ENHANCING THE INTERNATIONAL MOLECULAR EXCHANGE (IMEX): PROVIDING AN IMPROVED COMMUNITY-ORIENTED MOLECULAR INTERACTIONS

加强国际分子交换（IMEX）：提供改进的面向社区的分子相互作用

• 批准号: 10166532
• 负责人: Matteo Pellegrini
• 金额: $ 10.94万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-03-01 至 2022-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10166532
• 关键词: Address; Basic Science; Big Data; Big Data to Knowledge; Binding; Biological; Collaborations; Communities; Complex; Custom; Data; Data Analyses; Data Set; Databases; Deposition; Disease; Ensure; FAIR principles; Focus Groups; Goals; Grant; Human; Individual; International; Knowledge Discovery; Lead; Literature; Maintenance; Malignant Neoplasms; Manuals; Measures; Mediating; Metadata; Methods; Modeling; Molecular; Mutation; Outcome; Pathway Analysis; Pathway interactions; Post-Translational Protein Processing; Process; Production; Protein Databases; Proteins; Provider; Publications; Quality Control; Records; Registries; Regulation; Research; Research Personnel; Resources; Retrieval; Scientist; Set protein; Site; SwissProt; Text; Training; Translational Research; Triage; Update; data curation; design; experimental study; human disease; human interactome; improved; indexing; individualized medicine; innovation; interest; member; novel; outreach; research study; shared database; tool; web services; web site

Project Summary The IMEx Consortium (http://www.imexconsortium.org/) is an international collaboration between major public interaction data providers which captures experimental data through literature curation and deposition by bench scientists. IMEx member databases share and coordinate their curation efforts, using a central registry (IMExCentral: https://imexcentral.org/icentral/) to manage the selection of articles in order to provide a single, non-redundant, consistently-annotated set of protein interactions. In contrast to other currently active interaction databases, IMEx curators follow a detailed curation model which captures information on experimental methods and biologically important details such as essential binding regions and post-translational modifications, as well as mutations and their effect on protein interactions. This allows downstream users to analyze protein interaction networks and their regulation in normal and disease states. In this proposal we seek support for the continuation and extension of IMEx activities related to the curation and provision of interaction data with special emphasis on human interactome. Over the next five years, we will (1) augment the IMEx interaction dataset by curating information from at least 4000 new publications, providing tens of thousands of human protein interactions; (2) disseminate new and existing IMEx interaction records through a new, consortium-wide IMEx Protein Interaction Resource, which will include an interactive web site, a standards-compliant PSICQUIC web-service and ftp download site (customized subsets of the data will be provided to our long term collaborators, Reactome, UniProtKB and GO Consortium); (3) provide training for existing and new user communities on the use of protein interaction data and network analysis of cancer-related `big data'.

项目摘要 IMEx联盟（http：//www.imexconsortium.org/）是一个主要公共部门之间的国际合作组织。 交互数据提供器，通过文献整理和实验台沉积捕获实验数据 科学家IMEx成员数据库使用中央注册表共享和协调其策展工作 （IMExCentral：https：//imexcentral.org/icentral/）来管理文章的选择， 非冗余的，一致注释的蛋白质相互作用的集合。与其他当前活跃的互动相比， 数据库，IMEx策展人遵循详细的策展模型，捕捉实验方法的信息 以及生物学上重要的细节，如必需的结合区域和翻译后修饰， 突变及其对蛋白质相互作用的影响。这允许下游用户分析蛋白质相互作用 网络及其在正常和疾病状态下的调节。 在本提案中，我们寻求支持继续和扩大IMEx与策展有关的活动。 以及提供特别强调人类交互组的交互数据。未来五年，我们将 (1)通过从至少4000个新出版物中收集信息来扩充IMEx交互数据集， 数以万计的人类蛋白质相互作用;（2）传播新的和现有的IMEx相互作用记录 通过一个新的，联盟范围的IMEx蛋白质相互作用资源，其中将包括一个互动的网站， 符合标准的PSICQUIC Web服务和FTP下载站点（将 提供给我们的长期合作者，Reactome，UniProtKB和GO Consortium）;（3）提供培训， 现有的和新的用户社区使用蛋白质相互作用数据和网络分析癌症相关的 大数据。

项目成果

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions.

IMEx 冠状病毒相互作用组：冠状病毒科-宿主分子相互作用的演化图谱。

• DOI: 10.1101/2020.06.16.153817
• 发表时间: 2020
• 期刊: bioRxiv : the preprint server for biology
• 作者: Perfetto,L;Pastrello,C;Del-Toro,N;Duesbury,M;Iannuccelli,M;Kotlyar,M;Licata,L;Meldal,B;Panneerselvam,K;Panni,S;Rahimzadeh,N;Ricard-Blum,S;Salwinski,L;Shrivastava,A;Cesareni,G;Pellegrini,M;Orchard,S;Jurisica,I;Hermjakob,
• 通讯作者: Hermjakob,

Towards a unified open access dataset of molecular interactions.

• DOI: 10.1038/s41467-020-19942-z
• 发表时间: 2020-12-01
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Porras P;Barrera E;Bridge A;Del-Toro N;Cesareni G;Duesbury M;Hermjakob H;Iannuccelli M;Jurisica I;Kotlyar M;Licata L;Lovering RC;Lynn DJ;Meldal B;Nanduri B;Paneerselvam K;Panni S;Pastrello C;Pellegrini M;Perfetto L;Rahimzadeh N;Ratan P;Ricard-Blum S;Salwinski L;Shirodkar G;Shrivastava A;Orchard S
• 通讯作者: Orchard S

Bioinformatic identification of previously unrecognized amyloidogenic proteins.

• DOI: 10.1016/j.jbc.2022.101920
• 发表时间: 2022-05
• 期刊: JOURNAL OF BIOLOGICAL CHEMISTRY
• 影响因子: 4.8
• 作者: Rosenberg, Gregory M.;Murray, Kevin A.;Salwinski, Lukasz;Hughes, Michael P.;Abskharon, Romany;Eisenberg, David S.
• 通讯作者: Eisenberg, David S.

The IntAct database: efficient access to fine-grained molecular interaction data.

• DOI: 10.1093/nar/gkab1006
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Del Toro N;Shrivastava A;Ragueneau E;Meldal B;Combe C;Barrera E;Perfetto L;How K;Ratan P;Shirodkar G;Lu O;Mészáros B;Watkins X;Pundir S;Licata L;Iannuccelli M;Pellegrini M;Martin MJ;Panni S;Duesbury M;Vallet SD;Rappsilber J;Ricard-Blum S;Cesareni G;Salwinski L;Orchard S;Porras P;Panneerselvam K;Hermjakob H
• 通讯作者: Hermjakob H

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

• DOI: 10.1186/s12859-018-2118-1
• 发表时间: 2018-04-11
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Sivade Dumousseau M;Alonso-López D;Ammari M;Bradley G;Campbell NH;Ceol A;Cesareni G;Combe C;De Las Rivas J;Del-Toro N;Heimbach J;Hermjakob H;Jurisica I;Koch M;Licata L;Lovering RC;Lynn DJ;Meldal BHM;Micklem G;Panni S;Porras P;Ricard-Blum S;Roechert B;Salwinski L;Shrivastava A;Sullivan J;Thierry-Mieg N;Yehudi Y;Van Roey K;Orchard S
• 通讯作者: Orchard S