FlyMine 31.0

27 Oct 11 | in News + Release notes by Julie

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

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FlyMine 30.0

26 Jul 11 | in News + Release notes by Julie

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

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FlyMine 29.0

6 Jul 11 | in News + Release notes by Julie

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.

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FlyMine 28.0

29 Mar 11 | in News + Release notes by Julie

In Release 28.0 we have updated data from FlyBase to release FB2011_02 and updated several data sets to their most recent versions. Please see the data section of FlyMine for more details.

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FlyMine 27.0

18 Feb 11 | in News + Release notes by Julie

We are pleased to announce the 27th release of FlyMine. As well as more up-to-date data, there are several new features and bug fixes to make things easier for you.

Data

In this release 27.0 we have updated data from FlyBase to release FB2011_01 and updated several data sets to their most recent versions. Please see the data section of FlyMine for more details.

New Features

There are lots of new features we are really excited about:

• Improvements to the list upload procedure

  The list upload procedure is easier to use, having been redesigned to provide more help to the user

• Linking In

  There is now better support for linking in to FlyMine. As well as linking to report pages,
  you can link directly to query result sets, list analysis pages, or a choice of the two.

• Embedding Results on Your Pages

  In addition to the old method of using IFrames, you can now embed tables of data from FlyMine directly into your own pages using JavaScript.
  There is a full tutorial on this exploring some of its potential here. Among its benefits, is the
  ability to have full stylistic integration with your own page using native css styling.

• Meaningful Order for Templates

  The list of templates, which was previously simply ordered by template name,
  now shows templates according to popularity, so the most popular (and thus most useful, hopefully) templates will appear at the top,
  making it easier to discover helpful tools.

Updates

As well as new features, there are a few tweaks to the existing functionality:

• Stricter test correction on enrichment widgets
• More helpful filter options on enrichment widgets
• New “delete” button on lists page
• Report pages load faster (ajaxy magic means the interactions displayer doesn’t hold things up now)
• The QueryBuilder is more intuitive: selecting an item in the list will take you back to the original item after page refresh/reload
• Distinct values are easier to spot in query results – we’ve added a link to the column summary to help

Bug Fixes

And we haven’t stopped working to keep FlyMine bug-free…

• “Score” images now display correctly on search results
• Login bug concerning mixed case usernames fixed
• Fixed widget bug when viewing after exporting widget data
• Data isn’t repeated in the “miscellaneous” section on report pages

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FlyMine 26.0

6 Dec 10 | in News + Release notes by Julie

We are pleased to announce the release of FlyMine 26.0.  We have added a host of new features, improvements and bug fixes to make your research easier and more productive.  In Release 26.0 we have updated data from FlyBase to release FB2010_08 and updated several data sets to their most recent versions.  Please see the data section of FlyMine for more details.

(more…)

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Web services workshop

3 Nov 10 | in News by Richard

Did you know you can run queries in FlyMine using a web service from Perl/Java code? We have a half day workshop in Cambridge on November 16th that will show you how. More details here:

http://www.biomed.cam.ac.uk/gradschool/skills/intermine-users.html

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FlyMine 25.0

13 May 10 | in News + Release notes by Julie

In Release 25.0 we have updated data from FlyBase to release FB2010_04 and updated several data sets to their most recent versions. Please see the data section of FlyMine for more details.

DATA

• NEW – Stocks from FlyBase
• FIX – Feature type on genes corrected
• FIX – Clones loaded from FlyBase and BDGP merge

FEATURES

• FIX – `query` link in breadcrumbs
• FIX – occasional lag on list analysis page fixed
• FIX – outputting raw HTML for protein structure.alignment fixed
• FIX – removed confusing message on query history page
  • would output pathquery object if it was a bad query
• FIX -MicroArrayAssay.name is a dropdown now
• FIX -Removed obsolete Experiment.interactionDetectionMethod from model
• FIX – can use quicksearch with galaxy
• FIX – constraint form on querybuilder works correctly now

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Release 24.0

4 Apr 10 | in News + Release notes by Julie

In Release 24.0 we have updated data from FlyBase to release FB2010_03 and updated several data sets to their most recent versions. Please see the data section of FlyMine for more details.

DATA

• NEW – Homologues from KEGG

FEATURES

• NEW – added links to RatMine from pathway, GOTerm, protein domain
• UPDATE – QueryBuilder – removed tag filtering from constraint form.
• UPDATE – QueryBuilder – advanced options now open by default
• FIX – Sanger’s datasource name
• FIX – Can now customise the column titles for embedded templates
• UPDATE – Make Bonferroni algorithm less strict, see widgets for more details.
• FIX  – Corrected data bug that was duplicating a limited set of interactions.

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