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The aim ofTKCat (Tailored KnowledgeCatalog) is to facilitate the management of data from knowledgeresources that are frequently used alone or together in researchenvironments. In TKCat, knowledge resources are manipulated as modeleddatabase (MDB) objects. These objects provide access to the data tablesalong with a general description of the resource and a detail data modelgenerated withReDaMoR documentingthe tables, their fields and their relationships. These MDB are thengathered in catalogs that can be easily explored an shared. TKCatprovides tools to easily subset, filter and combine MDBs and create newcatalogs suited for specific needs.

This package has been presented at theuseR!2022conference and here aretheslides.

The TKCat R package is licensed underGPL-3.

install.packages("TKCat")

The following R packages available on CRAN are required:

• ReDaMoR: Relational DataModeler
• magrittr: AForward-Pipe Operator for R
• DBI: R Database Interface
• visNetwork: NetworkVisualization using ‘vis.js’ Library
• dplyr: A Grammar of DataManipulation
• ClickHouseHTTP: ASimple HTTP Database Interface to ‘ClickHouse’
• rlang: Functions for BaseTypes and Core R and ‘Tidyverse’ Features
• tidyselect: Selectfrom a Set of Strings
• getPass: Masked UserInput
• shiny: Web ApplicationFramework for R
• shinydashboard:Create Dashboards with ‘Shiny’
• DT: A Wrapper of theJavaScript Library ‘DataTables’
• htmltools: Tools forHTML
• readr: Read RectangularText Data
• jsonlite: A Simple andRobust JSON Parser and Generator for R
• jsonvalidate:Validate ‘JSON’ Schema
• base64enc: Tools forbase64 encoding
• markdown: RenderMarkdown with ‘commonmark’
• promises: Abstractionsfor Promise-Based Asynchronous Programming
• future: Unified Paralleland Distributed Processing in R for Everyone
• xml2: Parse XML
• Matrix: Sparse and DenseMatrix Classes and Methods
• uuid: Tools for Generatingand Handling of UUIDs
• crayon: Colored TerminalOutput
• roxygen2: In-LineDocumentation for R

And those are suggested:

• knitr: A General-PurposePackage for Dynamic Report Generation in R
• rmarkdown: DynamicDocuments for R
• stringr: Simple,Consistent Wrappers for Common String Operations
• RClickhouse: ‘YandexClickhouse’ Interface for R with Basic ‘dplyr’ Support
• data.tree: GeneralPurpose Hierarchical Data Structure
• BED: Biological EntityDictionary (BED)

devtools::install_github("patzaw/TKCat")

• Introduction toTKCat(vignette("TKCat"))

• Defining and using Requirements for KnowledgeManagement(vignette("TKCat-KMR-POK"))

• Thedm package provides similarfeatures but with different implementation choices. Here are the maindifferences:

  • Thedm data model feature is built upon thedatamodelr package whereasTKCat relies onReDaMoR.
  • Bothdm andTKCat provides mechanisms to check thefulfillment of the data model constrains and tools to automaticallytake advantage of them.
  • dm supports connection to many different DBMS. It also takeadvantage of constraints which are documented in the DBMS whenavailable.TKCat only supports theClickHouse system through theClickHouseHTTP orRClickhouse packages.
  • TKCat implements 3 main types of MDB based on files, memorytables or ClickHouse database. It also provides mechanisms toautomatically convert from and to any of these implementations.
  • TKCat supports catalogs of MDBs facilitating the exploration ofexisting data. It also allows the integration of different MDBsthrough the automatic identification of similar concepts(Collections) and the automatic conversion of the differentvocabulary on which they rely.