Liverpool AI link outs from PubMed IDs in User Comments and PubMed tables

Model/lib/wdk/model/records/commentTableQueries.xml

@@ -58,7 +58,7 @@
             <column name="project_id"/>
             <column name="comment_id"/>
             <column name="pmids"/>
-            <column name="pmids_link"/>
+            <column name="liverpool_ai_links"/>
             <column name="genecount"/>
             <column name="filecount"/>
             <column name="stable_id"/>
@@ -86,11 +86,18 @@
                   SELECT c.comment_target_id, c.project_name as project_id, c.comment_id,
                          ga.source_id, c.stable_id, c.comment_date, c.headline,
                          files.filecount, references.pmids, 
-                         CASE  WHEN (references.pmids is null) THEN ''
-                         WHEN REGEXP_LIKE(references.pmids , '^-?[[:digit:],.]*$') 
-                           THEN '<a href="/cgi-bin/pmid2title?pmids=' || references.pmids || ' ">' || references.pmids || '</a>' 
-                           ELSE '<a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=' || references.pmids  || ' ">' || references.pmids || '</a>' 
-                           END AS pmids_link,
+                         CASE WHEN (references.pmids is null) THEN ''
+                              WHEN INSTR(references.pmids, ',') = 0 THEN 
+                                '<a href="https://pgb.liv.ac.uk/aisum/?db=' || c.project_name || '&id=' || references.pmids || '&gene=' || ga.source_id || '" target="_blank">View AI Summary</a>'
+                              ELSE REPLACE(
+                                REGEXP_REPLACE(
+                                  references.pmids,
+                                  '([0-9]+)',
+                                  '<a href="https://pgb.liv.ac.uk/aisum/?db=' || c.project_name || '&id=\1&gene=' || ga.source_id || '" target="_blank">\1</a>'
+                                ),
+                                ',', ', '
+                              )
+                         END AS liverpool_ai_links,
                          gene_counts.geneCount,
                          &&selectReviewed&&
                          u.first_name || ' ' || u.last_name || ', ' || u.organization as user_name_org

Model/lib/wdk/model/records/geneRecord.xml

@@ -1688,6 +1688,10 @@ name" internal="true"/>
             <![CDATA[/cgi-bin/pmid2title?pmids=$$pmids$$]]>
           </url>
         </linkAttribute>
+        <columnAttribute name="liverpool_ai_links" 
+              displayName="AI Summary"
+              help="Experimental feature that aims to extract gene function summaries from publications. Links open in a new tab at our Liverpool colleagues' website.">
+        </columnAttribute>
         <columnAttribute name="genecount" displayName="# Related Genes"/>
         <columnAttribute name="comment_status" displayName="Status"/>
         <columnAttribute name="filecount" displayName="# Uploaded Files"/>
@@ -2653,6 +2657,8 @@ name" internal="true"/>
 	    <description><![CDATA[<i>Shown are references from the NCBI gene2pubmed database and from manual assignment by curators.</i>]]></description>
             <columnAttribute displayName="PubMed ID" name="pubmed_id"  internal="true"/>
             <columnAttribute displayName="doi" name="doi"  internal="true"/>
+            <columnAttribute displayName="Gene ID" name="source_id"  internal="true"/>
+            <columnAttribute displayName="Project ID" name="project_id"  internal="true"/>
 
             <linkAttribute name="pubmed_link"
                         displayName="PubMed ID" >
@@ -2684,6 +2690,23 @@ name" internal="true"/>
 
             <columnAttribute displayName="Title" name="title"/>
             <columnAttribute displayName="Authors" name="authors"/>
+
+            <linkAttribute
+              name="liverpool_ai_link"
+              displayName="AI Summary"
+	      help="Experimental feature that aims to extract gene function summaries from publications. Links open in a new tab at our Liverpool colleagues' website." >
+                 <displayText>
+                    <![CDATA[
+                    View AI Summary
+                    ]]>
+                 </displayText>
+                <url>
+                    <![CDATA[
+                    https://pgb.liv.ac.uk/aisum/?db=$$project_id$$&id=$$pubmed_id$$&gene=$$source_id$$
+                    ]]>
+                </url>
+            </linkAttribute>
+
             <propertyList name="includeInDumper"><value>true</value></propertyList>
           </table>
 

Model/lib/wdk/ontology/individuals.txt

@@ -302,7 +302,7 @@ GeneRecordClasses.GeneRecordClass.MetabolicPathwaysMPMP	http://edamontology.org/
 GeneRecordClasses.GeneRecordClass.MetabolicPathways	http://edamontology.org/topic_0753	Metabolic Pathways	GeneRecordClasses.GeneRecordClass	table	MetabolicPathways				transcript	2	record	download	
 GeneRecordClasses.GeneRecordClass.Alias	http://edamontology.org/topic_0219	Curation and Annotation	GeneRecordClasses.GeneRecordClass	table	Alias				transcript		record	download	
 GeneRecordClasses.GeneRecordClass.strain	http://edamontology.org/topic_3299	Evolutionary Biology	GeneRecordClasses.GeneRecordClass	attribute	strain				gene		record-internal	download	
-GeneRecordClasses.GeneRecordClass.PubMed	http://edamontology.org/topic_3068	Literature and Reference	GeneRecordClasses.GeneRecordClass	table	PubMed				transcript		record	download	
+GeneRecordClasses.GeneRecordClass.PubMed	http://edamontology.org/topic_3068	Literature and Reference	GeneRecordClasses.GeneRecordClass	table	PubMed				transcript	1	record	download	
 GeneRecordClasses.GeneRecordClass.Cellxgene	http://edamontology.org/topic_3308	Transcriptomics	GeneRecordClasses.GeneRecordClass	table	Cellxgene				transcript		record		
 GeneRecordClasses.GeneRecordClass.GeneLinkouts	http://edamontology.org/topic_3345	Data identity and mapping	GeneRecordClasses.GeneRecordClass	table	GeneLinkouts				transcript		record	download	
 GeneRecordClasses.GeneRecordClass.3dPreds	http://edamontology.org/topic_0081	Structure Analysis	GeneRecordClasses.GeneRecordClass	table	3dPreds				transcript	2	record	download