Introduction | Create an MDB: a minimal example | Loading example data | Creating a data model with ReDaMoR | Binding the model to the data in an MDB object | Adding information about an MDB | Documenting collection members | Writing an MDB in files | Leveraging MDB | HPO | ClinVar | CHEMBL | MDB implementations | Exploring information | Pulling, subsetting and combining | Filtering and joining | Merging MDBs with collections | Collections and collection members | Shared collections and merging | Merging without collection | A centralized catalog of MDB in ClickHouse (chTKCat) | Local TKCat | chTKCat | Pushing an MDB in a chTKCat instance | Specific operations on chMDB objects | Data organization in ClickHouse | Defining and using Requirements for Knowledge Management (KMR) | Appendices | chTKCat operations | Instantiating the ClickHouse database | Install ClickHouse, initialize and configure the TKCat instance | Cleaning and removing a TKCat instance | User management | Creation | Update | Drop | chMDB management | chMDB Creation | Populating chMDB | Deleting a chMDB | Collection management | Implementation | Data models | Default database | Modeled databases | TKCat collections | Creating a collection | Documenting collection members | Collection mapper functions | Remarks about supported data format and data types | Matrices of values | Documents stored as base64 values | References

Defining KMR | KMR organization | Define requirements | Table and mandatory features | Optional features | Possible values for feature properties | Measurements | KM specifications | Exploring requirements | Documenting MDB specifications | Simple example | Piece Of Knowledge (POK) | Helpers | KMR helpers | MDB helpers | POK objects

Introduction | Installation | From CRAN | Dependencies | From github | Creating and modifying relational data using the graphical user interface | Running the app | Model formalism | Data model example: the Human Phenotype Ontology | Tables | Foreign keys | App organization | The main menu | The model view | The edition view | Contextual help tour | Keyboard shortcuts | Adding foreign keys | Confronting data | Drafting a data model from data frames | Support of matrices | TKCat: Tailored Knowledge Catalog | Acknowledgments | References

Introduction | Citing BED | Installation | Dependencies | Installation from github | Possible issue when updating from releases <= 1.3.0 | Connection | Data model | Direct calls | Feeding the database | Caching | Exploring available data | Biological entities | Organisms | Identifiers of biological entities | Experimental platforms and probes | Managing identifiers | Retrieving all identifiers from a source | Preferred identifier | Checking identifiers | Identifier annotation | Products of molecular biology processes | Converting identifiers | Same entity and same organism: from one source to another | Same organism: from one entity to another | From one organism to another | Converting lists of identifiers | BEIDList | Converting data frames | Explore convertion shortest path between two identifiers | Notes about converting from and to gene symbols | An interactive dictionary: Shiny module | Session info

Installation and requirements | Development version from github | Vignette requirements | Building figures | Simple example: Animal cells | Defining UI elements | Setting element styles | Setting element attributes | Save and export widget | Mapping data: Wikipathways | 'shiny' applications | Building and inserting the figure (P1) | Interactions (P2) | Modifying the figure (P3) | Updating figure elements (P4) | Additional notes