FlyMine 6.1 contains a major overhaul of the way bags are handled. Bags can now only contain actual objects rather than identifiers or symbols. This means that any object in a bag has already been found in FlyMine which should reduce confusion. A sophisticated bag upload system has been added to aid in creating bags from external lists of identifiers.
PLEASE NOTE – most saved user content is automatically upgraded between FlyMine releases. In this case it was not possible to port some types of bags. These are still available in the 6.0 archive, please contact support [at] flymine.org if you have any queries about transferring bags.
Bags also now have a type (class) assigned to them – for example Gene, Protein, GOTerm. This means that when editing a constraint in a template query only bags of the correct type will be listed – so if the template requires you to enter a Gene identifier the bags dropdown will list any Gene bags in your profile. The same is true when creating/editing a query in the QueryBuilder, just add a constraint on the identifier, name, etc of a class and you will see available bags.
The ‘Bags’ page in MyMine (select ‘Bags’ or ‘MyMine’ from the top menu bar) now allows you to paste in a list of identifiers and select a type for the new bag. The input can be a mixture of different identifier types, for example if you wish to create a bag ofÂ Drosophilagenes if can be a mixture of CGxx, FBgnxx and symbols. In the case where an object can’t be found to that matches a particular input identifier, FlyMine will attempt to help. For example if the input list contains a UniProt protein identifier, but you choose to make a gene bag, the website will attempt to find a related gene. Any matches found in this way will be reported for you to choose which are added to your bag.
As an example, when creating a Gene bag from these identifiers: zen CG2328 FBgn0015379 Q8IML9_DROME unknown_name FlyMine will find a gene for each of the first three identifiers and find the gene for the Q8IML9_DROME protein. The “unknown_name” will be reported as not found.
Also new are bag details pages. These are accessible for any of your saved bags in the ‘Bags’ tab of MyMine. They have a similar layout to object details pages but run templates for all objects in your page. On the page for gene bags is the first of many ‘widgets’ we plan to add for a viewing and analysis of data in bags. Currently there a widget that graphs the genes from a bag that are over/under expressed in different tissues according to the FlyAtlas data set (www.flyatlas.org). Note that clicking on any of the bars in this graph allows you to create a new bag of genes in that category. More functionality will be available on these pages in release 7.0/
FlyMine 6.0 adds data from sevenÂ Dropsophila RNAi screens from the DRSC, microarray-based gene expression data from FlyAtlas and Transcriptional cis-regulatory modules (CRMs) from REDfly. Template queries have a new, succinct naming scheme and identifiers/names in results tables are now links to object details pages. Other data sources have been updated/added and there are numerous interface improvements.
NOTE – from release 6.0 FlyMine does not support saved bags of objects. User’s object bags have not been ported to release 6.0 but can still be retrieved from the release 5.0 archive. If any user wishes to use information from old object bags we recommend exporting from 5.0 as a list of appropriate identifiers and uploading to release 6.0. Please contact us if you require any help with this. All other saved information has been transferred to release 6.0.
An upcoming release of FlyMine will introduce a new system for uploading and managing bags of data.
- NEW – Microarray-based gene expression data forÂ D. melanogaster from FlyAtlas.
- NEW – High-throughput cell-based RNAi screens from theÂ Drosophila RNAi Screening Center.
- NEW – Transcriptional cis-regulatory modules (CRMs) forÂ D. melanogaster from REDfly.
- NEW – Probe sets from the Affymetrix GeneChip Drosophila Genome 2.0 Array.
- NEW – Syntenic regions betweenÂ D. melanogaster andÂ D. pseudoobscura.
- NEW – Orthologues and GO annotation forÂ S. pombe andÂ P. falciparum.
- NEW – Anatomy ontology forÂ Drosophila.
- UPDATE -Â D. melanogaster genome annotation updated to version 4.3.
- UPDATE – UniProt protein data is now at version 8.9.
- UPDATE – Worm RNAi data from WormBase 30th September 2006.
- UPDATE -Â D. melanogaster BACs are now loaded.
- UPDATE – Protein fragments from UniProt are now identified by an isFragment true/false attribute.
- UPDATE – Proteins now have a length (in amino acids) and molecularWeight (in Daltons).
- FIX – Protein interaction confidence scores restored.
- FIX – PCRProducts now reference the TilingPathSpan they create.
- FIX – Some unpublished microarray experiments have been removed.
- User Interface
- NEW – Names and identifiers in results tables now link to object details pages.
- NEW – Template names have been changed so that they now have a short name and a longer description. The short name is the main name and is displayed on the aspect pages, template search results and the object details pages. This shorter name has the format ‘query starting point(s)’ –> ‘query output’ and allows easier scanning of templates to find the one required. The longer description can be viewed when the template form is accessed.
- NEW – When running a template query the title and description is displayed above the results.
- NEW – The trail now includes a ‘Query’ link back to the template or Query Builder, i.e. now ‘Query -> Results’.
- UPDATE – It is no longer possible to create bags of objects from results or upload.
- UPDATE – Chromosomal locations are displayed in a more compact format (e.g. 2R:1598168-1676472).
- UPDATE – ‘History’ has been renamed to ‘My Mine’ and the layout improved.
- improved query and template XML import/export options.
- added a ‘Change Password’ tab.
- bag listing and upload pages have been combined.
- FIX – Searches in bags of strings are no longer case sensitive.
- FIX – After running a template query ‘Current Query’ will now return to the template form instead of the Query Builder page.
- FIX – To address a performance issue bag size is limited to 100 entries unless you are logged in (when the limit is much higher).
- There are no changes to tools available in release 6.0.
- Known issues
- There are currently no known issues with data in release 6.0.
FlyMine 5.0 adds genome annotation forÂ D. pseudoobscura (release 2.0 from FlyBase) andÂ A. mellifera (release 2.0 from Ensembl) with InParanoid orthologues to the other genomes in FlyMine. Also added are InParanoid orthologues to many other species and GO annotation for some of them. Interface improvements include the ability for users to tag favourite templates and to change their password.
- NEW: Genome annotation forÂ D. pseudoobscura version 2.0 from FlyBase.
- NEW: Genome annotation forÂ A. Mellifera release 2.0 from Ensembl version 37.
- NEW: InParanoid orthologues fromÂ D. melanogaster, D. pseudoobscura, A. gambiae, C. elegans andÂ A. mellifera to many other organisms.
- NEW: GO annotation (accessible via orthologues) forÂ M. musculus, R. ratticus, S. cerevisiae andÂ A. mellifera.
- NEW: Protein interaction and UniProt data for S. cerevisiae.
- NEW: IntergenicRegion class – objects to describe intergenic regions on chromosomes, sequence and overlapping features available. Genes now have references to upstream and downstream intergenic regions.
- UPDATE: Genome annotation forÂ A. gambiae updated to build AgamP3 from Ensembl version 37.
- FIX: INDAC microarray oligos now have sequences.
- FIX: OMIM disease names are no longer duplicated, new templates added to the Disease aspect.
- FIX: mRNA sequences no longer include intron sequences.
- FIX: Protein Interactions – some interactions referenced isoform ids so data didn’t merge correctly with other protein information. Now have correct UniProt accession.
- FIX: Protein interactions are now correctly assigned to Formstecher et al, 2005 – was fixed in IntAct.
- User Interface
- NEW: Favourite templates – logged in users can see a * beside template query names to select then as favourites. They are listed in a new ‘Favourites’ tab on the History page.
- NEW: Change password – users can now choose there own password when creating an account. Passwords can be changed when logged in by clicking on the username in the top menu bar.
- FIX: Missing class descriptions completed.
- NEW: Boolean fields are now constrained by a true/false dropdown.
- FIX: GBrowse images on object details pages are now oriented correctly for features on reverse strand. Also now show absolute coordinates.
- Known Issues
- Due to a change in format of XML from IntAct there are no confidence scores for protein interaction experiments, we will release a fixed version as soon as possible.
- Gene.goAnnotation collection not filled in for A. Gambiae genes, need to use Gene.annotations instead.
Major changes to layout and content of summary pages. These pages can now display the results of template queries inline to give immediate access to data. The http://www.flymine.org home page now shows aspect icons and query options. Many other interface improvements. Addition of Arbeitman et al, 2002 Drosophila time course microarray data and human disease gene matches from Homophila.
- NEW: microarray data from “Gene Expression During the Life Cycle ofÂ Drosophila melanogaster“, Arbeitman et al 2002.
- NEW: added data human disease gene matches from Homophila (http://superfly.ucsd.edu/homophila/).
- NEW: more protein interaction experiments from IntAct – see Protein Interaction aspect.
- NEW: Gene now has an “allGoAnnotation” collection that contains the term assigned to a gene plus all the parents of the term. Using this collection to find genes with a particular term will find all genes with that term *and* any with a more specific term.
- ENHANCEMENT: MRNA now references threePrimeUTR and fivePrimeUTR.
- ENHANCEMENT:Â D. melanogaster translation symbols now set from FlyBase.
- ENHANCEMENT:Â D. melanogaster chromosome bands now loaded from FlyBase.
- UPDATE:Â D. melanogaster genome annotation updated from 4.2 to 4.2.1.
- UPDATE: GO annotation and UniProt proteins updated.
- FIX:Â D. melanogaster regulatory regions from FlyBase now have chromosome location.
- FIX:Â D. melanogaster insertion sites and point mutations from FlyBase reference genes correctly.
- FIX:Â A. gambiae genes from Ensembl and InParanoid orthologues now merged correctly.
- NEW: a graph of interacting proteins on protein summary pages.
- NEW: graphs ofÂ D. melanogaster time course expression on gene details pages (Arbeitman et al, 2002).
- NEW: FASTA retrieval icon to access sequence of all features with sequence.
- FIX: insertion sites now displayed correctly on GBrowse.
- User Interface
- NEW: Template queries are now viewable inline on object summary pages.
- NEW: bags saved in history can now be subtracted from one another.
- NEW: Query constraint logic can now be manipulated within the query builder – can constrain A AND B/A OR B.
- NEW: Added Run query link to run a query directly from the History page.
- NEW: Template queries can now include a choice of several different output formats.
- ENHANCEMENT: Template search terms are highlighted in results lists.
- ENHANCEMENT: Template building integrated into query builder interface.
- Known issues
- DATA: Protein interactions from Formstecher et al, 2005 (PubMed: 15710747) are incorrectly assigned to Rain et al, 2001 (PubMed: 11196647) which in IntAct is a secondary reference.
- DATA: OMIM disease names contain the same text repeated multiple times.