The Open Biodiversity Knowledge Management System

OpenBiodiv utilizes semantic publishing workflows, text mining, common standards, ontology modelling and graph database technologies to establish a robust infrastructure for creating and managing a Biodiversity Knowledge Graph. OpenBiodiv encompasses data extracted from full-text article XMLs published by Pensoft and taxonomic treatments extracted by Plazi from journals of other publishers. The data from both sources are converted to RDF and are integrated in a graph database which contains the OpenBiodiv-O ontology and a RDF version of the GBIF taxonomic backbone. OpenBiodiv provides the following services: XML-to-RDF conversion workflow and software for JATS TaxPub XML versions of journal articles, RDF conversion of taxonomic hierarchies in CSV (example: GBIF taxonomic backbone), a triple store of close to one billion triples of facts and metadata extracted from literature, SPARQL endpoint, accessible for regular queries and federated queries with other domain-specific or generic endpoints, and predefined SPARQL queries reflecting different research questions. Within BiCIKL, OpenBiodiv will be developed to provide a LOD version of data liberated from the literature to make them interoperable with other data infrastructures throughout the biodiversity data life cycle.

OpenBiodiv 依托语义出版工作流、文本挖掘、通用标准、本体建模与图数据库技术，搭建起一套稳健的基础设施，用于创建与管理生物多样性知识图谱（Biodiversity Knowledge Graph）。该平台涵盖两类数据：一类为Pensoft出版的全本文献XML数据，另一类为Plazi从其他出版社期刊中提取的分类学处理文本。两类数据源均被转换为资源描述框架（Resource Description Framework，RDF）格式，并集成至包含OpenBiodiv-O本体以及全球生物多样性信息设施（Global Biodiversity Information Facility，GBIF）分类学主干数据的RDF版本的图数据库中。OpenBiodiv 提供以下服务：面向期刊文章JATS TaxPub XML格式的XML-to-RDF转换工作流与配套软件；针对CSV格式分类层级的RDF转换工具（示例：GBIF分类学主干数据）；存储近10亿条从文献中提取的事实与元数据三元组的三元组存储库；支持常规查询以及与其他领域特定或通用端点开展联合查询的SPARQL端点；以及适配不同研究问题的预定义SPARQL查询集。在BiCIKL项目框架内，OpenBiodiv 将得到进一步开发，以提供从文献中析出的数据的关联开放数据（Linked Open Data，LOD）版本，使其在生物多样性数据全生命周期中能够与其他数据基础设施实现互操作。

搜集汇总

背景与挑战

背景概述

OpenBiodiv是一个基于语义出版、文本挖掘和图数据库技术的生物多样性知识管理系统，它整合了来自期刊文章的XML数据和分类学处理数据，转换为RDF并构建了一个包含本体和GBIF分类学骨干的知识图谱。该系统提供XML到RDF转换、SPARQL查询端点等服务，旨在在BiCIKL项目中通过关联开放数据增强生物多样性数据在生命周期内的互操作性。