Graphical Collaborative Tooling for Vocabulary Mapping

[haydenbspence]

This is a preliminary analysis of tooling that may assist in the collaborative process of mapping vocabularies. They are presented in no specific order. Each has been evaluated on the following basic criteria:

• Has a graphical user interface and does not require command-line usage
• Provides real-time collaboration options
• Supports the primary task of mapping two or more vocabularies over creating or editing ontologies
• Is one or more of the following (open source, free, low cost)
• Has a moderate to easy learning curve

Title	Description	Pros	Cons
Gra.fo	A visual, collaborative, real-time ontology editor.	Strong real-time collaboration, graphical user interface, ability to handle complex relationships.	Not specifically designed for medical ontologies, some features might require a subscription.
Arches	An open-source platform designed for managing and disseminating cultural heritage data.	Open-source, robust mapping features, adaptable to various data types.	Originally designed for historical and archaeological data, requires some setup and configuration.
WebProtégé	A free, open-source platform for collaborative ontology editing developed by Stanford University.	Supports collaborative ontology editing, flexible user interface for building and managing ontologies.	Learning curve can be steep for non-technical users, not specifically designed for vocabulary mapping.
TopBraid EDG	A tool to manage metadata about various types of data, and offers mapping and integration features for handling various vocabularies.	Supports a broad range of data governance, robust mapping and integration features.	Not open-source, full features require paid version.
BioPortal	Web-based platform for sharing, browsing, and using ontologies in various formats.	Great for managing biomedical ontologies, wide range of supported formats.	Not designed for real-time collaboration, interface can be complex for new users.
OntoGraph	A web-based tool for visualizing, navigating, and editing RDF graphs.	Good for working with RDF graphs, visual navigation features.	Not explicitly designed for collaboration, learning curve for those unfamiliar with RDF.
Protege	An open-source platform for constructing domain models and knowledge-based applications with ontologies.	Powerful ontology editor, strong community support.	Steep learning curve, not designed specifically for real-time collaboration.
CmapTools	Tool designed for creating concept maps to represent semantic relationships.	User-friendly interface, suitable for creating visual representations.	Not specifically designed for ontology or vocabulary mapping.
Apache Jena	A Java framework for building Semantic Web and Linked Data applications.	Robust RDF, RDFS, OWL, and SPARQL support, includes rule-based inference engine.	Requires programming knowledge, not specifically designed for collaboration.
yEd Graph Editor	A tool for creating diagrams, including those necessary for vocabulary mapping.	High flexibility for different types of diagrams, user-friendly interface.	Not explicitly designed for ontology or vocabulary mapping, learning curve for complex diagrams.
MindMup	A user-friendly mind mapping tool that allows creating and sharing interactive mind maps.	Easy to use, supports collaboration, exports to various formats including JSON.	Not specifically designed for vocabulary mapping, advanced features may require paid version.
XMind	A full-featured mind mapping and brainstorming tool.	Broad range of diagram types, exports to various formats, including JSON.	Not specifically designed for vocabulary mapping, full features require paid version.
Freeplane	An open-source software for creating mind maps.	Open-source, supports creating complex connections and relationships.	Not specifically designed for ontology or vocabulary mapping.
Draw.io (diagrams.net)	A free online diagram software for making flowcharts, process diagrams, org charts, UML, ER, and network diagrams.	Wide variety of diagram types, intuitive user interface.	Not specifically designed for vocabulary mapping, advanced features might require some learning.

This list has been evaluated with the same basic criteria aside from the graphical user interface. This is for those proficient in R or Python. It's also assumed that git would satisfy the collaboration criteria as these tools are all code.

Title	Description	Pros	Cons
SKOS (Python)	Simple Knowledge Organization System provides a model for expressing the basic structure and content of concept schemes.	Widely used in the semantic web, good interoperability.	Requires understanding of RDF and semantic web concepts.
Owlready2 (Python)	A module for ontology-oriented programming in Python, it can load OWL 2.0 and RDFs ontologies and manipulate them transparently in Python.	Simplifies working with ontologies in Python, supports reasoning via HermiT.	Limited to Python, might have a learning curve for some users.
RDFLib (Python)	A Python library for working with RDF, a fundamental format for semantic web data.	Simplifies parsing, serializing, and manipulating RDF.	Understanding of RDF and semantic web concepts is necessary.
SPARQLWrapper (Python)	A simple Python wrapper around a SPARQL service to remotely execute your queries, useful for querying semantic web data.	Simplifies execution of SPARQL queries from Python.	Requires understanding of SPARQL and semantic web concepts.
rdflib.js (JavaScript)	A JavaScript library for parsing, serializing, and manipulating RDF data, useful if you're also comfortable with JavaScript.	Allows RDF manipulation in JavaScript.	Requires understanding of RDF and semantic web concepts, and JavaScript proficiency.
tidygraph (R)	An R package for graph manipulation that allows you to work with graph data structures.	Simplifies graph manipulation in R, integrates with the 'tidyverse'.	Requires proficiency in R, not specific to ontologies.
igraph (R)	A collection of network analysis tools with the emphasis on efficiency, portability, and ease of use.	Powerful network analysis features, supports R and Python.	Can have a steep learning curve, not specific to ontologies.

[DrUrwin]

We've developed a tool at the University of Nottingham called Carrot Mapper, it is used within the UK and internationally to map source data to the OMOP CDM, please feel free to have a look here:

https://carrot4omop.ac.uk/
https://github.com/Health-Informatics-UoN/carrot-docs

Carrot Mapper is:

• Free to use
• Open Source
• Open to collaboration for further development