Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes.
Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes.
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DOI：
10.1093/database/baaa079
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发表时间：
2020-11-20
期刊：
影响因子：
--
通讯作者：
Starr J
中科院分区：
文献类型：
--
作者：
Cui H;Zhang L;Ford B;Cheng HL;Macklin JA;Reznicek A;Starr J
为了在计算分析中使用公开的表型信息，已经努力将表型特征的描述从人类语言转换为本体化陈述。这种出版后的策展过程不仅缓慢而昂贵，而且由于不同的个人对一个角色的不同解释，它还承受着巨大的策展人之间的差异（包括策展人-作者之间的差异）。这个问题是任何以人为基础的智力活动所固有的。为了解决这个问题，如果我们要避免出版后的策展，作者在出版时使科学出版物在语义上清晰（即可计算）是关键的一步。为了帮助作者有效地产生物种表型，同时产生可计算的数据，我们正在试验一个作者驱动的本体开发方法，并开发和评估一系列的本体感知软件模块，将创建可扩展的物种描述，很容易在科学计算中使用。第一个软件模块原型称为测量记录器已开发，以帮助作者在定义连续测量，并在本文中报道。两个可用性研究的软件进行了22名本科生主修信息科学和32个生物学。结果表明，参与者可以使用测量记录器没有培训，他们发现它很容易使用有限的实践后。与会者还赞赏语义增强功能。Measurement Recorder的字符重用功能使参与者之间的字符收敛率提高了48%，并有可能进一步减少用户在定义字符时的错误。还发现了一系列软件设计问题，并进行了纠正。测量记录器使作者能够以语义清晰的方式记录测量，并沿着丰富表型本体。未来的工作包括将语义数据表示为资源描述框架（RDF）知识图，并在这种新的作者驱动的本体开发方法中描述作者作为领域知识提供者和本体工程师作为知识形式化者之间的分工。
To use published phenotype information in computational analyses, there have been efforts to convert descriptions of phenotype characters from human languages to ontologized statements. This postpublication curation process is not only slow and costly, it is also burdened with significant intercurator variation (including curator–author variation), due to different interpretations of a character by various individuals. This problem is inherent in any human-based intellectual activity. To address this problem, making scientific publications semantically clear (i.e. computable) by the authors at the time of publication is a critical step if we are to avoid postpublication curation. To help authors efficiently produce species phenotypes while producing computable data, we are experimenting with an author-driven ontology development approach and developing and evaluating a series of ontology-aware software modules that would create publishable species descriptions that are readily useable in scientific computations. The first software module prototype called Measurement Recorder has been developed to assist authors in defining continuous measurements and reported in this paper. Two usability studies of the software were conducted with 22 undergraduate students majoring in information science and 32 in biology. Results suggest that participants can use Measurement Recorder without training and they find it easy to use after limited practice. Participants also appreciate the semantic enhancement features. Measurement Recorder’s character reuse features facilitate character convergence among participants by 48% and have the potential to further reduce user errors in defining characters. A set of software design issues have also been identified and then corrected. Measurement Recorder enables authors to record measurements in a semantically clear manner and enriches phenotype ontology along the way. Future work includes representing the semantic data as Resource Description Framework (RDF) knowledge graphs and characterizing the division of work between authors as domain knowledge providers and ontology engineers as knowledge formalizers in this new author-driven ontology development approach.
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影响因子：
6.5
作者：
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通讯作者：
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影响因子：
1.2
作者：
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DOI：
10.1093/database/baw149
发表时间：
2016-12-26
影响因子：
5.8
作者：
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通讯作者：
Karp, Peter D.
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DOI：
10.1093/database/bav040
发表时间：
2015
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Dahdul W;Dececchi TA;Ibrahim N;Lapp H;Mabee P
通讯作者：
Mabee P
DOI：
10.1093/database/bas024
发表时间：
2012-05-02
影响因子：
5.8
作者：
Bunt, Stephanie M.;Grumbling, Gary B.;Millburn, Gillian H.
通讯作者：
Millburn, Gillian H.