bio.tools update for tool with id: asafind

data/asafind/asafind.biotools.json

@@ -3,9 +3,39 @@
     "additionDate": "2025-12-15T14:17:14.627791Z",
     "biotoolsCURIE": "biotools:asafind",
     "biotoolsID": "asafind",
+    "collectionID": [
+        "ELIXIR-CZ",
+        "Czech Republic"
+    ],
     "confidence_flag": "tool",
     "cost": "Free of charge",
-    "description": "ASAFind is a software that predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin. \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example can be found in diatoms and cryptophytes. The plastids in these groups of algae are not only surrounded by additional membranes compared to primary plastids (as found in red-, green- and glaucophyte algae), but also by an additional compartment between the second and third membrane, which is referred to as the periplastidic compartment. The N-terminal part of the pre-protein of nucleus-encoded diatom plastid proteins is an ER-type signal peptide, which is followed by a transit peptide, and the cleavage site between these two targeting domains is characterized by a characteristic sequence motif (“ASA-FAP”), such targeting pre-sequences are commonly referred to as bipartite targeting signals.",
+    "credit": [
+        {
+            "email": "mvohnoutova@jcu.cz",
+            "name": "Marta Vohnoutov\u00e1",
+            "orcidid": "https://orcid.org/0000-0002-8915-8626",
+            "typeEntity": "Person",
+            "typeRole": [
+                "Contributor",
+                "Developer",
+                "Maintainer"
+            ],
+            "url": "https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699"
+        },
+        {
+            "email": "agruber@prf.jcu.cz",
+            "name": "Ansgar Gruber",
+            "orcidid": "https://orcid.org/0000-0002-5876-4391",
+            "typeEntity": "Person",
+            "typeRole": [
+                "Primary contact",
+                "Developer",
+                "Documentor"
+            ],
+            "url": "https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401"
+        }
+    ],
+    "description": "ASAFind is a software that predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin. \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example can be found in diatoms and cryptophytes. ASAFind uses protein sequence data and external predictions of signal peptides (by the tools SignalP and TargetP), and predicts plastid proteins, and proteins that are targeted to the periplastidic compartment from these data; optionally, a graphical output can generated.",
     "documentation": [
         {
             "type": [
@@ -16,9 +46,9 @@
     ],
     "download": [
         {
-            "note": "Repository for local installation",
+            "note": "Download page on web-service, links to repository",
             "type": "Downloads page",
-            "url": "https://github.com/ASAFind/ASAFind-2",
+            "url": "https://asafind.jcu.cz/download-page/",
             "version": "2.0"
         }
     ],
@@ -29,7 +59,9 @@
         "type": "group"
     },
     "elixirCommunity": [
-        "Plant Sciences"
+        "Plant Sciences",
+        "Marine Metagenomics",
+        "Microbial Biotechnology"
     ],
     "elixirNode": [
         "Czech Republic"
@@ -40,12 +72,6 @@
     "function": [
         {
             "input": [
-                {
-                    "data": {
-                        "term": "Feature table",
-                        "uri": "http://edamontology.org/data_1270"
-                    }
-                },
                 {
                     "data": {
                         "term": "Protein sequence record",
@@ -57,33 +83,39 @@
                             "uri": "http://edamontology.org/format_1929"
                         }
                     ]
+                },
+                {
+                    "data": {
+                        "term": "Feature table",
+                        "uri": "http://edamontology.org/data_1270"
+                    }
                 }
             ],
             "operation": [
                 {
-                    "term": "Protein cleavage site prediction",
-                    "uri": "http://edamontology.org/operation_0422"
+                    "term": "Subcellular localisation prediction",
+                    "uri": "http://edamontology.org/operation_2489"
                 },
                 {
                     "term": "Sequence motif recognition",
                     "uri": "http://edamontology.org/operation_0239"
                 },
                 {
-                    "term": "Subcellular localisation prediction",
-                    "uri": "http://edamontology.org/operation_2489"
+                    "term": "Protein cleavage site prediction",
+                    "uri": "http://edamontology.org/operation_0422"
                 }
             ],
             "output": [
                 {
                     "data": {
-                        "term": "Plot",
-                        "uri": "http://edamontology.org/data_2884"
+                        "term": "Protein features",
+                        "uri": "http://edamontology.org/data_1277"
                     }
                 },
                 {
                     "data": {
-                        "term": "Protein features",
-                        "uri": "http://edamontology.org/data_1277"
+                        "term": "Plot",
+                        "uri": "http://edamontology.org/data_2884"
                     }
                 }
             ]
@@ -93,7 +125,7 @@
     "language": [
         "Python"
     ],
-    "lastUpdate": "2025-12-15T16:16:18.187289Z",
+    "lastUpdate": "2025-12-15T17:36:43.189214Z",
     "license": "CC-BY-SA-4.0",
     "link": [
         {
@@ -102,16 +134,38 @@
                 "Service"
             ],
             "url": "https://asafind.jcu.cz"
+        },
+        {
+            "note": "Information and source code, for local installation or development",
+            "type": [
+                "Repository"
+            ],
+            "url": "https://github.com/ASAFind/ASAFind-2"
         }
     ],
     "maturity": "Mature",
     "name": "ASAFind",
     "operatingSystem": [
-        "Linux",
-        "Mac"
+        "Mac",
+        "Linux"
     ],
     "owner": "martavohnoutova",
     "publication": [
+        {
+            "doi": "10.1111/tpj.70138",
+            "metadata": {
+                "date": "2025-06-01T00:00:00Z",
+                "journal": "Plant Journal",
+                "title": "ASAFind 2.0: multi-class protein targeting prediction for diatoms and algae with complex plastids"
+            },
+            "note": "Publication of the current version of ASAFind (2.0)",
+            "pmcid": "PMC12136025",
+            "pmid": "40464854",
+            "type": [
+                "Primary"
+            ],
+            "version": "2.0"
+        },
         {
             "doi": "10.1111/tpj.12734",
             "metadata": {
@@ -129,23 +183,27 @@
             "version": "1.0"
         },
         {
-            "doi": "10.1111/tpj.70138",
-            "metadata": {
-                "date": "2025-06-01T00:00:00Z",
-                "journal": "Plant Journal",
-                "title": "ASAFind 2.0: multi-class protein targeting prediction for diatoms and algae with complex plastids"
-            },
-            "pmcid": "PMC12136025",
-            "pmid": "40464854",
+            "doi": "10.48550/arXiv.2303.02509",
+            "note": "Benchmarking of the performance of the first version of ASAFind",
             "type": [
-                "Primary"
+                "Benchmarking study"
             ],
-            "version": "2.0"
+            "version": "1.0"
+        }
+    ],
+    "relation": [
+        {
+            "biotoolsID": "signalp",
+            "type": "uses"
+        },
+        {
+            "biotoolsID": "targetp",
+            "type": "uses"
         }
     ],
     "toolType": [
-        "Command-line tool",
         "Script",
+        "Command-line tool",
         "Web service"
     ],
     "topic": [
@@ -154,19 +212,19 @@
             "uri": "http://edamontology.org/topic_2229"
         },
         {
-            "term": "Genomics",
-            "uri": "http://edamontology.org/topic_0622"
+            "term": "Proteins",
+            "uri": "http://edamontology.org/topic_0078"
         },
         {
             "term": "Plant biology",
             "uri": "http://edamontology.org/topic_0780"
         },
         {
-            "term": "Proteins",
-            "uri": "http://edamontology.org/topic_0078"
+            "term": "Genomics",
+            "uri": "http://edamontology.org/topic_0622"
         }
     ],
     "version": [
         "2.0"
     ]
-}
+}