genSysRev_v1.RmdThis vignette shows the example comma specification based on the general systematic review registration form (v1.0). It can be initialized as follows:
initialized_genSysRev_v1 <-
comma::matrixMap_load(
"genSysRev_v1"
);The comma specification’s metadata is:
| field | content |
|---|---|
| title | Example comma specification based on the general systematic review registration form |
| author | Gjalt-Jorn Peters and Tugce Varol |
| date | 2023-05-05 |
| comments | This is an example form. You’re free to use it, but you may well be better off adjusting it to your project first. |
| version | 1.0 |
The specific contributor table for this comma specification is:
| Contributor | Project-group formation | Defining research goals | Synthesis plans | First entity draft | Entity feedback | Entity finalization | Screening procedure | Exclusion criteria | Search Strategy | Query development | Query translation | Preregistration | Query execution | Importing and merging of query hits | Grey literature | Communicating with authors | Validating search strategy | Deduplication | Preparing screening packages | Screening | Validation of screening | Processing screening results | Extraction | Validation of extraction | Processing extraction results | Preprocessing | Quality assessment | Synthesis analyses | Validation of the synthesis | Data management | Writing the first manuscript draft | Reviewing and editing the manuscript | Prepare a presentation | Give a presentation |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Example name 1 | ||||||||||||||||||||||||||||||||||
| Example name 2 | ||||||||||||||||||||||||||||||||||
This matrix maps contributions as follows (from specific to generic):
comma::show_contribution_mapping(
initialized_genSysRev_v1,
output = "markdown"
);Project-group formation: Forming working group by deciding on and inviting people [project_group]
– MAPS ONTO –>
Project administration: Management and coordination responsibility for the research activity planning and execution. [project_administration]
Defining research goals: Formulating research goals, including research questions and hypotheses [goals]
– MAPS ONTO –>
Conceptualization: Ideas; formulation or evolution of overarching research goals and aims. [conceptualization]
Synthesis plans: Devising the synthesis plans: which analyses will be conducted to achieve the research goals. [synthesis_plans]
– MAPS ONTO –>
Formal Analysis: Application of statistical, mathematical, computational, or other formal techniques to analyse or synthesize study data. [formal_analysis]
First entity draft: Producing the first draft of the entities to be extracted [entity_drafting]
– MAPS ONTO –>
Methodology: Development or design of methodology; creation of models [methodology]
Entity feedback: Providing feedback on the entities [entity_feedback]
– MAPS ONTO –>
Methodology: Development or design of methodology; creation of models [methodology]
Entity finalization: Producing the final specification of the entities to extract [entity_finalization]
– MAPS ONTO –>
Methodology: Development or design of methodology; creation of models [methodology]
Screening procedure: Developing the procedure for the screening: deduplication, software to use, masking procedure, etc. [screening_procedure]
– MAPS ONTO –>
Methodology: Development or design of methodology; creation of models [methodology]
Exclusion criteria: Formulating the exclusion criteria for screening [exclusion_criteria]
– MAPS ONTO –>
Conceptualization: Ideas; formulation or evolution of overarching research goals and aims. [conceptualization]
Search Strategy: Development of the search strategy, selection of databases and interfaces, designing procedures to contact authors, etc (note that this includes query development and translation). [search_strategy]
– MAPS ONTO –>
Methodology: Development or design of methodology; creation of models [methodology]
Query development: Development of the conceptual query (i.e. concepts and synonyms to search for as well as the logical operators to use to combine them) [query_development]
– MAPS ONTO –>
Conceptualization: Ideas; formulation or evolution of overarching research goals and aims. [conceptualization]
Query translation: Translating the query to the syntax and fields used by each used interface/database combination [query_translation]
– MAPS ONTO –>
Software: Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. [software]
Preregistration: Prepare and post the preregistration. [preregistration]
– MAPS ONTO –>
Project administration: Management and coordination responsibility for the research activity planning and execution. [project_administration]
Query execution: Entering the queries into the interfaces to search each database and exporting the hits into the chosen file format [query_execution]
– MAPS ONTO –>
Data curation: Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use. [data_curation]
Importing and merging of query hits: Importing the query hits and merging them into one file to prepare for screening [query_hits_merging]
– MAPS ONTO –>
Software: Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. [software]
Grey literature: Searching for grey literature [search_grey]
– MAPS ONTO –>
Data curation: Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use. [data_curation]
Communicating with authors: Contacting authors and handling further communications with them [search_author_contact]
– MAPS ONTO –>
Project administration: Management and coordination responsibility for the research activity planning and execution. [project_administration]
Validating search strategy: Validating the search strategy (e.g. checking whether sources that were already known to be relevant beforehand are indeed located) [search_validation]
– MAPS ONTO –>
Validation: Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs. [validation]
Deduplication: Deduplicating the query hits [deduplication]
– MAPS ONTO –>
Data curation: Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use. [data_curation]
Preparing screening packages: Preparing the screening packages for each screener [screening_packages]
– MAPS ONTO –>
Methodology: Development or design of methodology; creation of models [methodology]
Screening: Actual screening of query hits by applying the exclusion criteria [screening]
– MAPS ONTO –>
Data curation: Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use. [data_curation]
Validation of screening: Verification of screening decisions, for example by randomly sampling some decisions. If using multiple independent screeners, this also includes tasks related to reliability assessment and reconciliation. [screening_validation]
– MAPS ONTO –>
Validation: Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs. [validation]
Processing screening results: Processing screening results to prepare for following stages, and importing screening results to obtain final list of sources to acquire for extraction. This includes sampling (if sources are sampled at all). [screening_processing]
– MAPS ONTO –>
Software: Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. [software]
Extraction: Extraction of entities from the sources and registration of those entities in a machine-readable format. [extraction]
– MAPS ONTO –>
Investigation: Conducting a research and investigation process, specifically performing the experiments, or data/evidence collection. [investigation]
Validation of extraction: Verification of extracted entities, for example by randomly sampling some entities or extracted sources. If using multiple independent extractors, this also includes tasks related to reliability assessment and reconciliation. [extraction_validation]
– MAPS ONTO –>
Validation: Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs. [validation]
Processing extraction results: Importing the extracted entities into the software used for synthesis. [extraction_processing]
– MAPS ONTO –>
Software: Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. [software]
Preprocessing: Preparing the raw extracted entities for synthesis. [synthesis_preprocessing]
– MAPS ONTO –>
Software: Programming, software development; designing computer programs; implementation of the computer code and supporting algorithms; testing of existing code components. [software]
Quality assessment: Verifying the quality of the data that were produced from the extracted entities. [synthesis_quality_assessment]
– MAPS ONTO –>
Data curation: Management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use. [data_curation]
Synthesis analyses: Conducting the analyses that were planned to achieve the research goals. [synthesis]
– MAPS ONTO –>
Formal Analysis: Application of statistical, mathematical, computational, or other formal techniques to analyse or synthesize study data. [formal_analysis]
Synthesis analyses: Conducting the analyses that were planned to achieve the research goals. [synthesis]
– MAPS ONTO –>
Formal Analysis: Application of statistical, mathematical, computational, or other formal techniques to analyse or synthesize study data. [formal_analysis]
Validation of the synthesis: Verification of the synthesis analyses. If using multiple independent synthesists, this also includes tasks related to reliability assessment and reconciliation. [synthesis_validation]
– MAPS ONTO –>
Validation: Verification, whether as a part of the activity or separate, of the overall replication/reproducibility of results/experiments and other research outputs. [validation]
Data management: Setting up and maintaining the repositories that are used (Git, OSF, etc), as well as developing the data management plan. [data_management]
– MAPS ONTO –>
Resources: Provision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools. [resources]
Writing the first manuscript draft: Write the first version of the manuscript reporting on this project. [manuscript_first_draft]
– MAPS ONTO –>
Writing – original draft: Preparation, creation and/or presentation of the published work, specifically writing the initial draft (including substantive translation). [writing_original_draft]
Reviewing and editing the manuscript: Reading manuscript versions and providing (tracked) changes or comments. [manuscript_review_editing]
– MAPS ONTO –>
Writing – review & editing: Preparation, creation and/or presentation of the published work by those from the original research group, specifically critical review, commentary or revision – including pre- or post-publication stages. [writing_review_editing]
Prepare a presentation: Preparing slides or other materials for a presentation about this project. [presentation_prepare]
– MAPS ONTO –>
Project administration: Management and coordination responsibility for the research activity planning and execution. [project_administration]
Give a presentation: Give a presentation about this project. [presentation_present]
– MAPS ONTO –>
Project administration: Management and coordination responsibility for the research activity planning and execution. [project_administration]