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.
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