Abstract
PHI-Base is a database that it is accessible through the web and contains a catalogue of experimentally verified pathogen-host interactions from fungal, oomycete and bacterial pathogens and animal, plant, fungal and insect hosts. In 2016, researchers from Centre for Plant Biotechnology and Genomics at Universidad Politécnica de Madrid, Spain, released a semantic-based version of part of this database (named Semantic PHI) focusing on those interactions where the affected host are plants. This semantic version was created and published using FAIR methodology and was available through a SPARQL endpoint. In this paper is presented a proof of concept done to create an interface for Semantic PHI-Base dataset. A web tool that allows interacting and visualizing the interactions contained in Semantic PHI database using an easy interface was created. This tool represents a case study of interacting and visualizing the knowledge contained within a semantic dataset allowing the use of such dataset by users with no expertise in semantic technologies.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
- 2.
- 3.
- 4.
Two logical operators (AND, OR) can be applied between the parameters chosen by the user.
- 5.
- 6.
- 7.
- 8.
- 9.
References
Wulff, B.B.H., Horvath, D.M., Ward, E.R.: Improving immunity in crops: new tactics in an old game. Curr. Opin. Plant Biol. 14, 468–476 (2011). https://doi.org/10.1016/j.pbi.2011.04.002
Rodríguez Iglesias, A.: FAIR approaches applied to unraveling plant-pathogen interactions data and RNA processing evolution. http://oa.upm.es/44220/ (2016)
Paredes-Valverde, M.A., Valencia-García, R., Rodríguez-García, M.Á., Colomo-Palacios, R., Alor-Hernández, G.: A semantic-based approach for querying linked data using natural language. J. Inf. Sci. 42, 851–862 (2016). https://doi.org/10.1177/0165551515616311
Paredes-Valverde, M.A., Rodríguez-García, M.Á., Ruiz-Martínez, A., Valencia-García, R., Alor-Hernández, G.: ONLI: an ontology-based system for querying DBpedia using natural language paradigm. Expert Syst. Appl. 42, 5163–5176 (2015). https://doi.org/10.1016/j.eswa.2015.02.034
Rohamsted Research Institute. http://www.rothamsted.ac.uk
PHI-Base. http://www.phi-base.org/
Binns, D., Dimmer, E., Huntley, R., Barrell, D., O’Donovan, C., Apweiler, R.: QuickGO: a web-based tool for gene ontology searching. Bioinform. 25, 3045–3046 (2009). https://doi.org/10.1093/bioinformatics/btp536
Frontiers.: Publishing FAIR data: an exemplar methodology utilizing PHI-Base. Tech. Adv. Plant Sci. http://journal.frontiersin.org/article/10.3389/fpls.2016.00641/full
Wilkinson, M.D., Dumontier, M., Aalbersberg, I.J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., Santos, L.B., Bourne, P.E., Bouwman, J., Brookes, A.J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C.T., Finkers, R., Gonzalez-Beltran, A., Gray, A.J.G., Groth, P., Goble, C., Grethe, J.S., Heringa, J., Hoen, P.A.C. ’t, Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S.J., Martone, M.E., Mons, A., Packer, A.L., Persson, B., Rocca-Serra, P., Roos, M., Schaik, R. van Sansone, S.-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M.A., Thompson, M., Lei, J., van der Mulligen, E., van Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J., Mons, B.: The FAIR guiding principles for scientific data management and stewardship. Sci. Data. 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18
Mungall, C., Overton, J.A., Osumi-Sutherland, D., Haendel, M.: mbrush: Obo-relations, pp. 10–29. Zenodo (2015). https://doi.org/10.5281/zenodo.32899
Brinkman, R.R., Courtot, M., Derom, D., Fostel, J.M., He, Y., Lord, P., Malone, J., Parkinson, H., Peters, B., Rocca-Serra, P., Ruttenberg, A., Sansone, S.-A., Soldatova, L.N., Stoeckert, C.J., Turner, J.A., Zheng, J., Modeling biomedical experimental processes with OBI. J. Biomed. Semant. 1, S7 (2010). https://doi.org/10.1186/2041-1480-1-s1-s7
Ison, J., Kalaš, M., Jonassen, I., Bolser, D., Uludag, M., McWilliam, H., Malone, J., Lopez, R., Pettifer, S., Rice, P.: EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. Bioinform. 29, 1325–1332 (2013). https://doi.org/10.1093/bioinformatics/btt113
Malone, J., Holloway, E., Adamusiak, T., Kapushesky, M., Zheng, J., Kolesnikov, N., Zhukova, A., Brazma, A., Parkinson, H.: Modeling sample variables with an experimental factor ontology. Bioinform. 26, 1112–1118 (2010). https://doi.org/10.1093/bioinformatics/btq099
Dumontier, M., Baker, C.J., Baran, J., Callahan, A., Chepelev, L., Cruz-Toledo, J., Del Rio, N.R., Duck, G., Furlong, L.I., Keath, N., Klassen, D., McCusker, J.P., Queralt-Rosinach, N., Samwald, M., Villanueva-Rosales, N., Wilkinson, M.D., Hoehndorf, R.: The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J. Biomed. Semant. 5, 14 (2014). https://doi.org/10.1186/2041-1480-5-14
Arenas, M., Cuenca Grau, B., Kharlamov, E., Marciuska, S., Zheleznyakov, D.: Faceted search over ontology-enhanced RDF data. In: Proceedings of the 23rd ACM International Conference on Information and Knowledge Management, pp. 939–948. ACM, New York, NY, USA (2014)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Mesa-Polo, J.C., García-Salgado, R., Lagunes-García, G., Rodríguez-González, A., Rodríguez-Iglesias, A. (2019). Semantic PHI-Base Web Interface: A Web Tool to Interact and Visualize Plant-Pathogen Interactions Data. In: Alor-Hernández, G., Sánchez-Cervantes, J., Rodríguez-González, A., Valencia-García, R. (eds) Current Trends in Semantic Web Technologies: Theory and Practice. Studies in Computational Intelligence, vol 815. Springer, Cham. https://doi.org/10.1007/978-3-030-06149-4_10
Download citation
DOI: https://doi.org/10.1007/978-3-030-06149-4_10
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-06148-7
Online ISBN: 978-3-030-06149-4
eBook Packages: Intelligent Technologies and RoboticsIntelligent Technologies and Robotics (R0)