7. Ontology-related tools and services

Recipe Overview

Reading Time

15 minutes

Executable Code

No

Difficulty

Introducing ontology-related tools and services

Recipe Type

Survey / Review

Audience

Data Curator, Data Manager, Data Scientist, Ontologist, Software Engineer, Terminology Manager

Maturity Level & Indicator

not applicable

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7.1. Main Objectives

This recipe aims to provide an overview of tools available to perform a number of key operations using ontologies and relevant to FAIR processes: from ontology management to using ontology for annotation or performing ontology mapping.

It aims to serve as a starting point to identify tools for FAIRification tasks where ontologies and semantic frameworks are needed.

disclaimer

It is not intended to provide a comprehensive list covering all possible tools.

The lists of tools are generated either automatically by querying the bio.tools repository, or through manual curation. In this last instance, the list produced reflects what is being used in the industry and is influenced by the FAIRplus project partners that have been surveyed for the purpose of this work.

Warning

The content in these tables was generated in March 2021. For an updated contents, please check the FAIR tooling repository.

7.2. Requirements

• recipe dependency:

  • Selecting terminologies and ontologies

• knowledge requirement:

  • be familiar with ontologies and semantic annotation.

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7.3. FAIRification Objectives, Inputs and Outputs

Actions.Objectives.Tasks	Input	Output
ontology and terminology
text annotation

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7.4. Overview

The figure below shows different ontology-related operations and their relationships, together with related tools and recipes.

Fig. 7.2 Overview of key aspects in ontology associated processes

The table below is an overview of ontology strategies tools identified. Details of each tools are provided below.

Topic	Curated tools	Related tools in Bio.tools
Ontology annotation	ZOOMA	bioBERT
	NCBI BioPortal Annotator	PPR-SSM
	BioBert	HPO2GO
	Termite	Vapur
	PoolParty Semantic Suite	matscholar
	OntoMaton	CollaboNet
	Prodigy	Calchas
	OntoText	QTL TableMiner++(QTM)
		thbp
Ontology mapping	OxO	meshr
		locdb
Ontology management	AberOWL	ngly1
	BioPortal	Doc2Hpo
	Centree Ontology Manager	PlanGexQ
	OLS	GOcats
	Ontobee	RDFScape
	PoolParty	OntoBrowser
		QuickGO
		Circular Gene Ontology (CirGO)
Ontology engineering	eNanoMapper Slimmer
	OWLAPI
	Protégé
	ROBOT
	TopBraid Composer
	VocBench

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7.5. Operations

7.5.1. Ontology annotation

Ontoloy Annotation is the process of linking free text or data items to ‘tokens’ (defined terms from a lexicon) which provide semantic value. For example, “type 2 diabetes” can be annotated with corresponding term in the MONDO disease ontology.

Curated tools

Tool	Description	License	Topics	Resource Type	How to use
ZOOMA	A tool for mapping free text annotations to ontology term based on a curated repository of annotation knowledge.	EMBL-EBI Terms of Use	Ontology and terminology, Systems biology, Data identity and mapping	Web application, API	ZOOMA-Getting started
NCBI BioPortal Annotator	Get annotations for biomedical text with classes from the ontologies.	BioPortal Terms of Use	Ontology and terminology, Systems biology, Data identity and mapping	Web application, API	BioPortal help
BioBert	A biomedical language representation model designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering.	Apache 2.0	text mining, named-entity recognition, natural language processing	Python
Termite	Semantic enrichment to unlock the value of unstructured text and simplify the identification of new potential biomarker leads from scientific text.	Commercial license	Ontology and terminology
PoolParty Semantic Suite	Automate the handling of heterogeneous metadata systems and the creation of enterprise knowledge graphs.design knowledge graphs at your own pace and with speed. Create your own ontologies and custom schemes by reusing already existing ontologies such as FOAF, FIBO, schema.org and CHEBI, among others. Apply them to your existing taxonomies with ease.	Commercial license	Content enrichment, Data integration
OntoMaton	A tool facilitating ontology search and tagging functionalities within Google Spreadsheets.	CPAL license		Google Add-ons
Prodigy	A modern annotation tool for creating training and evaluation data for machine learning models. You can also use Prodigy to help you inspect and clean your data, do error analysis and develop rule-based systems to use in combination with your statistical models.	Commercial license	Data annotation	Python, Web application,API
OntoText	Connect and publish complex enterprise knowledge with standard-compliant semantic graph database; Customize and apply analytics to link documents to graphs, extract new facts, classify and recommend content.	Commercial license

Related tools in Bio.Tools

Tool	Description	License	Topics	Resource Type
bioBERT	A pre-trained weights of BioBERT, a language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc.	N/A	Medicine, Ontology and terminology, Natural language processing	Python
PPR-SSM	Personalized PageRank and semantic similarity measures for linking entities found in documents to concepts from domain-specific ontologies.	N/A	Imaging, Natural language processing, Data mining, Genotype and phenotype, Ontology and terminology	Java, Python
HPO2GO	Prediction of human phenotype ontology term associations using cross ontology annotation co-occurrences.Mapping between Human Phenotype Ontology (HPO) and Gene Ontology (GO) terms for the prediction of gene/protein - function - phenotype - disease associations.	GPL-3.0	Pathology, Protein interactions, Genotype and phenotype, Ontology and terminology, Gene expression	Command-line tool
Vapur	A Search Engine to Find Related Protein.Vapur is an online entity-oriented search engine for the COVID-19 anthology. Vapur is empowered with a semantic inverted index that is created through named entity recognition and relation extraction on CORD-19 abstracts.	N/A	Pathology, Ontology and terminology, Natural language processing, Enzymes	Python
matscholar	A Python library for materials-focused natural language processing (NLP). Named Entity Recognition and Normalization Applied to Large-Scale Information Extraction from the Materials Science Literature.	MIT	Chemistry, Ontology and terminology, Natural language processing	Command-line tool
CollaboNet	Collaboration of deep neural networks for biomedical named entity recognition.	MIT	Ontology and terminology, Natural language processing, Machine learning	Command-line tool
Calchas	A web based framework that takes advantage of domain specific ontologies, and Natural Language Processing, aiming to empower exploration of biomedical resources via semantic-based querying and search. The NLP engine analyzes the input free-text query and translates it into targeted queries with terms from the underlying ontology.	N/A	Medical informatics, Ontology and terminology, Natural language processing, Bioinformatics	Web application
QTL TableMiner++(QTM)	It is a command-line tool to retrieve and semantically annotate results obtained from QTL mapping experiments. It takes full-text articles from the Europe PMC repository as input and outputs the extracted QTLs into a relational database (SQLite) and text file (CSV).	Apache-2.0	Ontology and terminology	Command-line tool
thbp	Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries.	N/A	Anatomy, Ontology and terminology, Natural language processing

7.5.2. Ontology mapping

The process of determining correspondences between equivalent concepts in alternative ontologies, and other vocabularies. This may include mapping to convey different levels of granularity.

Curated tools

Tool	Description	License	Topics	Resource Type	How to use
OxO	A service for finding mappings (or cross-references) between terms from ontologies, vocabularies and coding standards.	EMBL-EBI Terms of Use	Ontology alignment	GUI and API

Related tools in Bio.Tools

Tool	Description	License	Topics	Type
meshr	A set of annotation maps describing the entire MeSH assembled using data from MeSH.	Apache-2.0	Medical informatics, Data quality management	Command-line tool, Library
locdb	Manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress).	N/A	Ontology and terminology, Data submission, annotation and curation, Proteins	Database portal

7.5.3. Ontology management

The process of managing ontologies and other vocabularies in semantic web-linked data environments.This includes policies for update and maintenance of constituent and new terms.

Curated tools

Tool	Description	License	Topics	Resource Type	How to use
OLS	a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions.	EMBL-EBI Terms of Use	Ontology and terminology	Web Application, API
BioPortal	A repository of biomedical ontologies.	BioPortal Terms of Use	Ontology and terminology	Web Application, API
PoolParty	Knowledge Engineering & Knowledge Graph Management. Taxonomy, ontology and linked dataset management.	Commercial license	Ontology and terminology
Centree Ontology Manager	A centralised, enterprise-ready resource for ontology management and transforms the experience of maintaining and releasing ontologies for research-led businesses.	Commercial license		Web application, API
Ontobee	A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis.	Apache 2.0		Web application
AberOWL	A framework for ontology-based access to biological data. It consists of a repository of bio-ontologies, a set of webservices which provide access to OWL(-EL) reasoning over the ontologies, and several frontends which utilise the ontology repository and reasoning services.			Web application, API

Related tools in Bio.Tools

Tool	Description	License	Topics	Type
ngly1	A repository for the NGLY1 Deficiency Knowledge Graph, the reasoning context to support hypothesis discovery for NGLY1 Deficiency-CDDG (DOID:0060728) research. The user can navigate the knowledge in the graph in the Neo4j Browser website.	N/A	Molecular interactions, pathways and networks, Ontology and terminology, Machine learning	Command-line tool
Doc2Hpo	Web application for efficient and accurate Human Phenotype Ontology (HPO) concept curation.	Unlicense	Genotype and phenotype, Ontology and terminology, Natural language processing	Web application
PlanGexQ	A user-friendly interactive tool for the curation and annotation of planarian morphologies and gene expression patterns in a centralized database.	N/A	Mathematics, Genotype and phenotype, Model organisms, Ontology and terminology, Gene expression
GOcats	Advances in gene ontology utilization improve statistical power of annotation enrichment.	N/A	Mapping, Ontology and terminology, Microarray experiment	Command-line tool
RDFScape	This is a project that brings Semantic Web features to the popular Systems Biology software Cytoscape. It allows to query, visualize and reason on ontologies represented in OWL or RDF within Cytoscape.		Systems biology, Ontology and terminology, Biology	Desktop application
OntoBrowser	The tool was developed to manage ontologies (and controlled terminologies e.g. CDISC SEND). The primary goal of the tool is to provide an online collaborative solution for expert curators to map code list terms (sourced from multiple systems/databases) to preferred ontology terms.	Apache 2.0	Ontology and terminology, Data identity and mapping	Web API, Web application
QuickGO	A fast browser for Gene Ontology terms and annotations.		Ontology and terminology	Web application
Circular Gene Ontology (CirGO)	Visualises non-redundant two-level hierarchically structured ontology terms from gene expression data in a 2D space.	GPL3.0	Ontology and terminology, Data visualisation, Gene expression	Command-line tool, Desktop application

7.5.4. Ontology engineering

Ontology engineering is the process of developing and maintaining ontologies during the ontology life cycle.

Curated tools

Tool	Description	License	Topics	Resource Type
Protégé	A free, open source ontology editor and a knowledge management system.	2-Clause BSD		Web application, Desktop application
ROBOT	An open source library and command-line tool for automating ontology development tasks. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks.	BSD 3-Clause License		Command-line tool
OWLAPI	A Java API and reference implmentation for creating, manipulating and serialising OWL Ontologies.	LGPL and Apache		API
eNanoMapper Slimmer	A slim tool to slim ontologies as part of ontology integration. It allows users to provide configuration files that specify which parts of an ontology should be kept and/or removed, allowing to just select parts of the ontology you like.	MIT license		Java
TopBraid Composer	TopBraid Composer Maestro Edition is used to develop ontology models, configure data source integration, and create semantic services and user interfaces.	Commercial license
VocBench	a web-based, multilingual, collaborative development platform for managing OWL ontologies, SKOS(/XL) thesauri, Ontolex-lemon lexicons and generic RDF datasets.	License		Desktop application

7.6. Implementation examples

To show how these tools can be used in real life examples, please check the related recipes.

• Selecting terminologies and ontologies

• Building an application ontology with ROBOT

7.7. References

References

7.7.1. What to read next?

FAIRsharing records appearing in this recipe:

• BioPortal
• CDISC
• CDISC Standard for Exchange of Nonclinical Data (CDISC SEND)
• Chemical Entities of Biological Interest (ChEBI)
• Comma-separated Values (CSV)
• Disease Ontology (DOID)
• Europe PubMed Central (Europe PMC)
• Gene Ontology (GO)
• Human Phenotype Ontology (HP)
• Monarch Disease Ontology (MONDO)
• Ontobee
• Ontology Cross Reference Service (OxO)
• Ontology Lookup Service (OLS)
• Resource Description Framework (RDF)
• Schema.org
• Simple Knowledge Organization System (SKOS)
• The FAIR Principles (FAIR)
• Web Ontology Language (OWL)
• bio.tools

7.8. Authors

Authors

Name	ORCID	Affiliation	Type	ELIXIR Node	Contribution
Fuqi Xu		EMBL-EBI			Writing - Original Draft, Software
Eva Marin del Pico		Barcelona Supercomputing Centre			Writing - Original Draft, Software
Sukhi Singh		The Hyve			Data curation, Software
Philippe Rocca-Serra		University of Oxford			Writing - Review & Editing

7.9. License

License

The Creative Commons 4.0 BY license

Contents

6. Requesting new terms 8. Building an application ontology with ROBOT