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Paleontology Knowledge Graph for Data-Driven Discovery

Journal of Earth Science 2024年第3期35卷 1024-1034页

作者： Yiying Deng Sicun Song junxuan fan Mao Luo Le Yao Shaochun Dong Yukun Shi Linna Zhang Yue Wang Haipeng Xu Huiqing Xu Yingying Zhao Zhaohui Pan Zhangshuai Hou Xiaoming Li Boheng Shen Xinran Chen Shuhan Zhang Xuejin Wu Lida Xing Qingqing Liang Enze Wang School of Resources and Environmental Engineering Hefei University of TechnologyHefei 230009China State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and PaleoenvironmentChinese Academy of SciencesNanjing 210008China School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling Nanjing UniversityNanjing 210023China State Key Laboratory for Mineral Deposits Research Nanjing UniversityNanjing 210023China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China Centre for Research and Education on Biological Evolution and Environment Nanjing UniversityNanjing 210023China State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesBeijing 100083China School of the Earth Sciences and Resources China University of GeosciencesBeijing 100083China

A knowledge graph(KG)is a knowledge base that integrates and represents data based on a graph-structured data model or *** have made efforts to construct geosciencerelated KGs to overcome semantic heterogeneity and facilitate knowledge representation,data integration,and text ***,there is currently no comprehensive paleontology KG or data-driven discovery based on *** this study,we constructed a two-layer model to represent the ordinal hierarchical structure of the paleontology KG following a top-down construction *** ontology containing 19365 concepts has been defined up to *** this basis,we derived the synonymy list based on the paleontology KG and designed corresponding online functions in the OneStratigraphy database to showcase the use of the KG in paleontological research.

关键词： paleontology knowledge graph ontology synonymy list OneStratigraphy big data ge-ology.

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重建深时地球生物多样性时空分布模式的思考

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科学通报 2024年第22期69卷 3252-3267页

作者：张书涵沈树忠王向东张华樊隽轩南京大学地球科学与工程学院关键地球物质循环前沿科学中心内生金属成矿机制研究国家重点实验室南京210023 中国科学院南京地质古生物研究所现代古生物学和地层学国家重点实验室南京210008

重建地球生物多样性演变历史是了解地球生命演化规律的关键.通过研究地质时期的生物多样性变化,能够追溯生命的起源、演化和灭绝过程,并探索其原因.然而,地球上曾经生活过的99%以上的生物都已经灭亡,其中只有一小部分保存为化石并被人... 详细信息

重建地球生物多样性演变历史是了解地球生命演化规律的关键.通过研究地质时期的生物多样性变化,能够追溯生命的起源、演化和灭绝过程,并探索其原因.然而,地球上曾经生活过的99%以上的生物都已经灭亡,其中只有一小部分保存为化石并被人类发现.因此,如何利用化石记录重建地球生物多样性变化的过程是一个非常复杂的科学难题.为了解决这一难题,需要从多方面入手.首先,建立含有时空信息的全球性大型综合数据库是研究深时生物多样性模式的必要条件,也是识别曾经发生过的重大生物事件的基础,以往的研究多集中在海洋无脊椎动物化石多样性的研究,目前仍然缺乏全球性的陆地生物多样性模式.其次,需要解决化石保存不完整和样本采集时空不均一的难题.近十几年来,随着海量数据的积累,大数据分析技术的发展,通过多学科交叉,在解决时空分辨率低和样本偏差等问题上发展了更有效的分析手段,但仍然任重道远.最后,新的大数据研究结果引发了对深时地球生物多样性变化的时空规律的许多新认识.随着研究的深入,五次生物大灭绝的灭绝幅度和灭绝率明显降低,需要以全球大数据为基础重新精确估算,其中二叠纪末生物大灭绝无疑仍是最大的一次,而泥盆纪晚期F/F和三叠纪末灭绝事件很可能算不上五大生物灭绝之二,白垩纪末生物大灭绝的持续时间和灭绝幅度也需要重新估算.此外,寒武纪-奥陶纪、石炭纪-二叠纪和新生代三大生物辐射事件也需要全球高分辨率化石数据验证.以人工智能和超级计算机等为手段建立的深时生态系统演变模型是实现古今对比的未来方向.这些研究将使我们对地球生物多样性历史有全方位的认识,也为现今的全球生态系统面临的问题提供深时参照.

关键词：深时大数据生物多样性生物大灭绝生态模型

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Paleobiogeographic Knowledge Graph:An Ongoing Work with Fundamental Support for Future Research

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地球科学学刊:英文版 2023年第5期34卷 1339-1349页

作者： Linna Zhang Zhangshuai Hou Boheng Shen Qing Chen Shaochun Dong junxuan fan State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and PalaeoenvironmentChinese Academy of SciencesNanjing 210008China School of Earth Sciences and Engineering and Frontiers Science Center for Critical Earth Material Cycling Nanjing UniversityNanjing 210023China State Key Laboratory for Mineral Deposits Research Nanjing UniversityNanjing 210023China

Paleobiogeography investigates geographical distributions of fossil organisms and controlling factors that affect their distributions in geological history,to reveal the macro-evolution and coordinated development of life and the *** is a crucial window for understanding the biosphere and the geographical *** two centuries of development,paleobiogeographic studies have led to the accumulation of significant amounts of knowledge and data;however,the voluminous outputs present the characteristics of an“isolated island”with a scattered,limited number of authoritative definitions of terminologies and semantic heterogeneity among *** makes data queries cumbersome,the rate of data reuse low,and data sharing more difficult.A knowledge graph(KG)has the advantage of expressing concepts and their semantic relations,which is an important tool for achieving data organization and fusion,and data mining;further,it is also a key technology for realizing the unrestricted sharing of paleobiogeographic *** our efforts over the past two years,a paleobiogeographic KG was developed based on the established construction procedure of the KG,which contains 273 concepts,172 properties,and 47 ***,the completion of this KG and the construction of a paleobiogeographic platform for display and analysis are now being carried out.

关键词： biogeographic unit knowledge base artificial intelligence paleobiogeographic platform knowledge inference knowledge graph

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How to Build a High-Resolution Digital Geological Timeline?

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Journal of Earth Science 2022年第6期33卷 1629-1632页

作者： Shuzhong Shen junxuan fan Xiangdong Wang Feifei Zhang Yukun Shi Shuhan Zhang State Key Laboratory for Mineral Deposits Research School of Earth Sciences and EngineeringFrontiers Science Center for Critical Earth Material CyclingNanjing UniversityNanjing210023China

1 QUESTION FORMULATION Time and space are the two basic axes to characterize the existence of matter. Without time, there would be no rate(“No dates, No rates”). The Earth has a history of approximately 4.5 billion years, leaving behind a myriad of geological records,and the geologic timeline is the only common language available to unravel the evolutionary history of the Earth.

关键词： approximate Resolution Earth

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深时重大生物和气候事件与全球变化:进展与挑战

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科学通报 2024年第2期69卷 268-285页

作者：沈树忠张飞飞王文倩王向东樊隽轩陈吉涛王博曹剑杨石岭张华李高军邓涛李献华陈骏南京大学地球科学与工程学院关键地球物质循环前沿科学中心内生金属成矿机制研究国家重点实验室南京210023 中国科学院南京地质古生物研究所现代古生物学与地层学国家重点实验室南京210008 中国科学院地质与地球物理研究所新生代地质与环境重点实验室北京100029 中国科学院古脊椎动物与古人类研究所脊椎动物演化与人类起源重点实验室北京100044 中国科学院地质与地球物理研究所岩石圈演化国家重点实验室北京100029

地球自5.4亿年前现代生态系统形成至今,发生了多次与碳循环扰动有关的重大气候事件.这些事件的触发机制、发展过程、环境变化及其伴随的生物响应型式为科学评估当今全球变化背景下生物多样性现状提供重要借鉴.然而,古-今生态系统变化时... 详细信息

地球自5.4亿年前现代生态系统形成至今,发生了多次与碳循环扰动有关的重大气候事件.这些事件的触发机制、发展过程、环境变化及其伴随的生物响应型式为科学评估当今全球变化背景下生物多样性现状提供重要借鉴.然而,古-今生态系统变化时间尺度大不相同,高分辨率关键环境因子(温度、CO_(2)、降雨量、海洋氧化还原条件等)在深时记录中亦难以获取,深时海陆生物多样性模式尚缺乏高分辨率记录.因此,当今全球变化与深时记录对比存在巨大鸿沟.地球5.4亿年以来大部分时间处于两极无冰的温室状态,期间伴随多次极冷和极热气候事件,但地球深时重大生物演化和气候事件的关系复杂.生物多样性在变冷的奥陶纪早期、晚古生代大冰期、晚新生代大冰期以及中-晚三叠世和白垩纪热室期均呈现稳定增加,而在奥陶纪末冰期快速降温期间和二叠纪末、三叠纪末、白垩纪末火山排气作用导致的快速升温过程中急剧下降.地质时期生物多样性对气候变化的不同响应型式表明,生物多样性变化的根本驱动因素可能不是简单的温度、大气CO_(2)浓度等环境因子的背景值高或低,而是环境因子的变化速率(环境变率).变率较小,环境相对稳定,生物有足够的时间适应环境变化,生物多样性不会丧失,甚至繁盛.反之,若环境因子变率过大,超出了生态系统的承受力,生物来不及适应,生物多样性就会显著降低,甚至引发大灭绝.已有模拟和计算表明,当今地球碳排放的速度有可能超过了地质历史时期任何一次生物大灭绝事件.因此,避免环境突变事件和生物大灭绝的再次发生成为政界、科学界和普通民众关注的焦点.打通地球多圈层界限,开展古-今地质记录、冷-热极端气候、海-陆生态系统和长-短时间尺度的综合对比研究,并通过建立适用于深时的地球系统模型,模拟重大生物和环境事件的背景与发生过程,是地球系统科学未来发展的重要方向.

关键词：深时极端气候重大生物事件环境变率全球变化地球系统模拟

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Paleogeographic evolution of the Lower Yangtze region and the break of the “platform-slope-basin” pattern during the Late Ordovician

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Science China Earth Sciences 2018年第5期61卷 625-636页

作者： Qing CHEN junxuan fan Linna ZHANG Xu CHEN CAS Key Laboratory of Economic Stratigraphy and Palaeogeography Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences Laboratory for Marine Geology Qingdao National Laboratory for Marine Science and Technology

Wide distribution of the black shales and diversification of the graptolite fauna in South China during the Late Ordovician resulted from its unique paleogeographic pattern, which was significantly affected by the paleogeographic evolution of the Lower Yangtze region. In the study, 120 Upper Ordovician sections from the Lower Yangtze region were collected, and a unified biostratigraphic framework has been applied to these sections to establish a reliable stratigraphic subdivision and correlation. Under the unified time framework, we delineate the distribution area of each lithostratigraphic unit, outline the boundary between the sea and land, and reconstruct the paleogeographic pattern for each graptolite zone. The result indicates that, with the uplift and expansion of the ‘Jiangnan Oldland' in the beginning of the late Katian, the oldland extended into the Yangtze Sea gradually from south to north, which finally separate the Jiangnan Slope and the Yangtze Platform. Consequently,the longstanding paleogeographic pattern of "platform-slope-basin" in South China was broken. The paleogeographic change led to sedimentary differentiation among the two sides of the ‘Jiangnan Oldland' during the Late Ordovician. This event also led to the closure of the eastern exit of the Upper Yangtze Sea, and formed a semi-closed, limited and stagnant environment for the development of the organic-rich black shales during the Late Ordovician. The major controlling factors of these paleogeographic changes in the Lower Yangtze region were not consistent from the Katian to the Hirnantian. In the late Katian, the sedimentary differentiation between the east and west sides mostly resulted from regional tectonic movement-the Kwangsian ***, during the Hirnantian, the whole Yangtze region became shallower, which was mostly influenced by the concentration of the Gondwana ice sheet and the consequent global sea level drop.

关键词：奥陶纪进化裂缝岩石层位学控制因素构造运动黑页岩沉积区

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Toward a stepwise Kwangsian Orogeny

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Science China Earth Sciences 2014年第5期57卷 379-387页

作者： CHEN Xu fan junxuan CHEN Qing TANG Lan HOU XuDong State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences College of Resources and Metallurgy Guangxi University

The Kwangsian Orogeny originated along the southeast coast of China and stepwise developed in a northwest *** includes two stages,a long locally varying uplift from the Late Ordovician to the early Silurian and a finally tectonic movement near the Silurian and Devonian *** Kwangsian uplift event shows a stepwise delay northwestwards from the southeastern coast area in Nemagraptus gracilis Biozone(Sa1)to the south side of the Xuefeng Mountains in or later than Cystograptus vesiculosus Biozone(R3)to Coronograptus cyphus Biozone(R4).In the southern of Yangtze Platform,the Yichang Uplift was droved by the Kwangsian Orogeny forming a diachronous stratigraphical break through Rhuddanian and *** distribution of the early Telychian lower marine red beds indicates a northwestward increase of the Cathaysian *** evidence may explain why the Kwangsian movement was marked by an angular disconformity during the Pridoli to earliest Devonian interval.

关键词：造山运动角度不整合东南沿海构造运动早志留世晚奥陶世局部变化沿海区域

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Ordovician graptolite-bearing strata in southern Jiangxi with a special reference to the Kwangsian Orogeny

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Science China Earth Sciences 2010年第11期53卷 1602-1610页

作者： Xu Chen YuanDong Zhang junxuan fan JunFeng Cheng QiJian Li Chinese Acad Sci Nanjing Inst Geol & Palaeontol State Key Lab Palaeobiol & Stratig Nanjing 210008 Peoples R China

The Ordovician graptolite sequence of the Yongxin-Chongyi area in southern Jiangxi was suggested as a standard for the correlation of Ordovician in the Zhujiang region of South China. Based on a restudy of the Upper Ordovician graptolites, the Shikou and Huamianlong formations are recognized herein as a part of the Hanjiang Formation, corresponding only to the Dipla-canthograptus caudatus-Diplacanthograptus spiniferus Zone. Two graptolite zones in the Longxi Formation of Yongxin and Chongyi, the Nemagraptus gracilis Zone and Climacograptus bicornis Zone, are redefined here. A rapid replacement of facies from the typical deep-water graptolitic black shale of Longxi Formation to the rapidly-accumulated, shallow-water clastic deposits of Hanjiang Formation indicates the tectonic initiation of the Kwangsian Orogeny. The thick clastic deposits of the Han-jiang Formation are proposed to come from a nearby source area that rose during the Kwangsian Orogeny. The D. caudatus-D. spiniferus graptolite Zone of the Hanjiang Formation indicates the initiation time of this tectonic event.

关键词： Longxi Formation Hanjiang Formation Sandbian Ordovician graptolite Kwangsian Orogeny

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Deep-time Paleogeographic Reconstruction Based on Database:Taking the South China T. approximatus Biozone(Early Ordovician) as an Example

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Acta Geologica Sinica(English Edition) 2019年第S1期93卷 76-79页

作者： ZHANG Linna fan junxuan CHEN Qing State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and Paleontology and Center for Excellence in Life and PaleoenvironmentChinese Academy of SciencesNanjing 210008China School of Earth Sciences and Engineering Nanjing UniversityNanjing 210023China CAS Key Laboratory of Economic Stratigraphy and Palaeogeography Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and PaleoenvironmentChinese Academy of SciencesNanjing 210008China

Paleogeography is a discipline that studies spatial distribution and evolutionary characteristics of geographic objects in earth history(Feng,2003;Feng et al.,2012).It focuses on the sediments,organisms and environmental proxies,most of which are preserved in the ***,a large amount of this geological and biological information was no longer preserved after the geological process of burial.

关键词： paleogeography deep-time GIS database

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Biostratigraphic correlation of the Ordovician black shales in Tarim Basin and its peripheral regions

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Science China Earth Sciences 2012年第8期55卷 1230-1237页

作者： CHEN Xu ZHANG YuanDong LI Yue fan junxuan TANG Peng CHEN Qing ZHANG YuanYuan Nanjing Institute of Geology and Palaeontology Chinese Academy of SciencesNanjing 210008China State Key Laboratory of Palaeobiology and Stratigraphy Nanjing 210008China Graduate University of Chinese Academy of Sciences Beijing 100049China

Ordovician black shales are widely distributed in the Tarim Basin and its peripheral regions,and some of them may serve as potential hydrocarbon source *** present study of the Ordovician graptolite fauna from these shales,together with the yielded conodonts and chitinozoans etc.,permits a refined correlation of the *** mainly on a new collecting of the graptolites and a study of the faunas in Kalpin and Kuruktag regions,and the successful identification of the new graptolite material from a few drill cores within the basin,we are able to update our knowledge of the Ordovician in the regions,and draw some conclusions:(1) The most widespread distribution of the black shales in the Tarim Basin and its peripheral regions,which correspond to the Nemagraptus gracilis Zone,may be related to a global sea-level rise during this time interval.(2) Black shales of Ordovician occur most frequently and extensively in the Kuruktag(also spelled as Quruq Tagh) region in east-ern Tianshan Mountains,spanning Tremadocian to mid-Katian(*** Zone) temporally and extending southeastwards into Manjiaer *** black shales of the *** Zone may even extend into the central Tarim Basin.(3) Three different bio-and litho-facies belts(Bachu:carbonate platform and reef belt;Kalpin-Aksu:marginal platform and upper slope belt;Wushi:slope belt) are recognized in the northwestern Tarim Basin.(4) The internationally well-correlated Saergan black shale,which has been considered to possess high potential for hydrocarbon source rock,may possess a restricted distribution in the Kalpin and Aksu areas.

关键词：塔里木盆地黑色页岩周边地区奥陶系地层对比笔石动物群库鲁克塔格阿克苏地区

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