Difference between revisions of "FlyBase:Links to and from FlyBase"

Latest revision as of 16:15, 27 September 2018

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/<search term>	http://flybase.org/search/humoral%20immune%20response
Symbol	http://flybase.org/search/symbol/<symbol>	http://flybase.org/search/symbol/dpp
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.

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.
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.

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 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

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 '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 can either be an ID or a short phrase (e.g. name of a pathway/reaction). Spaces are allowed, but tabs are not. This field cannot exceed 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

GenBank_dbinfo.txt

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

GenBank_linkout.txt

#Flybase ID	DBNAME  DBID        DBURL
FBgn0259750 GENBANK AAA86639    AAA86639
FBgn0005561 GENBANK AAB70249    AAB70249

Example 2

UniProt_dbinfo.txt

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

UniProt_linkout.txt

#Flybase ID	DBNAME  DBID      DBURL
FBgn0259750 UNIPROT O16117    entry/O16117
FBgn0005561	UNIPROT O16804    entry/O16804

When will my linkouts appear in FlyBase?

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.

@@ Line 48: / Line 48: @@
 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.
+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
+=== How to establish linkouts ===
-The linkout link targets (the web reports that the URLs redirect to) must provide data that isn't available in the FlyBase report.
+# [http://flybase.org/contact/email 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.
-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.
+# Validate your FlyBase IDs using our [http://flybase.org/convert/id ID Converter tool].
-Linkout data must be updated once a year. Linkout data that has not been updated in over a year will be dropped from FlyBase.
+# Construct your [[#Link_table linkout| link table]] and [[#Database_information_file| database information file]] making sure that you meet the guidelines set forth in [[#Linkout_requirements| Linkout Requirements]]
-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.
+# 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.
-FlyBase reserves the right to reject or remove linkouts if these requirements are not met.
+# Update your links at least once a year from the time of your previous submission.
-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.
+=== Linkout requirements ===
-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.
+* The linkout link targets (the web reports that the URLs redirect to) must provide data that isn't available in the FlyBase report.
-If accepted, you will be given an FTP login account that will be used to upload your linkouts to FlyBase.
+* 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.
-Validate your FlyBase IDs using our ID Converter tool.
+* Linkout data must be updated once a year. Linkout data that has not been updated in over a year will be dropped from FlyBase.
-Construct your linkout link table and database information files making sure that you meet the guidelines set forth in Linkout Requirements.
+* FlyBase IDs must be validated using our [http://flybase.org/convert/id ID Converter tool] to ensure that you are using current FlyBase IDs. Linkout links that refer to old FlyBase IDs will be automatically dropped.
-Login to ftp.flybase.org using your FTP account and deposit the appropriately named files.
+* FlyBase reserves the right to reject or remove linkouts if these requirements are not met.
-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 6 releases a year. The exact dates of each release are posted [http://flybase.org/static_pages/docs/release_schedule.html here].  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.
+=== Linkout Submission Format ===
-Link table
+==== 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
@@ Line 87: / Line 85: @@
 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.
+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.
@@ Line 93: / Line 91: @@
 Column 3 - DBID
-External database object id. This field cannot contain spaces and is limited to 255 characters.
+External database object id. This field can either be an ID or a short phrase (e.g. name of a pathway/reaction).  Spaces are allowed, but tabs are not.  This field cannot exceed 255 characters.
 Column 4 - DBURL
@@ Line 99: / Line 97: @@
 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
+==== 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
@@ Line 131: / Line 129: @@
 File examples
+==== Example 1 ====
+GenBank_dbinfo.txt
 <pre>
-Example 1-
 DBNAME  GENBANK
 BASEURL http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=
@@ Line 139: / Line 137: @@
 DESC    A genetic sequence database.
 EMAIL   johndoe@nowhere.com
+</pre>
+GenBank_linkout.txt
+<pre>
 #Flybase ID	DBNAME  DBID        DBURL
 FBgn0259750 GENBANK AAA86639    AAA86639
 FBgn0005561 GENBANK AAB70249    AAB70249
+</pre>
-Example 2-
+==== Example 2 ====
+UniProt_dbinfo.txt
+<pre>
 DBNAME  UNIPROT
 BASEURL http://www.uniprot.org/
@@ Line 151: / Line 155: @@
 DESC    A database of protein sequence and functional information.
 EMAIL   johndoe@nowhere.com
+</pre>
+UniProt_linkout.txt
+<pre>
 #Flybase ID	DBNAME  DBID      DBURL
 FBgn0259750 UNIPROT O16117    entry/O16117
 FBgn0005561	UNIPROT O16804    entry/O16804
 </pre>
+=== When will my linkouts appear in FlyBase? ===
+FlyBase performs 6 releases a year ([http://flybase.org/static/release_schedule 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.
 [[Category:Help]]