FlyBase:Links to and from FlyBase
- 1 Links to FlyBase
- 2 Links from FlyBase
Links to FlyBase
This section describes the various ways you can link from a resource (webpage, email, publication, etc.) to FlyBase. The links go to either a single data report or searches that can return one or more data reports.
Linking to a single report
When creating links from your resource to a FlyBase data report you need to use
followed by a valid FlyBase ID.
If the ID you have used no longer exists you will be redirected to a search that will return one or more IDs that correspond to the new record(s).
Linking to searches
FlyBase offers three types of URLs that provide access to our simple search interface. The first type of search performs a full text search across all data types (genes, alleles, clones, stocks, etc.). The second searches object symbols across all data types. The third type does a full text search across the data type specified. The table below illustrates the three types and provides example URLs. "<search term>" denotes the place where the terms you wish to search should be placed. You must ensure that they are URL encoded (spaces replaced with %20 and so on). "<FlyBase data type>" refers to a 4 letter code that denotes the ID namespace you wish to search (see FlyBase:Identifiers for more information).
|Full text||http://flybase.org/search/<search term>||http://flybase.org/search/humoral%20immune%20response|
|Full text within a data type||http://flybase.org/search/<FlyBase data type>/<search term>||http://flybase.org/search/FBgn/humoral%20immune%20response|
|Symbol within a data type||http://flybase.org/search/symbol/<FlyBase data type>/<search term>||http://flybase.org/search/symbol/FBal/dpp|
Links from FlyBase
FlyBase supports linkouts from any FlyBase object that has a stable FlyBase ID (e.g. FBxx[0-9]+) and a web report. Databases suitable for this kind of linking to FlyBase are those with mature data structures whose data are expressed in terms of FlyBase genetic objects that carry stable identifiers or as sequences that can be mapped to the reference sequence of a Drosophila species. FlyBase currently accepts linkout data in a simple spreadsheet table (see below), plus a summary record for the external database with link information and name. We are happy to consider additional linkout databases. Please contact us if you would like to contribute links to your database.
FlyBase-curated links and linkouts are displayed on the Report Pages in the most appropriate section of the Report. Linkouts are indicated by a Linkout label in parentheses after the field label. In addition, on the Gene Report, all FlyBase-curated links and linkouts are also grouped together in a single External crossreferences & Linkouts section.
- Contact us with a brief description of your database and links to your website. Please be sure to include links to your main site as well as the report pages that you would like us to link to.
- Validate your FlyBase IDs using our ID Converter tool.
- Construct your link table and database information file making sure that you meet the guidelines set forth in Linkout Requirements
- Contact us to let us know that you have finished preparing your files and are ready to make a submission. You will receive an email with instructions on how to upload your files. Multiple files should be tar gzipped or zip compressed into a single file.
- Update your links at least once a year from the time of your previous submission.
Please note that if you are establishing a single type of linkout between FlyBase and your site then only a single linking table and database information file is required. If you want to establish multiple types of linkouts then you need to submit a linking table and database information file for each type.
- The linkout link targets (the web reports that the URLs redirect to) must provide data that isn't available in the FlyBase report.
- Linkout links can only be established for the subset of FlyBase objects that you have additional data for. Links cannot lead to an error page, a blank report or a report that provides no additional data about the FlyBase object that is being linked from.
- Linkout data must be updated once a year. Linkout data that has not been updated in over a year will be dropped from FlyBase.
- FlyBase IDs must be validated using our ID Converter tool to ensure that you are using current FlyBase IDs. Linkout links that refer to old FlyBase IDs will be automatically dropped.
- FlyBase reserves the right to reject or remove linkouts if these requirements are not met.
Linkout Submission Format
The link table format is a simple 4 column tab delimited file. The description of the columns in order is show below. The filename of this file must use the form
Replace <dbname> with the value used in column 2 of the same file.
Column 1 - FlyBase ID
A valid FlyBase ID matching this regular expression: '^FB\w\w\d+\t'
Column 2 - DBNAME
Some unique/standard name for external database. Alpha-numeric only 'A-z0-9'. If you are submitting more than one linking table you need to ensure that the DBNAME is unique to each file. Reusing a DbName once it is used in another linking table is not permitted.
For example, if a group named "FLYLAB" wanted to establish links between FlyBase gene reports and 2 different types of analysis on their web site they could use "FLYLAB_EX1" and "FLYLAB_EX2" for the DbName column in their linkout files.
Column 3 - DBID
External database object id. This field cannot contain spaces and is limited to 255 characters.
Column 4 - DBURL
Relative link to external database web report. This is the text that will be appended to the base URL parameter that is defined in the database information file.
Database information file
The database information file contains the DbName that it corresponds to, the base URL to use for linkout hyperlinks, the homepage URL for your site and a brief description of your database. The filename of this file must use the form
Replace <dbname> with the value use in column 2 of the link table file that this file corresponds to.
The format of this file uses a simple FIELD<TAB>VALUE<NEWLINE> format. The field names are as follows
Line 1 - DBNAME
The DBNAME value used in column 2 of the link table.
Line 2 - BASEURL
The base URL to use when constructing links to your database.
Line 3 - HOMEURL
The homepage URL that represents the front page of your database.
Line 4 - DESC
A brief description of your database.
Line 5 - EMAIL
The email to use should we need to contact you.
DBNAME GENBANK BASEURL http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val= HOMEURL http://www.ncbi.nlm.nih.gov/ DESC A genetic sequence database. EMAIL email@example.com
#Flybase ID DBNAME DBID DBURL FBgn0259750 GENBANK AAA86639 AAA86639 FBgn0005561 GENBANK AAB70249 AAB70249
DBNAME UNIPROT BASEURL http://www.uniprot.org/ HOMEURL http://www.uniprot.org/ DESC A database of protein sequence and functional information. EMAIL firstname.lastname@example.org
#Flybase ID DBNAME DBID DBURL FBgn0259750 UNIPROT O16117 entry/O16117 FBgn0005561 UNIPROT O16804 entry/O16804
FlyBase performs 6 releases a year (schedule). In order for your linkouts to be included in any particular release we require that the necessary linkout files be uploaded no later than 3 weeks prior to our published release date.