Linking information for external database

Last Updated: December 2003

FlyBase currently accepts external database link data to gene reports in a simple spreadsheet table (tab-delimited, 4 columns), plus a summary record for each external DB with link info and name. This format may change. Most likely we will continue supporting this, but add an XML format that includes these tabular fields plus the database summary record. Update processing from data providers as well as stale-link checks will become automated.

The current update mechanism is to email to linkoutflybase.net

The link table

The link table looks like this:

#FlybaseID	DbName	  DbID		DbUrl (relative to base DBurl)
FBgn0000011	BDGPisx	  8078		ab
FBgn0000011	IFly	  FBgn0000011	../neural/abrupt.htm
FBgn0000014	IFly	  FBgn0000014	../segment/abdmla1.htm
FBgn0000014	KWgx	  FBgn0000014	FBgn0000014
                                

FlybaseID:

valid FlyBase ID, currently only FBgn is supported but others can be. '^FB\w\w\d+\t' is required for valid data line

DbName:

some unique/standard name for external database. Alpha-numeric only (\w+)

DbID:

external database object id (any opaque string)

DbUrl:

relative link to external database web report (this is the essential one, appended to Base DbURL for making hyperlink).

Each link table should have a common base-url, but you can provide as many tables as base-urls, with base summary record.

Database summary record

The database summary record looks like this, for Base-url, one per DbName ( == DBID here).

OPVR
{
DBID|BDGPisx
-- DbName database name; alphanumeric only; required;
unique/standard among bio-dbs; used in visible label (DbName:DbAcc) for hyperlinks

BURL|http://www.fruitfly.org/cgi-bin/ex/bquery.pl?qtype=report&searchfield=symbol&find=
-- Base url, *appending* database DbUrl returns proper page (required)

NAM|BDGP in situ Gene Expression Database
-- Full name of database (displayed in long reports; optional)

LKNA|BDGP in situ
-- Brief name, displayed in FlyBase summary reports (optional)

ICO|http://www.fruitfly.org/images/logo.gif
-- Database icon (not yet displayed; optional)

LKHE|BDGP in situ Expression Report with images
-- Database link help, long description for help pages (optional; html ok; todo)

LKFL|flybase-data-field-here
-- Database link field: FlyBase data field to link DbURL to (not yet implemented)
-- valid data fields are listed at http://flybase.net/docs/lk/fbhelp/
}

XML Database summary record

This summary record can also be provided as XML:

<OPVR>
<DBID>dbid-here</DBID><BURL>url-here</BURL>...
</OPVR>

An Example database summary:

OPVR
{
DBID|FlyGRID
BURL|http://biodata.mshri.on.ca/fly_grid/servlet/SearchResults?keywords=
NAM|Fly GRID, General Repository for Interaction Datasets
ICO|
LKNA|Fly GRID
LKHE|The General Repository for Interaction Datasets,
|<a href="http://biodata.mshri.on.ca:80/fly_grid/servlet/SearchPage">Drosophila melanogaster interaction site</a>.
}

OR ---

<OPVR>
<DBID>FlyGRID</DBID>
<BURL>http://biodata.mshri.on.ca/fly_grid/servlet/SearchResults?keywords=</BURL>
<NAM>Fly GRID, General Repository for Interaction Datasets</NAM>
<ICO></ICO>
<LKNA>Fly GRID</LKNA>
<LKHE>The General Repository for Interaction Datasets,
<a href="http://biodata.mshri.on.ca:80/fly_grid/servlet/SearchPage">Drosophila melanogaster interaction site</a>.
</LKHE>
</OPVR>