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Reference Manual F - Links to and from FlyBase
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Last updated: 17 December 2009 FlyBase provides stable links to FlyBase for use by other databases, and links to other databases from FlyBase. Links to FlyBase data items, and links between data items in FlyBase and other databases are described in the sections that follow. Drosophila Resources includes a linked list of additional databases likely to be of interest to users of FlyBase. F.1. FlyBase Identifier NumbersFlyBase assigns unique identifier numbers to several classes of object within the database. One reason for this is to allow unambiguous cross-references both within FlyBase and between FlyBase and other databases. FlyBase identifier numbers have the general form FBxxnnnnnnn where xx is an alphabetical code for the identifier class and nnnnnnn is a 7 digit number, padded with leading zeros. The following classes of object are now publicly available in FlyBase data:
Each object has a single Primary identifier number that is used to uniquely identify it in the database. An object may also have any number of Secondary identifier numbers. If an object has a secondary identifier number, it generally indicates that at some point an entry has been merged with or split from other entries in the database. This may have occured due to more data becoming available in the literature or due to correction of previous errors in the database. The rules for when primary identifier numbers become secondary are complex. Some examples are included below: A merge:If two entries A and B are found to refer to the same object, then a new primary identifier number will be given to the merged entry, and the old identifier numbers of entries A and B will be listed under this merged entry as secondary identifier numbers. A split (case 1):If one entry is found to correspond to two (or more) objects, e.g., entry A does, in fact, refer to objects X and Y, then X and Y, as new objects, each get new primary identifier numbers and the old primary identifier number of the suppressed entry A is listed as a secondary identifier number under both X and Y. A split (case 2):If one entry is found to correspond to two (or more) objects, e.g. entry A refers to objects A and X, then the existing entry for A and the new entry for X each get a new primary identifier number and the old primary identifier number of A is listed as a secondary identifier number under both A and X. If an object is simply renamed, i.e. its valid symbol in FlyBase is changed without there being a merge or a split, its primary identifier number does not change. The following classes of identifier were previously used in FlyBase, but are no longer in current use as identifier numbers in the database.
F.2. Links to external databasesFlyBase includes "pointers" to data kept by other databases in two different ways. FlyBase-curated links These are accession numbers that are incorporated into the FlyBase database, for sequence and certain other molecular data, and for reference data. Linkouts These links derive from linking tables that are maintained and provided to FlyBase by the external database. Linkouts are combined with FlyBase data for reporting on FlyBase web pages. F.2.1. FlyBase-curated linksAccession numbers from the following databases are currently incorporated into FlyBase records as FlyBase-curated links:
F.2.2. LinkoutsFlyBase 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. Linkout requirements
FlyBase reserves the right to reject or remove linkouts if these requirements are not met. How to establish linkouts
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. When will my linkouts appear in FlyBase?FlyBase performs 10 releases a year. The exact dates of each release are posted in our forum. We generally skip one month in the summer and then December. In order for your linkouts to be included in any particular release we require that the necessary linkout files be uploaded to our FTP site no later than 3 weeks prior to our published release date. Link table
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
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 '\w+'.
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.
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
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. File examplesExample 1- 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 johndoe@nowhere.com #Flybase ID DBNAME DBID DBURL FBgn0259750 GENBANK AAA86639 AAA86639 FBgn0005561 GENBANK AAB70249 AAB70249 Example 2-
DBNAME UNIPROT
BASEURL http://www.uniprot.org/
HOMEURL http://www.uniprot.org/
DESC A database of protein sequence and functional information.
EMAIL johndoe@nowhere.com
#Flybase ID DBNAME DBID DBURL
FBgn0259750 UNIPROT O16117 entry/O16117
FBgn0005561 UNIPROT O16804 entry/O16804
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