Software and Dependencies in Research Citation Graphs

Following the widespread digitalization of scholarship, software has become essential for research, but the current sociotechnical system of citation does not reflect this sufficiently. Citation provides context for research, but the current model for the respective research citation graphs does not integrate software. In this article, I develop a directed graph model to alleviate this, describe challenges for its instantiation, and give an outlook of useful applications of research citation graphs, including transitive credit.

[1]  Wendy Hui Kyong Chun,et al.  On Software, or the Persistence of Visual Knowledge , 2005, Grey Room.

[2]  Daniel S. Katz,et al.  Transitive Credit and JSON-LD , 2015 .

[3]  Daniel S. Katz Transitive Credit as a Means to Address Social and Technological Concerns Stemming from Citation and Attribution of Digital Products , 2014 .

[4]  Lior Shamir,et al.  Practices in source code sharing in astrophysics , 2013, Astron. Comput..

[5]  R. Peng Reproducible Research in Computational Science , 2011, Science.

[6]  Carole A. Goble,et al.  Better Software, Better Research , 2014, IEEE Internet Comput..

[7]  Daniel S. Katz,et al.  Software vs. data in the context of citation , 2016, PeerJ Prepr..

[8]  Marjorie M. K. Hlava,et al.  Beyond authorship: attribution, contribution, collaboration, and credit , 2015, Learn. Publ..

[9]  James Howison,et al.  Software in the scientific literature: Problems with seeing, finding, and using software mentioned in the biology literature , 2016, J. Assoc. Inf. Sci. Technol..

[10]  Qian Zhang,et al.  Software Citation Implementation Challenges , 2019, ArXiv.

[11]  Daniel S. Katz,et al.  Implementing Transitive Credit with JSON-LD , 2014, ArXiv.

[12]  Silvio Peroni,et al.  Setting our bibliographic references free: towards open citation data , 2015, J. Documentation.

[13]  S. Waqar Jaffry,et al.  Information extraction from scientific articles: a survey , 2018, Scientometrics.

[14]  Roberto Di Cosmo,et al.  Building the universal archive of source code , 2018, Commun. ACM.

[15]  Stephan Druskat,et al.  Citation File Format (CFF) , 2017 .

[16]  Carl Boettiger Citing R packages , 2012 .

[17]  Jenny Fry,et al.  Scholarship in the Digital Age: Information, Infrastructure, and the Internet , 2010, J. Assoc. Inf. Sci. Technol..

[18]  Arthur E. Kirkpatrick,et al.  Assessing open source software as a scholarly contribution , 2009, Commun. ACM.

[19]  Yasmin AlNoamany,et al.  Towards computational reproducibility: researcher perspectives on the use and sharing of software , 2018, PeerJ Prepr..

[20]  Yolanda Gil,et al.  Enhancing reproducibility for computational methods , 2016, Science.

[21]  E GARFIELD,et al.  Citation indexes for science; a new dimension in documentation through association of ideas. , 2006, Science.

[22]  Kai Li,et al.  How is R cited in research outputs? Structure, impacts, and citation standard , 2017, J. Informetrics.

[23]  G. Gutting The archaeology of knowledge , 1989 .

[24]  Victoria Stodden,et al.  Reproducible Research , 2019, The New Statistics with R.

[25]  Alva L. Couch,et al.  NSF Workshop on Supporting Scientific Discovery through Norms and Practices for Software and Data Citation and Attribution , 2015 .

[26]  Heather A. Piwowar,et al.  Altmetrics: Value all research products , 2013, Nature.

[27]  Jinghui Cheng,et al.  Activity-Based Analysis of Open Source Software Contributors: Roles and Dynamics , 2019, 2019 IEEE/ACM 12th International Workshop on Cooperative and Human Aspects of Software Engineering (CHASE).

[28]  Michael Brickenstein,et al.  swMATH - An Information Service for Mathematical Software , 2013, ICMS.

[29]  Suzie Allard,et al.  Trust and Authority in Scholarly Communications in the Light of the Digital Transition: setting the scene for a major study , 2014, Learn. Publ..

[30]  Daniel S. Katz,et al.  Journal of Open Source Software (JOSS): design and first-year review , 2017, PeerJ Comput. Sci..

[31]  Jeffrey Beck NISO Z39.96The Journal Article Tag Suite (JATS): What Happened to the NLM DTDs? , 2011, The journal of electronic publishing : JEP.

[32]  Steven A Greenberg,et al.  How citation distortions create unfounded authority: analysis of a citation network , 2009, BMJ : British Medical Journal.

[33]  Bruce Alberts,et al.  Making Data Maximally Available , 2011, Science.

[34]  Stephen R. Piccolo,et al.  Tools and techniques for computational reproducibility , 2016, GigaScience.

[35]  E. Garfield Citation analysis as a tool in journal evaluation. , 1972, Science.

[36]  Eleni Constantinou,et al.  Developers Expertise and Roles on Software Technologies , 2016, 2016 23rd Asia-Pacific Software Engineering Conference (APSEC).

[37]  Daniel S. Katz,et al.  Software citation principles , 2016, PeerJ Comput. Sci..

[38]  Barbara Kline Pope,et al.  Transparency in authors’ contributions and responsibilities to promote integrity in scientific publication , 2017, Proceedings of the National Academy of Sciences.

[39]  Anthony C. Woodbury,et al.  Reproducible research in linguistics: A position statement on data citation and attribution in our field , 2017 .

[40]  Jane Greenberg,et al.  Software citation, reuse and metadata considerations: An exploratory study examining LAMMPS , 2016, ASIST.

[41]  Hyoungjoo Park,et al.  Research software citation in the Data Citation Index: Current practices and implications for research software sharing and reuse , 2019, J. Informetrics.

[42]  Beth Plale,et al.  Software in Science: a Report of Outcomes of the 2014 National Science Foundation Software Infrastructure for Sustained Innovation (SI2) Meeting , 2014 .

[43]  M. Martone,et al.  A data citation roadmap for scientific publishers , 2017, Scientific Data.

[44]  Tomás Recio,et al.  On the evaluation of research software: the CDUR procedure , 2019, F1000Research.

[45]  Jennifer M. Urban,et al.  Shining Light into Black Boxes , 2012, Science.

[46]  C. Neylon,et al.  Article-Level Metrics and the Evolution of Scientific Impact , 2009, PLoS biology.

[47]  Alan Singleton,et al.  Bibliometrics and Citation Analysis; from the Science Citation Index to Cybermetrics , 2010, Learn. Publ..