Add prefixes: synbip.* (#1268)

This pull request introduces four new prefixes for the Synthetic Binding Protein Database (SYNBIP): PubMed paper: https://pubmed.ncbi.nlm.nih.gov/39413165/ Database: https://idrblab.org/synbip/ - `synbip.sbp`: IDs for the synthetic binding proteins (SBPs) - `synbip.bts`: IDs for the binding targets of SBPs - `synbip.pss`: IDs for the proteins scaffolds of SBPs - `synbip.epitope`: IDs for the SBP-target complex interactions --------- Co-authored-by: Mufaddal Naguthanawala <[email protected]> Co-authored-by: Ben Gyori <[email protected]>
biopragmatics · Nov 27, 2024 · 9f5c52d · 9f5c52d
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diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json
@@ -110118,6 +110118,142 @@
       }
     }
   },
+  "synbip.bts": {
+    "contact": {
+      "email": "[email protected]",
+      "name": "Fengcheng Li",
+      "orcid": "0000-0002-1846-639X"
+    },
+    "contributor": {
+      "email": "[email protected]",
+      "github": "nagutm",
+      "name": "Mufaddal Naguthanawala",
+      "orcid": "0009-0009-5240-7463"
+    },
+    "description": "Identifiers for the binding targets of synthetic binding proteins (SBP), describing the specific molecules or complexes that SBPs interact with for their intended applications",
+    "example": "st00576",
+    "github_request_issue": 1268,
+    "homepage": "http://synbip.idrblab.net",
+    "name": "Synthetic Binding Proteins Binding Target",
+    "pattern": "^st\\d+$",
+    "publications": [
+      {
+        "doi": "10.1093/nar/gkae893",
+        "pubmed": "39413165",
+        "title": "SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation",
+        "year": 2024
+      }
+    ],
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "bgyori",
+      "name": "Benjamin M. Gyori",
+      "orcid": "0000-0001-9439-5346"
+    },
+    "uri_format": "http://synbip.idrblab.net/data/bts/details/$1"
+  },
+  "synbip.epitope": {
+    "contact": {
+      "email": "[email protected]",
+      "name": "Fengcheng Li",
+      "orcid": "0000-0002-1846-639X"
+    },
+    "contributor": {
+      "email": "[email protected]",
+      "github": "nagutm",
+      "name": "Mufaddal Naguthanawala",
+      "orcid": "0009-0009-5240-7463"
+    },
+    "description": "Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics",
+    "example": "mt002305",
+    "github_request_issue": 1268,
+    "homepage": "http://synbip.idrblab.net",
+    "name": "Synthetic Binding Protein Epitope",
+    "pattern": "^mt\\d+$",
+    "publications": [
+      {
+        "doi": "10.1093/nar/gkae893",
+        "pubmed": "39413165",
+        "title": "SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation",
+        "year": 2024
+      }
+    ],
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "bgyori",
+      "name": "Benjamin M. Gyori",
+      "orcid": "0000-0001-9439-5346"
+    },
+    "uri_format": "http://synbip.idrblab.net/data/sbp-target-complex/details/$1"
+  },
+  "synbip.pss": {
+    "contact": {
+      "email": "[email protected]",
+      "name": "Fengcheng Li",
+      "orcid": "0000-0002-1846-639X"
+    },
+    "contributor": {
+      "email": "[email protected]",
+      "github": "nagutm",
+      "name": "Mufaddal Naguthanawala",
+      "orcid": "0009-0009-5240-7463"
+    },
+    "description": "Identifiers for the protein scaffolds of synthetic binding proteins (SBP), detailing their structural frameworks and roles in facilitating SBP function.",
+    "example": "ps048",
+    "github_request_issue": 1268,
+    "homepage": "http://synbip.idrblab.net",
+    "name": "Synthetic Binding Protein Protein Scaffold",
+    "pattern": "^ps\\d+$",
+    "publications": [
+      {
+        "doi": "10.1093/nar/gkae893",
+        "pubmed": "39413165",
+        "title": "SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation",
+        "year": 2024
+      }
+    ],
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "bgyori",
+      "name": "Benjamin M. Gyori",
+      "orcid": "0000-0001-9439-5346"
+    },
+    "uri_format": "http://synbip.idrblab.net/data/scaffold/details/$1"
+  },
+  "synbip.sbp": {
+    "contact": {
+      "email": "[email protected]",
+      "name": "Fengcheng Li",
+      "orcid": "0000-0002-1846-639X"
+    },
+    "contributor": {
+      "email": "[email protected]",
+      "github": "nagutm",
+      "name": "Mufaddal Naguthanawala",
+      "orcid": "0009-0009-5240-7463"
+    },
+    "description": "Identifiers for synthetic binding proteins, providing detailed information on their sequences, structures, targets, and functional properties for research, diagnostic, and therapeutic applications.",
+    "example": "sbp000002",
+    "github_request_issue": 1268,
+    "homepage": "http://synbip.idrblab.net",
+    "name": "Synthetic Binding Protein",
+    "pattern": "^sbp\\d+$",
+    "publications": [
+      {
+        "doi": "10.1093/nar/gkae893",
+        "pubmed": "39413165",
+        "title": "SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation",
+        "year": 2024
+      }
+    ],
+    "reviewer": {
+      "email": "[email protected]",
+      "github": "bgyori",
+      "name": "Benjamin M. Gyori",
+      "orcid": "0000-0001-9439-5346"
+    },
+    "uri_format": "http://synbip.idrblab.net/data/sbp/details/$1"
+  },
   "syoid": {
     "contributor": {
       "email": "[email protected]",

diff --git a/src/bioregistry/data/curated_papers.tsv b/src/bioregistry/data/curated_papers.tsv
@@ -55,5 +55,6 @@ pubmed	relevant	orcid	date_curated	relevancy_type	pr_added	notes
 39345624	1	0009-0009-5240-7463	2024-10-19	new_publication	1223	Publication for sgd and sgd.pathways
 39379619	1	0009-0009-5240-7463	2024-11-26	new_provider	1285	Provider for UniProt
 39401100	1	0009-0009-5240-7463	2024-11-20	new_publication	1264	Publication for intact and intact.molecule
+39413165	1	0009-0009-5240-7463	2024-11-20	new_prefix	1268	Identifiers for synthetic binding proteins
 39470701	1	0009-0009-5240-7463	2024-11-26	new_publication	1286	Publication for mobidb
 39498478	1	0009-0009-5240-7463	2024-11-25	new_publication	1283	Publication for gold