The LILY Database: Linking Lithology to IODP Physical, Chemical, and Magnetic Properties Data

During each expedition of the International Ocean Discovery Program and its precursor, the Integrated Ocean Drilling Program (jointly referred to as IODP), vast arrays of data are collected from drill cores. These data, which are accessible from the IODP LIMS (Laboratory Information Management System) database, include physical, chemical, and magnetic properties collected semi-continuously along cores using automated track systems, as well as a variety of analyses conducted on discrete subsamples taken from the cores. In addition, the lithology of all cores is described based on visual characteristics of the surface of split cores, visual examination of smear slides and thin sections, and compositional or mineralogical information derived from geochemical analyses. We extract basic lithologic information from this complex array of descriptive information and then tie that information to all other measurements. This new database is referred to as LIMS with Lithology (LILY). LILY currently contains over 34 million data from 89 km of core recovered on 42 expeditions conducted 2009-2019. Some uses of LILY include identifying the abundance of different lithologies, finding data from core intervals with a specific lithology, assessing the efficacy of coring systems in different lithologies, or characterizing and analyzing physical, chemical, and magnetic properties based on lithology. We illustrate the use of LILY by computing the grain density by lithology from over 24,000 moisture and density measurements and then use those grain densities, along with the large IODP bulk density dataset, to compute a new high-resolution porosity dataset with over 3.7 million new porosity estimates. CONTENT DESCRIPTION: The main LILY database is stored in the files with the suffix _DataLITH.csv. Each file contains IODP LIMS data with lithology and other metadata added. The file prefix gives the type of data. For example, AVS_DataLITH.csv contains the Automated Vane Shear (AVS) shear strength data paired with lithology and other metadata. A list of all data types is given in Supporting Information Table S1 of Childress et al. (submitted to AGU G-cubed). Other compressed data folders contain multiple files used in creating the LILY database: 1_RawDESC.zip: Contains 7,940 .csv files derived from the raw text content of the DESClogik Excel worksheets that was extracted, converted to comma separated value (.csv) format, and put into files with a consistent naming convention, without applying any corrections or conversions to the original text. Each file is the direct extraction of a tab from the DESC workbooks, available at https://web.iodp.tamu.edu/DESCReport/ 2_CoreSUMM.zip: Contains one file with Core Summary information, which includes the expedition, site, hole, core, coring type, top and bottom depths drilled, advances and recoveries, time and date of recovery, and the number of sections. These data are further paired with additional metadata (expanded core type, latitude, longitude, and water depth). Coordinates and water depth for each hole are derived from LIMS (and the JANUS database at http://www-odp.tamu.edu/database/ for older expeditions). 3_RawDATA.zip: Contains the raw track/discrete dataset downloaded by expedition from IODP LIMS database and placed in folders for each type of data (AVS, CARB, SRM, etc.) 4_RawLITH.zip: Contains 42 .csv files, with one file for each expedition. Each file contains all lithologic description (prefix, principal and suffix, etc.) information for an entire expedition, as it was originally described. These have been transformed to a consistent format and paired with consistent identification information and additional metadata. Headers are normalized across all expeditions and SampleID information is standardized. 5_CleanLITH: Contains 42 .csv files. Each file contains all lithologic description (prefix, principal and suffix) information for an entire expedition. The lithologic descriptions have been standardized to a consistent nomenclature using the dictionary given in Support Information Table S4 of Childress et al. (submitted to AGU G-cubed). These data are further paired with additional metadata (e.g., degree of consolidation, expanded core type, latitude, longitude, and water depth).

国际大洋发现计划（International Ocean Discovery Program, IODP）及其前身综合大洋钻探计划的每一次科考航次中，研究人员均会从钻探获取的岩芯中采集海量数据。此类数据可通过IODP实验室信息管理系统（Laboratory Information Management System, LIMS）数据库获取，涵盖两类内容：一是利用自动化岩芯扫描系统沿岩芯半连续采集的物理、化学及磁学性质数据，二是对岩芯离散子样本开展的各类分析结果。

此外，所有岩芯的岩性描述均基于以下依据：劈开岩芯表面的视觉特征、涂片与薄片的镜下观察结果，以及地球化学分析得到的成分或矿物学信息。我们从这一庞杂的描述性数据集中提取基础岩性信息，并将其与所有其他测量数据进行关联整合，这一新数据库被命名为带岩性信息的LIMS（Lithology-integrated LIMS, LILY）。

目前LILY数据库包含2009至2019年间42个科考航次获取的89千米岩芯对应的超过3400万条数据。LILY的典型应用场景包括：识别不同岩性的丰度、检索特定岩性对应的岩芯段数据、评估不同岩性环境下钻探系统的取芯效率，以及基于岩性对物理、化学及磁学性质进行表征与分析。

我们以实例演示LILY的使用方法：先对超过24000条湿度与密度测量数据按岩性类别计算颗粒密度，随后利用这些颗粒密度与庞大的IODP体积密度数据集，计算得到包含超过370万条新孔隙度估算值的高分辨率孔隙度数据集。

### 内容说明
LILY主数据库存储于后缀为`_DataLITH.csv`的文件中。每个文件均包含添加了岩性及其他元数据的IODP LIMS数据，文件名前缀代表对应的数据类型。例如，`AVS_DataLITH.csv`包含了与岩性及其他元数据关联的自动叶片剪切（Automated Vane Shear, AVS）抗剪强度数据。所有数据类型的完整列表可参见Childress等人（提交至AGU G-cubed）的辅助信息表S1。

其余压缩数据文件夹包含构建LILY数据库所需的全部源文件：
1. `1_RawDESC.zip`：包含7940个`.csv`格式文件，这些文件由DESClogik Excel工作表的原始文本内容提取并转换为逗号分隔值格式，采用统一命名规范生成，未对原始文本进行任何校正或转换操作。每个文件直接对应DESC工作簿中的一个工作表，相关内容可通过https://web.iodp.tamu.edu/DESCReport/ 获取。
2. `2_CoreSUMM.zip`：包含一份岩芯概要信息文件，涵盖航次、站位、钻孔、岩芯、取芯类型、钻探上下深度、进尺与岩芯回收率、回收时间与日期，以及岩芯段数量等核心信息。此类数据还额外关联了扩展岩芯类型、纬度、经度与水深等元数据。每个钻孔的坐标与水深数据源自LIMS数据库；对于早期航次，则取自http://www-odp.tamu.edu/database/的JANUS数据库。
3. `3_RawDATA.zip`：包含按航次从IODP LIMS数据库下载的原始扫描/离散数据集，并按数据类型（AVS、CARB、SRM等）分文件夹存储。
4. `4_RawLITH.zip`：包含42个`.csv`格式文件，每个文件对应一个科考航次，存储了该航次全部岩芯的原始岩性描述信息（前缀、主岩性、后缀等）。这些文件已转换为统一格式，并关联了统一的标识信息与额外元数据。所有航次的文件表头已完成标准化，样本ID（SampleID）信息也已统一规范。
5. `5_CleanLITH`：包含42个`.csv`格式文件，每个文件对应一个科考航次的全部岩性描述信息（前缀、主岩性与后缀）。岩性描述已采用Childress等人（提交至AGU G-cubed）辅助信息表S4中的词典统一为标准化命名规范，并额外关联了固结程度、扩展岩芯类型、纬度、经度与水深等元数据。