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new FlyBase data reports

Don Gilbert gilbertd at bio.indiana.edu
Mon Aug 31 17:10:19 EST 1998

new FlyBase data reports

New reporting of genes, aberrations, alleles and references are
available from your FlyBase server (e.g., http://flybase.bio.indiana.edu/).  
These are labelled "new" in the results when you search these data
sections. The old reports remain available. If these new versions are
acceptable, FlyBase will retire the old ones.  As you use FlyBase,
please try the new reports, and let us know of comments or problems
you find. Many of the changes were added as a result of your helpful

Highlights of the new reports:

Abstracts -- All reports now include a brief computer-generated
abstract of the information. Later on, better human-written abstracts
will replace many of these.
Brevity -- Standard reports are now reasonably brief with sections for
fuller information (alleles, references, attributed data). The full
report option can produce large reports (some 200+ pages for genes
like Ubx, Adh, w, N, and up to 1000 pages for lacZ). With options
for allele tables, reference lists and attributed data sections, you
can get at all the information without a full report, we hope.

Reference reports -- these are expanded and redesigned.  They include
abstracts where available from PubMed or FlyBase services. Included
also are links to a journal's full paper where PubMed offers these.
There are now links to gene and aberration data that are attributed
to a reference. References can be fetched in Refer and Endnote
application formats as an option.

Output options -- The new HTML output is designed, we hope,
to read and print better than old reports. A simple HTML option is
available that looks much like the old reports. Also available are
plain text and labelled data output formats.

Body part reports -- Links to body part vocabulary reports are
available. This is very preliminary. Where reports include body part
terms, such as in expression patterns and alleles with phenotype
data, these link to a new report function. To learn for example
what is "adult thorax" and how it fits within a hierarchy of
Drosophila body parts, see these links.  A few of these include images
locating the body part, and more will be forthcoming.

Other updates -- A new section of information attributed to references
is available (Attributed data). More hyperlinks within FlyBase and to
other genomic information are available.  References in full
reports include a full citation with title, and reference lists can be
sorted by author, year or ID.
Language translation -- American English and British English are
useful translations.  For testing, there is a French translation, but it
is word substitution only, without grammar translation.  If you find
this useful, we could offer other languages this way.  If it reads
atrociously without the grammar translation, we will drop this.

More user preferences -- See the Preferences section of the FlyBase
server to style reports to your taste.  Choose language translation
and display options such as simple/fancy HTML, superscript and greek
symbol display.

Slowness -- The new report program is somewhat slower than the old
one.  It does more work behind the scenes.  It should not be
greatly slower though.  Let us know if you find problems with this.

-- d.gilbert--biocomputing--indiana-u--bloomington-in-47405
-- gilbertd at bio.indiana.edu

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