Table 2.

Example application cases of biomedical semantic annotation tools

Application Case (AC)	The role of semantic annotation tool in the AC	Biomedical resources relevant for the AC (or representative examples, if multiple)
Semantic search of biomedical tools and services [6]	Sematic search of biomedical tools and services enabled by semantic annotation of users’ (free-form) queries with concepts from UMLS Metathesaurus	Catalogs of and social spaces created around biomedical tools and services, e.g.: - myExperiment (http://www.myexperiment.org/) - BioCatalogue (https://www.biocatalogue.org/)
Semantic search of domain specific scientific literature [74]	Semantic annotation of PubMed entries with ontological concepts related to genes and proteins	Ontologies used for the annotation of biomedical references (PubMed entries): - Gene Ontology - GO (http://geneontology.org/) - Universal Protein Resource - UniProt (http://www.uniprot.org/uniprot/)
Improved clinical decision making [75]	Extraction of key clinical concepts (UMLS-based) required for supporting clinical decision making; the concepts are extracted from biomedical literature and clinical text sources	Sources of biomedical texts used to support decision making: - PubMed Central (PMC) Open Access Subset (https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/) - MEDLINE abstracts (https://www.nlm.nih.gov/bsd/pmresources.html)
Unambiguous description of abbreviations [10]	Extended (long) forms of abbreviations are matched against both UMLS and DBpedia concepts, thus not only disambiguating the long forms, but also connecting UMLS and DBpedia KBs	Allie - a search service for abbreviations and their long forms (http://allie.dbcls.jp/)