Responsible Metrics Dashboard

Code repo including the code to calculate the underlying metrics as well as the Shiny app to present the results.

Forked with many thanks from https://github.com/quest-bih/dashboard

Repo overview

Put all the scripts that are directly involved in preparing data for use in the dashboard in the prep/ folder. Please indicate what scripts/software/data sources are used to generate the inputs for these in a comment in the code itself.

Put the final output data of these scripts in the shiny_app/data/ folder. These should only include the data that the dashboard Shiny app uses directly to generate plots.

The shiny_app/ folder contains the code that is run to generate the Shiny app.

Data preparation pipeline

1. Original data set based on Web of Science and Dimensions search

The following columns came from a search of Web of Science and Dimensions

| Column | Type | Details | |------------------------|-------------|----------------------------------------| | doi | string | Digital Object Identifier | | city | string | The university medical centre (UMC) | | year_published | numeric | Year of publication | | early_access | numeric | | | year_searched | numeric | | | email | string | Corresponding author email | | corr_author | string | Corresponding author | | authors | string | Semicolon delimited author list | | affiliations | string | Author affiliations | | type | string | Article type | | pmid_wos | numeric | Pubmed ID (Web of Science) | | wos_categories | string | | | language | string | Language of article (Web of Science) | | category_for | json | | | mesh_terms | json | | | pmid_dimensions | numeric | Pubmed ID (Dimensions) | | is_for_match | boolean | | | is_wos_match | boolean | | | is_multidisciplinary | boolean | | | is_book | boolean | | | is_retracted | boolean | | | approach | categorical | One of three approaches used to id UMC | | specificity_any_TF | numeric | | | specificity_any_TFU | numeric | |

2. Open access information

The data set from (1.) is joined by pmid_dimensions with open access information to provide the following additional columns

| Column | Type | Details | |-------------|-------------|--------------------------------------| | color | categorical | Type of Open Access provided | | issn | string | International Standard Serial Number | | journal | string | Name of journal | | publisher | string | Name of publisher | | date | date | |

3. Trial registry number (TRN) reporting

The data set from (2.) is joined by doi with TRN reporting information to provide the following additional columns

| Column | Type | Details | |------------------|---------|-----------------------------------------------| | is_human_ct | boolean | Is this a clinical trial | | abs_trn_1 | string | TRN found in abstract (1) | | abs_trn_2 | string | TRN found in abstract (2) | | abs_trn_3 | string | TRN found in abstract (3) | | abs_trn_4 | string | TRN found in abstract (4) | | abs_trn_5 | string | TRN found in abstract (5) | | abs_trn_6 | string | TRN found in abstract (6) | | abs_registry_1 | string | Registry corresponding to TRN in abstract (1) | | abs_registry_2 | string | Registry corresponding to TRN in abstract (2) | | abs_registry_3 | string | Registry corresponding to TRN in abstract (3) | | abs_registry_4 | string | Registry corresponding to TRN in abstract (4) | | abs_registry_5 | string | Registry corresponding to TRN in abstract (5) | | abs_registry_6 | string | Registry corresponding to TRN in abstract (6) | | si_trn_1 | string | TRN found in secondary information (1) | | si_trn_2 | string | TRN found in secondary information (2) | | si_trn_3 | string | TRN found in secondary information (3) | | si_trn_4 | string | TRN found in secondary information (4) | | si_registry_1 | string | Registry corresponding to TRN in SI (1) | | si_registry_2 | string | Registry corresponding to TRN in SI (2) | | si_registry_3 | string | Registry corresponding to TRN in SI (3) | | si_registry_4 | string | Registry corresponding to TRN in SI (4) |

4. Animal research

All unique values from pmid_dimensions column from (3.) are tested for whether they would appear in a search for animal research developed by Hooijmans et al (2010), using https://codeberg.org/bgcarlisle/PubmedIntersectionCheck

The resulting data set is joined by pmid_dimensions to the data set from (3.) to provide the following additional column (see merge-animals-and-sciscore.R for details)

| Column | Type | Details | |-------------|---------|----------------------------------------------------| | is_animal | boolean | Does this paper reflect experimentation on animals |

5. Robustness metrics

The data set from (4.) is joined by the pmid_dimensions column with robustness metrics provided by Sciscore to provide the following additional columns (see merge-animals-and-sciscore.R for details)

| Column | Type | Details | |----------------------------|---------|-----------------------------------------------| | sciscore | numeric | Summary robustness score provided by Sciscore | | iacuc | boolean | Presence of an IACUC statement | | irb | boolean | Presence of an IRB statement | | sex | boolean | Reporting of sex of research subjects | | blinding | boolean | Reporting of blinding | | randomization | boolean | Reporting of randomization | | power | boolean | Presence of a power calculation | | cell_line_auth | | | | antibody_detected | | | | antibody_with_rrid | | | | antibody_rrid_suggested | | | | organism_detected | | | | organism_with_rrid | | | | organism_rrid_suggested | | | | tool_detected | | | | tool_with_rrid | | | | tool_rrid_suggested | | | | cell_line_detected | | | | cell_line_with_rrid | | | | cell_line_rrid_suggested | | | | cell_line_contaminated | | | | plasmid_detected | | | | plasmid_with_rrid | | | | plasmid_rrid_suggested | | |

6. Open code and open data

The data set from (5.) is joined by doi, city and year_published to provide the following additional columns

| Column | Type | Description | |------------------------|-------------|-----------------------------------| | success | boolean | | | origin | categorical | | | article | string | DOI | | is_open_data | boolean | Whether the article has open data | | open_data_category | categorical | Location of open data | | is_open_code | boolean | Whether the article has open code | | open_data_statements | string | Extracted open data statement | | open_code_statements | string | Extracted open code statement |

7. Prepare UMC names

The UMC names in the city column are now all in lower case. Capitalize them with umc-names-caps.R