Transgenic alleles now have a “Transgenic product class” field that uses Sequence Ontology (SO) term(s) to describe the nature of the encoded product, so that it is easier for you to see whether it is useful for your experiments. The transgenic product class terms we use fall into 4 broad types:

• wild_type (together with either cDNA or genomic_DNA to describe the nature of the coding sequence, if known).
• a term describing a structural change relative to wild-type (e.g. missense_variant, inframe_deletion)
• a term describing a functional change relative to wild-type (e.g. dominant_negative_variant, polypeptide_post_translational_processing_variant)
• a term describing a sequence targeting reagent (sgRNA, RNAi_reagent).

The field is located in the General Information and Nature of the Allele sections of the Allele Reports.

To get a list of all transgenes that encode a particular type of gene product, either click on the SO term in the “Transgenic product class” field of an individual Allele Report, or use the Vocabularies tool to go to the relevant Term Report. On the Term Report, click on the Alleles button in the Annotations section to get a hist list of all the matching transgenic alleles. For example, the wild_type term lists over 28,000 transgenic alleles, while missense_variant lists almost 7800 alleles.

FlyBase has updated the DRSC Integrative Ortholog Prediction Tool (DIOPT) to version 9.1. This update is derived from the latest data available from the DRSC's DIOPT tool and includes the following orthology prediction algorithms: Compara, eggNOG, Hieranoid, Homologene, InParanoid, OMA, OrthoDB, OrthoFinder, OrthoInspector, OrthoMCL, Panther, Phylome, SonicParanoid, and Domainoid.

DIOPT 9.1 now also includes predictions for A. gambiae (African malaria mosquito) and E. coli.

As with previous versions, DIOPT 9.1 predictions can be accessed from the FlyBase home page using the “Homologs” search tool, or viewed on gene reports (“Orthologs” and “Paralogs” sections).

For further details regarding DIOPT and its features, please visit the DRSC's DIOPT website.

1. The NIG-Fly sgRNA collection consists of fly stocks containing transgenic constructs designed for CRISPR/Cas9-based mutation of a gene. Each construct constitutively expresses a single sgRNA that targets a gene of interest.
2. The NIG-Fly KO collection consists of fly stocks, each carrying a knockout of a gene of interest, generated using stocks from the NIG-Fly sgRNA collection.

1. The cGAS/STING Signaling Pathway has been added. This is an anti-viral pattern recognition pathway which has only recently been described in flies.
2. Pathway groups are now available in a their own separate, downloadable tsv file in the Gene Groups Section of the Current Release page.
3. The pathway physical interaction networks (e.g. EGFR Signaling Pathway) now show all pathway genes, regardless of whether they have any curated physical interaction data with other members and so more accurately reflect experimental knowledge.

1. The GenExel collection, a set of P{EP} insertion lines that have been sequence mapped to the genome.
2. A set of GAL4 driver lines characterized as part of the KDRC K-Gut Project as being expressed in the gut. These lines were originally generated by the Rubin lab at the Janelia Research Campus, and the GAL4 driver is expressed under the control of a putative enhancer fragment.

• 1422 phenotype annotations,
• 951 alleles/transgenes,
• 729 GO annotations,
• 636 Disease Ontology statements,
• 706 genetic interactions,
• 280 fly stocks,
• 250 expression statements,
• 231 physical interactions,
• 106 cell line associations,
• 83 mapped mutations,
• 20 gene model updates,
• and built a Fly Board election survey!

See the 2021_06 Release Notes for details of changes to the FlyBase database for this release.

• switch between log2-converted and linear presentation of signal/coverage subsets profiles,
• switch between topographical/tilted and vertical alignment of subsets profiles, and
• select desired vertical spacing of subsets profiles (up to complete separation without overlaps)

• Links to MARRVEL (Model organism Aggregated Resources for Rare Variant ExpLoration) have been added to the ‘Key Links’ section at the top of gene reports. MARRVEL facilitates the study of rare human variants by integrating human gene and variant information with key biological data from model organism orthologs. Links on human gene reports in FlyBase go directly to the corresponding MARRVEL page (e.g. human PTEN), while links on D. melanogaster gene reports go to an intermediate page showing the human orthologs of the fly gene (e.g. fly Pten).
• The ‘Key Links’ section on gene reports for human and other model organisms now includes a link to the corresponding page at the Alliance of Genome Resources. For example, see the Hsap\PTEN report.
• In the “Expression Data” section of gene reports, linkouts to single-cell expression resources are now available: DRscDB and EMBL-EBI Single Cell Expression Atlas. These linkouts provide a list of single-cell RNA-seq datasets in which expression of the gene has been observed, with tools for further exploring those datasets.
• FlyBase has also added two new categories to the Drosophila Online Resources page. A variety of useful links pertaining to “Cell Lines and Cell Culture” and “DNA Reagents” can now be found in these new sections.

• Back-end improvements to improve usability and efficiency
• Reference search indicates if a paper has already been curated, eliminating duplicated effort
• Certain data-types are pre-populated within the FTYP form based on text-mining
• Easier searching via synonyms for genes to associate with the publication
• A new ‘dataset’ flag for large-scale genome-style studies; this will mean authors only need to add the small number of genes that have been further studied within their publication
• Authors of reviews will be contacted with a slimmed down version of FTYP to associate genes with their reviews
• Options to give FlyBase more data about cell lines used
• A new data-type if the author has used chemicals to investigate phenotypes
• A new data-type if the author has investigated a new member of a signaling pathway
• Authors can now indicate if their paper contains a technical advance or new resource which may be useful to the fly community
• If none of the data-types listed in FTYP apply, we now give the author an option to tell us what kind of data is in the publication
• Authors are encouraged to submit ‘Gene Snapshots’ about uncharacterized genes they have studied in their paper

FlyBase now reflects gene model annotation and genome assembly information for D. melanogaster only. As of this release (FB2020_03), annotation and assembly information for these species has been retired: D. simulans, D. ananassae, D. pseudoobscura and D. virilis. This follows retirement of such information in release FB2018_06 for the following species: D. erecta, D. grimshawi, D. mojavensis, D. persimilis, D. sechellia, D. willistoni, D. yakuba. For the status of these gene model annotations, please see the NCBI page Eukaryotic genomes annotated at NCBI.

The FlyBase BLAST tool will continue to support queries against the reference genomes of these retired species, but not queries against annotated transcripts or proteins. For the current and future releases, there will be no JBrowse or GBrowse view of the gene model annotations for the species. FASTA and GFF files for the retired gene model annotations and assemblies will still be available on the FlyBase FTP site ftp://ftp.flybase.net/genomes/, but they will not be updated. The related gene reports will persist, containing various types of curated information (phenotypes, expression, publications), as well as links to sequence information at external sites like NCBI Gene in the "CrossReferences" section, though these links may go stale over time.

We emphasize that this decision was carefully deliberated, made in consultation with the FlyBase advisory board and our partners at the NCBI, to allow FlyBase to redirect its energies from these rarely used resources to other aspects of the project that are more heavily used by the Drosophila community. Please see this NCBI Announcement to learn more about their Drosophila gene annotation resources.

Our ID Converter tool is now called ID Validator. This tool will accept a list of FlyBase symbols/IDs (for any data type) and, where necessary/possible, update them to their current versions. It will also convert certain external IDs (GenBank nucleotide/protein accessions, UniProt accessions, PubMed IDs) into their equivalent FlyBase IDs. The output is provided as a validation table that can either be downloaded as a file or exported to a FlyBase HitList for futher processing (including conversion between data types).

• Performance fix for large lists of items.
• Converting FlyBase IDs into other data classes (e.g. allele to gene or polypeptide to gene) is no longer supported. To accomplish this, first upload your list to ID Validator, export to a HitList, and then convert your list into the desired data class using the HitList convert button.
• The use of symbol synonyms for validating your symbol lists can be enabled or disabled.
• Validation is now restricted to only D. melanogaster by default with the option to include other species if desired.
• Cases where a single ID is now represented by multiple FlyBase records or multiple IDs are now merged into a single FlyBase record are flagged with a '!' to indicate that you may want to review the validation for your use case.
• A subset of validated items can be selected for export by using the checkbox next to each item.
• Items that have been updated are indicated with a yellow background.

• Powerful new hitlist management
  General searches now go to mixed data-class hitlists with lots of information and links in each hit item; lists can be filtered by data class and species. Hitlists with a single data class also have a compact tabular view. Analysis tools and list export for download, etc. are all there too.
  The main search is also now available in every FlyBase page, as a second option of the familiar "Jump to Gene" search bar in the page header.
• Enhanced Report pages
  FlyBase 2.0 report pages look more modern, with a fluid layout and new features like the navigation panel. Look for improvements to many report types, including greatly expanded Dataset Reports. The redesigned references section is an embedded hitlist management tool in itself, with options for filtering, sorting, and exporting reference lists. The Gene Report has many specific enhancements, with new summaries including GO summary ribbons and protein domain graphics.
• New tools and features
  Try the new Sequence Downloader, and take a look at JBrowse if you haven't seen it yet. Other tools will be augmented in the coming months as well.
• Better under the hood, too
  The FlyBase 2.0 website includes a modern API for better programmatic access to data.

*Polytene images were first made available in October 2016.
**A full map correspondence table of recombination, cytology and sequence map values for D. melanogaster genes on the reference genome assembly is available in the Maps section of the FlyBase Resources page.

*Recombination map data were first made available in FB2016_05 (September 2016).
**The new "Recombination map" section was first released in FB2017_01 (February 2017).