to the report page of that gene. In the summary section (upper left) you will find a class called 'orthologues' where all orthologues are listed. Alternatively, you can use the template Gene --> Orthologues, or any related template. If you would like to fine orthologues of more than one gene at once, make a list of these genes and use the template mentioned before.

- Note: all data on orthologues are from the InParanoid database.

Q. How do I find which GO terms my gene has been annotated with?

A template query is available for this query: Gene --> GO terms. Apart from the name and identifier of the GO term, the result page also shows the evidence code that supports the term as well as qualifier. These evidence codes correspond to broad categories of experimental or other support. For more information about these evidence codes, go to http://www.geneontology.org/GO.evidence.shtml. The qualifier column is used for flags that modify the interpretation of an annotation. Allowable values are 'contributes_to', 'colocalizes_with' and 'NOT'. 'colocalizes_with' is used only with cellular component terms. 'contributes_to' is used only with molecular function terms. 'NOT' is used with terms from any of the three ontologies. Not every term has a qualifier attached to it.

Another template is also available: Gene --> GO terms and parents of those terms. This will show all GO terms associated with the gene, as well as all parents of this term. If 'isPrimaryAssignment' is 'true' then that GO term was actually assigned to the gene. Likewise if it is false then the GO term is some more general parent term.

- More information on GO annotation can be found at http://www.geneontology.org/GO.contents.doc.shtml.

Q. How do I find regulatory regions and/or binding sites associated with a gene?

A template query is available to find all regulatory regions: Gene [D. melanogaster] --> Regulatory regions + chromosomal locations and lengths of these regions.

A template query is available to find all binding sites: Gene [D. melanogaster] --> TF Binding sites + chromosomal locations and factors that bind these sites.

A template query is available to find all regulatory binding sites and all binding sites within these region: Gene [D. melanogaster] --> Regulatory regions + TF binding sites overlapping these regions.

Within the FlyMine database model, all regulatory elements (enhancers, transcription factor binding sites and CRMs) are all in the 'regulatoryRegions' class. Within that class, there are enhancers from FlyBase (in the 'enhancer' class), CRMs from REDfly (in the 'TFmodule' class), transcription factor binding sites from REDfly (in the 'TFBindingSite' class) and elements from FlyBase.

- Note: we currently only have regulatory information for Drosophila genes.

Q. How can I find the actual sequence of an object in FlyMine?

You can find the sequence of any object via the FASTA buttons on its report page.

Q. How can I retrieve sequences for more than one object all at once?

Make a list of the objects (genes, proteins, ...) you're interested in and display it as a result page. At the bottom of this page, there is an option to export the corresponding sequences in FASTA format.

Currently, the FASTA export option will export the sequences belonging to objects in the first visible (i.e. not hidden) column only. Therefore, if that column does not contain any sequence-linked objects, the FASTA export option will not be activated. Columns can be moved to the first position by using the arrows in the header. If objects appear more than once in the column, the sequence will only be exported once.

Q. When I search for Orthologues I get two different 'types', orthologues and inparalogues - what does this mean and what do the scores mean?

According to Sonnhammer and Koonin (Pubmed 12446146), orthologues and paralogues can be defined as the following:

Orthologous genes: genes in two species that have directly evolved from a single gene in the last common ancestor and are likely to be functionally related.

Paralogous genes: homologous genes related by a duplication event. Might be in the same or in a different genome.

Inparalogous genes: genes that derive from a duplication event after a speciation of interest. Inparalogs are together orthologs to the corresponding orthologous gene/genes in the other species.

The orthologues and inparalogues in FlyMine come from the inparanoid program (http://inparanoid.sbc.su.se) which calculates scores as follows:

The inparanoid program calculates orthologue and inparalogue clusters, pairwise between two organisms, by first finding the best recipricol blast match for each gene. This becomes the seed-orthologue to which inparalogues are clustered. Each member in the cluster receives an inparalog score which reflects the distance to the seed-orthologue. A score of 1.0 means there is identical distance to the seed orthologue (and so all orthologues in the cluster will have an inparanoid score of 1.0). Each inparalogue in the cluster will have a score less than one which reflects how similar it is to the seed orthologue. In addition to the inparanoid score, each orthologue within the cluster has a bootstrap score, which is the confidence that this seed-ortholog pair are true orthologues. (This is estimated by sampling how often the pair is found as recipricolly best matches by a bootstrapping procedure applied to the original Blast alignment).

Download in other formats:

Plain Text