### 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'.

The following is a list of possible tags to use in a Pubmed query:

0 / 100
0%

### Filter options

#### Summary filtered data

#### Filter

##### Remove duplicates

Remove preprints with existing peer reviewed publication. Matching of publications is done based on a fuzzy matching of the titles.

##### Dataset selection

A logical filter for the datasets can be specfied. For example: 'Not in orcid And in scholar' means to only show publications that are in Google scholar and at the same time not in ORCID.

##### Cutoff year

Only publications within the year limits are shown.

##### OA status

Only the publications with the selected OA status are shown.

### 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 selection'

To reverse the filter, press 'Reset 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.

### ‌

### Grey zone (Sci-hub)

Retrieve fulltext links of closed publications from sci-hub

## 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).

### 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.

### Contact

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
##
## 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
## [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_1.6.0
##
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7               tidyr_1.1.3              listenv_0.8.0
##  [4] shinyWidgets_0.6.0       visNetwork_2.0.9         assertthat_0.2.1
##  [7] digest_0.6.27            utf8_1.2.2               parallelly_1.27.0
## [10] mime_0.11                R6_2.5.1                 odbc_1.3.2
## [13] evaluate_0.14            httr_1.4.2               ggplot2_3.3.5
## [16] pillar_1.6.2             rlang_0.4.11             lazyeval_0.2.2
## [19] data.table_1.14.0        rentrez_1.2.3            jquerylib_0.1.4
## [22] blob_1.2.2               DiagrammeR_1.0.6.1       shinyjs_2.0.0
## [25] stringr_1.4.0            htmlwidgets_1.5.3        bit_4.0.4
## [28] munsell_0.5.0            compiler_4.1.0           httpuv_1.6.2
## [31] xfun_0.25                pkgconfig_2.0.3          globals_0.14.0
## [34] htmltools_0.5.2          tidyselect_1.1.1         shinyTree_0.3.0
## [37] tibble_3.1.4             uzhOS_1.0                codetools_0.2-18
## [40] XML_3.99-0.7             fansi_0.5.0              future_1.22.1
## [43] viridisLite_0.4.0        crayon_1.4.1             dplyr_1.0.7
## [46] withr_2.4.2              later_1.3.0              grid_4.1.0
## [49] jsonlite_1.7.2           xtable_1.8-4             gtable_0.3.0
## [52] lifecycle_1.0.0          DBI_1.1.1                magrittr_2.0.1
## [55] scales_1.1.1             stringi_1.7.4            promises_1.2.0.1
## [58] bslib_0.2.5.1            ellipsis_0.3.2           generics_0.1.0
## [61] vctrs_0.3.8              RColorBrewer_1.1-2       tools_4.1.0
## [64] bit64_4.0.5              glue_1.4.2               purrr_0.3.4
## [67] hms_1.1.0                parallel_4.1.0           fastmap_1.1.0
## [70] colorspace_2.0-2         shinydashboardPlus_2.0.2 shinydashboard_0.7.1
## [73] plotly_4.9.4.1           knitr_1.33               sass_0.4.0