Skip to content

Latest commit

 

History

History
154 lines (119 loc) · 6.6 KB

script_descriptions.md

File metadata and controls

154 lines (119 loc) · 6.6 KB

Script Descriptions

The scripts below were used in the case study to assess use of the Human Disease Ontology in the publication:

Assessing Resource Use: A Case Study with the Human Disease Ontology. DATABASE. Accepted, awaiting publication.

These scripts are found in the scripts/ directory and listed below under the section of the case study they apply to, with a brief description. Later in this document a description of what each script accomplished and its file inputs and outputs are given.

Obtain Use Records

  1. citedby_full_procedure.R: used to obtain "cited by" and MyNCBI collection records.
  2. pub_searches.R: used to obtain and analyze search records.

Curating Use Information

No scripts were used in curation. Instead, open the DO_uses-published_2022 Google Sheet to review curated information.

Evaluate Use

citedby_RNA.R citedby_analysis.R citedby_manual_count_plot.R compare_citedby_search.R

Detailed Description of Scripts Used in Publication

  1. citedby_full_procedure.R

    • Purpose: Obtain publication records from PubMed and Scopus that cite one or more of the official DO publications (referred to as "cited by"), load DO's MyNCBI collection, merge all of the records from these sources together, and append results to existing DO_uses-published_2022 Google Sheet.
    • Input:
      1. data/citedby/collection.txt: 2022-11-17 download of DO's MyNCBI collection.
    • Output:
      1. data/citedby/do_cb_pm_summary_by_id.rda: full, untidied PubMed "cited by" results, obtained 2022-11-10.
      2. data/citedby/do_cb_scop_by_id.rda: full, untidied Scopus "cited by" results, obtained 2022-11-10.
      3. data/citedby/do_collection_pm_summary.rda: full, untidied MyNCBI collection publication summary results from PubMed, obtained 2022-11-10.
      4. data/citedby/do_collection_pmc_summary.rda: full, untidied MyNCBI collection publication summary results from PubMed Central (PMC), obtained 2022-11-10.
      5. data/citedby/DO_citedby.csv: merged and tidied citations from all sources.

  2. pub_searches.R

    • Purpose: Obtain publication records via search against PubMed, PubMed Central (PMC), and Europe PMC databases that may have used the DO.
    • Input: None
    • Output:

      • Raw search results, obtained 2022-11-09:

        1. Europe PMC: data/lit_search/epmc_search_raw.RData
        2. PubMed: data/lit_search/pubmed_search_raw.RData
        3. PMC: data/lit_search/pmc_search_raw.RData

      • Raw results for additional identifiers, obtained 2022-11-09: 4. PubMed: data/lit_search/pm_search_raw-IDs.RData 5. PMC: data/lit_search/pmc_search_raw-IDs.RData

      • Tidied search results 6. Europe PMC: data/lit_search/epmc_search_results.csv 7. PubMed: data/lit_search/pubmed_search_results.csv 8. PMC: data/lit_search/pmc_search_results.csv

        data/lit_search/search_res_n.csv data/lit_search/actual_search_terms.csv graphics/lit_search/epmc_search_overlap.png graphics/lit_search/epmc_search_overlap-min10.png graphics/lit_search/pmc_search_overlap.png graphics/lit_search/pm_search_overlap.png data/lit_search/src_comparison.csv graphics/lit_search/search_src_overlap-venn.png graphics/lit_search/search_src_overlap-upset.png graphics/lit_search/total_hits-graph.png graphics/lit_search/total_hits-legend.png graphics/lit_search/total_hits-complete.png

citedby_RNA.R - Purpose: - Input: - Output: 1. graphics/citedby/RNA_pubs_over_time.png 2. graphics/citedby/RNA_pubs_over_time-by_type.png 3. graphics/citedby/RNA_pubs_over_time-by_pub_type.png

citedby_analysis.R - Purpose: - Input: 1. data/citedby/DO_citedby.csv - Output: data/citedby/analysis/time_to_review.csv data/citedby/analysis/MyNCBI_collection_cites-mid2021.csv data/citedby/analysis/citedby_source_count.csv data/citedby/analysis/review_time_summary.csv data/citedby/analysis/status_uses_count.csv data/citedby/analysis/use_type_count.csv data/citedby/analysis/tool_roles_count.csv data/citedby/analysis/research_area_count.csv data/citedby/analysis/disease_count.csv data/citedby/analysis/use_case_count.csv

graphics/citedby/analysis/DO_cited_by_count.png graphics/citedby/analysis/citedy_source_overlap-venn.png

citedby_manual_count_plot.R - Purpose: - Input: 1. data/citedby/counts/citedby_counts-manual.csv - Output: 2. data/citedby/counts/citedby_counts-manual_smry.csv 3. graphics/citedby/citedby_manual_comparison_2021.png 4. graphics/citedby/citedby_manual_comparison_2022.png

compare_citedby_search.R - Purpose: - Input: 1. data/citedby/DO_citedby.csv - Output:

data/lit_search/src_comparison.csv data/lit_search/epmc_search_results.csv data/cb_search_compare/citedby_search_comparison.csv data/cb_search_compare/search_uniq.csv graphics/cb_search_compare/citedby_search_comparison.png graphics/cb_search_compare/search_unique_pub_type.png

Additional Scripts in this Repository

Three additional scripts in this repository were used to evaluate the impact of the DO outside of published literature but these impact measures, specific to the DO, are not included in the publication.

  1. alliance_disease_record_counts.R: count of disease records in databases belonging to the Alliance of Genome Resources.
  2. bioconductor_stats.R: unique IP download statistics for DO-dependent R packages 'DOSE' and 'DO.db'.
  3. cfde_disease_record_counts.R: count of disease records in databases belonging to the Common Fund Data Ecosystem (CFDE).

Details

data/alliance/disease_counts-full_by_obj.csv data/alliance/disease_counts-disobj_by_obj.csv data/alliance/disease_counts-disease_by_obj.csv data/alliance/disease_counts-unique_diseases.csv graphics/alliance_disobj_plot.png graphics/alliance_full_record_plot.png

data/bioc_DO_stats.csv data/bioc_DO_stats-1yr-distinctIP.csv graphics/bioc_DO_stats-distinctIP.png graphics/bioc_DO_stats-1yr-distinctIP.png

  • Input: data/cfde/CFDE_data-program_sample_disease.csv
  • Output:
    1. data/cfde/cfde_disease_counts.csv
    2. graphics/cfde_disease.png