Populous: A Tool for Populating an Ontology
Populous: A Tool for Populating an Ontology
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Populous：填充本体的工具
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发表时间：
2011
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通讯作者：
R. Stevens
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作者：
S. Jupp;M. Horridge;L. Iannone;J. Klein;S. Owen;J. Schanstra;K. Wolstencroft;R. Stevens
我们介绍了Populous，这是一个开源应用程序，用于为本体收集内容并大量填充该本体。Populous为作者提供了一个基于表的表单，其中列被绑定以获取特定本体的值；用户可以通过本体的有意义标签从本体中选择一个概念，为给定的实体给出一个值。填充的表被馈送到模板中，然后可以用来生成本体的公理。《Populous》将知识收集与概念化分离；它还将用户从通常的本体创作工具中移除。可用性：下载，源和视频通过http://www.e-lico.eu/ populous。像Protege和OBOEdit这样的本体构建环境为手工编写公理提供了便利。这些工具对于捕获本体的形式至关重要。然而，许多本体很大，其中相当大的部分是由相同公理模式的重复构成的，只是在该模式内的填充物中有所不同。为了避免手工操作的单调乏味和潜在错误，可以填充模板并生成模式的公理，从而避免手动编写许多公理。Populous[1]通过为任何本体作者提供一个熟悉的基于表单填充表的用户界面来填充本体模式或模板来实现这一点。行与被描述的实体相关联；列被绑定到属性，单元格被限制从特定的本体或本体的片段获取值。当作者填写模板时，他或她将被引导在模板中放置适当的值。然后可以使用OWL脚本语言将该表的内容转换为目标本体的公理。Populous是RightField的扩展1，它用于创建包含基于本体的电子表格内容限制的Excel文档。RightField主要用于生成数据注释的电子表格模板；Populous扩展了RightField以支持知识收集和本体生成。Populous和RightField都是在BSD许可下发布的开源跨平台Java应用程序。他们使用Apache-POI 2与微软文档进行交互并操作Excel电子表格。1 http://www.rightfield.org.uk 2 http://poi.apache.org OWL和OBO两种本体都可以上传到Populous。用户还可以直接从biopportal浏览和加载本体。一旦本体被加载，它们就会被推理器分类，并且可以检查基本的类层次结构。可以从本体中选择术语，为表中特定单元格选择允许的值创建验证集。来自本体实体的标签可以在单元格中使用，而不仅仅是URI或URI片段。Populous允许添加自由文本，即使单元格有关联的验证范围；这些值以红色突出显示，当在验证集中找不到合适的候选词时，它们可以作为新词或建议词的占位符。Populous支持使用本体预处理器语言3 （OPPL）模式，以便从已填充的模板生成新的OWL公理。OPPL是曼彻斯特OWL语法的扩展，用于选择、添加和删除公理，它有一个用于操作本体的脚本解释器。OPPL模式中的变量通过Populous模式向导使用列名映射到表中的列。我们已经与生物学家一起使用Populous来填充肾脏和泌尿途径本体b[2]的大部分。Populous是支持本体创作过程的工具“拼图”中的另一块。它开始填补术语请求系统和手动公理编写系统之间的空白，它提供了一种“填写”模板的机制，这种机制可以根据组成本体的本体对模板进行验证。我们认为Populous是一种让领域专家参与创作过程的手段，这些领域专家不是本体专家，任何本体作者都可以更有效地填充他们的本体内容。感谢：我们感谢Mikel Egana Aranguren对《Populous》的建议、要求和测试。这项工作由e-LICO项目EU/FP7/ICT-2007.4.4和SysMO-DB BBSRC拨款BBG0102181资助。
We present Populous, an open source application for gathering content for an ontology and populating that ontology en masse. Populous presents authors with a table-based form where columns are tied to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity. Populated tables are fed into templates that can then be used to generate the ontology’s axioms. Populous separates knowledge gathering from the conceptualisation; it also removes users from the usual ontology authoring tools. Availability: Download, source and video via http://www.e-lico.eu/ populous. Ontology building environments such as Protege and OBOEdit offer facilities for the manual authoring of axioms. Such tools are vital for capturing an ontology’s form. Many ontologies are, however, large with considerable portions formed of repetitions of the same pattern of axioms, varying only in the fillers within that pattern. To avoid the tedium and potential errors of doing this manually, templates can be filled and the axioms for the pattern generated, avoiding the manual authoring of many axioms. Populous [1] does this by presenting a familiar form-filling table-based user interface for any ontology authors to populate ontology patterns or templates. Rows are tied to the entities being described; columns are tied to properties and the cells constrained to take values from particular ontologies or fragments of an ontology. As an author fills out the template, he or she is guided to place appropriate values within the template. The content of this table can then be transformed into the axioms of the target ontology with an OWL scripting language. Populous is an extension of RightField,1 which is used for creating Excel documents that contain ontology based restrictions on a spreadsheet’s content. RightField is primarily designed for generating spreadsheet templates for data annotation; Populous extends RightField to support knowledge gathering and ontology generation. Populous and RightField are both open source, cross platform Java applications released under the BSD licence. They use the Apache-POI 2 for interacting with Microsoft documents and manipulating Excel spreadsheets. 1 http://www.rightfield.org.uk 2 http://poi.apache.org Both OWL and OBO ontologies can be uploaded into Populous. Users can also browse and load ontologies directly from BioPortal. Once the ontologies are loaded they are classified by a reasoner and the basic class hierarchy can be inspected. Terms can be selected from the ontology to create validation sets for values that are permitted for a particular selection of cells in the table. Labels from an ontology’s entities can be used within a cell, not just URI or URI fragments. Populous allows the addition of free text, even if the cell has an associated validation range; these values are highlighted in red and can act as placeholders for new or suggested terms when no suitable candidate can be found in the validation set. Populous supports the use of the Ontology Pre-Processor Language 3 (OPPL) patterns in order to generate new OWL axioms from the populated template. OPPL is an extension of Manchester OWL Syntax to select, add and remove axioms and it has an interpreter for scripts that manipulate the ontology. Variables from the OPPL pattern are mapped to columns from the table using the column name through the Populous pattern Wizard. We have used Populous with biologists to populate large portions of a kidney and urinary pathway ontology [2]. Populous is another piece in the ‘jigsaw’ of tools that support the ontology authoring process. It starts to fill the gap between the term request system and the manual axiom authoring systems by providing a mechanism for ‘filling out’ templates in such a way that they can be validated against the ontologies with which the ontology is being composed. We see Populous as a means for engaging domain experts who are not ontology experts in the authoring process and any ontology author to more effectively populate their ontology’s content. Acknowledgements: We acknowledge Mikel Egana Aranguren for his advice, requirements and testing of Populous. This work was funded by the e-LICO project— EU/FP7/ICT-2007.4.4 and by SysMO-DB BBSRC grant BBG0102181.