fileName;variableName;description;levels;type;response
charite_open_data_2020.csv;article;{ODDPub} DOI of the articles screened;{different values};character;pre-loaded
charite_open_data_2020.csv;is_open_data;"{ODDPub} Automatically detected Open Data state by ODDPub; here only TRUE cases used for Open Data screening workflow";TRUE;logical;pre-loaded
charite_open_data_2020.csv;open_data_category;{ODDPub} Automatically detected type of data repository, presence of data availability statement in the article or data detection in supplement;{different values};character;pre-loaded
charite_open_data_2020.csv;is_open_code;{ODDPub} Automatically detected Open Code state by ODDPub;"TRUE;FALSE";logical;pre-loaded
charite_open_data_2020.csv;open_data_statements;{ODDPub} Automatically detected Open Data statement in the article fulltext;{different values};character;pre-loaded
charite_open_data_2020.csv;open_code_statements;{ODDPub} Automatically detected Open Code statement in the article fulltext;{different values};character;pre-loaded
charite_open_data_2020.csv;reference_to_data;"{Numbat} Availability of reference to 'raw' data - data availability statement if present or any passage in the article fulltext; 'n_a' stays for article type that does not generate new data";"yes;no;n_a;unsure";character;single choice
charite_open_data_2020.csv;identifier;{Numbat} Dataset identifier (either a DOI or a link/repository+accession code) to the dataset containg files;{different open text entries};character;open text field
charite_open_data_2020.csv;own_or_reuse_data;"{Numbat} Ownership of data: data generated by the article author(s) ('own_open-data') or by the different contibutor(s) ('open_data_reuse'); the reuse of own data is also possible which is documented here as 'own_open-data' with clear commentaries about reuse";"own_open-data;open_data_reuse;unsure";character;single choice
charite_open_data_2020.csv;data_in_supplement;{Numbat} Article independent dataset sharing in the data repository or plattform, and support by metadata;"yes;no;unsure";character;single choice
charite_open_data_2020.csv;findability;{Numbat} Findability of dataset in the stated data repository via stated accession code;"yes;no;unsure";character;single choice
charite_open_data_2020.csv;data_access;"{Numbat} Accessibility of dataset in stated location; 'resticted' dataset(s) require registration or application to access them";"yes;no;restricted;unsure";character;single choice
charite_open_data_2020.csv;is_machine_readable_format;"{Numbat} Machine readable dataset file format; 'format_unknown' for cases when no format is documented in the metadata or could not be exctracted from the file naming, or the file is too heavy to be downloaded (>200 Mb)";"yes;no;unsure;format_unknown";character;single choice
charite_open_data_2020.csv;machine_readable_format_excel;{Numbat} Excel file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_csv;{Numbat} CSV file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_txt;{Numbat} TXT file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_spss;{Numbat} SPSS file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_other_text_formats;{Numbat} Other, not listed yet, text or table file formats;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_video;{Numbat} Video file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_audio;{Numbat} Audio file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_picture;{Numbat} Image file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_fasta_fastq;{Numbat} FASTA or FASTQ file format (nucleotide sequences);"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_raw;{Numbat} RAW file format (image);"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_genetic_sequences;{Numbat} Other, not listed yet, file formats of genetic sequences;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_subject_specific_format;{Numbat} Other, not listed yet, subject specific file formats;"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;machine_readable_format_unsure;{Numbat} Unsure which file format the dataset belongs to (commentaries are expected here);"1;NULL";character;part of multiple choice selection
charite_open_data_2020.csv;illustrative_files;{Numbat} Only for file formats Video, Audio, Image, RAW, Unsure:  datasets with visual elements should have more than just illustrative character, i.e. figures from the article stored in the data repository are not sufficient;"yes;no;inapplicable;unsure";character;single choice
charite_open_data_2020.csv;analytical_replication;"{Numbat} Representation of sufficient 'rawness', e.g. for data replication in a different study. No precise distinction between replication and absence of replication is possible. Tendency to a positive response can be documented as 'replication', and a confident opinion about replication as 'yes'; tendency to a negative response can be documented as 'no_replication', and a confident opinion about absence of replication as 'no'";"yes;no;replication;no_replication";character;single choice
charite_open_data_2020.csv;assessment;{Numbat} Final decision about opennes of examined dataset (not applicable here on all datasets for the examined article, i.e. on article-level assessment). The response 'unsure' does not appear in the final output as it is interim result for discussion during reconciliation;"open_data;no_open_data";character;single choice
charite_open_data_2021.csv;doi;{ODDPub} DOI of the articles screened;{different values};character;pre-loaded
charite_open_data_2021.csv;is_open_data;"{ODDPub} Automatically detected Open Data state by ODDPub; here only TRUE cases used for Open Data screening workflow";TRUE;logical;pre-loaded
charite_open_data_2021.csv;open_data_category;{ODDPub} Automatically detected type of data repository, presence of data availability statement in the article or data detection in supplement;{different values};character;pre-loaded
charite_open_data_2021.csv;is_open_code;{ODDPub} Automatically detected Open Code state by ODDPub;"TRUE;FALSE";logical;pre-loaded
charite_open_data_2021.csv;open_data_statements;{ODDPub} Automatically detected Open Data statement in the article fulltext;{different values};character;pre-loaded
charite_open_data_2021.csv;open_code_statements;{ODDPub} Automatically detected Open Code statement in the article fulltext;{different values};character;pre-loaded
charite_open_data_2021.csv;reference_to_data;"{Numbat} Availability of reference to 'raw' data - data availability statement if present or any passage in the article fulltext; 'n_a' stays for article type that does not generate new data";"yes;no;n_a";character;single choice
charite_open_data_2021.csv;findability;{Numbat} Findability of dataset in the stated data repository via stated accession code;"yes;no;unsure";character;single choice
charite_open_data_2021.csv;data_identifier;{Numbat} Dataset identifier (either a DOI or a link/repository+accession code) to the dataset containg files;{different open text entries};character;open text field
charite_open_data_2021.csv;not_a_supplement;{Numbat} Article independent dataset sharing in the data repository or plattform, and support by metadata;"yes;no;unsure";character;single choice
charite_open_data_2021.csv;repository;"{Numbat} Repository name in which examined dataset was detected: available through the tags list retrieved from re3data.org registry and completed manually based on the previously detected repositores in the medical context; list extension was possible during extraction";"4D Nucleome Consortium data portal;Addgene;ADNI;AIBL;ArrayExpress;BBMRI.nl;BCAC;BioImage;BioProject;BioStudies;cancer.gov;CATs;Center for Health Protection;Center for Statistical Genetics;clinicaltrials.gov;Code Ocean;Connectone;dbGaP;DDBJ;decipher;DRYAD;DZNE;Edmond;EMPIAR;ENCODE;EuMCCR;European genome-phenome archive;European Nucleotide Archive;EWAS Catalog;Fairdata.fi;FASTGenomics;figshare;FlowRepository;GitHub;GitLab;gnomAD browser;GNPS;GoDMC;GTDB;gtexportal;GWAS;Harvard Dataverse;heiDATA;HISAT2;HOCOMOCO;ICGC;immuneAccess;Kaggle;LCSB;Lead BDS;Linnarsson Lab;Mass Spectrometry Interactive Virtual Environment;Mendeley Data;MetaboLights;Metabolomics Workbench;Microbiome;MorphoSource;Mouse Genome Informatics;National Cancer Institute;NCBI Gene Expression Omnibus;NGDC Genome Sequence Archive;NCBI Genomic Data Commons;NCBI Nucleotide;NCBI Protein;NCBI Sequence Read Archive;NCBI Trace Archive;NeuroVault;NGDC BioProject;NITRC;OMICSCIENCE;OpARA;Open Science Framework;OpenNeuro;PGS Catalog;ProteomeXchange;PRoteomics IDEntifications Database;PTB-OAR;R2 Genomics Analysis and Visualization Platform;SASBDB;Single Cell Portal;Synapse;TCIA;Terra;The Electron Microscopy Data Bank;U.S. Census Bureau;Virtual Trials Archives;Worldwide Protein Data Bank;Zenodo;ZivaHub";character;tags
charite_open_data_2021.csv;year_of_data_publication;"{Numbat} Year of the last (reasonable) update of the examined dataset in form ""YYYY""";"1993;2008;2010;2011;2012;2013;2014;2015;2016;2017;2018;2019;2020;2021;2022";character;open text field
charite_open_data_2021.csv;data_access;"{Numbat} Accessibility of dataset in stated location; 'resticted' dataset(s) require registration or application to access them";"yes;no;restricted;unsure";character;single choice
charite_open_data_2021.csv;dataset_license;{Numbat} Availability of metadata about standard license for datasets, e.g. Creative Commons;"yes;no;unsure";character;single choice
charite_open_data_2021.csv;license_name;"{Numbat} License name detected; list extension was possible during extraction";"CC BY;CC BY-NC;CC BY-NC-ND;CC BY,CC0;CC0;GNU GPLv3;Public Domain";character;tags
charite_open_data_2021.csv;own_or_reuse_data;"{Numbat} Ownership of data: data generated by the article author(s) ('own_open-data') or by the different contibutor(s) ('open_data_reuse'); the reuse of own data is also possible which is documented here as 'own_open-data' with clear commentaries about reuse";"own_open-data;open_data_reuse;unsure";character;single choice
charite_open_data_2021.csv;machine_readable_format;"{Numbat} Machine readable dataset file format; 'format_unknown' for cases when no format is documented in the metadata or could not be exctracted from the file naming, or the file is too heavy to be downloaded (>200 Mb)";"yes;no;unsure;format_unknown";character;single choice
charite_open_data_2021.csv;machine_readable_format_excel;{Numbat} Excel file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_csv_tsv;{Numbat} CSV or TSV file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_txt_docs;{Numbat} TXT or DOCS file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_other_text_formats;{Numbat} Other, not listed yet, text or table file formats;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_video;{Numbat} Video file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_audio;{Numbat} Audio file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_picture;{Numbat} Image file format;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_fasta_fastq;{Numbat} FASTA or FASTQ file format (nucleotide sequences);"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_raw;{Numbat} RAW file format (image);"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_genetic_sequences;{Numbat} Other, not listed yet, file formats of genetic sequences;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_subject_specific_format;{Numbat} Other, not listed yet, subject specific file formats;"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;machine_readable_format_unsure;{Numbat} Unsure which file format the dataset belongs to (commentaries are expected here);"1;NULL";character;part of multiple choice selection
charite_open_data_2021.csv;illustrative_files;{Numbat} Only for file formats Video, Audio, Image, RAW, Unsure:  datasets with visual elements should have more than just illustrative character, i.e. figures from the article stored in the data repository are not sufficient;"yes;no;inapplicable;unsure";character;single choice
charite_open_data_2021.csv;analytical_replication;"{Numbat} Representation of sufficient 'rawness', e.g. for data replication in a different study. No precise distinction between replication and absence of replication is possible. Tendency to a positive response can be documented as 'replication', and a confident opinion about replication as 'yes'; tendency to a negative response can be documented as 'no_replication', and a confident opinion about absence of replication as 'no'";"yes;no;replication;no_replication";character;single choice
charite_open_data_2021.csv;open_data_assessment;{Numbat} Final decision about opennes of examined dataset (not applicable here on all datasets for the examined article, i.e. on article-level assessment). The response 'unsure' does not appear in the final output as it is interim result for discussion during reconciliation;"open_data;no_open_data";character;single choice
dutch_umc_open_data.csv;doi;{ODDPub} DOI of the articles screened;{different values};character;pre-loaded
dutch_umc_open_data.csv;is_open_data;"{ODDPub} Automatically detected Open Data state by ODDPub; here only TRUE cases used for Open Data screening workflow";TRUE;logical;pre-loaded
dutch_umc_open_data.csv;open_data_category;{ODDPub} Automatically detected type of data repository, presence of data availability statement in the article or data detection in supplement;{different values};character;pre-loaded
dutch_umc_open_data.csv;is_open_code;{ODDPub} Automatically detected Open Code state by ODDPub;"TRUE;FALSE";logical;pre-loaded
dutch_umc_open_data.csv;open_data_statements;{ODDPub} Automatically detected Open Data statement in the article fulltext;{different values};character;pre-loaded
dutch_umc_open_data.csv;open_code_statements;{ODDPub} Automatically detected Open Code statement in the article fulltext;{different values};character;pre-loaded
dutch_umc_open_data.csv;reference_to_data;"{Numbat} Availability of reference to 'raw' data - data availability statement if present or any passage in the article fulltext; 'n_a' stays for article type that does not generate new data";"yes;no;n_a;unsure";character;single choice
dutch_umc_open_data.csv;findability;{Numbat} Findability of dataset in the stated data repository via stated accession code;"yes;no;unsure";character;single choice
dutch_umc_open_data.csv;data_identifier;{Numbat} Dataset identifier (either a DOI or a link/repository+accession code) to the dataset containg files;{different open text entries};character;open text field
dutch_umc_open_data.csv;not_a_supplement;{Numbat} Article independent dataset sharing in the data repository or plattform, and support by metadata;"yes;no;unsure";character;single choice
dutch_umc_open_data.csv;repository;"{Numbat} Repository name in which examined dataset was detected: available through the tags list retrieved from re3data.org registry and completed manually based on the previously detected repositores in the medical context; list extension was possible during extraction";"ArrayExpress;BioProject;BioStudies;cancer imaging archive;DataVerseNL;dbGaP;DRYAD;European genome-phenome archive;European Nucleotide Archive;figshare;GitHub;Harvard Dataverse;NCBI Gene Expression Omnibus;NCBI Sequence Read Archive;Open Science Framework;OpenNeuro;Pride Archive ProteomeXchange Consortium;PRoteomics IDEntifications Database;TCIA;Zenodo";character;tags
dutch_umc_open_data.csv;year_of_data_publication;"{Numbat} Year of the last (reasonable) update of the examined dataset in form ""YYYY""";"2016;2017;2018;2019;2020;2021;2022";character;open text field
dutch_umc_open_data.csv;data_access;"{Numbat} Accessibility of dataset in stated location; 'resticted' dataset(s) require registration or application to access them";"yes;no;restricted;unsure";character;single choice
dutch_umc_open_data.csv;dataset_license;{Numbat} Availability of metadata about standard license for datasets, e.g. Creative Commons;"yes;no;unsure";character;single choice
dutch_umc_open_data.csv;license_name;"{Numbat} License name detected; list extension was possible during extraction";"CC BY;CC BY,CC0;CC0";character;tags
dutch_umc_open_data.csv;own_or_reuse_data;"{Numbat} Ownership of data: data generated by the article author(s) ('own_open-data') or by the different contibutor(s) ('open_data_reuse'); the reuse of own data is also possible which is documented here as 'own_open-data' with clear commentaries about reuse";"own_open-data;open_data_reuse";character;single choice
dutch_umc_open_data.csv;machine_readable_format;"{Numbat} Machine readable dataset file format; 'format_unknown' for cases when no format is documented in the metadata or could not be exctracted from the file naming, or the file is too heavy to be downloaded (>200 Mb)";"yes;unsure;format_unknown";character;single choice
dutch_umc_open_data.csv;machine_readable_format_excel;{Numbat} Excel file format;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_csv_tsv;{Numbat} CSV or TSV file format;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_txt_docs;{Numbat} TXT or DOCS file format;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_other_text_formats;{Numbat} Other, not listed yet, text or table file formats;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_video;{Numbat} Video file format;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_audio;{Numbat} Audio file format;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_picture;{Numbat} Image file format;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_fasta_fastq;{Numbat} FASTA or FASTQ file format (nucleotide sequences);"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_raw;{Numbat} RAW file format (image);"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_genetic_sequences;{Numbat} Other, not listed yet, file formats of genetic sequences;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_subject_specific_format;{Numbat} Other, not listed yet, subject specific file formats;"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;machine_readable_format_unsure;{Numbat} Unsure which file format the dataset belongs to (commentaries are expected here);"1;NULL";character;part of multiple choice selection
dutch_umc_open_data.csv;illustrative_files;{Numbat} Only for file formats Video, Audio, Image, RAW, Unsure:  datasets with visual elements should have more than just illustrative character, i.e. figures from the article stored in the data repository are not sufficient;"yes;no;inapplicable;unsure";character;single choice
dutch_umc_open_data.csv;analytical_replication;"{Numbat} Representation of sufficient 'rawness', e.g. for data replication in a different study. No precise distinction between replication and absence of replication is possible. Tendency to a positive response can be documented as 'replication', and a confident opinion about replication as 'yes'; tendency to a negative response can be documented as 'no_replication', and a confident opinion about absence of replication as 'no'";"yes;no;replication;no_replication";character;single choice
dutch_umc_open_data.csv;open_data_assessment;{Numbat} Final decision about opennes of examined dataset (not applicable here on all datasets for the examined article, i.e. on article-level assessment). The response 'unsure' does not appear in the final output as it is interim result for discussion during reconciliation;"open_data;no_open_data";character;single choice
IRR_2_raters_article_level.csv;doi;{ODDPub} DOI of the article used for IRR calucation (random choice);{different values};character;NA
IRR_2_raters_article_level.csv;username;{Numbat} Decoded/anonymised username who participated in Open Data validation;"rater 1;rater2";character;NA
IRR_2_raters_article_level.csv;final_assessment;{Manually processed} Combined result of possible final open data assessments: if indicated 'open_data'/'no_open_data'/'unsure_open_data' - originates from column 'open_data_assessment', if indicated 'open_data_reuse' - originates from column 'own_or_reuse_data', if indicated 'restricted' - originates from column 'data_access', if indicated 'n_a' - originates from column 'reference_to_data';"open_data;no_open_data;unsure_open_data;open_data_reuse;restricted;n_a";character;NA
IRR_2_raters_dataset_level.csv;doi;{ODDPub} DOI of the article used for IRR calucation (random choice);{different values};character;NA
IRR_2_raters_dataset_level.csv;data_identifier;{Numbat} Dataset identifier (either a DOI or a link/repository+accession code) to the dataset containg files which were overlapping by all raters and were used for IRR calculation;{different open text entries};character;NA
IRR_2_raters_dataset_level.csv;username;{Numbat} Decoded/anonymised username who participated in Open Data validation;"rater 1;rater2";character;NA
IRR_2_raters_dataset_level.csv;final_assessment;{Manually processed} Combined result of possible final open data assessments: if indicated 'open_data'/'no_open_data'/'unsure_open_data' - originates from column 'open_data_assessment', if indicated 'open_data_reuse' originates from column 'own_or_reuse_data', if indicated 'restricted' - originates from column 'data_access', if indicated 'n_a' - originates from column 'reference_to_data';"open_data;no_open_data;unsure_open_data;open_data_reuse;restricted;n_a";character;NA
IRR_3_raters_article_level.csv;doi;{ODDPub} DOI of the article used for IRR calucation (random choice);{different values};character;NA
IRR_3_raters_article_level.csv;username;{Numbat} Decoded/anonymised username who participated in Open Data validation;"rater 1;rater2;rater 3";character;NA
IRR_3_raters_article_level.csv;final_assessment;{Manually processed} Combined result of possible final open data assessments: if indicated 'open_data'/'no_open_data'/'unsure_open_data' - originates from column 'open_data_assessment', if indicated 'open_data_reuse' originates from column 'own_or_reuse_data', if indicated 'restricted' - originates from column 'data_access', if indicated 'n_a' - originates from column 'reference_to_data';"open_data;no_open_data;unsure_open_data;n_a";character;NA
IRR_3_raters_dataset_level.csv;doi;{ODDPub} DOI of the article used for IRR calucation (random choice);{different values};character;NA
IRR_3_raters_dataset_level.csv;data_identifier;{Numbat} Dataset identifier (either a DOI or a link/repository+accession code) to the dataset containg files which were overlapping by all raters and were used for IRR calculation;{different open text entries};character;NA
IRR_3_raters_dataset_level.csv;username;{Numbat} Decoded/anonymised username who participated in Open Data validation;"rater 1;rater2;rater 3";character;NA
IRR_3_raters_dataset_level.csv;final_assessment;{Manually processed} Combined result of possible final open data assessments: if indicated 'open_data'/'no_open_data'/'unsure_open_data' - originates from column 'open_data_assessment', if indicated 'open_data_reuse' originates from column 'own_or_reuse_data', if indicated 'restricted' - originates from column 'data_access', if indicated 'n_a' - originates from column 'reference_to_data';"open_data;no_open_data;unsure_open_data;open_data_reuse;restricted;n_a";character;NA