Abstract
The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB’s large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.
Highlights
Consistent practice of data citation facilitates and incentivizes data sharing and reuse because it could be counted as professional recognition for data providers as citations of journal and other types publications
We focus on analyzing citations to the Protein Data Bank (PDB) data repository
The data is available for download from, in either NXML markup language or plain text
Summary
Consistent practice of data citation facilitates and incentivizes data sharing and reuse because it could be counted as professional recognition for data providers as citations of journal and other types publications. Currently no commonly agreed data citation practice has been adopted. It is not clear which practice standard or policy gains the most adoption, nor is how they reflect the impact of the data being cited. The Protein Data Bank (PDB) [1,2,3,4,5,6,7,8] is the worldwide repository of experimentally determined structures of proteins, nucleic acids, and complex assemblies, including drug-target complexes. The PDB annotates structures according to standards set by the wwPDB [9] and provides unique identifiers and DOIs for its datasets.
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