RECODE: Relational Ecological COrpus for Data Extraction

RECODE is a manually annotated corpus of ecological and taxonomic literature, aimed at training and fine-tuning models for automated extraction of occurrence and trait data from unstructured text. Documents present have been annotated and validated by experts familiar with the traits of the included taxa (currently spiders and insects). Furthermore, this dataset is goal-oriented and published simultaneously with a complementary R package (arete) and a practical case of its usage for both finetuning and validation. Table of Contents The following are all the elements contained in the archive ./recode.zip: recode, directory. Contains metadata.csv, containing the metadata for each entry in RECODE. Also subdivides into all available taxa: currently ./insecta and ./araneae. These directories subdivide by annotator if available. If not, .tsv files are placed under a ./all directory. Finally, annotation files are named by the focus taxa they belong to and their document ID. metadata.csv ./araneae ./insecta r, directory. Contains the script used to calculate the values and plots present in the describing manuscript as well as all necessary files. These include two .csv tables containing taxonomic information on the species annotated in the dataset. These are supplied instead of being generated as part of the script as: 1) this data is prone to becoming outdated; 2) the method used to extract this information requires internet access. script_publish.R taxa_table_insects.csv taxa_table_spiders.csv plots, directory. Contains all plots created in R that appear on the release version of the describing manuscript. FIG_1.png FIG_3.png FIG_4.png FIG_5.png FIG_6.pngRECODE是一个经人工标注的生态学与分类学文献语料库（corpus），旨在训练并微调用于从非结构化文本（unstructured text）中自动提取物种出现记录与性状数据的模型。语料库内所有文档均由熟悉所纳入类群（当前为蜘蛛与昆虫）性状的专家完成标注与验证。此外，该数据集为目标导向型数据集，同步发布了配套的R语言包（arete），以及用于模型微调与验证的实际应用案例。 ### 目录 以下为./recode.zip压缩包内包含的全部内容： 1. **recode/** 目录 内含元数据（metadata）文件metadata.csv，存储RECODE语料库中每条数据的元数据。该目录同时按类群划分为两个子目录：当前为`./insecta`（昆虫纲）与`./araneae`（蜘蛛纲）。若标注者信息可获取，这些类群目录将进一步按标注者细分；若无法获取标注者信息，则.tsv格式的标注文件将置于`./all`子目录下。最终的标注文件以其所属的目标类群及文档ID命名。 包含的文件与子目录： - metadata.csv - ./araneae - ./insecta 2. **r/** 目录 内含用于生成描述性论文中统计值与图表的脚本，以及所有必需的辅助文件。其中包含两份.csv格式的表格，存储了本数据集已标注物种的分类学信息。此处直接提供该分类学数据而非在脚本中自动生成，原因有二：其一，该类数据易随时间推移过时；其二，提取该信息的方法需要联网访问外部资源。 包含的文件与子目录： - script_publish.R - taxa_table_insects.csv - taxa_table_spiders.csv 3. **plots/** 目录 内含所有出现在描述性论文正式发布版本中的R语言生成图表。 包含的文件： - FIG_1.png - FIG_3.png - FIG_4.png - FIG_5.png - FIG_6.png