Future of FlyMine

Dear FlyMine users,
We regret to announce that FlyMine will only be updated until December 2008/ January 2009. After that the final version will be kept live for as many years as it is still significantly used. Condolences would be appreciated and can be sent to support@flymine.org!
There are a couple of reasons for this change. Currently there is a great opportunity to develop a medically-focussed database using the InterMine system developed during the FlyMine project: we plan to generate a resource valuable to the broader biomedical research community and for which there will be little overlap with other resources worldwide. In addition, our most recent funding reviewers expressed concern at perceived overlap with FlyBase, leading us to re-evaluate where we could most effectively contribute.
Fortunately, FlyBase is keen to cover the loss of functionality provided to the Drosophila community either by adopting InterMine or by developing similar functionality themselves. In order to assess priorities for users we will be carrying out a survey jointly with FlyBase and encourage you to take part.
Drosophila data will still be available through the InterMine platform as part of the modENCODE project. In addition, the NIH is reviewing an application to incorporate InterMine functionality as part of the yeast (SGD), rat (RGD) and zebrafish (ZFIN) model organism databases.
During the FlyMine project our group developed the open source InterMine system, which is software used to create data warehouses with a flexible web interface. InterMine reduces the effort needed to build and maintain both small and large-scale data warehouses, while providing flexible querying, powerful operations on lists and integrated analysis tools.
InterMine has become a successful project in its own right and is being adopted by a growing number of groups for their own database projects. It has made real progress in enabling the creation of integrated databases and providing biologists with advanced functionality, and we will continue its development. We thank all users of FlyMine for contributing to this success by providing feedback and suggestions.
The FlyMine/ InterMine Team

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Release 14.0

In Release 14.0 we have updated data from FlyBase to release FB2008_06 and many sources are updated to the latest versions. We have added an autocompletion feature for many constraints in template queries and QueryBuilder. This means that as you type, for example a GO term or protein domain name, suggested matches will be provided.

Data

Data from FlyBase is updated to the FB2008_06 release and many other sources have been updated to the latest versions, specific changes are detailed below. For a complete list of all data included in FlyMine see the ‘Data’ tab above.

  • NEW - Drosophila genes now have a field ‘flyBaseFeatureType’ field for the gene type e.g. protein_coding, miRNA_gene.
  • NEW - D. melanogaster microRNATargets now have chromosome locations and appear in GBrowse.
  • FIX - C. elegans genes and proteins are now correctly linked to one another.
  • NEW – CRM and binding sites from REDfly now have an evidence field which contains information about the experiment.
  • FIX – More probesets from AffyMetrix are correctly mapped to genes, including those with predicted transcripts
  • NEW – A new tissue, the salivary gland, has been added to the FlyAtlas dataset.

Data integration

In this release we further improved the data integration system to update old identifiers for Drosophila genes that are provided by many data sources to match a current FlyBase identifier. We now include only current FlyBase genes that have a genome location (see 13.0 release notes for more details).

Data sources

Most data, including all genes and proteins, have been assigned a dataset. A dataset includes the source of the data, dataset name and URL, allowing you to quickly and easily find the origin of the data.

Autocompletion

Many name fields in template queries and the QueryBuilder now have type-ahead autocompletion to assist in selecting valid terms. As you start to type, possible matches are fetched from FlyMine; the text you have typed can match anywhere within the terms and multiple words can be matched. This is particularly useful for GO terms or protein domain names.

Removing list entries

It is now possible to remove entries from one of your lists. On the List Analysis page you can now select entries in the list and use the new ‘Edit’ menu to delete them from your list or add them to another existing list.

User interface

  • NEW – added linkouts for genes to BDGP in situ and for alleles to FlyBase
  • FIX – you can now access the lists and query history section of MyMine when not logged in. This allows you to delete your temporary lists.
  • FIX – GLEANR symbols are no longer low quality matches when using them to upload a list of Drosophila genes.
  • FIX – template and list search pages no longer reset the search term when using the back button.

Template web services

  • FIX – the ‘Show link with constraint values highlighted in red’ now highlights every value correctly
  • FIX – various javascript errors in Internet Explorer 6.0 have been fixed that prevented the results count from being updated.
  • NEW – results are returned with the correct file extension which makes it easier for programs to correctly open the file
  • FIX – you can now login while on the template web services page
  • FIX – template form correctly updates on error

Widgets

  • NEW – extra columns added to the widget export
  • FIX – enrichment widgets include more digits when displayed in scientific notation
  • FIX – enrichment widgets no longer overlap when displayed
  • NEW – statistical enrichment widgets now link to documentation on the method of calculation used

Release 13.0

In Release 13.0 we have improved integration of data with old Drosophila gene identifiers from several sources, this information is now applied to a current FlyBase gene where possible. We have also added allele and phenotype information from FlyBase and miRNA target predictions from miRBase. Data from FlyBase is updated to the FB2008_05 release and other sources have been updated to the latest version. User interface improvements focus on uploading and saving lists. We have also launched a RESTful web service allowing queries to be run from scripts and remote sites.

Data integration

In this release we have made a major effort to update old identifiers for Drosophila genes that are provided by many data sources to match a current FlyBase identifier. We have done this with a synonym lookup, for example when we download data from a particular source that references gene CG12802 which is no longer a current gene identifier but is a synonym (an old identifier) for FBgn0250818. Where an old identifier did not match a single gene we did not load data for it. As a result we have improved data integration, you should see more data attached to current genes and no longer see old genes with data from only one source.

Data

We have added Drosophila allele and phenotype data from FlyBase and miRNA target predictions from miRBase. Data from FlyBase is updated to the FB2008_05 release and many other sources have been updated to the latest versions, new data are detailed below. For a complete list of all data included in FlyMine see the ‘Data’ tab above.

  • NEW - Drosophila melanogaster allele and phenoytype data from FlyBase.
  • NEW - Drosophila melanogaster predicted miRNA targets from miRBase.
  • UPDATE – three new RNAi screens added from DRSC.

Saving lists

We have enhanced creation of lists from results tables and fixed some selection issues.

  • NEW – a ‘Selection’ bar below the results table tracks objects that have been selected.
  • NEW – where the same object appears on multiple rows, selecting it once will select all rows even if on different pages.
  • FIX – performance of list creation from results improved.
  • FIX – selecting individual objects from multiple pages now works correctly.
  • FIX – selecting a whole column then de-selecting some rows now works as expected.

Web Services

We have begun to introduce RESTful web services to enable access to FlyMine data from scripts and other web sites. We are working on adding client APIs and further features.

  • It is now possible to run an XML query via a simple URL and get results as XML, or tab separated formats. See documentation for more.
  • All public template queries can be executed for any values and HTML results embedded in a remote web page. So if you run a web site presenting Drosophila data you can fetch results live from FlyMine to view alongside your own. Please contact us if you any questions about this. See documentation for more.

List upload

  • NEW – organism name is now displayed for issues on list confirmation page.
  • FIX – fixed problems uploading from a file on some versions of Safari.
  • FIX – improved performance and fixed unresponsive script errors when clicking ‘Add all’ with very large numbers (hundreds) of issues on upload confirmation page.
  • FIX – improved error messages for incorrect file names typed into file upload box.
  • FIX – improved disabling of paste/browse options on list upload page.

User interface

  • NEW – the List Analysis page menu bar has a ‘Find’ option to search for a particular identifier in the list.
  • NEW – the Lists tab now has a ‘Copy’ option. Select a list and type a new name to create a copy, or select multiple lists and they will be named automaticaly. You can copy public lists as well your own lists.
  • NEW – option to show/hide descriptions in the Template and List tabs.
  • NEW – widgets on List Analysis pages now show a count of objects that have no data for the widget.
  • FIX – linking to FlyBase with a list of genes from the List Analysis page now works with large lists.
  • NEW – link to FlyExpress with a list of genes from List Analsyis page.
  • NEW – added links to external databases in enrichment widgets.
  • NEW – link to BDGP in situ data from gene report pages.

Release 12.0

Release 12.0 of FlyMine adds genome annotation for the ten additional Drosophila species included in FlyBase release FB2008_02. Homology data between the 12 Drosophila species from the 12 Genomes Consortium (2007) paper. Data from BDGP in situ and genetic interactions from BioGRID are also added. We have also added more widgets for analysing lists of genes and improved the style and layout of the list analysis page.

Data

Many existing data sources have been updated to the latest versions, new data sources are detailed below. For a complete list of all data included in FlyMine see the ‘Data’ tab above.

  • NEW - Drosophila 12 genomes. We have added genome annotation for the additional ten sequenced Drosophila genomes from FlyBase release FB2008_02.
  • NEW - Drosophila 12 genomes homology – homology between 12 Drosophila genomes, data from the 12 Genomes Consortium (2007). PubMed 17994087
  • NEW – BDGP in situ expression patterns.
  • NEW – Genetic Interaction data for D. melanogaster, C. elegans and S. cerevisiae from BioGRID.
  • NEW – Probe sets from the Affymetrix GeneChip Drosophila Genome 1.0 Array.
  • FIX – Some InParanoid cluster names have been fixed.
  • FIX – ProteinDomain name and shortName were both showing the short name, now fixed.
  • FIX - Drosophila UTRs and CDSs now have FlyBase as evidence.
  • FIX – Evidence for REDfly TFBindingSites now fixed.

List Analysis

The layout of list analysis pages has been improved. New ‘List Info’ and ‘Link Outs’ sections are added to the top ot the page. Widgets have had a style update, more can be displayed on the screen at once and a menu allows you to open/close them. Loading times of the list analysis page has been greatly improved. Details of new widgets are given below.

  • NEW – Orthologues widget – for a list of genes shows counts of orthologues in other organisms using data from InParanoid and homology between the 12 Drosophila genomes.
  • NEW – BDGP in situ expression patterns widget. For a list of genes display the counts expressed or not expressed at the stage ranges tested.
  • NEW – BDGP in situ term enrichment. For a list of genes see if any ImaGO terms assigned by BDGP are statistically enriched.
  • NEW – Genetic Interactions widget. For a list of genes show genes that genetically interact and the count of genes from the list that they interact with. Data from BioGRID.
  • NEW – For a list of Drosophila genes export all directly to FlyBase’s HitList page.
  • NEW – Data from enrichment widgets can now be exported as tab or comma separated files.
  • FIX – no longer get an exception after adding elements to an existing list then clicking ‘view all results’ on list analysis page.

Other fixes

  • FIX – Column summary buttons and option to save a list now appear on all results tables.
  • FIX – Exporting results has been made much faster.
  • FIX – GFF3 export now only exports unique rows.
  • FIX – Bug with exporting results in IE6 fixed.
  • FIX – List upload now ignores duplicate identifiers even if the case doesn’t match.
  • FIX – Links to KEGG pathways on the KEGG web site have been corrected.
  • FIX – Improved error messages when importing invalid query XML.
  • FIX – Constraining a field in the QueryBuilder to ‘has no value’ sometimes didn’t work, now fixed.

Release 11.0

Release 11.0 of FlyMine includes an update of data from FlyBase, expression data related to Tiffin motifs has been added and many other data sources are updated. We have also added new widgets and improved menus on results and list analysis pages.

Data

The D. melanogaster genome has been updated to release 5.5 from FlyBase. Many other data sources have been updated to recent versions, see the Data tab for more details.

  • FIX – We now follow part-of relationships when computing transitive closure on the the Gene Ontology. This means that queries that include parents/children of terms now follow part-of relationships as do the GO enrichment widgets.
  • FIX - D. melanogaster UTRs and CDSs are now retrieved correctly from FlyBase
  • FIX – Some minor changes have been made to the ProteinInteraction class – unused attributes have been removed, interacting regions is now filled in.
  • UPDATE – InterPro domains for each protein are now retrieved from UniProt with details of the domains taken from InterPro. We now include domains for more organisms.
  • UPDATE – As of October 2007, the Drosophila DNAse I footprint (FlyReg) database has fully merged with the REDfly database. The FlyReg website will no longer be updated. Therefore, FlyMine now loads the FlyReg transcription factor binding sites directly from the REDfly database.
  • UPDATE – All REDfly identifiers have been updated.
  • UPDATE - C. elegans RNAi phenotype data from WormBase have been remodeled. Every phenotype now has a flag for ‘Observed’: true/false. Some phenotypes show a penetrance range.
  • NEW – Five more D. melanogaster RNAi screens added from the DRSC.
  • NEW – A subset of Tiffin motifs are now correlated with known expression patterns.

Orthologues

We have changed the way we present orthologue data from InParanoid to make it simpler and more obvious. Orthologues and Paralogues now appear in a single Homologue class which has a type of ‘orthologue’ or ‘inParalogue’, we no longer use the terms ‘main’ and ‘secondary’. Please contact us if you have any problems with this.

When viewing a list of genes on a list analysis page there is now an orthologue conversion section in the top right. Select an organism to view a results page of orthologues in that organism to export or create a new list.

Widgets

New widgets have been added to protein and genome feature list analysis pages. Enrichment widgets now include the option to choose Benjamini-Hochberg or Bonferroni error correction. Benjamini-Hochberg is the default and is less stringent. Enrichment and table widgets can now be opened in a new window and have the option to select multiple categories (e.g. multiple GO terms) and display/export all data from those categories.

  • NEW – A chromosome distribution widget is now shown on list analysis pages for any located genome feature (e.g. genes, exons, binding sites).
  • NEW – Enrichment widgets added to protein list analysis page:
    • InterPro protein domains.
    • GO terms (queried via corresponding genes).
    • UniProt protein features.
    • UniProt keywords.
  • NEW – Enrichment widget results can be filtered on maximum p-value.
  • FIX – clicking on bars of chromosome distribution widget now gives correct results with multi-organism lists.
  • FIX – links on GO enrichment now give results for A. gambiae and A. mellifera

List upload

  • NEW – ‘Add all’/’Remove all’ links added to each issue section on list upload page – making large lists easier to manage.
  • NEW – Issues on the confirmation page now have links to open report pages in a new window.
  • FIX – Confirmation page no longer resets if an invalid list name is entered.
  • FIX – List name is no longer pre-filled with the last entered list name.

Other user interface changes

  • NEW – Template query forms include an ‘XML’ link to export an XML representation of the query.
  • NEW – Export, Create List and Add To List are now in a menu bar above results tables, combined with previous/next navigation.
  • NEW – Open/closed state of sections on report and list analysis sections is now ‘sticky’ for your current session.
  • FIX – Improvements to error checking and messages when importing XML queries/templates.
  • FIX – Selections don’t reset if an invalid name entered when performing list combination operations.
  • FIX – Improved error handling on results page when selecting objects to save and list name.

Release 10.0

Release 10.0 of FlyMine includes an update of data from FlyBase, a new A. gambiae gene expression data set and some user interface changes.

Data

The D. melanogaster genome has been updated to release 5.4 from FlyBase. We have added a new microarray-based gene expression data set for the life cycle of A. gambiae. ‘Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster.’ (Koutsos et al 2007 - PubMed).

Other data changes:

  • FIX – duplicate introns have been removed for D. melanogaster and D. pseudoobscura, FlyMine used to infer introns but they are now imported from FlyBase.
  • FIX – introns are now created on the correct strand for A. gambiae and A. mellifera.
  • FIX – orthologues for A. gambiae, A. mellifera and A. aegypti now reference genes as well as translations, they will now appear in results of more template queries.
  • FIX - D. pseudoobscura ‘Unknown’ assembly groups are no longer created as chromosomes.
  • FIX – the ‘localised’ category has been removed for fly-FISH expression data, the data now just shows whether a gene is expressed or not at a particular stage.

List Conversion

The List analysis page has a new ‘Convert’ section for instant conversion between common types (genes, proteins, transcripts and exons). Counts of each type are displayed for a list – e.g. the numbers of proteins, transcripts and exons found for a list of genes. Clicking on the type will bring up a results table from which you can export identifiers, sequence or create a new list.

External links

We have added links to more external databases from report pages – e.g. to model organism databases and REDfly. We now have a simple configuration system for links so if you have suggestions of other databases it would by useful to link to please let us know – support[at]flymine.org.

Tutorial and FAQ

We have added a tutorial on creating and using lists in FlyMine, see the help page. There is also a list of Frequently Asked Questionslinked to from the header.

User interface changes

  • NEW – the queries run when clicking on graphs or tables in list analysis widgets now include more information.
  • NEW – number of rows shown in results tables is remembered.
  • FIX – performance improvement for uploading lists with more than 1000 elements.
  • FIX – fixed problem where user was logged out or history was lost when returning to the home page.
  • FIX – uploading a list from a file is fixed on Safari.
  • FIX – it is now more obvious when long text entries have been truncated in results tables.
  • FIX – fixed ‘div has no properties’ error in templates tab if user created two templates with the same title.