JAL-4036 updated help about new UniProt API

[jalview.git] / help / help / html / features / uniprotsequencefetcher.html

diff --git a/help/help/html/features/uniprotsequencefetcher.html b/help/help/html/features/uniprotsequencefetcher.html
index 25d1a17..1d368ef 100644 (file)
--- a/help/help/html/features/uniprotsequencefetcher.html
+++ b/help/help/html/features/uniprotsequencefetcher.html
@@ -32,14 +32,11 @@
   allows sequences to be located via gene name, keywords, or even
   <em>via</em> manual cross-referencing from UniProt or other
   bioinformatics websites.
-  <br/>
   <br />
-  <strong>Please Note:</strong>Versions of Jalview older than 2.11.2.3 may need a configuration change
-  in order to access freetext search. Please see this post:
-  <a
-    href="https://discourse.jalview.org/t/uniprot-free-text-search-not-working-in-jalview-2-11-2-2-and-earlier/1825">https://discourse.jalview.org/t/uniprot-free-text-search-not-working-in-jalview-2-11-2-2-and-earlier/1825</a>
-  in Jalview's discussion forum for a workaround.
   <br />
+  <strong>Please Note:</strong>UniProt updated their API in July 2022.  Versions of Jalview older than 2.11.2.4 will not work with the July 2022 UniProt free text search.
+  <br />
+  <strong>The new UniProt API has a different search syntax</strong> for ranges of dates and numbers, and different query fields for advanced searches.  The general syntax of combining queries remains the same.  Because of these differences, your previously saved searches will not appear in the dropdown list next to the search box.  If you need to access these old searches they can be found in your <code>~/.jalview_properties</code> file with the label <code>CACHE.UNIPROT_FTS</code>.  If you want to transfer them to the new API search then copy the values to the <code>CACHE.UNIPROT_2022_FTS</code> label (or rename the existing label if the new one does not exist) (see the <a href="uniprotqueryfields.html">UniProtKB query fields</a> page).
   <p>
     To open the UniProt Sequence Fetcher, select UniProt as the database
     from any <a href="seqfetch.html">Sequence Fetcher</a> dialog (opened
@@ -78,8 +75,7 @@
     <li><strong><a name="text-search">Complex queries
           with the UniProt query Syntax</a></strong> The text box also allows complex
       queries to be entered. The table below provides a brief overview
-      of the supported syntax (see <a href="uniprotqueryfields.html">query
-        fields for UniProtKB</a>):
+      of the supported syntax (see the <a href="uniprotqueryfields.html">UniProtKB query fields</a> page for more details):
       <table border="1" width="95%">
         <tr>
           <td><code>human antigen</code></td>
@@ -144,7 +140,7 @@
             acids.</td>
         </tr>
         <tr>
-          <td><code>citation:(author:Arai author:Chung)</code></td>
+          <td><code>(lit_author:Arai) AND (lit_author:Chung)</code></td>
           <td>All entries with a publication that was coauthored by
             two specific authors.</td>
         </tr>
@@ -171,7 +167,7 @@
     like to be displayed or removed.</p>
   <p>
     <em>The UniProt Free Test Search Interface was introduced in
-      Jalview 2.10.0</em>
+      Jalview 2.10.0 and updated to the July 2022 API in Jalview 2.11.2.4</em>
   </p>
 </body>
-</html>
\ No newline at end of file
+</html>