Some qualifiers can be converted into URLs giving the users an option to open external web pages for a selected gene or marker.

A regular procedure of loading the annotation tracks allows adding such qualifier links during loading by specifying values in [QualifierLinks] section of the INI file, for example:

[QualifierLinks]
; Some qualifiers can be shown as hyper-links.
; Link qualifier name-value to external sources.
; %s in the link is where a qualifier value is positioned.
;QUALIFIER_NAME=PLACEHOLDER_URL
;ID="http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=%s"
; The line above would result in the qualifier "ID" shown as a hyper-link. For example, if ID="Os1g123", the URL would be "http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/?name=Os1g123"
Name="https://phytozome-next.jgi.doe.gov/report/transcript/Gmax_Wm82_a4_v1/%s"

The hyper-link should contain a placeholder (%s) that will be replaced by the value of the selected qualifier. In the example above, if the qualifier Name has the value Glyma.01G117100.1, the URL will be converted to "https://phytozome-next.jgi.doe.gov/report/transcript/Gmax_Wm82_a4_v1/Glyma.01G117100.1"

The qualifier links can be added later, after the track has been loaded. To do this, issue the command 

add qualifier_link {mapSetId | path}

Suppose we want to add a link to the qualifier 'ec' for the MapSetId:41. The URL to the Enzyme web page for the value 2.7.11.1 would be "https://enzyme.expasy.org/EC/2.7.11.1" .


PS> add qualifier_link 41
Map set: /Glycine max/Wm82.a4.v1

Existing qualifier links (qualifier name and URL):
Name          https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Gmax&searchText=transcriptName:%s
KOG           https://www.ncbi.nlm.nih.gov/Structure/cdd/%s
Pfam          http://pfam.xfam.org/family/%s
Panther       http://www.pantherdb.org/panther/familyList.do?searchType=basic&fieldName=all&organism=all&listType=6&fieldValue=%s
KO            https://www.genome.jp/dbget-bin/www_bget?%s
GO            https://www.ebi.ac.uk/QuickGO/term/%s
Transcript    https://www.ncbi.nlm.nih.gov/nuccore/%s

Track 'Gene models':
[0] Best-hit-arabi-name ( 78,306 records) : AT1G01020.1
[1]         Description ( 73,459 records) : (1 of 1) 1.1.1.141 - 15-hydroxyprostaglandin dehydrogenase (NAD(+)) / 15-hydroxyprostaglandin dehydrogenase
[2]                  GO ( 44,937 records) : GO:0000049
[3]                  KO ( 21,255 records) : K00001
[4]                 KOG ( 27,398 records) : KOG0001
[5]                Name ( 86,256 records) : Glyma.01G000100.1
[6]             Panther ( 78,210 records) : PTHR10000,PTHR10000:SF13
[7]                Pfam ( 66,725 records) : PF00004
[8] RibosomalFrameshift (     25 records) : Ribosomal frameshift occurs at positions 13752514-13752516.
[9]             Synonym ( 72,921 records) : Glyma.01G103700
[10]  ancestorIdentifier ( 55,193 records) : Glyma.01G000100.1.Wm82.a2.v1
[11]       arabi-defline ( 70,946 records) : 1,2-alpha-L-fucosidases
[12]        arabi-symbol ( 34,239 records) : (AT)SRC2,SRC2
[13]                  ec ( 25,481 records) : 1.1.1.1
[14]             longest ( 86,256 records) : 0
[15]               pacid ( 86,256 records) : 41077002

Which qualifier will provide value for the URL? Type the line [number]: 13

Select the line number corresponding to the qualifier that will supply the value for the URL.


Qualifier: 'ec', track: 'Gene models'
Example values:
        3.1.1.4
        3.6.1.9
        5.3.4.1
        2.7.7.6

Type the URL (%s in the URL will be replaced by the value of the selected qualifier): https://enzyme.expasy.org/EC/%s
Value 'https://enzyme.expasy.org/EC/%s' for qualifier 'ec' will be inserted. (Y/N)?Y
DATA_VERSION updated
1 record have been inserted or updated

Verify the correctness of the inserted qualifier link by running the command 'list qualifier_link':


PS> list qualifier_link 41
Existing qualifier links (qualifier name and URL):
Name          https://phytozome.jgi.doe.gov/pz/portal.html#!gene?organism=Gmax&searchText=transcriptName:%s
KOG           https://www.ncbi.nlm.nih.gov/Structure/cdd/%s
Pfam          http://pfam.xfam.org/family/%s
Panther       http://www.pantherdb.org/panther/familyList.do?searchType=basic&fieldName=all&organism=all&listType=6&fieldValue=%s
KO            https://www.genome.jp/dbget-bin/www_bget?%s
GO            https://www.ebi.ac.uk/QuickGO/term/%s
Transcript    https://www.ncbi.nlm.nih.gov/nuccore/%s
ec            https://enzyme.expasy.org/EC/%s

Optional: use regular expression to extract substrings and form hyperlinks inside the text qualifier value

A qualifier link can be embedded into into a longer text of the qualifier value. For example, 'Dbxref' can contain multiple identifiers, each of them can be used to construct a hyperlink:

Gene3D:G3DSA:2.40.50.140,InterPro:IPR003871,InterPro:IPR012340,Pfam:PF02721,Superfamily:SSF50249

Use a regular expression to extract sub-strings that will be converted into the hyperlink inside the text. 

Add the qualifier link for the qualifier 'Dbxref'. Provide the corresponding URL (e.g., https://www.ebi.ac.uk/interpro/entry/InterPro/%s) and supply the regular expression to find a proper identifier in the text and convert it into a link:

For the link to Interpro, the regex might look like Interpro:(IPR\d+)

Add more qualifier links, they can refer to the same qualifier as before ('Dbxref' again). This will show the qualifier value with multiple hyper-links: