Securing and developing the IPD-MHC database to enhance research into livestock diseases

保护和开发 IPD-MHC 数据库以加强对牲畜疾病的研究

• 批准号: BB/M011488/1
• 负责人: John Hammond
• 金额: $ 67.45万
• 依托单位: The Pirbright Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM011488%2F1
• 关键词: Securing; developing; IPD; MHC; database

The Immuno Polymorphism Database (IPD) (https://www.ebi.ac.uk/ipd/) is a set of specialist databases that contain curated sequence datasets of polymorphic immune genes. Developed and maintained by the Anthony Nolan, these databases help save the lives of people with blood cancer by matching donors major histocompatibility complex (MHC; (also known as HLA in humans) to prevent rejection. One of these databases is IPD-MHC, a repository of non-human MHC genes that includes the major farmed animals species; cattle, sheep, pigs, trout and salmon. All these species exhibit high degrees of variation within their MHC genes. This diversity differentially influences how the adaptive and innate immune systems respond to pathogens and vaccines. Therefore a greater understanding of this diversity and the tools to analyse it offer a significant advance to our broad capability to examine immune function in these fundamental food producing species.Since the first release in 2003, IPD-MHC has become the central source of curated and annotated comparative MHC data and nomenclature globally. The website now receives nearly 250 visitors every day and over 500 sequences were submitted in 2013 from all over the world. However, this success has created problems. The database and website have never been specifically funded. IPD-MHC has existed as an 'in kind' project that the research community and bioinformaticians at Antony Nolan have considered important enough to create and continue. The demands that the level of traffic has created mean that this model is no longer sustainable. Indeed, there is already a chronic lack of development and this data repository is in danger of becoming redundant. This proposal will support a dedicated IPD-MHC bioinformatician located at Anthony Nolan to work alongside the other IPD bioinformaticians. Their role will be to unify the individual species websites, incorporate the extensive chicken MHC data as a key farmed animal and create one streamlined data submission processes. Once this is in place, the capability of IPD-MHC will be significantly enhanced to accept a greater range of data and an expanded suite of analysis tools will be imbedded to allow advanced analysis for non-bioinformaticians. IPD-MHC still has overwhelming support from the research community, Anthony Nolan and the offer of free infrastructure from the European Bioinformatics Institute. This project is aimed at securing this central resource and expertise in the UK, to benefit this important UK research community and reach out to the rest of the world as part of the global food security agenda.

免疫多态性数据库（IPD）（https://www.ebi.ac.uk/ipd/）是一组专家数据库，其中包含多态性免疫基因的策划序列数据集。这些数据库是由Anthony Nolan开发和维护的，通过与捐助者相匹配的主要组织相容性复合物（MHC；（也称为人类中的HLA）来防止拒绝。这些数据库之一是iPD-MHC，这些数据库之一，包括大型农场的动物群，这些数据库是coit sheep and picit sheep;其MHC基因内的变化程度都不同地影响了适应性和先天的免疫系统对病原体和疫苗的反应，因此对这种多样性有更大的了解，并分析其在2003年的核心范围内，对我们的首次发行了，它可以为我们的广泛的命名提供。该网站在全球范围内每天都有近250名访问者，2013年从全球提交了500多个序列。但是，这种成功造成了问题。数据库和网站从未获得专门资助。 IPD-MHC已成为一个“亲切”项目，研究社区和安东尼·诺兰（Antony Nolan）的生物信息学家认为这足以创建和继续。交通水平的要求意味着该模型不再可持续。确实，已经长期缺乏发展，并且该数据存储库有多余的危险。该提案将支持位于安东尼·诺兰（Anthony Nolan）的专用IPD-MHC生物信息学家与其他IPD生物信息学家一起工作。他们的作用是统一各个物种网站，将广泛的鸡肉MHC数据纳入关键的养殖动物，并创建一个简化的数据提交过程。一旦到位，IPD-MHC的能力将得到显着增强，以接受更大的数据，并且将嵌入扩展的分析工具，以允许对非生物信息学家进行高级分析。 IPD-MHC仍然得到了研究界，Anthony Nolan的压倒性支持，并提供了欧洲生物信息学研究所的免费基础设施。该项目旨在确保英国的这种中央资源和专业知识，以使这个重要的英国研究社区受益，并作为全球粮食安全议程的一部分与世界其他地区联系。

项目成果

Allelic nomenclature for the duplicated MHC class II DQ genes in sheep.

绵羊中重复的 MHC II 类 DQ 基因的等位基因命名法。

• DOI: 10.1007/s00251-018-1096-9
• 发表时间: 2019
• 期刊: Immunogenetics
• 影响因子: 3.2
• 作者: Ballingall KT

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex.

• DOI: 10.1093/nar/gkw1050
• 发表时间: 2017-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Maccari G;Robinson J;Ballingall K;Guethlein LA;Grimholt U;Kaufman J;Ho CS;de Groot NG;Flicek P;Bontrop RE;Hammond JA;Marsh SG
• 通讯作者: Marsh SG

P013 Development of the IPD-MHC database

P013 IPD-MHC数据库的开发

• DOI: 10.1016/j.humimm.2016.07.078
• 发表时间: 2016
• 期刊: Human Immunology
• 影响因子: 2.7
• 作者: Robinson J

IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics.

• DOI: 10.1186/s12859-023-05624-2
• 发表时间: 2023-12-21
• 期刊: BMC bioinformatics
• 影响因子: 3

Nomenclature report for killer-cell immunoglobulin-like receptors (KIR) in macaque species: new genes/alleles, renaming recombinant entities and IPD-NHKIR updates

• DOI: 10.1007/s00251-019-01135-8
• 发表时间: 2019-11-29
• 期刊: IMMUNOGENETICS
• 影响因子: 3.2
• 作者: Bruijnesteijn, Jesse;de Groot, Natasja G.;Bontrop, Ronald E.
• 通讯作者: Bontrop, Ronald E.