Harmonizing plant metabarcoding pipelines in Europe to support monitoring activities in the field of plants and their functional organismic networks

协调欧洲植物元条形码管道，以支持植物及其功能性有机网络领域的监测活动

• 批准号: 532161749
• 负责人: Professorin Dr. Birgit Gemeinholzer
• 金额: --
• 依托单位: Universitaire Ziekenhuizen
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/532161749?language=en
• 关键词: Harmonizing; plant; metabarcoding; pipelines; Europe

Plants, as autotrophs, are the drivers of terrestrial ecosystems. It is estimated that two out of five plant species are threatened with extinction, which probably also affects other organisms. Plant metabarcoding (the analysis of environmental DNA (eDNA) for taxonomic identification) can be standardized and automated, suits large-scale, high-throughput, long-term monitoring, and enables biodiversity surveys at a scale and accuracy previously unattainable. All European conservation initiatives are based on species occurrence, and indicator species form the basis for conservation decision-making. However, public and private sector stakeholders need rapid, accurate, and cost-effective methods to monitor plant biodiversity. The transnational and transdisciplinary METAPLANTCODE project will test, optimize and provide best practice recommendations for pan-European case studies on plant metabarcoding, optimize analysis pipelines for species identification and develops easy-to-use reference databases to be implemented in European and national infrastructures. Gaps will be identified and specified. In collaboration with BIOSCAN Europe, ELIXIR communities and others, best practice documents on FAIR publication of plant metabarcode data in GBIF and INSDC databases will be published and organized. Through the use of AI, multimodal DL models will be implemented in novel tools for stand-alone metabarcoding analyses, compatible with the ELIXIR infrastructure, to leverage multiple data sources for species-level identification (sequence data, text data, taxonomic classification datasets, and ecological analyses). We will improve the accuracy of species identification through GBIF datasets and metadata (GBIF, EUNIS, Biolflor) and incorporate regional, national, and international botanical taxonomic checklists, Red Lists, and floras for species level identification by mobilization to the Catalogue of Life (COL) through COL ChecklistBank. The taxonomic and floristic literature will be semantically enriched with new entity recognition and relationship extraction modules to support optimized metabarcoding identification of species by domain-specific descriptive/phenotypic features (e.g., habitats, features, soil characteristics, biotic interactions). An interface is provided to link taxonomic names to treatments, identify homonyms and synonyms, e.g., for conversion and annotation of flora, red lists, and ecological treatments. At project end, all METAPLANTCODE products will be FAIR+ available. From project start on knowledge transfer with participating partners and stakeholders will be fostered. Relevant stakeholders will be identified, priorities set, communication channels established, monitored and revised as needed. We will increase efforts to engage stakeholders and conduct training and outreach to ensure that plant metabarcoding is routinely used as a standard for biodiversity monitoring in Europe and beyond in the future.

植物作为自养生物，是陆地生态系统的驱动者。据估计，五分之二的植物物种面临灭绝的威胁，这可能也影响到其他生物。植物元条形码（用于分类鉴定的环境DNA（eDNA）分析）可以标准化和自动化，适合大规模，高通量，长期监测，并使生物多样性调查的规模和精度以前无法达到。所有欧洲的保护举措都是基于物种的出现，而指标物种构成了保护决策的基础。然而，公共和私营部门的利益相关者需要快速，准确和具有成本效益的方法来监测植物生物多样性。跨国和跨学科的METAPLANTCODE项目将测试、优化和提供泛欧植物元条形码案例研究的最佳实践建议，优化物种识别的分析管道，并开发易于使用的参考数据库，供欧洲和国家基础设施使用。将查明并具体说明差距。与BIOSCAN Europe、ELIXIR社区和其他机构合作，将出版和组织关于FAIR在GBIF和INSDC数据库中发布植物元条形码数据的最佳实践文件。通过使用人工智能，多模式DL模型将在与ELIXIR基础设施兼容的独立元条形码分析的新工具中实现，以利用多个数据源进行物种级识别（序列数据，文本数据，分类学分类数据集和生态分析）。我们将通过GBIF数据集和元数据（GBIF，EUNIS，Biolflor）提高物种识别的准确性，并通过COL ChecklistBank将区域，国家和国际植物分类检查表，红色名录和植物区系用于物种水平识别。分类学和植物区系文献将在语义上丰富新的实体识别和关系提取模块，以支持通过特定领域的描述性/表型特征（例如，生境、地貌、土壤特性、生物相互作用）。提供了一个接口，用于将分类名称链接到治疗，识别同音异义词和同义词，例如，用于植物群、红色名录和生态处理的转换和注释。在项目结束时，所有的METAPLANTCODE产品将是公平的+可用。从项目开始，将促进与参与伙伴和利益攸关方的知识转让。将确定相关利益攸关方，确定优先事项，建立沟通渠道，并根据需要进行监测和修订。我们将加大努力，让利益攸关方参与进来，并开展培训和外联活动，以确保植物元条形码今后在欧洲和其他地区被例行用作生物多样性监测的标准。