Table 3.

List of tools for data curation with ontologies, annotation data exchange format and tools for ontology editing

Use	Tool	Summary	Reference/URL
Data curation/annotation	Noctua	web-based tool for collaborative editing of models of biological processes	http://noctua.berkeleybop.org/
	PubSearch	TAIR in-house literature curation tool	https://www.ncbi.nlm.nih.gov/pubmed/18428773
	Protein2GO	EBI’s GO annotation tool	https://sourceforge.net/projects/protein2go/
	TOAST	community curation tool for GO and PO annotations	https://www.ncbi.nlm.nih.gov/pubmed/22859749
	CANTO	web-based literature curation tool	https://academic.oup.com/bioinformatics/article/30/12/1791/382357/Canto-an-online-tool-for-community-literature
	Textpresso Central	web-based text mining and literature curation (with plug ins for Noctua)	doi: 10.1186/s12859-018-2103-8.
	CACAO	community annotation tool used in undergraduate competitions	https://gowiki.tamu.edu/wiki/index.php/Category:CACAO
	Table Editor	application for easily editing spreadsheet-formatted data with associated ontologies	https://incatools.github.io/table-editor/?config=.%2Fconfig.yaml
	PhenoteFX	phenotype curation	http://phenotefx.readthedocs.io/en/latest/
Annotation data exchange formats	GAF2	file format for ontology annotation data exchange	http://geneontology.org/page/go-annotation-file-format-20
	RDF	Resource Description Framework
	Phenopackets	an extensible data model and data exchange format for phenotype data	https://github.com/phenopackets/phenopacket-format/wiki/Overview-of-Phenotype-Exchange-Format
	BioLink model	schema for biological data and associations	https://biolink.github.io/biolink-model/
Ontology editors	Protégé	ontology editing tool	http://protege.stanford.edu/