Creating an ignorance-base: Exploring known unknowns in the scientific literature.
Creating an ignorance-base: Exploring known unknowns in the scientific literature.
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DOI：
10.1016/j.jbi.2023.104405
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发表时间：
2023-07
影响因子：
4.5
通讯作者：
Hunter, Lawrence E.
中科院分区：
文献类型：
--
作者：
Boguslav, Mayla R.;Salem, Nourah M.;White, Elizabeth K.;Sullivan, Katherine J.;Bada, Michael;Hernandez, Teri L.;Leach, Sonia M.;Hunter, Lawrence E.
关键词：
科学发现通过探索新的和未知的领域而取得进展。更具体地说，它是通过将未知的未知先转化为已知的未知，然后转化为未知的过程来推进的。在过去的几十年里，研究人员开发了许多知识库来捕获和连接已知知识，这使得主题探索和实验结果的上下文成为可能。但认识到未知因素对于找到最相关的问题及其答案也是至关重要的。以前关于已知未知的工作试图理解它们、对它们进行注释并使它们的识别自动化。然而，目前还不存在捕捉这些未知因素的知识库，几乎没有工作集中于科学家如何利用它们来追踪给定的主题或实验结果，以寻找开放的问题和新的探索途径。我们在这里表明，未知的知识库可以连接到基于本体论的生物医学知识，以加速产前营养领域的研究。我们提出了第一个无知基础，通过组合分类器来识别无知陈述(缺失或不完整知识的陈述，暗示知识的目标)和产前营养文献中的生物医学概念而创建的知识库。这个知识库将文献中提到的生物医学概念与作者对它们的无知声明放在一起。使用我们的系统，对维生素D和产前健康主题感兴趣的研究人员能够通过搜索丰富的无知陈述的概念来发现三个新的探索途径(免疫系统、呼吸系统和大脑发育)。这些都埋藏在许多标准丰富的概念中。此外，我们利用无知基础丰富了与维生素D和自然早产相关的基因列表相关的概念，并在一个隐含的领域(神经科学)找到了一个新兴的研究主题(大脑发育)。研究人员可以从神经科学领域寻找这些无知说法的潜在答案。我们的目标是帮助学生、研究人员、资助者和出版商更好地了解我们集体对科学的无知(已知未知)的状态，以便通过继续阐明和关注已知未知及其各自的科学知识目标来帮助加速研究。
Scientific discovery progresses by exploring new and uncharted territory. More specifically, it advances by a process of transforming unknown unknowns first into known unknowns, and then into knowns. Over the last few decades, researchers have developed many knowledge bases to capture and connect the knowns, which has enabled topic exploration and contextualization of experimental results. But recognizing the unknowns is also critical for finding the most pertinent questions and their answers. Prior work on known unknowns has sought to understand them, annotate them, and automate their identification. However, no knowledge-bases yet exist to capture these unknowns, and little work has focused on how scientists might use them to trace a given topic or experimental result in search of open questions and new avenues for exploration. We show here that a knowledge base of unknowns can be connected to ontologically grounded biomedical knowledge to accelerate research in the field of prenatal nutrition. We present the first ignorance-base, a knowledge-base created by combining classifiers to recognize ignorance statements (statements of missing or incomplete knowledge that imply a goal for knowledge) and biomedical concepts over the prenatal nutrition literature. This knowledge-base places biomedical concepts mentioned in the literature in context with the ignorance statements authors have made about them. Using our system, researchers interested in the topic of vitamin D and prenatal health were able to uncover three new avenues for exploration (immune system, respiratory system, and brain development) by searching for concepts enriched in ignorance statements. These were buried among the many standard enriched concepts. Additionally, we used the ignorance-base to enrich concepts connected to a gene list associated with vitamin D and spontaneous preterm birth and found an emerging topic of study (brain development) in an implied field (neuroscience). The researchers could look to the field of neuroscience for potential answers to the ignorance statements. Our goal is to help students, researchers, funders, and publishers better understand the state of our collective scientific ignorance (known unknowns) in order to help accelerate research through the continued illumination of and focus on the known unknowns and their respective goals for scientific knowledge.
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影响因子：
5.8
作者：
Bornigen, Daniela;Tranchevent, Leon-Charles;Moreau, Yves
通讯作者：
Moreau, Yves
DOI：
10.1093/bioinformatics/btx466
发表时间：
2017-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Zerva C;Batista-Navarro R;Day P;Ananiadou S
通讯作者：
Ananiadou S
影响因子：
3
作者：
Boguslav MR;Hailu ND;Bada M;Baumgartner WA Jr;Hunter LE
通讯作者：
Hunter LE
影响因子：
14.9
作者：
Gene Ontology Consortium;Blake JA;Dolan M;Drabkin H;Hill DP;Li N;Sitnikov D;Bridges S;Burgess S;Buza T;McCarthy F;Peddinti D;Pillai L;Carbon S;Dietze H;Ireland A;Lewis SE;Mungall CJ;Gaudet P;Chrisholm RL;Fey P;Kibbe WA;Basu S;Siegele DA;McIntosh BK;Renfro DP;Zweifel AE;Hu JC;Brown NH;Tweedie S;Alam-Faruque Y;Apweiler R;Auchinchloss A;Axelsen K;Bely B;Blatter M-;Bonilla C;Bouguerleret L;Boutet E;Breuza L;Bridge A;Chan WM;Chavali G;Coudert E;Dimmer E;Estreicher A;Famiglietti L;Feuermann M;Gos A;Gruaz-Gumowski N;Hieta R;Hinz C;Hulo C;Huntley R;James J;Jungo F;Keller G;Laiho K;Legge D;Lemercier P;Lieberherr D;Magrane M;Martin MJ;Masson P;Mutowo-Muellenet P;O'Donovan C;Pedruzzi I;Pichler K;Poggioli D;Porras Millán P;Poux S;Rivoire C;Roechert B;Sawford T;Schneider M;Stutz A;Sundaram S;Tognolli M;Xenarios I;Foulgar R;Lomax J;Roncaglia P;Khodiyar VK;Lovering RC;Talmud PJ;Chibucos M;Giglio MG;Chang H-;Hunter S;McAnulla C;Mitchell A;Sangrador A;Stephan R;Harris MA;Oliver SG;Rutherford K;Wood V;Bahler J;Lock A;Kersey PJ;McDowall DM;Staines DM;Dwinell M;Shimoyama M;Laulederkind S;Hayman T;Wang S-;Petri V;Lowry T;D'Eustachio P;Matthews L;Balakrishnan R;Binkley G;Cherry JM;Costanzo MC;Dwight SS;Engel SR;Fisk DG;Hitz BC;Hong EL;Karra K;Miyasato SR;Nash RS;Park J;Skrzypek MS;Weng S;Wong ED;Berardini TZ;Huala E;Mi H;Thomas PD;Chan J;Kishore R;Sternberg P;Van Auken K;Howe D;Westerfield M
通讯作者：
Westerfield M
影响因子：
4.5
作者：
Agarwal S;Yu H
通讯作者：
Yu H