From 9f5c52dbe5a97d6086cf15195e9b9c1e5799815b Mon Sep 17 00:00:00 2001 From: Mufaddal Naguthanawala <110353148+nagutm@users.noreply.github.com> Date: Tue, 26 Nov 2024 20:50:22 -0500 Subject: [PATCH] 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 Co-authored-by: Ben Gyori --- src/bioregistry/data/bioregistry.json | 136 ++++++++++++++++++++++++ src/bioregistry/data/curated_papers.tsv | 1 + 2 files changed, 137 insertions(+) diff --git a/src/bioregistry/data/bioregistry.json b/src/bioregistry/data/bioregistry.json index cf1425fdc..64127506a 100644 --- a/src/bioregistry/data/bioregistry.json +++ b/src/bioregistry/data/bioregistry.json @@ -110118,6 +110118,142 @@ } } }, + "synbip.bts": { + "contact": { + "email": "lifengcheng@zju.edu.cn", + "name": "Fengcheng Li", + "orcid": "0000-0002-1846-639X" + }, + "contributor": { + "email": "m.naguthana@hotmail.com", + "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": "b.gyori@northeastern.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "uri_format": "http://synbip.idrblab.net/data/bts/details/$1" + }, + "synbip.epitope": { + "contact": { + "email": "lifengcheng@zju.edu.cn", + "name": "Fengcheng Li", + "orcid": "0000-0002-1846-639X" + }, + "contributor": { + "email": "m.naguthana@hotmail.com", + "github": "nagutm", + "name": "Mufaddal Naguthanawala", + "orcid": "0009-0009-5240-7463" + }, + "description": "Identifiers for synthetic binding protein-target complexes, detailing their components, 3D structures and docking statistics", + "example": "mt002305", + "github_request_issue": 1268, + "homepage": "http://synbip.idrblab.net", + "name": "Synthetic Binding Protein Epitope", + "pattern": "^mt\\d+$", + "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": "b.gyori@northeastern.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "uri_format": "http://synbip.idrblab.net/data/sbp-target-complex/details/$1" + }, + "synbip.pss": { + "contact": { + "email": "lifengcheng@zju.edu.cn", + "name": "Fengcheng Li", + "orcid": "0000-0002-1846-639X" + }, + "contributor": { + "email": "m.naguthana@hotmail.com", + "github": "nagutm", + "name": "Mufaddal Naguthanawala", + "orcid": "0009-0009-5240-7463" + }, + "description": "Identifiers for the protein scaffolds of synthetic binding proteins (SBP), detailing their structural frameworks and roles in facilitating SBP function.", + "example": "ps048", + "github_request_issue": 1268, + "homepage": "http://synbip.idrblab.net", + "name": "Synthetic Binding Protein Protein Scaffold", + "pattern": "^ps\\d+$", + "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": "b.gyori@northeastern.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "uri_format": "http://synbip.idrblab.net/data/scaffold/details/$1" + }, + "synbip.sbp": { + "contact": { + "email": "lifengcheng@zju.edu.cn", + "name": "Fengcheng Li", + "orcid": "0000-0002-1846-639X" + }, + "contributor": { + "email": "m.naguthana@hotmail.com", + "github": "nagutm", + "name": "Mufaddal Naguthanawala", + "orcid": "0009-0009-5240-7463" + }, + "description": "Identifiers for synthetic binding proteins, providing detailed information on their sequences, structures, targets, and functional properties for research, diagnostic, and therapeutic applications.", + "example": "sbp000002", + "github_request_issue": 1268, + "homepage": "http://synbip.idrblab.net", + "name": "Synthetic Binding Protein", + "pattern": "^sbp\\d+$", + "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": "b.gyori@northeastern.edu", + "github": "bgyori", + "name": "Benjamin M. Gyori", + "orcid": "0000-0001-9439-5346" + }, + "uri_format": "http://synbip.idrblab.net/data/sbp/details/$1" + }, "syoid": { "contributor": { "email": "cthoyt@gmail.com", diff --git a/src/bioregistry/data/curated_papers.tsv b/src/bioregistry/data/curated_papers.tsv index e0acad0cb..d3397094a 100644 --- 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