发表机构
Bhargava Systems Research Inc.; Cornell University; Johns Hopkins University（Bhargava系统研究公司; 康奈尔大学; 约翰斯·霍普金斯大学）
机构由 AI 辅助整理，请以论文原文为准。AI 中文总结
PaperAtlas从640万篇开放获取文章中自动构建计算方法与软件图谱，覆盖约107万计算类摘要，识别出软件名称并评估与现有注册表的匹配，提供开源网络服务。
AI 中文摘要
计算方法与软件分散在日益难以人工审阅的文献中，而经过整理的注册表仅收录了可用资源的一部分。我们提出了PaperAtlas，一个从PubMed Central开放获取语料库中自动构建的图谱。在筛查的6,446,741篇摘要中，1,074,191篇被分类为计算类，其中为1,074,140篇提取了符合模式的有效记录。在这些记录中，描述算法、软件包或网络服务器的267,893篇论文形成了1,438个聚类，在限制到父级生物医学类别后保留了1,000个聚类。在与至少五个bio.tools条目关联的296个聚类中，最常见的EDAM主题的平均集中度为61.7%，而排列检验下为26.4%。在31,180个不同的软件和网络服务器名称中，61.0%在bio.tools、PyPI、CRAN、Bioconductor或Bioconda中缺乏严格匹配。在语料库中具有定义论文的12,207个bio.tools条目中，56.6%被端到端恢复，而在其定义出版物进入图谱的8,265个条目中，这一比例增至83.6%。PaperAtlas完全开源，并作为网络服务器在bhargavaresearch.org/paperatlas提供。
英文摘要
Computational methods and software are dispersed across a literature that is increasingly difficult to review manually, while curated registries capture only a subset of available resources. We present PaperAtlas, an automatically constructed atlas derived from the PubMed Central open-access corpus. Of 6,446,741 abstracts screened, 1,074,191 were classified as computational, with schema-valid records extracted for 1,074,140. Among these, 267,893 papers describing an algorithm, software package or web server formed 1,438 clusters, with 1,000 retained after restriction to parent-level biomedical categories. In 296 clusters linked to at least five bio.tools entries, the mean concentration of the most frequent EDAM topic was 61.7%, compared with 26.4% under permutation. Of 31,180 distinct software and web-server names, 61.0% lacked a strict match in bio.tools, PyPI, CRAN, Bioconductor or Bioconda. Among 12,207 bio.tools entries with defining papers in the corpus, 56.6% were recovered end to end, increasing to 83.6% among the 8,265 entries whose defining publication entered the atlas. PaperAtlas is fully open source and available as a web server at bhargavaresearch.org/paperatlas.
