ricgraph_toc_documentation.md

Table of contents Ricgraph documentation

This table of contents has been generated automatically.

• Ricgraph - Research in context graph
  • What is Ricgraph?
    • Motivation
    • Main contributions of Ricgraph
    • How to use Ricgraph (very short)
    • Read more about Ricgraph
  • Why Ricgraph?
  • Examples
  • Ricgraph in bullet points
  • Next steps
    • Further information about Ricgraph
    • Steps to take if you would like to install Ricgraph and harvest data
    • Steps to take if you would like to use Ricgraph
    • Read this in case you would like to extend Ricgraph
    • Ricgraph website
  • Contact
• Implementation details
  • Person identifiers
  • Person-root node in Ricgraph
  • Research outputs connected to persons
  • Example research questions
  • Videos of Ricgraph
  • Properties of nodes in Ricgraph
• Ricgraph videos
  • Video Start with ORCID to find software
  • Video Find persons who contributed to a publication
  • Video Find outputs and organizations from a person
  • Video Traverse Utrecht University organizations
  • Video Find output common to two persons
  • Video Ricgraph Explorer
  • Epilogue
• Ricgraph Explorer
  • Working with Ricgraph Explorer
    • Research question “What are the research results of person A”
    • Other research questions
  • How to start Ricgraph Explorer
  • Home page
  • Search page
  • Person options page
  • Organization options page
  • Results page
  • Browsing Ricgraph
  • Showing a privacy statement or privacy measures document
• Future work
• Ricgraph harvest scripts
  • Introduction to harvest scripts
  • Organization abbreviation
  • Harvest of OpenAlex (harvest_openalex_to_ricgraph.py)
  • Harvest of Pure (harvest_pure_to_ricgraph.py)
    • Limit the amount of data to harvest from Pure
    • Pure READ and Pure CRUD API
    • Pure harvesting of projects
  • Harvest of Utrecht University data sets (harvest_yoda_datacite_to_ricgraph.py)
  • Harvest of Utrecht University staff pages (harvest_uustaffpages_to_ricgraph.py)
  • Harvest of software from the Research Software Directory (harvest_rsd_to_ricgraph.py)
  • Order of running the harvest scripts
  • How to make your own harvesting scripts
• Install and configure Ricgraph
  • Ricgraph Makefile
  • Installation instructions for a single user
    • Neo4j
    • Memgraph
  • Requirements
  • Steps to take
  • Install Neo4j Desktop
    • Post-install steps Neo4j Desktop
  • Install Bloom configuration
  • Download Ricgraph
  • Use a Python virtual environment and install Python requirements
    • Using Python's venv module
    • Using a Python Integrated development environment (IDE)
    • Notable dependencies used in Ricgraph:
  • Ricgraph initialization file
    • Settings for graph database backend
    • Extending Ricgraph with new properties in the nodes
    • RICGRAPH_NODEADD_MODE
  • Using Ricgraph
  • Dumping and restoring the Ricgraph database
    • Create a Neo4j Desktop database dump of Ricgraph
    • Create a Neo4j Community Edition database dump of Ricgraph
    • Restore a Neo4j Desktop database dump of Ricgraph in Neo4j Desktop
    • Restore a Neo4j Desktop database dump of Ricgraph in Neo4j Community Edition
    • Restore a Neo4j Community Edition database dump of Ricgraph in Neo4j Community Edition
  • Ricgraph on Windows
• Ricgraph known bugs
  • Error while emptying Ricgraph with Neo4j
    • Solution for Neo4j Desktop
    • Solution for Neo4j Community Edition
• Ricgraph miscellaneous scripts
  • Construct a Ricgraph from a csv file (construct_ricgraph_from_csv.py)
  • Import nodes and edges from a csv file, raw version (ricgraph_import_raw_from_csv.py)
  • Export nodes and edges to a csv file, raw version (ricgraph_export_raw_to_csv.py)
  • Delete personal data from Ricgraph (delete_personal_data.py)
  • Count the number of organizations that contributed to a category (count_organizations_contributed_to_category.py)
  • Export nodes to a file (export_person_identifiers.py and export_person_node_properties.py)
  • Script to enrich persons (enrich_orcids_scopusids.py)
  • Script to find person identifiers pointing to different persons (find_double_pids.py)
  • Create a table of contents of the Ricgraph documentation (create_toc_documentation.py)
  • Create an index of the Ricgraph documentation (create_index_documentation.py)
  • Create the Ricgraph REST API documentation (convert_openapi_to_mddoc.py)
• Ricgraph publications, presentations, use, and mentions
  • Ricgraph publications
  • Ricgraph presentations
  • Ricgraph newsletters
  • Ricgraph use
  • Ricgraph mentions
  • Arjan Sieverink presents Ricgraph at Pure International Conference 2023
• Query and visualize Ricgraph
  • Start Neo4j Desktop
  • How to use Bloom
    • Install the Bloom configuration file
    • Open Bloom
    • Execute queries
    • Actions while clicking on a node
    • Visualization of nodes
• Ricgraph REST API
  • Installation of the Ricgraph REST API
  • Use of the Ricgraph REST API
  • Generate the Ricgraph REST API documentation page
• Ricgraph script writing
  • How to make your own harvesting scripts
  • General program structure of a Python script using Ricgraph
  • Structure of a Python script that is harvesting data
  • Function calls for inserting nodes
  • Function call for unifying personal identifiers
  • Function calls to create, read (find), update and delete (CRUD) nodes
  • Function calls to get neighbors of nodes
• Index Ricgraph documentation
• Table of contents Ricgraph documentation
• Ricgraph as a server on Linux
  • Check the requirements
  • Install and start Neo4j Community Edition
    • Post-install steps Neo4j Community Edition
  • Install and start Memgraph
  • Create a ricgraph user and group
  • Create a Python virtual environment and install Ricgraph in it
  • Run Ricgraph scripts from the command line or as a cronjob
    • In case you have installed Ricgraph as a server
    • In case you have installed Ricgraph for a single user
    • Using the Makefile
  • Use a service unit file to run Ricgraph Explorer and the Ricgraph REST API
  • Use Apache, WSGI, and ASGI to make Ricgraph Explorer and the Ricgraph REST API accessible from outside your virtual machine
    • Introduction Apache webserver
    • Installation Apache
    • Post-install steps Apache
  • Use Nginx, WSGI, and ASGI to make Ricgraph Explorer and the Ricgraph REST API accessible from outside your virtual machine
    • Introduction Nginx webserver
    • Installation Nginx
    • Post-install steps Nginx
  • Restore a Neo4j Desktop database dump of Ricgraph in Neo4j Community Edition
  • How to install Ricgraph and Ricgraph Explorer on SURF Research Cloud
  • How to solve an AttributeError: Neo4jDriver object has no attribute executequery
• Ricgraph - Research in context graph REST API
  • How to use
  • Technicalities
  • Base URL
  • Endpoints
    • GET /person/search
    • GET /person/all_information
    • GET /person/share_research_results
    • GET /person/collaborating_organizations
    • GET /person/enrich
    • GET /organization/search
    • GET /organization/all_information
    • GET /organization/information_persons_results
    • GET /organization/enrich
    • GET /competence/search
    • GET /competence/all_information
    • GET /broad_search
    • GET /advanced_search
    • GET /get_all_personroot_nodes
    • GET /get_all_neighbor_nodes
    • GET /get_ricgraph_list
• Ricgraph comparison
  • General overview
  • Extendability
• Ricgraph in a container
  • Notes on the Ricgraph Podman container
  • Install Podman
  • Install and run the Ricgraph Podman container
  • Advanced use of the Ricgraph Podman container