Database (Oxford). 2022 Feb 2;2022. doi: 10.1093/database/baac001.
Critical to answering large-scale questions in biology is the integration of knowledge from different disciplines into a coherent, computable whole. Controlled vocabularies such as ontologies represent a clear path toward this goal. Using survey questionnaires, we examined the attitudes of biologists toward adopting controlled vocabularies in phenotype publications. Our questions cover current experience and overall attitude with controlled vocabularies, the awareness of the issues around ambiguity and inconsistency in phenotype descriptions and post-publication professional data curation, the preferred solutions and the effort and desired rewards for adopting a new authoring workflow. Results suggest that although the existence of controlled vocabularies is widespread, their use is not common. A majority of respondents (74%) are frustrated with ambiguity in phenotypic descriptions, and there is a strong agreement (mean agreement score 4.21 out of 5) that author curation would better reflect the original meaning of phenotype data. Moreover, the vast majority (85%) of researchers would try a new authoring workflow if resultant data were more consistent and less ambiguous. Even more respondents (93%) suggested that they would try and possibly adopt a new authoring workflow if it required 5% additional effort as compared to normal, but higher rates resulted in a steep decline in likely adoption rates. Among the four different types of rewards, two types of citations were the most desired incentives for authors to produce computable data. Overall, our results suggest the adoption of a new authoring workflow would be accelerated by a user-friendly and efficient software-authoring tool, an increased awareness of the challenges text ambiguity creates for external curators and an elevated appreciation of the benefits of controlled vocabularies.
要回答生物学中的大规模问题，关键是将不同学科的知识整合到一个连贯、可计算的整体中。受控词汇表（如本体论）代表了实现这一目标的明确途径。我们使用问卷调查，研究了生物学家在表型出版物中采用受控词汇表的态度。我们的问题涵盖了他们对受控词汇表的当前经验和总体态度、对表型描述中歧义性和不一致性问题以及发表后专业数据整理的认识、首选解决方案，以及采用新的创作工作流程的努力和期望回报。结果表明，尽管受控词汇表的存在很普遍，但它们的使用并不常见。大多数受访者（74%）对表型描述中的歧义感到沮丧，并且强烈认为（平均同意得分为 4.21 分），作者整理可以更好地反映表型数据的原始含义。此外，绝大多数（85%）的研究人员如果新的创作工作流程产生的数据更一致且歧义更少，他们会尝试新的创作工作流程。更多的受访者（93%）表示，如果与正常情况相比，额外的 5%的工作量就可以尝试和可能采用新的创作工作流程，但更高的费率会导致采用率大幅下降。在四种不同类型的奖励中，两种类型的引文是作者生成可计算数据的最理想激励措施。总体而言，我们的研究结果表明，用户友好且高效的软件创作工具、提高对文本歧义给外部整理者带来的挑战的认识，以及对受控词汇表的益处的重视，都将加速新创作工作流程的采用。
