Release 16.0

In Release 16.0 we have updated data from FlyBase to release FB2009_04 and many sources are updated to the latest versions, the way we include proteins has been redesigned so that all isoforms from UniProt are loaded. We have introduced a significant new feature to querying (‘outer joins’) and improved general query and export performance.

Data

Data from FlyBase is updated to the FB2009_04 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.

  • UPDATE – We now include all isoforms of proteins from UniProt.
  • UPDATE – Gene Ontology (GO) data assigned to genes has been re-modelled to now include relationship types between terms. Genes no longer have an allGoAnnotation collection to model transitive closure of the ontology, instead use the GoAnnotation.relations.parents collection.
  • NEW – We now load deficiencies/deletions and aberrations from FlyBase
  • FIX – TransposableElementInsertionSite features now have orientations, these are displayed in GBrowse.
  • FIX – Rat genes now have synonyms, organisms and datasets correctly attached
  • FIX – Drosophila mRNA now have synonyms and datasets correctly attached
  • FIX – ESTs now have locations
  • FIX – Dmel proteins from UniProt are correctly attached to genes.
  • FIX – All genes and proteins now have a datasource.
  • UPDATE – Cytological location data now available
  • UPDATE – Proteins and transcripts are now linked
  • NEW – Predicted miRNA targets
  • NEW – Drosophila development ontology
  • NEW – Synonyms now have datasets, so you can tell who is using which identifier.
  • UPDATE – Anopheles proteins now loaded for correct strain.
  • UPDATE - Apis mellifera genome removed.

Query system

In a major update to the query system it is now possible to choose whether columns include information that must be present to produce a row in the results or should just be shown if a value is present. This is best illustrated with an example. Consider an organism that has a thousand genes but only 900 are known to code for a protein. In FlyMine there would be 1000 genes and 900 of them would be related to a protein. You can now query for genes and related proteins in two ways:

  1. ‘inner join’ – You create a query with two columns, the first for the gene identifier, the second with the protein identifier. Only 900 rows are return, those that don’t have a protein aren’t included. This is how all queries worked before this release.
  2. ‘outer join’ – You create the same query but specify the gene to protein relationship as an ‘outer join’. This will return all 1000 genes in the first column and have empty cells in the second column for the 100 genes that don’t have a protein.

Organise your lists

You can now apply aritrary tags to your saved lists both on the list analysis page and in MyMine. Tags can be any label you like to help you categorise your saved information, one list can have multiple tags applied. You can filter lists by tag from the Lists view page.

Export

Improvements to the internals of InterMine have made exporting large datasets significantly faster – you should find download speeds around an order of magnitude better.

User interface

  • NEW – web service API is available.
  • FIX – Creating a list after converting between orthologues now works.
  • NEW – link to ArrayExpress atlas is available on certain report pages.
  • NEW – link to FlyBase appears on list analysis pages for alleles and insertions.
  • FIX – Foreign characters display properly
  • FIX – Chromosome distribution widget now excludes rubbish chromosomes from its calculations.
  • FIX – 404 error page improved.
  • FIX – List information on the report page is now at the top, for increased visibility
  • FIX – Export display issues fixed for Internet Explorer.
  • FIX – Fixed some slow algorithms displaying results data.
  • FIX – Fixed error in “Add Column” function where there are no extra columns to add.
  • FIX – Fixed “View all” button on Sequence residues.
  • UPDATE – Export now has column headings at the top.
  • FIX – Performance of widget queries improved.
  • FIX – Wildcards in queries are exported correctly.
  • UPDATE – Collection sizes are updated using AJAX on report pages.
  • UPDATE – UTRs now present in GBrowse
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Release 15.0

In Release 15.0 we have updated data from FlyBase to release FB2008_08 and many sources are updated to the latest versions.

Data

Data from FlyBase is updated to the FB2008_08 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 – FlyMine now loads all types interactions from the BioGRID for D. melanogaster, C. elegans and S. cerevisiae. Currently, no distinction is made between protein and genetic interactions. All of them (the ones from IntAct as well as the ones from the BioGRID) are now called ‘Interaction’. The Interaction Term allows to search for a particular interaction, eg phenotypic enhancement, two hybrid.
  • NEW – Affymetrix Probesets from the GeneChip D. melanogaster Genome 1.0 and 2.0 Arrays now have locations and mapped genes, obtained from the Ensembl database. FlyMine only loads probesets that match to at least one gene. More information on the Ensembl probeset mappings, can be found at Ensembl help
  • NEW – Loaded all aberrations from FlyBase including Drosdel deletions and they are now called ChromosomeStructureVariation. Each feature type is represented by a seperate sub-class: ChromosomalDeletion, ChromosomalDuplication, ChromosomalInversion, and ChromosomalTranslocation.
  • FIXED – The Ensembl id is correctly set for human genes.
  • NEW – Gene.flybaseFeatureType has been renamed to Gene.featureType.
  • FIXED – all MRNAs now have Translations.
  • FIXED – UTRs now have chromosome locations and appear in GBrowse.

Export

In this release, we’ve extended and improved the export system. We’ve optomised and configured the export process which has resulted in marked speed improvements. Also, we’ve added new functionality.

User interface

  • NEW – you can now have a dash in a list name
  • NEW – links on the allele list page directly to FlyBase
  • NEW – links on the allele list page to convert list to genes
  • FIXED – improved error handling throughout the site, including the QueryBuilder, template and query import pages
  • FIXED – the quick search now handles special characters correctly so you can search for any identifier, eg.
  • FIXED – selected records in your list stay highlighted even if you navigate away and then back to the list analysis page
  • FIXED – template form handles wildcards correctly

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

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.