Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
Skip to main content
Springer Nature Link
Log in

Semantic Graph Analysis for Federated LOD Surfing in Life Sciences

  • Conference paper
  • First Online:
Semantic Technology (JIST 2017)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 10675))

Included in the following conference series:

Abstract

Currently, Linked Open Data (LOD) is increasingly used when publishing life science databases. To facilitate flexible use of such databases, we employ a method that uses federated query search along a path of class–class relationships. However, an effective method for federated query search requires analysis of the structure the relationships form for LOD datasets. Therefore, we constructed a graph of class–class relationships among 43 SPARQL endpoints and analyzed the connectivity of the graph. As a result, we found that (1) the sizes of connected components follow a power law; thus we should deal with the classes separately according to the size of connected components, (2) only the largest and second largest connected components have paths among classes from two or more SPARQL endpoints, and the datasets of each of the two connected components share ontologies, and (3) key classes that connect SPARQL endpoints are primarily upper-level concepts in the biological domain.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

Notes

  1. 1.

    http://www4.wiwiss.fu-berlin.de/drugbank/sparql.

  2. 2.

    https://id.nlm.nih.gov/mesh/sparql.

  3. 3.

    https://dba-rdf.biosciencedbc.jp/sparql.

  4. 4.

    http://data.organic-edunet.eu/sparql.

  5. 5.

    http://sparql.wikipathways.org.

References

  1. Heim, P., Hellmann, S., Lehmann, J., Lohmann, S., Stegemann, T.: RelFinder: revealing relationships in RDF knowledge bases. In: Chua, T.-S., Kompatsiaris, Y., Mérialdo, B., Haas, W., Thallinger, G., Bailer, W. (eds.) SAMT 2009. LNCS, vol. 5887, pp. 182–187. Springer, Heidelberg (2009). https://doi.org/10.1007/978-3-642-10543-2_21

    Chapter  Google Scholar 

  2. Yamaguchi, A., Kozaki, K., Lenz, K., Yamamoto, Y., Masuya, H., Kobayashi, N.: Semantic data acquisition by traversing class-class relationships over linkedopen data. In: 6th Joint International Conference (JIST 2016), LNCS 10055, pp. 136-151(2016)

    Google Scholar 

  3. Vasilevsky, N., Johnson, T., Corday, K., Torniai, C., Brush, M., Segerdell, E., Wilson, M., Shaffer, C., Robinson, D., Haendel, M.: Research resources: curating the new eagle-i discovery system. Database 2012, bar067 (2012). https://doi.org/10.1093/database/bar067

    Article  Google Scholar 

  4. Yamamoto, Y., Yamaguchi, A., Bono, H., Takagi, T.: Allie: a database and a search service of abbreviations and long forms. Database 2011, bar013 (2011). https://doi.org/10.1093/database/bar013

    Google Scholar 

  5. Belleau, F., Nolin, M.A., Tourigny, N., Rigault, P., Morissette, J.: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inform. 41(5), 706–716 (2008)

    Article  Google Scholar 

  6. Gile, C.L., Bollacker, K.D., Lawrence, S.: CiteSeer: an automatic citation indexing system. In: Proceedings of the Third ACM Conference on Digital Libraries (DL 98), pp. 89–98 (1998)

    Google Scholar 

  7. Piñero, J., Queralt-Rosinach, N., Bravo, À., Deu-Pons, J., Bauer-Mehren, A., Baron, M., Sanz, F., Furlong, L.I.: DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database (2015). https://doi.org/10.1093/database/bav028

  8. Jupp, S., Malone, J., Bolleman, J., Brandizi, M., Davies, M., Garcia, L., Gaulton, A., Gehant, S., Laibe, C., Redaschi, N., Wimalaratne, S.M., Martin, M., Le Novére, N., Parkinson, H., Birney, E., Jenkinson, A.M.: The EBI RDF platform: linked open data for the life sciences. Bioinformatics 30(9), 1338–1339 (2014)

    Article  Google Scholar 

  9. Hassanzadeh, O., Miller, R.J.: Automatic Curation of Clinical Trials Data in LinkedCT. In: Arenas, M., Corcho, O., Simperl, E., Strohmaier, M., d’Aquin, M., Srinivas, K., Groth, P., Dumontier, M., Heflin, J., Thirunarayan, K., Staab, S. (eds.) ISWC 2015. LNCS, vol. 9367, pp. 270–278. Springer, Cham (2015). https://doi.org/10.1007/978-3-319-25010-6_16

    Chapter  Google Scholar 

Download references

Acknowledgments

This work was supported by JSPS KAKENHI grant numbers 17K00434, 17K00424 and 17H01789, and by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).

Author information

Authors and Affiliations

  1. Database Center for Life Science (DBCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba, 277-0871, Japan

    Atsuko Yamaguchi & Yasunori Yamamoto

  2. The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan

    Kouji Kozaki

  3. RIKEN BioResource Center (BRC), 3-1-1, Koyadai, Tsukuba, Ibaraki, 305-0074, Japan

    Hiroshi Masuya & Norio Kobayashi

  4. Advanced Center for Computing and Communication (ACCC), RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan

    Hiroshi Masuya & Norio Kobayashi

Authors
  1. Atsuko Yamaguchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kouji Kozaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yasunori Yamamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hiroshi Masuya
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Norio Kobayashi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Atsuko Yamaguchi .

Editor information

Editors and Affiliations

  1. Griffith University, Brisbane, Queensland, Australia

    Zhe Wang

  2. Dresden University of Technology, Dresden, Germany

    Anni-Yasmin Turhan

  3. Griffith University, Brisbane, Queensland, Australia

    Kewen Wang

  4. Tianjin University, Tianjin, China

    Xiaowang Zhang

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Yamaguchi, A., Kozaki, K., Yamamoto, Y., Masuya, H., Kobayashi, N. (2017). Semantic Graph Analysis for Federated LOD Surfing in Life Sciences. In: Wang, Z., Turhan, AY., Wang, K., Zhang, X. (eds) Semantic Technology. JIST 2017. Lecture Notes in Computer Science(), vol 10675. Springer, Cham. https://doi.org/10.1007/978-3-319-70682-5_18

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-70682-5_18

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-70681-8

  • Online ISBN: 978-3-319-70682-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation