Table 2 Example application cases of biomedical semantic annotation tools

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/)