A Database of Drosophila Genes & Genomes

 

News and Announcements

FlyBase News
hide Report on the November 2007 FlyBase survey ... Mar 2008

Report on the results of the FlyBase survey undertaken November 2007.

We were very pleased that respondents find that FlyBase is proving a valuable resource, with 65% of using FlyBase once a day or more and 80% finding FlyBase invaluable or very helpful in their genetic research activities. We were also pleased that most respondents who had contacted us for help found our response very good or good (88%). For a detailed breakdown of the results please see the acompanying PDF.

More importantly, your responses have been key in setting our priorities for the future, and we urge you to continue to give us suggestions for how we can improve the ability of FlyBase to assist your research. We need to understand FlyBase users' needs in order to make best use of our limited resources. We received too many suggestions to discuss all of them in this summary, and although all the points that were raised are being considered by the FlyBase team, we would like to highlight here a few of the lessons we learned from the survey.

  • Formalizing the structure of the data can result in reports that are not easy to read and understand. On the one hand users want to find out the basics of what is known about a gene from a short summary written in plain English. On the other hand using "controlled vocabularies" or "ontologies" is essential to produce a database that can be effectively searched (if different terms are used to describe the same thing, then to find all the entries for that thing, you would have to search with all possible terms; if you always use the same term, then one search is comprehensive). These contrasting needs were also reflected in the responses we received, for example when we asked "Are there data that are difficult to interpret because of formatting or presentation?" we received these two opposing responses:
    • "The automated descriptions of gene function are very poor. I reckon that's because GO doesn't work. GO and controlled vocabulary is great for informatics, but awful for the average grad student wanting to do genetics."
    • "The textual descriptions of gene expression are utterly useless for the computational community. Someone should sit down and translate them into the official vocabulary."
    We recognize that both approaches are essential: controlled vocabularies for effective searching and textual descriptions for summarizing subtle aspects of genetic, phenotypic and expression information. We have realized that no single approach will solve all problems, so we will be providing a variety of summaries. We will transfer "Red Book" summaries for the classical markers and visible phenotypes in the adult. Many users found Tom Brody's Interactive Fly a good source of information, and he has kindly agreed to supply FlyBase with his gene summaries. In addition we will set up a gene wiki, so that users can contribute to gene summaries, both in an attributed way or adding to a collective summary. We are investigating other approaches as well and welcome your further suggestions.
  • We are currently working hard to eliminate the problem that one can click on a data topic only to discover there is nothing in that category (empty matryoshka). If you haven't already noticed it, you can use Profile Manager to set your own configurations of which parts of the gene report are open by default.
  • We are significantly accelerating literature incorporation into FlyBase. We will describe our detailed plans separately, but one important feature will be to seek your help, by asking authors to give us key bits of information from the paper on a data entry web site. A number of users also asked for protein interaction data and information about useful reagents, such as antibodies. We will begin to incorporate these data types in the next several months.
  • The phenotypic and expression data need to be improved, and methods developed to improve our ability to search for genes with similar phenotypes or expression patterns.
  • Many of you would like FlyBase search tools to guess, "like Google", at what you are looking for when you type something that is not in the database. FlyBase provides the equivalent of Google spell-checking for symbols by including in the database extensive symbol synonyms. If you search for a known variant of a gene or other symbol, the record will be found. We plan to provide additional help by offering Google-style suggestions based on extension of the letters you have already typed. We will not, however, be able to provide search tools that test for all possible variants of what you have typed (even Google doesn't do that).
  • Information about orthologs and gene families need to be improved. We are replacing the current ortholog identifiers with gene symbols, and if possible names, from the other species. We are also evaluating optimal ways to present alignments and relationships amongst orthologs and gene families, and we expect the first results of these efforts to be publicly accessible in the next several months.
  • We had been concerned that those FlyBase users at great distance from our servers in Indiana might have much slower access to FlyBase; if so, this would have argued for the establishment of FlyBase mirrors around the globe. Here is the perception of the speed of the website from those countries with substantial numbers of survey respondents:
     
    Total
    Fast
    Acceptable
    Slow
    Canada
    29
    13 (45%)
    13 (45%)
    3 (10%)
    France
    58
    20 (34%)
    36 (62%)
    2 (3%)
    Germany
    52
    23 (44%)
    26 (50%)
    3 (6%)
    Spain
    32
    14 (44%)
    17 (53%)
    1 (3%)
    UK
    116
    41 (35%)
    61 (52%)
    14 (12%)
    USA
    481
    138 (29%)
    276 (57%)
    63 (13%)
    It can be seen that there is no correlation between the speed of FlyBase site and the country of access; therefore we concluded that mirrors would not improve speed of access to FlyBase. Rather, we expect that the speed of access reflects a complex set of issues such as local network conditions, capacity and configuration of individual desktops, browser choices and other issues that are largely out of our control.
hide The FB2008_02 release ... Feb 2008

Dear Colleagues,

The current FB2008_02 release embodies the first update containing a full set of gene records and annotations from the 12 fully sequenced Drosophila species. The sequences and annotations of these 12 genomes represent a community-wide effort, with the initial results published by the Drosophila 12 Genomes Consortium in Nature 450: 203-218 (FBrf0200326) and more than 40 companion papers.

In FB2008_02, the 11 non-melanogaster annotation sets correspond to the consensus GLEANR gene models used by the Drosophila 12 Genomes Consortium. The version 1.0 GLEANR annotations for 10 species (excluding D.melanogaster and D.pseudoobscura) were fully incorporated into FlyBase beginning with database release FB2008_01. The current version 2.1 GLEANR annotations of the D. pseudoobscura genome replace the previous version 2.0 annotation set and are newly presented in FB2008_02. Where the connection was obvious, the GLEANR gene models have been associated with pre-existing FlyBase genes. The D. melanogaster annotation set is continuously updated, with version 5.5 being current in FB2008_02. However, it should be noted that the initial analyses for the Drosophila 12 Genomes Consortium publications were based on comparisons with the version 4.3 D. melanogaster annotation set. This annotation set along with the current annotations of the other 11 species will be archived to allow continued reference to these canonical analysis sets.

Over the next several release cycles, we expect to update a small subset of annotations in non-melanogaster species. These are necessary to comply with GenBank requirements regarding annotation submissions which are currently in process. These changes will include merges of annotations that share coding sequences into a single multi-transcript gene model, removal or truncation of annotations that artifactually span sequence gaps, and elimination of spurious short annotations of less than 50 residues lacking orthology support. In the longer term, we will establish procedures for the research community to contribute modifications to these annotation sets.

We are excited with the unprecedented research opportunities that these new genomes represent.

Sincerely,

The FlyBase Consortium

hide Fly Genomes in Nature ... Nov 2007

FlyBase is pleased to call your attention to the publication of the main community papers describing the sequence and analysis of the 12 Drosophila genomes in the November 8 issue of Nature.

These papers and more than 40 companion papers that are being published over the next few months in several journals represent the initial results of analyses of an incredibly rich body of information. This is a landmark event in the long and wonderful history of Drosophila genetics and genomics, and marks a new phase in comparative genomics.

We are indebted to our colleagues who participated in this community effort and are confident that both the Drosophila and the greater scientific community will benefit from their efforts. On behalf of these communities, we wish to thank the National Human Genome Research Institute (NHGRI) of NIH for funding the sequencing effort and the participating sequencing centers for producing the sequences and assemblies.

FlyBase is actively working on finalizing the annotation sets for display in FlyBase and for their submission to GenBank on behalf of the Drosophila 12 Genomes Consortium. FlyBase will also provide access to other important data sets from these initial analyses. If you have suggestions/requests for information sets from these analyses that you would like to see displayed or accessible from FlyBase, please use our Contact FlyBase form to send us these suggestions.

The specific references for the main papers are:

Drosophila 12 Genomes Consortium, 2007. Evolution of genes and genomes on the Drosophila phylogeny.
Nature 450, 203-218 (8 November).

and

Stark et al., 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Nature 450, 219-232 (8 November).

hide Textpresso for Fly ... Oct 2007

FlyBase is pleased to announce the addition of a link to "Textpresso for Fly", a full-text search engine for the biological literature of the Drosophilidae. Textpresso for Fly currently contains 20,000 full text articles and 39,000 abstracts from the Drosophila literature.

Searches with keywords yield hits that consist of abstracts and (where available) complete sentences from the full text of the matching papers. In addition, more powerful and refined searches can be done with the use of categories. Categories are collections of conceptually related words whose occurrences have been marked up in the full text. For example, if one is interested in finding papers discussing the regulation of bcd, one would type the keyword "bcd" and specify the category "regulation". The search engine then returns sentences from full texts that contain at least one mention of the gene 'bcd' and at least one word or phrase from the list of terms comprising the "regulation" category. The lists of ~100 category types and their constituent terms are easily accessed from the Textpresso site. Links from the Textpresso reports lead users to the FyBase reference reports, from which the FlyBase-curated data can be accessed.

The link to "Textpresso for Fly" may be found in the "Resources" menu of the navigation bar.

FlyBase Announcements
hide FB2008_03 Released ... Mar 2008

Dear Colleagues,

FlyBase is pleased to announce the release of FB2008_03. For more information on this release please see the Release Notes.

Our next release (FB2008_04) has been scheduled for Friday April 25th, 2008. Please visit this forum thread for updates and other information about FB2008_04.

Sincerely,

The FlyBase Consortium

hide BLAST Upgrade and FlyBase Forum ... Dec 2007

FlyBase is pleased to announce changes to our BLAST service and a new FlyBase forum.

BLAST

Our BLAST service has undergone a significant overhaul to improve the user interface and make the results easier to view. Here are a few new features to look for:

  • Improved user interface.
  • Improved documentation.
  • Improved result page layout.
  • Added overview graphic of BLAST results
  • Added ability to download the "Hit" sequence in FASTA format.
  • Added ability to send BLAST hits to other FlyBase tools when searching annotated genes or proteins.
  • Upgraded BLAST engine to NCBI BLAST 2.2.17

We hope you enjoy these enhancements.

FlyBase Forum

We would also like to announce the immediate availability of the new FlyBase forum. The FlyBase forum provides a place for reading news from FlyBase, posting announcements, job postings, asking questions about FlyBase to us and the community. It also provides a general discussion area, a place for posting and discussing experimental protocols, and a place to search or offer stocks and reagents. To post messages you must register.

Many of the BLAST improvements and the request for a forum came directly from you so please continue to let us know what you think through the Contact FlyBase form.

Regards,
FlyBase

hide Apollo Support ... Sep 2006

From this point forward FlyBase will be providing Apollo viewable annotation data in chado-xml format only. The latest version of Apollo has been modified to retrieve annotation data via the web in this format. Therefore, we recommend that you upgrade to the latest available version of Apollo

We will no longer provide annotation data in GAME-XML format and while Apollo is still able to load and view existing GAME-XML data the data files must be available on the local machine as web retrieval of GAME files is no longer supported.

Please be aware that when Apollo is retrieving annotation data from the web it is obtaining precomputed chunks of xml. While the pieces have been generated to not span any gene models retrieval by sequence range may not result in the exact sequence requested being loaded into Apollo.

Please use the contact FlyBase form to send questions and requests for help to FlyBase.

hide Linkouts in FlyBase ... Mar 2006

FlyBase offers direct "linkouts" from our gene report pages to other web-based Drosophila data services. . The FlyBase Consortium wishes to thank the organizers and developers of these data sets for helping us provide a great deal of valuable information on Drosophila genes and genomes.

  • BDGP in situ Gene Expression Database (http://toy.lbl.gov:8888/cgi-bin/ex/insitu.pl)
  • Drosophila melanogaster Exon Database (http://proline.bic.nus.edu.sg/dedb/index.html)
  • Drosophila RNAi Screening Center (http://www.flyrnai.org/)
  • FLIGHT - Integrating Genomic and High-Throughput data (http://flight.licr.org/)
  • Fly GRID Interaction Data (http://biodata.mshri.on.ca:80/fly_grid/servlet/SearchPage)
  • FlyMine - integrated genomics and proteomics (http://www.flymine.org/)
  • NCBI Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/projects/geo/)
  • Heidelberg Database for RNAi Phenotypes (http://www.dkfz-heidelberg.de/signaling/ernai/ernai.html)
  • Hybrigenics Drosophila PIMRider (http://pim.hybrigenics.com/pimriderext/droso/index.html)
  • Yale Developmental Gene Expression (http://genome.med.yale.edu/Lifecycle/)
  • InParanoid computed orthology calls (http://inparanoid.cgb.ki.se/index.html)
  • PANTHER ClassificationSystem (http://www.pantherdb.org/)

In addition to these links FlyBase also provide direct links to the Drosophila records in the major international nucleotide, protein and bibliographic databases.

Community News & Announcements
hide Drosophila Researcher Genealogy ... May 2008

Are you in the academic lineage from Thomas Hunt Morgan? The Drosophila Researcher Genealogy begun by Keith Maggert has been expanded and incorporated into the Academic Tree Project. You can now log in and add yourself, your students, your advisors, and collaborators to the tree for Drosophila researchers. The Fly Tree currently includes over 1200 people. Put yourself on the tree at http://www.academictree.org/flytree/

Questions and comments can be directed to Mike Dietrich at: Michael.DietrichlinkDartmouth.edu

hide Pam Lewis's Artwork ... Apr 2008

The family of Ed Lewis has finished a project that Ed Lewis started before his death: to publish the amazing artwork of his wife, Pam. An on-line version of this book can be accessed at http://www.fruitfly.org/lewis/Site/Back.html. Several of her pen and ink and watercolors have been used in posters for scientific meetings. The Lewis family invites you to enjoy them.

hide Seymour Benzer Obituary ... Dec 2007

Dear Colleagues,

It is with sadness that FlyBase notes the passing of one of the true giants of genetics, Seymour Benzer on Nov. 30. Not only did he establish the basic concept of the complementation unit (cistron) through his groundbreaking work on the rII genes in phage T4 in the early days of molecular biology, but he then switched fields completely and founded the modern era of neurogenetics through his seminal work on neurobiology and behavior in Drosophila. The legacy of this work is immense. Just as importantly, he was a dear friend and mentor to many of us and we shall miss him.

hide The Drosophila Board White Paper 2007 ... Nov 2007

Dear Fly Person,

I am writing to ask for your comments on the Drosophila Board White Paper 2007 draft. The White Paper is extremely important for informing funding agencies including the NIH and NSF of our top research priorities for the next 2-3 years. Past White Papers have helped to justify funding for valuable community resources such as insertion mutations, cDNA collections, FlyBase and fly and molecular stock centers. The Drosophila Board White Paper 2007 draft has been assembled by the Board of Directors based on input from many members of the community. For it to accurately reflect the community's priorities, we need your input now. Please download the draft and send me your comments. Do you agree with the priorities? Is something important to your research missing? Are there things in the document you do not agree with? Please send comments even if it is only to endorse the White Paper. The White Paper is most powerful when backed by everyone in the research community including students, postdocs and PI's. Your opinion matters! Download the Drosophila Board White Paper 2007 draft at:

http://flybase.org/static_pages/news/whitepapers/DrosBoardWP2007_DRAFT_11_06_07.pdf

Send comments to trudy_mackaylinkncsu.edu with "White Paper" on the subject line.

Deadline for comments: November 30, 2007.

Thank you for your help,

Trudy Mackay
For the Drosophila Board of Directors

hide 2008 Drosophila Image Award competition ... Nov 2007

Dear Drosophila Colleagues,

This is the first (and only) call for submissions for the 2008 Drosophila Image Award. The award will be presented at the upcoming Drosophila Research Conference in San Diego on April 3, 2008.

Finalists and winners of the past awards can be viewed at: http://www.drosophila-images.org/

The Image Award program has been initiated in recognition of the important role that compelling images have played in Drosophila research. To encourage and celebrate the continuing creation of such images, finalist images will be displayed on the opening evening of the conference, at which time the winner will be presented with a plaque.

The Award will be given to the most striking image that clearly conveys a point of important biological information in Drosophila research. All images that have been or will be published in a primary research journal in 2007 are eligible. Submissions can be made electronically to imageawardlinklists.berkeley.edu

We encourage you to submit your work for consideration. Submissions are open until Jan. 28, 2008

Please see http://www.drosophila-images.org/ for more details and complete instructions for submission.

Sincerely,
The Drosophila Image Award Committee:
Michelle Arbeitman
David Bilder
Ross Cagan
Brian Calvi
Peter Lawrence

hide Bloomington Drosophila Stock Center - U.S. Drosophila Import Permits ... Oct 2007

The Bloomington Stock Center is now providing new web pages on U.S. Import Permits.

hide modENCODE Request ... Aug 2007

The groups within the modENCODE project would like community input in deciding on a list of transcription factors to test for genome-wide binding sites using ChIP-chip and ChIP-Seq methods. The availability of suitable antibodies as well as community priorities are important factors in deciding which transcription factors will be mapped first.

Please visit the modENCODE project wiki pages to nominate and vote on the transcription factors that you believe should have high priority. (You will need to create an account, but it should only take a minute or two.)

hide Drosophila Network News (bionet.drosophila)
  • Search and read Drosophila network news at www.bio.net
  • Post a new article to dros/bionet.drosophila via the BIOSCI mail-Usenet gateway: droslinknet.bio.net