Adds synonyms, antonyms, and related terms to UI

Improves domain concept clarity by displaying synonyms, antonyms,
and related terms for biological processes. Enhances user understanding
and access to relevant terminology for each concept.

Author: halaarar

shiny_app/app.R

@@ -1260,6 +1260,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "A chemical reaction in which its product or intermediate accelerates the same reaction. Supports nonlinear self-reinforcement and chemical self-organization."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-catalysis, autocatalysis, self-reinforcing reaction"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "heterocatalysis, enzyme-catalyzed"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "chemical oscillation, nonlinear dynamics")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1285,6 +1294,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "A protein kinase phosphorylates its own amino acid residues (cis or trans), tuning its conformation, catalytic activity, localization, and signaling dynamics."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-phosphorylation, cis-phosphorylation, intramolecular phosphorylation"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "dephosphorylation, heterophosphorylation"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "autokinase")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1311,6 +1329,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "The process by which a protein removes phosphate groups from itself, typically through intrinsic phosphatase activity or conformational changes that reverse autophosphorylation."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-dephosphorylation, autophosphatase activity, intrinsic phosphatase"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "autophosphorylation, heterophosphatase"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "autophosphorylation, phosphatase activity")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1336,6 +1363,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "The process where an acetyltransferase acetylates itself, adding acetyl groups to its own lysine residues, often affecting protein activity or stability."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-acetylation, cis-acetylation, intrinsic acetyltransferase activity"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "deacetylation, heteroacetylation"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "histone modification, lysine acetylation, protein acetylation")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1361,6 +1397,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "The process by which a protein removes methyl groups from itself through intrinsic demethylase activity, reversing the effects of methylation."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-demethylation, intrinsic demethylase activity"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "automethylation, heteromethylation"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "protein methylation, demethylase activity, epigenetic regulation")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1386,6 +1431,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "An E3 ubiquitin ligase attaches ubiquitin to itself, altering its stability, proteasomal targeting, and signaling functions depending on chain type and site."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-ubiquitination, cis-ubiquitination, auto-ubiquitylation"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "deubiquitination, heteroubiquitination"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "protein degradation")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1412,6 +1466,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "A gene product regulates transcription of the same gene through positive or negative feedback, tuning gene expression dynamics, noise, and homeostasis."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-regulation, autonomous regulation, homeostatic control"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "heteroregulation, external regulation"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "homeostasis, feedback control")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1438,6 +1501,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "Small diffusible molecules synthesized and detected by bacteria. Their accumulation with increasing cell density triggers coordinated community-wide transcriptional changes."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-induction, auto-stimulation, positive feedback induction"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "autorepression, negative feedback"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "autoactivation, positive feedback")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1464,6 +1536,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "Intrinsic structural interactions prevent inappropriate activation of a protein, maintaining it in an inactive state until relieved by ligand binding, structural rearrangement, or post-translational modification."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-inhibition, negative autoregulation, self-repression"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "autoactivation, positive autoregulation"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "negative feedback, autorepression")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",
@@ -1490,6 +1571,15 @@ ui <- navbarPage(
               p(style = "color: #555; margin-bottom: 15px;",
                 "Self-degradation mediated by endogenous lytic enzymes, occurring during programmed cell death, post-mortem breakdown, or engineered microbial lysis systems."),
 
+              div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
+                h5("Synonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "self-cleavage, autocatalytic cleavage, self-proteolysis"),
+                h5("Antonyms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0 0 12px 0; padding-left: 10px; color: #666; font-size: 14px;", "heterolysis, trans-cleavage"),
+                h5("Related Terms", style = "color: #2c3e50; font-size: 14px; margin-bottom: 8px;"),
+                p(style = "margin: 0; padding-left: 10px; color: #666; font-size: 14px;", "autocatalysis")
+              ),
+
               div(style = "background: #ffffff; padding: 15px; border-radius: 6px; margin: 15px 0; border: 1px solid #f0f0f0;",
                 h5("Core Ontology Relations", style = "color: #2c3e50; font-size: 14px; margin-bottom: 10px;"),
                 tags$ul(style = "margin: 0; padding-left: 20px; color: #555;",