HELP DOCUMENT FOR 
"Interactive Fly Hierarchy: cross-index to FlyBase genes"

A new allied database, The Interactive Fly, developed and maintained by
Tom and Judy Brody, is now accessible on all FlyBase servers in the
Allied Data directory.  The Interactive Fly provides overviews of
various developmental and cellular processes, with the foundation
information coming from Drosophila but with considerable integration of
information from vertebrate systems as well.  According to the Brody's,
it has been developed to make the Drosophila world more accessible to
the non-specialist.  In addition to the overviews, the Brody's maintain
gene records with links to FlyBase, and maintain lists of genes that
participate in the developmental and cellular processes that are
described.

In order to make these gene lists more accessible and more readily
connected to FlyBase as well, FlyBase has developed a hierarchical view
of the Interactive Fly entitled "Interactive Fly Hierarchy: cross-index
to FlyBase genes".  This hierarchy is accessible in two FlyBase
directories: Allied Data and Genes.  The hierarchy provides an overview
of the Interactive Fly with links to the specific Interactive Fly
pages, as well as gene lists with links to the individual gene records
in FlyBase and the Interactive Fly.  

The hierarchy and the gene lists should be viewed as a work in
progress, and we appreciate all input from the community.
Comments/corrections about the Interactive Fly should be addressed to
the Brody's at jgb@access.digex.net.  Comments/corrections about the
hierarchy should be addressed to flybase-updates@morgan.harvard.edu.

The top page of the hierarchy lists the main section headings of the
hierarchy.  Some of the hierarchical branches are short and end on this
page.  Others go deeper and are linked to separate hierarchy pages.
The conventions we use in displaying the hierarchy are as follows:

- Roman boldface terms are intermediary steps in the hierarchy presented
  on a given page.  
- Roman boldface hyperlinked terms link to a subsidiary hierarchy on 
  another page.  
- Roman plaintext hyperlinked terms link to a gene list.  
_ Italicized terms are endpoints that are under construction and do not
  yet link to any further pages.
- The hyperlinked (*) symbols link the term to its appropriate page in 
  the Interactive Fly.

At the end of the hierarchical branches are gene lists.  When you 
click on a term connecting to a gene list (Roman plaintext), a page
such as the following appears:

Tissue and Organ Development
-Morphogenesis and organogenesis in the embryo (*)
--Organs and organ systems
---Mesoderm and muscle (*)
----Other transcription factors

             FlyBase Gene (search for synonyms)         Interactive Fly
Symbol              Name              Accession           Description 

 aop             anterior open        FBgn0000097            aop 
 ct                 cut               FBgn0004198            ct 
 da              daughterless         FBgn0000413            da 
 Dif  Dorsal-related immunity factor  FBgn0011274            none 
 dl                dorsal             FBgn0000462            dl 
 dmyc-???          dmyc ???           none                   dmyc-??? 
 emc          extra macrochaetae      FBgn0000575            emc 
 gcm         glial cells missing      FBgn0014179            gcm 
 mam             mastermind           FBgn0002643            mam 

The terms at the top of the page describe the hierarchy leading down to
this gene list.  Under the heading FlyBase name, there are three columns:

- "Symbol" lists the valid FlyBase gene symbol.  In a few cases, the
  Interactive Fly uses a gene symbol that is not presently in FlyBase.  
  Such cases are noted with a "-???" suffix, as in the case of dmyc-???.
- "Name" lists the valid FlyBase full name for this gene.  Again, "???"
  indicates that this name is not presently in FlyBase.
- "Accession" is the FlyBase gene identifier (FBgn number), hyperlinked
  to that gene entry in FlyBase.

Under Interactive Fly, there is one column:

_ "Description" reiterates the valid FlyBase symbol, linked to the gene
  page in the Interactive Fly.

The Interactive Fly frequently uses gene names or symbols that FlyBase
considers synonyms rather than valid names or symbols.  The hyperlinked
phrase "search for synonyms" located next to the "FlyBase Gene" heading
connects to SymbolSearch, a FlyBase tool that enables you to enter a
synonym (or valid) gene name or symbol and connects you to the valid 
FlyBase gene record.