Searching Biomedical Literature with Anatomy Ontologies

  • Thomas Wächter
  • Dimitra Alexopoulou
  • Heiko Dietze
  • Jörg Hakenberg
  • Michael Schroeder
Part of the Computational Biology book series (COBO, volume 6)

Summary

Many ontologies and vocabularies have been designed to annotate genes and gene products based on evidence from literature. They are also useful to search literature systematically. GoPubMed is such an ontology-based literature search engine. It allows users to explore PubMed search results with hierarchical vocabularies such as the Gene Ontology or MeSH.We demonstrate the use of GoPubMed and MeshPubMed to answer questions relating to anatomy. Then, we discuss MousePubMed, the adaption of GoPubMed to vocabularies used in the Edinburgh Mouse Atlas with genes, tissues, and developmental stages. We develop a specific text mining algorithm for MousePubMed and demonstrate its usefulness by evaluating it on the Mouse Atlas. For nearly 1500 genes and over 10.000 triples of gene, tissue and stage, we are able to reconstruct with MousePubMed 37% of genes, 31% of gene-tissue associations and 13% of gene-tissue-stage associations from PubMed abstracts. These figures are encouraging as only abstracts are used.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Altun ZF, Hall DH (eds) (2002-2006) WormAtlas. http://www.wormatlas.orgGoogle Scholar
  2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, DolinskiK, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S,Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology:tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–9.Google Scholar
  3. Azuma N, Tadokoro K, Asaka A, Yamada M, Yamaguchi Y, Handa H, Matsushima S,Watanabe T, Kida Y, Ogura T, Torii M, Shimamura K, Nakafuku M (2005) Transdifferentiation of the retinal pigment epithelia to the neural retina by transfer of the Pax6transcriptional factor. Hum Mol Genet, 14(8):1059–68.Google Scholar
  4. Baldock RA, Bard JB, Burger A, Burton N, Christiansen J, Feng G, Hill B, Houghton D,Kaufman M, Rao J, Sharpe J, Ross A, Stevenson P, Venkataraman S,Waterhouse A, Yang Y, Davidson DR (2003) EMAP and EMAGE: a framework for understanding spatiallyorganized data. Neuroinformatics 1(4):309–25.Google Scholar
  5. Bard JL, Kaufman MH, Dubreuil C, Brune RM, Burger A, Baldock RA, Davidson DR(1998) An internet-accessible database of mouse developmental anatomy based on a systematicnomenclature. Mech Dev 74(1–2):111–120.CrossRefGoogle Scholar
  6. Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, MuellerLA, Yoon J, Doyle A, Lander G, Moseyko N, Yoo D, Xu I, Zoeckler B, Montoya M,Miller N, Weems D, Rhee SY (2004) Functional annotation of the Arabidopsis genomeusing controlled vocabularies. Plant Physiol 135(2):745–55.Google Scholar
  7. Berneis K, RizzoM(2005) Ldl size: does it matter? Swiss Med Wkly 134(49–50):720–4.Google Scholar
  8. Bodenreider O (2004) The Unified Medical Language System (UMLS): integratingbiomedical terminology. Nucl Acid Res 32:D267–70.CrossRefGoogle Scholar
  9. Brinckmann A, Rüther K, Williamson K, Lorenz B, Lucke B, Nrnberg P, Trijbels F,Janssen A, Schuelke M (2006) De novo double mutation in PAX6 and mtDNA tRNA(Lys) associated with atypical aniridia and mitochondrial disease. J Mol Med.Google Scholar
  10. Corcho O, Fernandez-Lopez M, Gomez-Perez A (2003) Methodologies, tools and languagesfor building ontologies: where is their meeting point? Data Knowl Eng 46(1):41–64.Google Scholar
  11. Couto FM, Silva MJ, Coutinho P (2005) Finding genomic ontology terms in text usingevidence content. BMC Bioinformatics 6(1):S21.CrossRefGoogle Scholar
  12. Doms A, Schroeder M (2005) GoPubMed: Exploring PubMed with the GeneOntology.Nucl Acid Res 33(Web Server Issue):W783–6.Google Scholar
  13. Duineveld AJ, Stoter R, Weiden MR, Kenepa B, Benjamins VR. Wondertools?: a comparativestudy of ontological engineering tools. Int J Hum-Comput Stud 52(6):1111–33.Google Scholar
  14. Ehrler F, Geissbuehler A, Jimeno A, Ruch P (2005) Data-poor categorization and passageretrieval for gene ontology annotation in Swiss-Prot. BMC Bioinformatics 6(1):S23.Google Scholar
  15. Fang Z, Cone K, Sanchez-Villeda H, Polacco M, McMullen M, Schroeder S, Gardiner J,Davis G, Havermann S, Yim Y, Vroh Bi I, Coe E (2003) iMap: a database-driven utility tointegrate and access the genetic and physical maps of maize. Bioinformatics 19:2105–11.CrossRefGoogle Scholar
  16. Grumbling G, Strelets V (2006) FlyBase: anatomical data, images and queries. Nucl AcidRes 34(Database issue):D484–8.Google Scholar
  17. Harbach RE, Knight KL (1980) Taxonomist’s Glossary of Mosquito Anatomy. PlexusPublishing Inc, Marlton, NJ, USA.Google Scholar
  18. Jaiswal P, Avraham A, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY,Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Ware D, Zapata F (2005) PlantOntology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. CompFunct Genom 6(7–8):388–97.CrossRefGoogle Scholar
  19. Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, ZhaoW, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S,Casstevens TM, Buckler ES, Stein L, McCouch S (2002) Gramene: a bird’s eye view ofcereal genomes. Nuc Acids Res 34(Database issue):D717–23.Google Scholar
  20. Jensen LJ, Saric J, Bork P (2006) Literature mining for the biologist: from informationretrieval to biological discovery. Nat Rev Genet 7:119–129.CrossRefGoogle Scholar
  21. Kleinjan DA, Seawright A, Mella S, Carr CB, Tyas DA, Simpson TI, Mason JO, PriceDJ, van Heyningen V (2006) Long-range downstream enhancers are essential for Pax6expression. Dev Biol.Google Scholar
  22. Lambrix P, Habbouche M, Perez M (2003) Evaluation of ontology development tools forbioinformatics. Bioinformatics 19(12):1564–71.CrossRefGoogle Scholar
  23. Müller H-M, Kenny EE, Sternberg PW (2003) Textpresso: an ontology-based informationretrieval and extraction system for biological literature. PLoS Biol 2.Google Scholar
  24. Ogren PV, Cohen KB, Acquaah-Mensah GK, Eberlein J, Hunter L (2004) The compositionalstructure of Gene Ontology terms. Pac Symp Biocomput. 214–25.Google Scholar
  25. Perez-Iratxeta C, Perez AJ, Bork P, Andrade MA (2003). Update on XplorMed: A webserver for exploring scientific literature. Nucl Acid Res 31(13):3866–8.CrossRefGoogle Scholar
  26. Rosse C, Mejino JLV (2003) A Reference Ontology for Bioinformatics: The FoundationalModel of Anatomy. Journal of Biomedical Informatics 36:478–500.CrossRefGoogle Scholar
  27. Thut CJ, Rountree RB, Hwa M, Kingsley DM(2001) A large-scale in situ screen providesmolecular evidence for the induction of eye anterior segment structures by the developinglens. Dev Biol 231(1):63–76.CrossRefGoogle Scholar
  28. Uschold M (1996) Building Ontologies: Towards a Unified Methodology. Conf BritComp Soc SIG Exp Sys, Cambridge, UK.Google Scholar
  29. Vincent PL, Coe EH, Polacco ML (2003) Zea mays ontology – a database of internationalterms. Trends Plant Sci 8(11):517–20.Part IIIAnatomy Ontologies and Spatio-Temporal AtlasesCrossRefGoogle Scholar

Copyright information

© Albert Burger, Duncan Davidson, Richard Baldock 2008

Authors and Affiliations

  • Thomas Wächter
  • Dimitra Alexopoulou
  • Heiko Dietze
  • Jörg Hakenberg
  • Michael Schroeder

There are no affiliations available

Personalised recommendations