Difference between revisions of "FlyBase:RefMan F."

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[[FlyBase:Identifiers|FlyBase Identifiers (FBIDs)]]
 
[[FlyBase:Identifiers|FlyBase Identifiers (FBIDs)]]
 +
 +
== FlyBase Identifier Numbers ==
 +
 +
FlyBase 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.  Some data classes, such as FBsf, use more than 7 digits.
 +
 +
The following classes of object are now publicly available in FlyBase data:
 +
 +
{| class="wikitable"
 +
|-
 +
! Data Class !! Description
 +
|-
 +
| FBab || aberration
 +
|-
 +
| FBal || allele
 +
|-
 +
| FBba || balancer/genotype variant
 +
|-
 +
| FBcl || clone
 +
|-
 +
| FBgn || gene
 +
|-
 +
| FBim || image
 +
|-
 +
| FBig || interaction
 +
|-
 +
| FBlc || large dataset metadata
 +
|-
 +
| FBmc || molecular construct
 +
|-
 +
| FBms || molecular segment
 +
|-
 +
| FBpp || polypeptide
 +
|-
 +
| FBrf || reference
 +
|-
 +
| FBsf || sequence feature
 +
|-
 +
| FBst || stock
 +
|-
 +
| FBtc || cell line
 +
|-
 +
| FBti || transposable element insertion
 +
|-
 +
| FBtp || transgenic construct or natural transposon
 +
|-
 +
| FBtr || transcript
 +
|}
 +
 +
 +
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.
 +
 +
FBan - annotation
 +
  
 
[[FlyBase:Links to and from FlyBase|Links to and from FlyBase]]
 
[[FlyBase:Links to and from FlyBase|Links to and 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
 +
 +
'''http://flybase.org/reports'''
 +
 +
followed by a valid [[FlyBase:Identifiers|FlyBase ID]].
 +
 +
e.g.
 +
* http://flybase.org/reports/FBgn0000119
 +
* http://flybase.org/reports/FBpp0086821
 +
* http://flybase.org/reports/FBal0012091
 +
 +
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 [http://en.wikipedia.org/wiki/Percent-encoding 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).
 +
 +
{| class="wikitable" border="1"
 +
|-
 +
! Search Type
 +
! URL
 +
! Example
 +
|-
 +
| Full text
 +
| <nowiki>http://flybase.org/search/simple/<search term></nowiki>
 +
| http://flybase.org/search/simple/humoral%20immune%20response
 +
|-
 +
| Symbol search
 +
| <nowiki>http://flybase.org/search/simple/symbol/<symbol></nowiki>
 +
| http://flybase.org/search/simple/symbol/dpp
 +
|-
 +
| Full text within a data type
 +
| <nowiki>http://flybase.org/search/simple/<FlyBase data type>/<search term></nowiki>
 +
| http://flybase.org/search/simple/FBgn/humoral%20immune%20response
 +
|}
 +
 +
== 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.
 +
 +
Linkout requirements
 +
 +
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 the 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.
 +
 +
How to establish linkouts
 +
 +
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.
 +
If accepted, you will be given an FTP login account that will be used to upload your linkouts to FlyBase.
 +
Validate your FlyBase IDs using our ID Converter tool.
 +
Construct your linkout link table and database information files making sure that you meet the guidelines set forth in Linkout Requirements.
 +
Login to ftp.flybase.org using your FTP account and deposit the appropriately named files.
 +
Contact us to let us know that you have completed your submission.
 +
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.
 +
 +
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
 +
 +
<dbname>_linkout.txt
 +
 +
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 '\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.
 +
 +
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
 +
 +
<dbname>_dbinfo.txt
 +
 +
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.
 +
 +
File examples
 +
 +
Example 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
 +
 +
 +
 +
 +
  
 
[[Category:DONE]]
 
[[Category:DONE]]
 +
[[Category:Help]]

Revision as of 15:22, 20 February 2014

Links to and from FlyBase (RefMan F)

FlyBase Identifiers (FBIDs)

FlyBase Identifier Numbers

FlyBase 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. Some data classes, such as FBsf, use more than 7 digits.

The following classes of object are now publicly available in FlyBase data:

Data Class Description
FBab aberration
FBal allele
FBba balancer/genotype variant
FBcl clone
FBgn gene
FBim image
FBig interaction
FBlc large dataset metadata
FBmc molecular construct
FBms molecular segment
FBpp polypeptide
FBrf reference
FBsf sequence feature
FBst stock
FBtc cell line
FBti transposable element insertion
FBtp transgenic construct or natural transposon
FBtr transcript


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.

FBan - annotation


Links to and 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

http://flybase.org/reports

followed by a valid FlyBase ID.

e.g.

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).

Search Type URL Example
Full text http://flybase.org/search/simple/<search term> http://flybase.org/search/simple/humoral%20immune%20response
Symbol search http://flybase.org/search/simple/symbol/<symbol> http://flybase.org/search/simple/symbol/dpp
Full text within a data type http://flybase.org/search/simple/<FlyBase data type>/<search term> http://flybase.org/search/simple/FBgn/humoral%20immune%20response

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.

Linkout requirements

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 the 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.

How to establish linkouts

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. If accepted, you will be given an FTP login account that will be used to upload your linkouts to FlyBase. Validate your FlyBase IDs using our ID Converter tool. Construct your linkout link table and database information files making sure that you meet the guidelines set forth in Linkout Requirements. Login to ftp.flybase.org using your FTP account and deposit the appropriately named files. Contact us to let us know that you have completed your submission. 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.

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

<dbname>_linkout.txt

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 '\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.

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

<dbname>_dbinfo.txt

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.

File examples

Example 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

  1. 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

  1. Flybase ID DBNAME DBID DBURL

FBgn0259750 UNIPROT O16117 entry/O16117 FBgn0005561 UNIPROT O16804 entry/O16804

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