FlyMine 35.0 Released

We’re happy to announce a new release of FlyMine.  We’ve updated all of our data sets to the newest versions and added lots of exciting features. See the data sources page for a full list of data sources and their versions.

Interactions

We have changed the way we model interactions to make the results of your searches easier for you to understand and analyse.  All the interaction template searches have been updated to use the new model.  In addition, we previously modeled interactions as a ‘matrix expansion’ – which means all possible interactions within a complex would be shown.  We have changed this so that only bait-prey interactions are shown (called a spoke-expansion).  However you can still infer all the possible interactions using the ‘all interactors’ field.  Please email us if you would like more information concerning this.

Sharing Lists

You can now share your lists with your colleagues and collaborators.  Simply add your colleagues email address to your list in ‘MyMine’.  They will be sent an email asking if they would like to accept the list.  Note that the list is still controlled by you – they can just see a copy so only you can modify it.  They can of course, create a copy of the list which will then be theirs to modify.  Again, please email us if you would like more information on this feature.

Background Distribution on Analysis Widgets

You can now specify your own background distribution for the enrichment widgets on the list analysis pages.  You need to have your preferred distribution saved as a list.  Each widget then has the option to select the list you wish to use.  If you are logged in you can save this as your default preference.

Please email us: support@flymine.org for any help on these new features.

FlyMine 34.0

We’re happy to announce a new release of FlyMine. We’ve updated all of our data sets to the newest versions and added lots of exciting features.

Query Results

We’ve updated the query results in FlyMine. You can now sort your results, filter on any value, add edit or remove columns and much more. See here for the full list.

Widgets

You can now embed FlyMine widgets onto any HTML page. See here for details.

Other

* RNAi screens correctly show up in keyword search results.
* Disease name is now a link so you can click for more information.
* We’ve added links from genes to BioGRID

FlyMine 33.0

Data

New Expression Data

Genome-wide RNA_seq expression data for D. melanogaster have been added.  This data was produced by the modENCODE project (www.modencode.org) and analysed by FlyBase, who calculated a single value for the expression level of each gene at each developmental stage or tissue (see http://flybase.org/reports/FBrf0212041.html for more details).  This data is available on report pages for each gene and can searched through template queries (for example: www.flymine.org/query/template.do?name=Gene_RNA_seq and www.flymine.org/query/template.do?name=RNA_seq_Genes).

Improved RNAi Data

RNAi data for D. melanogaster is now loaded from http://www.genomernai.org.  This data provides a number of new RNAi experiments and improved phenotype descriptions for both new and existing RNAi experiments.  See the RNAi templates to learn more about this data (for example: http://www.flymine.org/query/template.do?name=Gene_RNAi&scope=all and http://www.flymine.org/query/template.do?name=RNAiScreen_genes&scope=all)

Yeast Interactions are back

Due to popular demand, we have put the yeast interaction data back into FlyMine.

Website

List Analysis

  • Your list is automatically mapped to other organisms via orthologs loaded from Ensembl and TreeFam
  • Orthologue and Interactions widgets have been restored (after a user request)

Region Search

  • Extend regions at both sides by entering a value in the new input box
  • Download links are icons
  • Added the option to download chromosome sequence

Export

  • GFF3 export correctly storing parents’ relationship
  • “Hidden” export menu now direct links on results tables
  • FIX – Export works correctly when all columns of an outer join are removed
  • FIX – Missing attributes restored in fasta format

List Upload

  • Specific object types can have a different example list on Bag Upload page, eg. protein accessions displayed if a user selected proteins, gene identifiers displayed if a user selected gene.
  • Go back in history to the filled in form, preserves the input values.
  • “Match on case” – checkbox added to list upload form to toggle case sensitivity

Report page

  • Delay fixed – caching intelligently now
  • Templates displayed in summary also displayed in “Other” category
  • Displayers show nice “No Results” message if data fails to load
  • Displayers by default loaded through AJAX to speed up page loading. Can be set to display immediately without waiting for the DOM to render.
  • Left aligned displayers to make more readable
  • FIX – counts in overlapping features displayer are now correct
  • Protein sequence – added a new displayer
  • Protein Structure ATM: turned into a popup window
  • FIX – links to Reactome correct now

QueryBuilder

  • Add toggle to show/hide empty fields in the QueryBuilder tree
  • Added a button to save/update then run template
  • FIX – if a user clicks [SHOW] in the query builder twice really fast, the field only gets added once
  • FIX – displaying messages too late when the constaint logic is edited
  • FIX – can now build templates with Chrome
  • FIX – deleting a query from query history doesn’t forward user to my mine
  • FIX – prevented name of last saved query becoming the default name in the text box

Query results

  • The values the user selected on the template form are displayed on the results page
  • Updated results table with an exact count of results when available

Template form

  • Show OR logic when appropriate
  • Fixed hyphen breaking on auto-complete in template search on template list page

MyMine

  • Timestamps are now client specific and handle timezones correctly
  • Prompt users if they want to delete a list that’s being used by a query
  • Login/create account page improvements
  • Cookie saved remembering the list order preference(s).
  • Show the new size of a list after upgrade.
  • MyMine table sorting correctly
  • Renaming lists now works as expected

Other

  • FIX – Importing templates with ONE OF constraints works correctly
  • FIX – 4 year old bug which prevented LOOKUP constraints for non-bioentities from working correctly with wildcards
  • FIX – If you remove columns when exporting number of rows returned is not changed

FlyMine 32.0

FlyMine 32.0 has been released today with new and updated data and lots of bug fixes.  Please see the data section of FlyMine for more details.

External Links

  • NEW – more and better links to YeastMine and RatMine
  • FIX – Links to FlyBase from the list anlaysis page
  • FIX – Links to Reactome from pathway report pages

Other

  • FIX – bug preventing renaming lists and queries twice
  • NEW – timestamps are now client specific
  • FIX – query results with outer joins are easier to read
  • UPDATE – template queries are easier to build
  • FIX – bug preventing the import of queries with ONE OF constraint
  • NEW – downloading widget results on list analysis pages is easier and faster
  • FIX – sorting of lists and queries is fixed in MyMine
  • FIX –  hyphens no longer break auto-completion in queries
  • NEW – list tagging now supported by web services
  • FIX – LOOKUP constraints querying non bioentities with wildcards now work correctly
  • NEW – list upload examples now suggest identifiers based on the type you select.

FlyMine 31.0

We are happy to announce we have a released a new version of FlyMine.  We have updated some data sets, added a few new features and fixed some bugs.

Human Readable Labels

The labels for the data in FlyMine come from the field and table names from the database.

We have updated this to use user-friendly labels instead in an effort to make the labels more human readable.

Open ID

You can now log in to FlyMine using your Gmail or Yahoo account.  Simply click on the “Log in” link and follow the intructions.

Region Search

  • Additional parameter allows users to extend regions at both sides
  • Can create lists by feature types for all results or for an individual region
  • Results show gene symbols as well as DB identifier
  • Fixed by when exporting a long list of objects to galaxy caused a “Request-URI Too Large” error
  • Now works correctly with subclasses

Web Services

  • NEW: region search The ability to search for genomic features by interval (the Regions tab of the web-app) has been exposed as a web-service resource. Region data can be converted to lists, or downloaded directly as GFF3, FASTA or BED.
  • NEW: token authentication A new authentication mechanism has been introduced which has advantages over the current system of sending username and password details. The use of tokens means that users can authenticate requests without having to send their username and password, thus minimising chances of these being compromised. Tokens can be replaced without having to change login details, or indeed disabled entirely, meaning web-service access to user data can be forbidden on a user-by-user basis. This authentication mechanism is to be preferred to the current mechanism. One important benefit is the ability to make authenticated requests (for dealing with lists for instance) from the browser.
  • NEW: Ruby client Our commitment to supporting the range of languages used by bio-informatians has been extended to Ruby, which has a growing community based around the Bio-Ruby project. The Ruby client libraries are available from [https://rubygems.org/gems/intermine rubygems.org]. For documentation please visit [http://www.intermine.org/docs/ruby-docs].
  • NEW: Exporting BED from webservice queries In addition to GFF3 and FASTA, the BED biological standard format is supported from web-service queries.
  • NEW: Column summary data The column summary data (visible when clicking on the ? icon on a results table) is now available via web-services when passing the ”’summaryPath”’ parameter to a query or template results request.
  • NEW: Code generation The ability to generate code to run queries is now available programmatically via a web-service. Please see the WebService wiki page for details.

Export

  • New export format – BED
  • Fixed bugs that caused export to fail when:
    • feature didn’t have location info
    • sequence feature was not the root class, eg. Pathways.genes
    • all columns of an outer join are removed

Report Pages

We have added new widgets to the report pages:

  • Publications displayer orders by number of genes mentioned
  • New Pathways displayer shows pathways from other Mines for orthologues of current gene
  • New RGD disease displayer shows disease ontology terms from RatMine for orthologues of current gene
  • New viewer shows interactions, GO terms etc on publication report page

Data

  • New species from OMIM: human, rat and mouse.
  • YeastMine is now live, so we have removed yeast data from FlyMine, including publication, pathways, GO and interaction data.

Network Displayer

  • Added help text for different file types
  • Large datasets are now handled correctly. If there are too many interactions (> 2000) a link to download the data is shown instead of the displayer: 
    The network contains more than 2000 elements, the interaction can become sluggish in the displayer.
Please [Download the network data] and import it to [Cytoscape desktop] and use Force-Directed Layout
to view or [view interaction data] in a table.

Templates

  • Radio buttons stay checked when selecting/deselecting list constraint
  • Clicking on the “query >” breadcrumb to get back to the template form works correctly
  • Editing constraints for nested classes (eg. Gene > homologue > organism) doesn’t break model browser
  • In query builder, “Show results” button greyed out and not clickable anymore
  • After editing a template, if the user clicked on a template on the home page they would be directed to the previous template they had been editing.
  • Can now import template queries containing “ONE OF” constraints
  • Added option to delete trackers to the template import form. This allows superusers to export/import templates from other Mines, but save the usage information.
  • Fixed error when running a template with a bag constraint in an attribute and a lookup constraint in its parent

Miscellaneous

  • FIX – keyword search now handles booleans correctly
  • FIX – pathway widget correctly filters for KEGG pathways
  • UPDATE – widget data easier to download
  • UPDATE – list upload form has default organism selected, leading to less issues when uploading lists
  • FIX – links to other mines is cleverer, so results appear faster
  • FIX – report pages are now cached speeding up loading times

FlyMine 30.0

We have changed the way the lists are handled between FlyMine releases.

After each FlyBase release, we build a new FlyMine database and release a new version of FlyMine.  It is possible that genes saved in a user’s list have been merged or deleted from the new FlyBase database.  Previously, the FlyMine team upgraded everyone’s lists for them automatically.  This has the drawback of being time-consuming and opaque to the users.

So we have updated our system to require the user to manually resolve any conflicts.  Usually there will be no changes and no action will need to be taken.  However, if a user’s list has changed in FlyBase, users must go to the “My Mine” section of FlyMine and upgrade their lists manually before the list can be used.

You can check the status of your lists by visiting the “Lists” page in the “My Mine” section of FlyMine at http://www.flymine.org/query/mymine.do.  In the last column will be the list’s status:

  1. Current – The list is current, no action is needed
  2. Not current – The list is in the queue to be upgraded, you may have to wait a minute or so.
  3. Upgrade – The list contains genes that have been merged or deleted and needs to be upgraded.  Click on the “Upgrade” link and follow the instructions.

We hope the new system will be an improvement and make it more clear if list contents change over time.

UPDATES AND BUG FIXES

  • NEW – Sequence features can be exported as a file or sent to Galaxy in UCSC BED format
  • NEW – We now use human readable names for data labels and column names; previously we used the database field name
  • NEW – The region search has an additional parameter that allows you to extend your regions at both sides
  • NEW – Expression enrichment widget for Probesets
  • FIX – Some yeast and worm genes had not merged properly, the duplicates have now been removed
  • NEW – Better link outs to more external databases

FlyMine 29.0

In Release 29.0, we have updated data from FlyBase, BDGP and all other data sets to their most recent versions. Please see the data section of FlyMine for specific details.  We’ve also added lots of new functionality and redesigned several key areas of the site.  See below for specific details.

New Report Pages

Report pages have had a major design and technical overhaul. Based on a lot of feedback we’ve redesigned the header section of the page, added section headers for easy navigation in the page and added a new information section on the right hand side. The main changes:

  • Data is presented in compact inline lists where appropriate, e.g. synonyms, for greater readability.
  • New graphical data displayers have been added for homologues, expression data.
  • New section headers appear as tab bar that docks to the top of the screen as you scroll, the relevant header is highlighted when the section is in view.
  • Query results are greyed out if they do not have any results.
  • The various tables and lists of data have expanders, togglers and collapsers.
  • Related collections have been grouped together, for example now you would find CRMs and TFBindingSites under Regulation.
  • You can quickly move across categories of content through a sticky menu. This is a compromise that lets us show you all of the content we have for a given object at once, while allowing you to skip to the things you really want to see.

Search by Region

We have added a new search the Genomic Region Search which provides users the tool to query a huge amount of genomic sequence features such as genes, exons, etc. hosted in Flymine, with a list of chromosomal regions/intervals of users’ interests as input.  Located on the “Region” tab on menu bar to start the options page on which users can select species and feature types, and input their chromosomal regions (please read the help text on top of the page for more format information). After submitting the query, the results page will display all the features that overlap with the user’s regions. It’s also easy to export the results in different formats.

List Upload page redesign

  • List analysis is visually split into the stages of list upload, verifying identifier matches and the analysis itself.
  • A default list name (based on type of items, date and time) is generated
  • List upload verification stage now shows you how many items and additional matches you have in a list, allowing you to add groups of them while informing you if you have more matches to add to the list.

Other Layout changes

  • Removed breadcrumbs on right side
  • Tab behaviour: no tab is active on results and report pages
  • In the query builder page, changed links so they look like the ones on template form and added the green button Show Result in the top too.
  • Moved Contact Us link, removed contextual help.

Web Services

In addition the changes below, all our client libraries now have corresponding code generators accessible from the web interface to help you start writing your code.

We have added:

  • List functionality
    • Retrieval of details and inspection. Logged in users can retrieve their own list details.
    • Queries against lists (including private lists, if logged in).
    • Renaming
    • Deletion
    • Creation, from lists of identifiers, and queries.
    • Appending.
    • Union/Intersection/Symmetric Difference
    • Subtraction (Asymmetric Difference)
    • List membership (which lists is an object in) Many services support tagging.
  • Biological webservices:
    • Getting results as GFF3 and Fasta is now supported.
  • Possible Path Values:
    • Users can get summaries of the values a path may represent, along with frequency details.
  • Template and Query upload services:
  • Templates and queries can be saved to a user’s profile.
  • Resource reporting – users are able to check if an optional service has been enabled.
  • Schemata for result formats (xsd for XML and json-schema for JSON)

See WebService for details.  Later this summer we are holidng a webinar in which we review the available web services in detail.  If you are interested in attending, please let us know!  info[at]flymine.org

Python Library

There is a new client library for our webservices API written in Python. This offers access to a very broad range of webservice functions, including the new list webservices. There are complete API docs available at our docs section.  See PythonClient

JavaScript library

This has been made more flexible and extensible, and includes helpers for accessing services beyond query results. The main changes regard content presentation in the default table display, with a number of rendering bug fixes and UI improvements. The latest version is 0.2.  See JavaScriptClient

Perl Library

Now with access to all webservice features, including lists and possible path values. The major addition here however is character safe result parsing using structured message formats. Also there have been a number of method additions and improvements to make common jobs easy, such as shortcuts for adding all attributes on a class, or iterating over a query’s result-set. Lists and queries are broadly interchangable (both can be used as sources of results, or used in list operations, or in list constraints). All constraint types are now supported, including list and loop constraints.

In addition, a separate optional module, Webservice::InterMine::Bio provides access to the new biological webservices.  See PerlWebServiceAPI

Java Library

The Java webservice client now has paging support in its requests, along with better, more thorough documentation.  See JavaClient

Data

  • New data from OMIM
  • Data from UniProt for all Drosophilas, not just melanogaster
  • Introns collection added to gene
  • We’ve also removed several datasets – Tiffin, protein structures, InParanoid orthologues, all bee and pombe data.

Keyword Search

  • Keyword search correctly handles special characters
  • You can now use a wildcard as the first character of a search string

Updates and Bug Fixes

  • UPDATE – Add LIKE and NOT LIKE to input boxes of constraints
  • UPDATE – The dropdowns of lists in the template form are in alphabetical order
  • FIX – Query Builder constraint logic is case insensitive and displays A and B instead of A,B
  • FIX – Template export works when select single or multiple templates on MyMine and Templates tab
  • FIX – Forgotten password link sends a message with the URL
  • FIX – Input a filter value or select a category in Templates (or List) page , select a template (or a list), click ‘Back’: the page still displays the filter edited and/or the category selected
  • FIX – When copying one or more lists the name is automatically generated
  • UPDATE – Javascript and CSS are now minified
  • DELETED – Removed Excel export
  • NEW – Display different content on homepage if new user
  • NEW – Users can change column header descriptions
  • FIX – Error generated when clicking on summary button twice
  • FIX – Bug which caused templates to not appear on the correct report page
  • FIX – Search box toggle on homepage displays correct help text
  • FIX – Nav trail now displayed in the query builder
  • FIX – Multi-Value template parameters now comma-safe
  • UPDATE – Entrez gene identifier, pathway and protein domain names are now links in results tables, making it easier to find the data you want.
  • UPDATE – Ontology name is now a dropdown in queries so you don’t have to guess the exact name of the ontology you need.
  • UPDATE – Pathways have been added to the keyword search so you can filter your search results by pathway.