Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/help/help/html/features/seqfetch.html b/help/help/html/features/seqfetch.html
index e726c49..7d4a389 100755 (executable)
--- a/help/help/html/features/seqfetch.html
+++ b/help/help/html/features/seqfetch.html
@@ -38,7 +38,7 @@
       the database you want to retrieve sequences</strong> from the database
     chooser.
   </p>
-  <img src="selectfetchdb.gif" align="left" width="480" height="204"
+  <img src="selectfetchdb.gif" align="left"
     alt="Database selection dialog for fetching sequences (introduced in Jalview 2.8)">
   <p>
     The databases are shown as a tree, and ordered alphabetically;
@@ -69,17 +69,36 @@
         accession ids</strong> (as a semi-colon separated list), or press the
       &quot;Example&quot; button to paste the example accession for the
       currently selected database into the retrieval box. Finally, press
-      &quot;OK&quot; to initiate the retrieval.</li>
+      &quot;OK&quot; to initiate the retrieval.
+      <br />
+      For the PDB and UniProt sequence fetchers, choose the "Retrieve IDs" tab
+      to search for accession ids.</li>
   </ol>
 
-  <p>If you use the WSDBFetch sequence fetcher services (EMBL,
-    UniProt, PFAM, and RFAM) in work for publication, please cite:</p>
-  <p>
-    Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
-    J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
-    R. <br> SOAP-based services provided by the European
-    Bioinformatics Institute.<br> Nucleic Acids Res. 33(1):W25-W28
-    (2005) <br> <br>
-  </p>
+  <p>If you use the Sequence Fetcher, please remember to cite the
+    corresponding services (linked to below):</p>
+  <ul>
+    <li>Ensembl - <a
+      href="https://github.com/Ensembl/ensembl-rest/wiki#citing">The
+        Ensembl REST API</a></li>
+    <li>EMBL/EMBLCDS - Provided by the <a
+      href="https://www.ebi.ac.uk/ena/browser/api/#/ENA_Browser_Data_API/getFlatFileUsingGET">European
+        Nucleotide Archive's ENA Data API</a><br />
+    <em>Note: Versions of Jalview prior to 2.11.1.1 employed the
+        XML endpoint of the ENA browser, which was retired in August
+        2020.</em></li>
+    <li>Uniprot - Free Text Search and Retrieval via the <a
+      href="https://www.uniprot.org/help/api">Uniprot REST API</a></li>
+    <li>PDB - Free Text Search via the <a
+      href="https://www.ebi.ac.uk/pdbe/api/doc/search.html">PDBe
+        REST API</a> and retrieval via <a
+      href="https://www.ebi.ac.uk/Tools/dbfetch/">WSDbFetch</a><br />
+      Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate
+      J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez
+      R. <br> SOAP-based services provided by the European
+      Bioinformatics Institute.<br> Nucleic Acids Res.
+      33(1):W25-W28 (2005) <br> <br>
+    </li>
+  </ul>
 </body>
 </html>