![](bg7.png)
of BioVerbNet. Journal of Biomedical Semantics,
10(2):12.
Courtot, M., Bug, W., Gibson, F., Lister, A. L., Malone,
J., Schober, D., Brinkman, R. R., and Ruttenberg, A.
(2008). The OWL of biomedical investigations. In
Proceedings of the Fifth OWLED Workshop on OWL:
Experiences and Directions, page 12pp.
Degtyarenko, K., De Matos, P., Ennis, M., Hastings, J.,
Zbinden, M., McNaught, A., Alc
´
antara, R., Dar-
sow, M., Guedj, M., and Ashburner, M. (2007).
ChEBI: a database and ontology for chemical enti-
ties of biological interest. Nucleic Acids Research,
36(suppl 1):D344–D350.
Devanbu, P. T. and Litman, D. J. (1996). Taxonomic plan
reasoning. Artificial Intelligence, 84(1-2):1–35.
Dolbey, A., Ellsworth, M., and Scheffczyk, J. (2006).
BioFrameNet: A domain-specific FrameNet exten-
sion with links to biomedical ontologies. In Second In-
ternational Workshop on Formal Biomedical Knowl-
edge Representation (KR-MED 2006), CEUR Work-
shop Proceedings Vol. 222, pages 87–94.
Dumontier, M., Baker, C. J., Baran, J., Callahan, A., Che-
pelev, L., Cruz-Toledo, J., Rio, N. R. D., Duck, G.,
Furlong, L. I., Keath, N., Klassen, D., McCusker,
J. P., Queralt-Rosinach, N., Samwald, M., Villanueva-
Rosales, N., Wilkinson, M. D., and Hoehndorf, R.
(2014). The semanticscience integrated ontology (sio)
for biomedical research and knowledge discovery.
Journal of Biomedical Semantics, 5(1):14.
Entrez Gene (2020). https://www.ncbi.nlm.nih.gov.
Fern
´
andez, M., Cantador, I., L
´
opez, V., Vallet, D., Castells,
P., and Motta, E. (2011). Semantically enhanced
Information Retrieval: An ontology-based approach.
Journal of Web Semantics, 9(4):434–452.
Fillmore, C. J. (1976). Frame semantics and the nature of
language. Annals of the New York Academy of Sci-
ences, 280(1):20–32.
Fleischmann, A., Darsow, M., Degtyarenko, K., Fleis-
chmann, W., Boyce, S., Axelsen, K. B., Bairoch,
A., Schomburg, D., Tipton, K. F., and Apweiler,
R. (2004). Intenz, the integrated relational enzyme
database. Nucleic Acids Research, 32(suppl 1):D434–
D437.
FlyBase Consortium (2003). The flybase database of the
drosophila genome projects and community literature.
Nucleic Acids Research, 31(1):172–175.
FrameNet (2020). https://framenet.icsi.berkeley.edu.
Gene Ontology Consortium (2011). The gene ontology:
enhancements for 2011. Nucleic Acids Research,
40(D1):D559–D564.
Hu, W., Qiu, H., Huang, J., and Dumontier, M. (2017).
BioSearch: a semantic search engine for Bio2RDF.
Database, 2017.
Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K. F.,
Itoh, M., Kawashima, S., Katayama, T., Araki, M.,
and Hirakawa, M. (2006). From genomics to chemical
genomics: new developments in kegg. Nucleic Acids
Research, 34(suppl 1):D354–D357.
Kipper, K., Korhonen, A., Ryant, N., and Palmer, M.
(2008). A large-scale classification of English verbs.
Language Resources and Evaluation, 42(1):21–40.
Kipper-Schuler, K. (2005). VerbNet: A broad-coverage,
comprehensive verb lexicon. PhD thesis, University
of Pennsylvania.
Kirby, B. J., Symonds, W. T., Kearney, B. P., and Mathias,
A. A. (2015). Pharmacokinetic, pharmacodynamic,
and drug-interaction profile of the hepatitis C virus
NS5B polymerase inhibitor sofosbuvir. Clinical Phar-
macokinetics, 54(7):677–690.
Klingstr
¨
om, T., Soldatova, L., Stevens, R., Roos, T. E.,
Swertz, M. A., M
¨
uller, K. M., Kala
ˇ
s, M., Lambrix,
P., Taussig, M. J., Litton, J.-E., Landegren, U., and
Bongcam-Rudlof, E. (2013). Workshop on labortory
protocol standards for the molecular methods data-
base. New Biotechnology, 30(2):109–113.
Kohlschein, C., Klischies, D., Paulus, A., Burgdorf, A.,
Meisen, T., and Kipp, M. (2018). An extensible se-
mantic search engine for biomedical publications. In
2018 IEEE 20th International Conference on e-Health
Networking, Applications and Services (Healthcom),
pages 1–6.
Lenat, D. B., Prakash, M., and Shepherd, M. (1985). Cyc:
Using common sense knowledge to overcome brittle-
ness and knowledge acquisition bottlenecks. AI mag-
azine, 6(4):65–65.
Liang, J., Zhang, Y., Xiao, Y., Wang, H., Wang, W., and
Zhu, P. (2017). On the transitivity of hypernym-
hyponym relations in data-driven lexical taxonomies.
In Proceedings of the Thirty-First AAAI Conference
on Artificial Intelligence, AAAI’17, page 1185–1191.
AAAI Press.
Lippincott, T., Rimell, L., Verspoor, K., and Korhonen,
A. (2013). Approaches to verb subcategorization
for biomedicine. Journal of Biomedical Informatics,
46(2):212–227.
Miller, G. A. (1995). Wordnet: A lexical database for en-
glish. Communications of the ACM, 38(11):39–41.
Minsky, M. (1974). A framework for representing knowl-
edge. Artificial Intelligence Memo No. 306, Mas-
sachusetts Institute of Technology A.I. Laboratory.
Palmer, M., Gildea, D., and Kingsbury, P. (2005). The
Proposition Bank: An annotated corpus of semantic
roles. Computational Linguistics, 31(1):71–106.
Raphael, B. (1964). SIR: A computer program for seman-
tic information retrieval. PhD thesis, Massachusetts
Institute of Technology, Cambridge, USA.
Rijgersberg, H., Van Assem, M., and Top, J. (2013). Ontol-
ogy of units of measure and related concepts. Seman-
tic Web, 4(1):3–13.
Ringwald, M., Eppig, J. T., Kadin, J. A., and Richardson,
J. E. (2000). Gxd: a gene expression database for the
laboratory mouse: current status and recent enhance-
ments. Nucleic Acids Research, 28(1):115–119.
Rosse, C. and Mejino Jr, J. L. (2003). A reference on-
tology for biomedical informatics: the foundational
model of anatomy. Journal of Biomedical Informat-
ics, 36(6):478–500.
Salton, G., Wong, A., and Yang, C. S. (1975). A vector
Semantic Search for Biomedical Texts using Predicate-Argument Structure
305