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On the Role of Focus-Sensitivity for a Typology of Presupposition Triggers 焦点敏感性在预设触发类型中的作用
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-01-01 DOI: 10.1093/jos/ffac011
Alexander Göbel
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引用次数: 1
CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature. 基于import报告和文献的CIDO本体更新和宿主对COVID-19感染反应的二次分析。
IF 1.6 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-08-28 DOI: 10.1186/s13326-021-00250-4
Anthony Huffman, Anna Maria Masci, Jie Zheng, Nasim Sanati, Timothy Brunson, Guanming Wu, Yongqun He

Background: With COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span of time, we often lose an integrative and comprehensive picture of host-coronavirus interaction (HCI) mechanisms. As of early April 2021, the ImmPort database has stored 7 studies (with 6 having details) that cover topics including molecular immune signatures, epitopes, and sex differences in terms of mortality in COVID-19 patients. The Coronavirus Infectious Disease Ontology (CIDO) represents basic HCI information. We hypothesize that the CIDO can be used as the platform to represent newly recorded information from ImmPort leading the reinforcement of CIDO.

Methods: The CIDO was used as the semantic platform for logically modeling and representing newly identified knowledge reported in the 6 ImmPort studies. A recursive eXtensible Ontology Development (XOD) strategy was established to support the CIDO representation and enhancement. Secondary data analysis was also performed to analyze different aspects of the HCI from these ImmPort studies and other related literature reports.

Results: The topics covered by the 6 ImmPort papers were identified to overlap with existing CIDO representation. SARS-CoV-2 viral S protein related HCI knowledge was emphasized for CIDO modeling, including its binding with ACE2, mutations causing different variants, and epitope homology by comparison with other coronavirus S proteins. Different types of cytokine signatures were also identified and added to CIDO. Our secondary analysis of two cohort COVID-19 studies with cytokine panel detection found that a total of 11 cytokines were up-regulated in female patients after infection and 8 cytokines in male patients. These sex-specific gene responses were newly modeled and represented in CIDO. A new DL query was generated to demonstrate the benefits of such integrative ontology representation. Furthermore, IL-10 signaling pathway was found to be statistically significant for both male patients and female patients.

Conclusion: Using the recursive XOD strategy, six new ImmPort COVID-19 studies were systematically reviewed, the results were modeled and represented in CIDO, leading to the enhancement of CIDO. The enhanced ontology and further seconary analysis supported more comprehensive understanding of the molecular mechanism of host responses to COVID-19 infection.

背景:随着新冠肺炎仍处于大流行阶段,广泛的研究产生了越来越多的数据和知识。由于许多研究都是在短时间内发表的,我们经常失去对宿主冠状病毒相互作用(HCI)机制的综合和全面的了解。截至2021年4月初,ImmPort数据库已存储了7项研究(其中6项有详细信息),涉及新冠肺炎患者的分子免疫特征、表位和死亡率性别差异等主题。冠状病毒传染病本体论(CIDO)代表了基本的HCI信息。我们假设CIDO可以作为平台来表示来自ImmPort的新记录信息,从而加强CIDO。方法:将CIDO用作语义平台,对6项ImmPort研究中报告的新识别知识进行逻辑建模和表示。建立了一种递归的可扩展本体开发(XOD)策略来支持CIDO的表示和增强。还进行了二次数据分析,以分析来自这些ImmPort研究和其他相关文献报告的HCI的不同方面。结果:6篇ImmPort论文所涵盖的主题被确定为与加拿大国际开发署现有的代表重叠。CIDO建模强调了严重急性呼吸系统综合征冠状病毒2型病毒S蛋白相关的HCI知识,包括其与ACE2的结合、导致不同变体的突变,以及与其他冠状病毒S蛋白相比的表位同源性。还鉴定了不同类型的细胞因子特征,并将其添加到CIDO中。我们对新冠肺炎两项细胞因子组检测队列研究的二次分析发现,女性患者感染后共有11种细胞因子上调,男性患者共有8种细胞因子下调。这些性别特异性基因反应是新建模的,并在CIDO中得到了体现。生成了一个新的DL查询来展示这种集成本体表示的好处。此外,发现IL-10信号通路对男性患者和女性患者都具有统计学意义。结论:采用递归XOD策略,对6项新的新冠肺炎免疫研究进行了系统回顾,并在CIDO中对结果进行了建模和表示,从而增强了CIDO。增强的本体论和进一步的分离分析支持更全面地理解宿主对新冠肺炎感染反应的分子机制。
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引用次数: 0
The Origin of Cross-Cultural Differences in Referential Intuitions: Perspective Taking in the Gödel Case 参照直觉跨文化差异的起源:Gödel案例的视角
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-08-07 DOI: 10.1093/jos/ffab010
Jincai Li
How do proper names refer? This question about reference is critical for philosophers studying language, linguists investigating meaning and reference, and psycholinguists interested in how children acquire names. Over the past century, philosophers have put forward two classical theories to explain the link between a name and the entity it refers to, i.e., the descriptivist theory proposed by Frege (1892/1948), Russell (1905) and Searle (1958) among others, and the causal-historical view most notably advocated by Kripke (1980). On the former account, a name gets its referent through associated definite descriptions. Thus, when a speaker uses a name, they typically refer to whoever best fits the descriptive content attached to that name. For instance, the name “Kamala Harris” refers to the lady Kamala Harris because she is the sole individual who could uniquely satisfy the descriptive content “the first female vice president of the United States” that is commonly associated with the name nowadays. In contrast, according to the Kripkean causal-historical view, a name refers to a person via a link that is originated in the initial naming ceremony and then gets passed down through a community of speakers. Kripke contends that proper names are rigid designators and they continue to refer to the individuals who were initially given the name, even when they turn out to have none of the properties that speakers associate with this name (1980). That means, on the causal-historical picture, the name “Kamala Harris” would still refer to the person Kamala Harris even if she had not been elected the vice president of the United States. In the philosophical literature, the received wisdom is that Kripke supported his causalhistorical view of reference with the famous “Gödel” thought experiment. Suppose the only thing most people have heard about the mathematician Kurt Gödel is that he is the person who proved the incompleteness of arithmetic, which thus is the only possible definite description these people could associate with Gödel. And now imagine that the person who bears this name (Kurt Gödel) didn’t actually prove the theorem, but instead stole it from a fellow named Schmidt who did all the work. In this case, the descriptivist theory predicts that the name “Gödel” would refer to Schmidt, because Schmidt is the person best fitting
专有名称如何指代?这个关于指称的问题对于研究语言的哲学家,研究意义和指称的语言学家,以及对儿童如何获得名字感兴趣的心理语言学家来说是至关重要的。在过去的一个世纪里,哲学家们提出了两种经典理论来解释名称与其所指代的实体之间的联系,即Frege(1892/1948)、Russell(1905)和Searle(1958)等人提出的描述主义理论,以及Kripke(1980)最引人注目的因果历史观点。在前一种情况下,名称通过相关的确定描述获得其所指。因此,当演讲者使用一个名称时,他们通常指的是最适合该名称附带的描述性内容的人。例如,“卡玛拉·哈里斯”这个名字指的是卡玛拉·哈里斯女士,因为她是唯一一个能够独特地满足“美国第一位女副总统”这一描述内容的人,这一描述内容如今通常与这个名字联系在一起。相反,根据Kripkean的因果历史观点,一个名字是通过一个链接来指代一个人的,这个链接起源于最初的命名仪式,然后通过说话者的社区传递下去。Kripke认为专有名称是一种严格的指示,它们继续指代最初被赋予该名称的个人,即使他们最终没有说话者与该名称相关的任何属性(1980)。这意味着,在因果历史的图景中,“卡玛拉·哈里斯”这个名字仍然指的是卡玛拉·哈里斯这个人,即使她没有被选为美国副总统。在哲学文献中,公认的智慧是克里普克用著名的“Gödel”思想实验来支持他的因果史观。假设大多数人听说过的关于数学家Kurt Gödel的唯一一件事就是他是证明了算术不完备性的人,因此这是这些人能联想到Gödel的唯一可能的明确描述。现在想象一下,拥有这个名字的人(Kurt Gödel)实际上并没有证明这个定理,而是从一个名叫施密特的家伙那里偷来的,他做了所有的工作。在这种情况下,描述主义理论预测“Gödel”这个名字指的是施密特,因为施密特是最合适的人选
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引用次数: 4
A Note on the Cardinalities of Sets of Scalar Alternatives 关于标量备选集的基数的注记
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-06-25 DOI: 10.1093/jos/ffab011
S. Mascarenhas
Formal theories of scalar implicature appeal crucially to a set of alternatives. These are the alternative statements that a speaker could have made but chose not to in pragmatic accounts, and the alternative statements that figure in the computation of exhaustivity operators in grammatical approaches. I show that the three sufficiently explicit theories of alternatives in the literature generate sets of alternatives that grow at least exponentially as a function of the input, and that these theories generate very large sets even for relatively small inputs. For pragmatic accounts of scalar implicature, I argue these results are hard or impossible to square with what we know independently about manipulating alternatives from the psychology of human reasoning. I propose that they pose a weaker but more general challenge for grammatical approaches, since alternatives as required by exhaustivity operators occur elsewhere in grammar, for example as part of the semantics of operators like “only” and “even.”
标量蕴涵的形式理论对一组备选方案至关重要。这些是说话者本可以在语用中做出但选择不做的替代陈述,以及在语法方法中计算穷竭运算符的替代陈述。我展示了文献中三个足够明确的选择理论产生的选择集,至少作为输入的函数呈指数增长,并且这些理论即使对于相对较小的输入也会产生非常大的选择集。对于标量蕴涵的实用主义解释,我认为这些结果很难或不可能与我们从人类推理心理学中独立了解的操纵选择相一致。我认为它们对语法方法构成了较弱但更普遍的挑战,因为穷竭运算符所要求的替代出现在语法的其他地方,例如作为“only”和“even”等运算符的语义的一部分。
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引用次数: 0
The Contribution of Gestures to the Semantics of Non-Canonical Questions 手势对非规范问题语义的贡献
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-06-14 DOI: 10.1093/JOS/FFAB007
Michela Ippolito
The symbolic gesture MAT (mano a tulipano) used by native speakers of Italian characterizes non-canonical wh questions when used both as a co-speech and pro-speech gesture. MAT can be executed with either a fast tempo contour or a slow tempo contour. Tempo is semantically significant: descriptively, a fast tempo characterizes a biased but information-seeking non-canonical question; a slow tempo characterizes a rhetorical non-canonical question. I argue that the fast contour is the default tempo of MAT and that it brings about a biased interpretation. Slowing down the movement occurs when the feature [slow] is added: the semantic contribution of this feature is to add the presupposition that the question is resolved in the conversational context, resulting in the rhetorical interpretation of the question.
意大利语母语者使用的象征性手势MAT (mano a tulipano)在作为共同言语和支持言语的手势使用时具有非规范的wh问题特征。MAT可以用快节奏轮廓或慢节奏轮廓来执行。语速在语义上是重要的:在描述上,快的语速是一个有偏见但寻求信息的非规范问题的特征;慢节奏是修辞性非规范问题的特点。我认为快速轮廓是MAT的默认节奏,它带来了有偏见的解释。当添加[slow]特征时,动作会减慢:该特征的语义贡献是添加了问题在会话上下文中得到解决的前提,从而导致对问题的修辞解释。
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引用次数: 2
Subclausal Local Contexts 分条款的地方背景
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-06-03 DOI: 10.1093/JOS/FFAB004
A. Anvari, Kyle Blumberg
One of the central topics in semantic theory over the last few decades concerns the nature of local contexts. Recently, theorists have tried to develop general, non-stipulative accounts of local contexts (Ingason, 2016; Mandelkern & Romoli, 2017a; Schlenker, 2009). In this paper, we contribute to this literature by drawing attention to the local contexts of subclausal expressions. More specifically, we focus on the local contexts of quantificational determiners, e.g. ‘all’, ‘both’, etc. Our central tool for probing the local contexts of subclausal elements is the principle Maximize Presupposition! (Percus, 2006; Singh, 2011). The empirical basis of our investigation concerns some data discussed by Anvari (2018b), e.g. the fact that sentences such as ‘All of the two presidential candidates are crooked’ are unacceptable. In order to explain this, we suggest that the local context of determiners needs to contain the information carried by their restrictor. However, no existing non-stipulative account predicts this. Consequently, we think that the local contexts of subclausal expressions will likely have to be stipulated. This result has important consequences for debates in semantics and pragmatics, e.g. those around the so-called “explanatory problem” for dynamic semantics (Heim, 1990; Schlenker, 2009; Soames, 1982).
在过去的几十年里,语义理论的中心议题之一是局部语境的性质。最近,理论家们试图发展对当地背景的一般的、非规定性的解释(Ingason, 2016;Mandelkern & Romoli, 2017a;Schlenker, 2009)。在本文中,我们通过提请注意分条款表达的局部上下文来贡献这一文献。更具体地说,我们关注定量限定词的局部语境,例如“all”、“both”等。我们探索子条款要素的局部语境的核心工具是最大化预设原则!(Percus, 2006;辛格,2011)。我们调查的经验基础涉及Anvari (2018b)讨论的一些数据,例如,“所有两个总统候选人都是扭曲的”这样的句子是不可接受的。为了解释这一点,我们建议限定词的局部上下文需要包含限定词所携带的信息。然而,没有现有的非规定帐户预测到这一点。因此,我们认为很可能必须规定分条款用语的当地情况。这一结果对语义学和语用学的争论产生了重要影响,例如围绕动态语义学的所谓“解释问题”(Heim, 1990;Schlenker, 2009;兜,1982)。
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引用次数: 3
Why and how to engage expert stakeholders in ontology development: insights from social and behavioural sciences. 为什么以及如何让专家利益相关者参与本体开发:来自社会和行为科学的见解。
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-03-23 DOI: 10.1186/s13326-021-00240-6
Emma Norris, Janna Hastings, Marta M Marques, Ailbhe N Finnerty Mutlu, Silje Zink, Susan Michie

Background: Incorporating the feedback of expert stakeholders in ontology development is important to ensure content is appropriate, comprehensive, meets community needs and is interoperable with other ontologies and classification systems. However, domain experts are often not formally engaged in ontology development, and there is little available guidance on how this involvement should best be conducted and managed. Social and behavioural science studies often involve expert feedback in the development of tools and classification systems but have had little engagement with ontology development. This paper aims to (i) demonstrate how expert feedback can enhance ontology development, and (ii) provide practical recommendations on how to conduct expert feedback in ontology development using methodologies from the social and behavioural sciences.

Main body: Considerations for selecting methods for engaging stakeholders are presented. Mailing lists and issue trackers as existing methods used frequently in ontology development are discussed. Advisory boards and working groups, feedback tasks, consensus exercises, discussions and workshops are presented as potential methods from social and behavioural sciences to incorporate in ontology development.

Conclusions: A variety of methods from the social and behavioural sciences exist to enable feedback from expert stakeholders in ontology development. Engaging domain experts in ontology development enables depth and clarity in ontology development, whilst also establishing advocates for an ontology upon its completion.

背景:在本体开发中纳入专家利益相关者的反馈对于确保内容适当、全面、满足社区需求以及与其他本体和分类系统可互操作非常重要。然而,领域专家通常没有正式参与本体开发,而且关于如何最好地进行和管理这种参与,几乎没有可用的指导。社会和行为科学研究通常涉及工具和分类系统开发中的专家反馈,但很少涉及本体开发。本文旨在(i)展示专家反馈如何增强本体开发,以及(ii)就如何使用社会科学和行为科学的方法在本体开发中进行专家反馈提供实用建议。主体:介绍了选择利益相关者参与方法的考虑因素。讨论了本体开发中常用的邮件列表和问题跟踪方法。咨询委员会和工作组、反馈任务、共识练习、讨论和研讨会被认为是社会和行为科学纳入本体发展的潜在方法。结论:社会科学和行为科学中存在各种方法,可以在本体开发中获得专家利益相关者的反馈。让领域专家参与本体开发可以使本体开发具有深度和清晰度,同时也可以在本体完成后为其建立倡导者。
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引用次数: 0
Deferred Reference of Proper Names 专有名称的延迟引用
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-03-08 DOI: 10.1093/JOS/FFAB001
Katarzyna Kijania-Placek, P. Banás
In this paper, we argue that proper names have deferred uses. Following Geoffrey Nunberg, we describe the deferred reference mechanism by which a linguistic expression refers to something in the world by exploiting a contextually salient relation between an index and the referent in question. Nunberg offered a thorough analysis of deferred uses of indexicals but claimed that proper names do not permit such uses. We, however, offer a number of examples of uses of proper names which pass grammatical tests for deferred usage, as put forward by Nunberg.
在本文中,我们认为专有名称具有延迟用途。按照Geoffrey Nunberg的说法,我们描述了递延引用机制,通过这种机制,语言表达通过利用索引和所指之间的上下文显著关系来引用世界上的事物。纽伯格对指数的延迟使用进行了全面的分析,但声称专有名称不允许这样的使用。然而,我们提供了一些专有名称用法的例子,这些例子通过了Nunberg提出的递延用法的语法测试。
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引用次数: 3
Disjunction in Negative Contexts: A Cross-Linguistic Experimental Study 否定语境中的析取:跨语言实验研究
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-01-01 DOI: 10.1093/jos/ffab002
Oana Lungu, Anamaria Fălăuș, F. Panzeri
This squib reports experimental findings from a study investigating the interpretation of simple disjunction in negative contexts in four languages: Italian, French, English, Romanian. We provide evidence that casts doubt on the robustness of the distinction between PPI disjunction languages and non-PPI disjunction languages. The difference turns out to be less clear-cut than assumed in the theoretical (e.g., Szabolcsi 2002, Spector 2014, Nicolae 2017) or experimental literature (e.g., Crain 2012, Guasti et al. 2017). The results reported here inform current accounts of positive polarity and flesh out some methodological issues raised by the various tasks used in experimental investigations of the polarity sensitivity of disjunction.
本文报道了一项研究的实验结果,该研究调查了四种语言(意大利语、法语、英语、罗马尼亚语)在否定语境中对简单分离的解释。我们提供的证据对PPI分离语言和非PPI分离语言之间区别的鲁棒性产生了怀疑。事实证明,这种差异并不像理论(例如,Szabolcsi 2002, Spector 2014, Nicolae 2017)或实验文献(例如,Crain 2012, Guasti et al. 2017)中假设的那样明确。这里报告的结果为目前关于正极性的描述提供了信息,并充实了在分离极性敏感性的实验研究中使用的各种任务所提出的一些方法问题。
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引用次数: 5
The Semantics of Emotive Markers and Other Illocutionary Content 情绪标记语与其他言外内容的语义
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2021-01-01 DOI: 10.1093/jos/ffab005
J. Rett
I coin the term ‘emotive markers’ to describe words like fortunately and alas which encode not-at-issue information about the speaker’s emotive attitude towards the content of the utterances they occur in. I argue that there are important differences emotive markers and other encoders of not-at-issue content, in particular utterance modifiers like frankly or evidential adverbs like apparently. In contrast to these, emotive markers can result in Moore’s Paradox and always range over their local argument. I conclude that the contribution of emotive markers should be treated as ‘illocutionary content’, on par with the speaker’s other Discourse Commitments (Gunlogson, 2001), and I model this analysis in the dynamic sub-sentential update framework in Farkas and Bruce (2010).
我创造了“情感标记”这个词来描述像“幸运”和“唉”这样的词,它们编码了关于说话者对话语内容的情感态度的非争议信息。我认为情绪标记和非争议内容的其他编码器存在重要差异,特别是像坦率这样的话语修饰语或像显然这样的证据副词。与此相反,情感标记可能导致摩尔悖论,并且总是超出其局部争论的范围。我的结论是,情绪标记的贡献应该被视为“言外内容”,与说话者的其他话语承诺一样(Gunlogson, 2001),我在Farkas和Bruce(2010)的动态子句更新框架中对这一分析进行了建模。
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引用次数: 22
期刊
Journal of Biomedical Semantics
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