iCite Database Snapshot 2024-07

This is a database snapshot of the iCite web service (provided here as a single zipped CSV file, or compressed, tarred JSON files). In addition, citation links in the NIH Open Citation Collection are provided as a two-column CSV table in open_citation_collection.zip. iCite provides bibliometrics and metadata on publications indexed in PubMed, organized into three modules:<br>Influence: Delivers metrics of scientific influence, field-adjusted and benchmarked to NIH publications as the baseline.<br>Translation: Measures how Human, Animal, or Molecular/Cellular Biology-oriented each paper is; tracks and predicts citation by clinical articles<br>Open Cites: Disseminates link-level, public-domain citation data from the NIH Open Citation Collection<br>Definitions for individual data fields:<br>pmid: PubMed Identifier, an article ID as assigned in PubMed by the National Library of Medicine<br>doi: Digital Object Identifier, if available<br>year: Year the article was published<br>title: Title of the article<br>authors: List of author names<br>journal: Journal name (ISO abbreviation)<br>is_research_article: Flag indicating whether the Publication Type tags for this article are consistent with that of a primary research article<br>relative_citation_ratio: Relative Citation Ratio (RCR)--OPA's metric of scientific influence. Field-adjusted, time-adjusted and benchmarked against NIH-funded papers. The median RCR for NIH funded papers in any field is 1.0. An RCR of 2.0 means a paper is receiving twice as many citations per year than the median NIH funded paper in its field and year, while an RCR of 0.5 means that it is receiving half as many citations per year. Calculation details are documented in Hutchins et al., PLoS Biol. 2016;14(9):e1002541.<br>provisional: RCRs for papers published in the previous two years are flagged as "provisional", to reflect that citation metrics for newer articles are not necessarily as stable as they are for older articles. Provisional RCRs are provided for papers published previous year, if they have received with 5 citations or more, despite being, in many cases, less than a year old. All papers published the year before the previous year receive provisional RCRs. The current year is considered to be the NIH Fiscal Year which starts in October. For example, in July 2019 (NIH Fiscal Year 2019), papers from 2018 receive provisional RCRs if they have 5 citations or more, and all papers from 2017 receive provisional RCRs. In October 2019, at the start of NIH Fiscal Year 2020, papers from 2019 receive provisional RCRs if they have 5 citations or more and all papers from 2018 receive provisional RCRs.<br>citation_count: Number of unique articles that have cited this one<br>citations_per_year: Citations per year that this article has received since its publication. If this appeared as a preprint and a published article, the year from the published version is used as the primary publication date. This is the numerator for the Relative Citation Ratio.<br>field_citation_rate: Measure of the intrinsic citation rate of this paper's field, estimated using its co-citation network.<br>expected_citations_per_year: Citations per year that NIH-funded articles, with the same Field Citation Rate and published in the same year as this paper, receive. This is the denominator for the Relative Citation Ratio.<br>nih_percentile: Percentile rank of this paper's RCR compared to all NIH publications. For example, 95% indicates that this paper's RCR is higher than 95% of all NIH funded publications.<br>human: Fraction of MeSH terms that are in the Human category (out of this article's MeSH terms that fall into the Human, Animal, or Molecular/Cellular Biology categories)<br>animal: Fraction of MeSH terms that are in the Animal category (out of this article's MeSH terms that fall into the Human, Animal, or Molecular/Cellular Biology categories)<br>molecular_cellular: Fraction of MeSH terms that are in the Molecular/Cellular Biology category (out of this article's MeSH terms that fall into the Human, Animal, or Molecular/Cellular Biology categories)<br>x_coord: X coordinate of the article on the Triangle of Biomedicine<br>y_coord: Y Coordinate of the article on the Triangle of Biomedicine<br>is_clinical: Flag indicating that this paper meets the definition of a clinical article.<br>cited_by_clin: PMIDs of clinical articles that this article has been cited by.<br>apt: Approximate Potential to Translate is a machine learning-based estimate of the likelihood that this publication will be cited in later clinical trials or guidelines. Calculation details are documented in Hutchins et al., PLoS Biol. 2019;17(10):e3000416.<br>cited_by: PMIDs of articles that have cited this one.<br>references: PMIDs of articles in this article's reference list.<br>Large CSV files are zipped using zip version 4.5, which is more recent than the default unzip command line utility in some common Linux distributions. These files can be unzipped with tools that support version 4.5 or later such as 7zip.<br>Comments and questions can be addressed to [e-mail]

本数据集为iCite网络服务的数据库快照，以单个压缩CSV文件或tar打包压缩的JSON文件形式提供。此外，NIH开放引文集合中的引文链接以两栏CSV表格的形式存放在open_citation_collection.zip中。

iCite为PubMed收录的文献提供文献计量学指标与元数据，分为三个模块：
1. **影响力模块**：提供经领域校正、以美国国立卫生研究院（National Institutes of Health, NIH）资助文献为基准的科学影响力计量指标。
2. **转化模块**：衡量每篇文献偏向人类、动物还是分子/细胞生物学的程度，并追踪、预测临床文章对其的引用情况。
3. **开放引文模块**：发布来自NIH开放引文集合的链路级公共领域引文数据。

### 各数据字段定义：
`pmid`：PubMed编号（PubMed Identifier），即美国国家医学图书馆（National Library of Medicine）在PubMed中为文献分配的唯一识别ID。
`doi`：数字对象标识符（Digital Object Identifier, DOI），若文献可获取则提供该字段。
`year`：文献发表年份。
`title`：文献标题。
`authors`：作者姓名列表。
`journal`：期刊名称（采用ISO缩写格式）。
`is_research_article`：标识该文献的出版物类型标签是否符合原创研究文章标准的标志位。
`relative_citation_ratio`：相对引文比率（Relative Citation Ratio, RCR）——NIH办公室（OPA）的科学影响力计量指标。该指标经领域与时间校正，以NIH资助文献为基准。任意领域内NIH资助文献的RCR中位数为1.0。RCR为2.0意味着该文献每年获得的引文数是其所属领域、发表同年份NIH资助文献中位数的2倍；RCR为0.5则意味着其每年获得的引文数仅为对应基准的一半。该指标的计算细节详见Hutchins等人发表于PLoS Biol. 2016;14(9):e1002541的研究。
`provisional`：发表于前两年的文献的RCR会被标记为“临时”，以反映新近发表文献的引文计量指标不如成熟文献稳定。若发表于上一年度的文献获得5次及以上引文，即便其发表时长不足一年，也会提供临时RCR。所有发表于上上年的文献均会被赋予临时RCR。当前年度以NIH财年（始于每年10月）为准。例如，在2019年7月（NIH 2019财年），2018年发表且获得5次及以上引文的文献会被标记临时RCR，且2017年发表的所有文献均会被标记临时RCR。2019年10月，即NIH 2020财年伊始，2019年发表且获得5次及以上引文的文献会被标记临时RCR，2018年发表的所有文献均会被标记临时RCR。
`citation_count`：引用该文献的唯一文献总数量。
`citations_per_year`：该文献自发表以来每年获得的平均引文数。若该文献同时以预印本和正式出版物形式发布，则以正式出版物的年份作为其主要发表年份。该指标为相对引文比率的分子。
`field_citation_rate`：基于该文献的共引网络估算得到的其所属领域固有引文率。
`expected_citations_per_year`：与该文献具有相同领域引文率且发表于同年的NIH资助文献每年获得的平均引文数。该指标为相对引文比率的分母。
`nih_percentile`：该文献的RCR在所有NIH资助文献中的百分位排名。例如，95%意味着该文献的RCR高于95%的NIH资助文献。
`human`：该文献属于人类、动物或分子/细胞生物学类别的MeSH主题词（MeSH terms）中，归类为人类类别的占比。
`animal`：上述分类中，归类为动物类别的MeSH主题词占比。
`molecular_cellular`：上述分类中，归类为分子/细胞生物学类别的MeSH主题词占比。
`x_coord`：生物医药三角图（Triangle of Biomedicine）上该文献的X轴坐标。
`y_coord`：生物医药三角图（Triangle of Biomedicine）上该文献的Y轴坐标。
`is_clinical`：标识该文献符合临床文章定义的标志位。
`cited_by_clin`：引用该文献的临床文章的PubMed编号列表。
`apt`：近似转化潜力（Approximate Potential to Translate, APT），基于机器学习估算该文献被后续临床试验或指南引用的可能性。其计算细节详见Hutchins等人发表于PLoS Biol. 2019;17(10):e3000416的研究。
`cited_by`：引用该文献的所有文章的PubMed编号列表。
`references`：该文献参考文献列表中所收录文献的PubMed编号列表。

大型CSV文件采用zip 4.5版本压缩，该版本较部分主流Linux发行版默认的unzip命令行工具更新。此类文件可使用支持zip 4.5及以上版本的工具（如7zip）进行解压。

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