Author information
Enter one or more of the following IDs:
To retrieve publications from Pubmed a query has to be specified. An example query with a dummy name can generated by pressing 'Example Pubmed Query'.
Additional information can found here.The following is a list of possible tags to use in a Pubmed query:
Upsetplot (alternative to Venn Diagram)
A Upset plot is an alternative to a Venn Diagram in that it shows the size of different sets in which the publications can be found.
Table of publications
The Table below showing the list of publications can be further filtered.
Individual publications can be selected by directly clicking on the respective rows and the filter can be applied by pressing 'Apply row selection'
To reverse the filter, press 'Reset row selection'.
A Citation list of all displayed publications can be generated by pressing 'Bibtex citation'. This will start on confirmation and will be displayed underneath the table where also the possibility for download as a file exists.
Documentation
Overview
This application provides functionality to retrieve publication records from multiple sources (such as ORCID) to provide an overview of the completeness of the respective source together with the open access status of all publications.
Data Sources
Currently it is possible to retrieve publications from ORCID, Pubmed, Google scholar and Publons.
Guide
The following describes a step by step example use case of the app.
First step
As a first step, at least one identifier of the author of interest needs to be obtained. For each of the following identifiers first go to the respective webpage:
and then search for the author. Navigate to the profile of the researcher of interest. Copy the identifier and paste it into the corresponding field in the app (alternatively it is possible to directly copy the URL).
For Pubmed a search query has to be specified instead of an identifier. When pressing 'Example Pubmed Query' in the app, a simple example query is generated which needs to be adapted (!). For more information on how to write Pubmed queries go to this help page.
Furthermore there are two additional options that can be selected. The first one is the possibility to use Crossref for matching publications from Google scholar to other sources. The use of Crossref is not strictly needed but might find additional matches of publications from different sources than the standard matching. The drawback of using Crossref is the much longer time it takes to complete (usually several minutes). It is therefore recommended to first try without this option and only enable it when the quality of the publication matching is poor (or there are known missing links). The second additional option is to retrieve citation data from the NIH Open Citation Collection.
Second step
After entering at least one identifier, show report can be pressed to start retrieval
and merging of the publication data. This will happen in the background and the
app will update as soon as new data becomes available. Depending on the number
of identifiers and the number of publications this can take several minutes.
Third step
The obtained data can now be explored using the Histogram on the right hand side and the Table underneath it.
The data can be filtered by using the given selection buttons in the box on the left hand side with the title Filter options.
Filtering options include by dataset, by year and by open access (OA) status. Most useful
for the comparison of the publications in different sources is the option to filter by dataset.
This follows a logical selection of the datasets, e.g. In Orcid and In Publons
(i.e. orcid & publons in code) means to only show the publications that are in ORCID and
in Publons at the same time, In Orcid or In Publons would mean all publications
that are in either Publons or ORCID (or both), Not in Orcid and In Publons
are the ones that are not in ORCID but at the same time are in Publons.
The Upset plot underneath the filter box shows a convenient overview of the different sets that can be found in the data. This plot is also the main visualization if one is only interested in updating the different sources since it is immediately visible which sources are complete and which are not.
Fourth step
Above the table listing the publications, the button Bibtex citation can be pressed to generate a .tex citation file
of all the entries in the table. The resulting content will appear underneath the table in a new box and can be downloaded by pressing
Download Bibtex citation. This file in turn can be uploaded within the web page of the respective
profile to update the publications in that source.
Methods
Open access status
The open access status is retrieved from Unpaywall and
relies on the DOI of a publication. Since Google scholar does not use DOI's it is possible that
the open access status for certain publications is unknown.
Preprints are defined as having oa == "green" and best_oa_location.version == "submittedVersion" or
oa == "green" and best_oa_location.version == "publishedVersion" and first_oa_location.version == "submittedVersion"
(i.e. peer reviewed publication linked in unpaywall).
About
Source code
The source code can be found on www.github.com/markrobinsonuzh/os_monitor.
Bug reports
If you encounter problems please open an issue on Github at www.github.com/markrobinsonuzh/os_monitor/issues. Please make a short description of the error you encounter and provide the input that you used (like the ORCID or Google scholar ID). General feedback and feature requests are of course also welcome.
License
This software is licensed under the MIT License.
Contact
If you have other questions do not hesitate to contact us:
Reto Gerber: reto.gerber@uzh.ch
Mark D Robinson: mark.robinson@mls.uzh.ch
Session Info
sessionInfo()
## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] shiny_1.7.1
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.8 tidyr_1.2.0
## [3] listenv_0.8.0 shinyWidgets_0.6.4
## [5] visNetwork_2.1.0 assertthat_0.2.1
## [7] digest_0.6.29 utf8_1.2.2
## [9] parallelly_1.30.0 mime_0.12
## [11] R6_2.5.1 odbc_1.3.3
## [13] evaluate_0.14 httr_1.4.2
## [15] ggplot2_3.3.5 pillar_1.7.0
## [17] rlang_1.0.1 lazyeval_0.2.2
## [19] data.table_1.14.0 rentrez_1.2.3
## [21] jquerylib_0.1.4 blob_1.2.2
## [23] DiagrammeR_1.0.8 shinyjs_2.1.0
## [25] stringr_1.4.0 htmlwidgets_1.5.4
## [27] bit_4.0.4 munsell_0.5.0
## [29] xfun_0.25 compiler_4.1.0
## [31] httpuv_1.6.5 pkgconfig_2.0.3
## [33] globals_0.14.0 htmltools_0.5.2
## [35] tidyselect_1.1.1 shinyTree_0.3.0
## [37] tibble_3.1.6 uzhOS_1.0
## [39] codetools_0.2-18 XML_3.99-0.8
## [41] fansi_1.0.2 future_1.23.0
## [43] viridisLite_0.4.0 crayon_1.5.0
## [45] dplyr_1.0.8 withr_2.4.3
## [47] later_1.3.0 grid_4.1.0
## [49] jsonlite_1.7.3 xtable_1.8-4
## [51] gtable_0.3.0 lifecycle_1.0.1
## [53] DBI_1.1.1 magrittr_2.0.2
## [55] scales_1.1.1 cli_3.2.0
## [57] stringi_1.7.6 promises_1.2.0.1
## [59] bslib_0.3.1 ellipsis_0.3.2
## [61] generics_0.1.2 vctrs_0.3.8
## [63] RColorBrewer_1.1-2 tools_4.1.0
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## [69] parallel_4.1.0 fastmap_1.1.0
## [71] colorspace_2.0-2 shinydashboardPlus_2.0.4.9000
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## [75] knitr_1.33 sass_0.4.0