Table 1. Glossary.

Term	Definition	Source
Annotation	Process of coding selected parts of documents or other resources to identify the presence of ontology entities.	Michie et al., 2018.
Annotation guidance manual	Written guidance on how to identify and tag pieces of text from intervention evaluation reports with specific codes relating to entities in the ontology.
Basic Formal Ontology (BFO)	An upper level ontology consisting of continuants and occurrents developed to support integration, especially of data obtained through scientific research.	Arp et al., 2015.
Entity	Anything that exists, that can be a continuant or an occurrent as defined in the Basic Formal Ontology.	Arp et al., 2015.
EPPI-Reviewer	A web-based software program for managing and analysing data in all types of systematic review (meta- analysis, framework synthesis, thematic synthesis etc). It manages references, stores PDF files and facilitates qualitative and quantitative analyses such as meta- analysis and thematic synthesis. It also has a facility to annotate published papers.	Thomas et al., 2010; EPPI-Reviewer 4: http://eppi.ioe.ac.uk/eppireviewer4/ EPPI-Reviewer Web Version: https://eppi.ioe.ac.uk/ eppireviewer-web/
GitHub	A web-based platform used as a repository for sharing code, allowing version control.	https://github.com/
Inter-rater reliability	Statistical assessment of similarity and dissimilarity of coding between two or more coders. If inter-rater reliability is high this suggests that ontology entity definitions and labels are being interpreted similarly by the coders.	Gwet, 2014. Handbook of inter-rater reliability: The definitive guide to measuring the extent of agreement among raters. Gaithersburg, Advanced Analytics.
Interoperability	Two systems are interoperable if data coming from each system can be used by the other system. Note: An ontology is interoperable with another ontology if it can be used together with or re-uses parts from the other ontology	http://www.obofoundry.org/principles/fp-010- collaboration.html
Issue tracker	An online log for problems identified by users accessing and using an ontology.	BCIO Issue Tracker: https://github.com/ HumanBehaviourChangeProject/ontologies/issues
OBO Foundry	The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate.	Smith et al., 2007; www.obofoundry.org/
Ontology	A standardised framework providing a set of terms that can be used for the consistent annotation (or “tagging”) of data and information across disciplinary and research community boundaries.	Arp et al., 2015.
Parent class	A class within an ontology that is hierarchically related to one or more child (subsumed) classes such that all members of the child class are also members of the parent class and all properties of the parent class are also properties of the child class.	Arp et al., 2015.
Reconciliation	The process of discussing differences between the annotations of two paired annotators on the same papers. Differences are discussed before a final reconciled version of coding for each paper is produced.	Stan et al., 2014.
ROBOT	An automated command line tool for ontology workflows.	Jackson et al., 2019, http://robot.obolibrary.org
Unique resource identifier (URI)	A string of characters that unambiguously identifies an ontology or an individual entity within an ontology. Having URI identifiers is one of the OBO Foundry principles.	http://www.obofoundry.org/principles/fp-003-uris.html
Web Ontology Language (OWL)	A formal language for describing ontologies. It provides methods to model classes of “things”, how they relate to each other and the properties they have. OWL is designed to be interpreted by computer programs and is extensively used in the Semantic Web where rich knowledge about web documents and the relationships between them are represented using OWL syntax.	https://www.w3.org/TR/owl2-quick-reference/