OntoGene in BioCreative II

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2008 Oct 18

PMID 18834491

Citations 19

Authors

Fabio Rinaldi

Thomas Kappeler

Kaarel Kaljurand

Gerold Schneider

Manfred Klenner

Simon Clematide

Michael Hess

Jean-Marc von Allmen

Pierre Parisot

Martin Romacker

Therese Vachon

Affiliations

Soon will be listed here.

Abstract

Background: Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the critical pieces of information that are needed to direct current and future research investment.

Results: In this report we describe approaches taken within the scope of the second BioCreative competition in order to solve two aspects of this problem: detection of novel protein interactions reported in scientific articles, and detection of the experimental method that was used to confirm the interaction. Our approach to the former problem is based on a high-recall protein annotation step, followed by two strict disambiguation steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which deliver high-precision results while maintaining reasonable recall. The detection of the experimental methods is tackled by a pattern matching approach, which has delivered the best results in the official BioCreative evaluation.

Conclusion: Although the results of BioCreative clearly show that no tool is sufficiently reliable for fully automated annotations, a few of the proposed approaches (including our own) already perform at a competitive level. This makes them interesting either as standalone tools for preliminary document inspection, or as modules within an environment aimed at supporting the process of curation of biomedical literature.

Citing Articles

OGER++: hybrid multi-type entity recognition.

Furrer L, Jancso A, Colic N, Rinaldi F J Cheminform. 2019; 11(1):7.

PMID: 30666476 PMC: 6689863. DOI: 10.1186/s13321-018-0326-3.

Entity recognition in the biomedical domain using a hybrid approach.

Basaldella M, Furrer L, Tasso C, Rinaldi F J Biomed Semantics. 2017; 8(1):51.

PMID: 29122011 PMC: 5679148. DOI: 10.1186/s13326-017-0157-6.

Strategies towards digital and semi-automated curation in RegulonDB.

Rinaldi F, Lithgow O, Gama-Castro S, Solano H, Lopez A, Muniz Rascado L Database (Oxford). 2017; 2017(1).

PMID: 28365731 PMC: 5467564. DOI: 10.1093/database/bax012.

Automatic query generation using word embeddings for retrieving passages describing experimental methods.

Aydin F, Husunbeyi Z, Ozgur A Database (Oxford). 2017; 2017.

PMID: 28077568 PMC: 5225401. DOI: 10.1093/database/baw166.

Automated detection of discourse segment and experimental types from the text of cancer pathway results sections.

Burns G, Dasigi P, de Waard A, Hovy E Database (Oxford). 2016; 2016.

PMID: 27580922 PMC: 5006090. DOI: 10.1093/database/baw122.

References

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A . The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004; 22(2):177-83. DOI: 10.1038/nbt926. View

Temkin J, Gilder M . Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics. 2003; 19(16):2046-53. DOI: 10.1093/bioinformatics/btg279. View

Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I . Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics. 2004; 20(5):604-11. DOI: 10.1093/bioinformatics/btg452. View

SWANSON D . Fish oil, Raynaud's syndrome, and undiscovered public knowledge. Perspect Biol Med. 1986; 30(1):7-18. DOI: 10.1353/pbm.1986.0087. View

Krauthammer M, Nenadic G . Term identification in the biomedical literature. J Biomed Inform. 2004; 37(6):512-26. DOI: 10.1016/j.jbi.2004.08.004. View

Chen L, Liu H, Friedman C . Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics. 2004; 21(2):248-56. DOI: 10.1093/bioinformatics/bth496. View

Song Y, Kim E, Lee G, Yi B . POSBIOTM-NER: a trainable biomedical named-entity recognition system. Bioinformatics. 2005; 21(11):2794-6. DOI: 10.1093/bioinformatics/bti414. View

Settles B . ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics. 2005; 21(14):3191-2. DOI: 10.1093/bioinformatics/bti475. View

Ananiadou S, Kell D, Tsujii J . Text mining and its potential applications in systems biology. Trends Biotechnol. 2006; 24(12):571-9. DOI: 10.1016/j.tibtech.2006.10.002. View

10.

Chun H, Tsuruoka Y, Kim J, Shiba R, Nagata N, Hishiki T . Extraction of gene-disease relations from Medline using domain dictionaries and machine learning. Pac Symp Biocomput. 2006; :4-15. View

11.

Krallinger M, Valencia A . Text-mining and information-retrieval services for molecular biology. Genome Biol. 2005; 6(7):224. PMC: 1175978. DOI: 10.1186/gb-2005-6-7-224. View

12.

Pyysalo S, Salakoski T, Aubin S, Nazarenko A . Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches. BMC Bioinformatics. 2006; 7 Suppl 3:S2. PMC: 1764446. DOI: 10.1186/1471-2105-7-S3-S2. View

13.

Rinaldi F, Schneider G, Kaljurand K, Hess M, Romacker M . An environment for relation mining over richly annotated corpora: the case of GENIA. BMC Bioinformatics. 2006; 7 Suppl 3:S3. PMC: 1764447. DOI: 10.1186/1471-2105-7-S3-S3. View

14.

. The Universal Protein Resource (UniProt). Nucleic Acids Res. 2006; 35(Database issue):D193-7. PMC: 1669721. DOI: 10.1093/nar/gkl929. View

15.

Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C . IntAct--open source resource for molecular interaction data. Nucleic Acids Res. 2006; 35(Database issue):D561-5. PMC: 1751531. DOI: 10.1093/nar/gkl958. View

16.

Fundel K, Kuffner R, Zimmer R . RelEx--relation extraction using dependency parse trees. Bioinformatics. 2006; 23(3):365-71. DOI: 10.1093/bioinformatics/btl616. View

17.

Clegg A, Shepherd A . Benchmarking natural-language parsers for biological applications using dependency graphs. BMC Bioinformatics. 2007; 8:24. PMC: 1797812. DOI: 10.1186/1471-2105-8-24. View

18.

Pyysalo S, Ginter F, Heimonen J, Bjorne J, Boberg J, Jarvinen J . BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinformatics. 2007; 8:50. PMC: 1808065. DOI: 10.1186/1471-2105-8-50. View

19.

Smith L, Tanabe L, Ando R, Kuo C, Chung I, Hsu C . Overview of BioCreative II gene mention recognition. Genome Biol. 2008; 9 Suppl 2:S2. PMC: 2559986. DOI: 10.1186/gb-2008-9-s2-s2. View

20.

Morgan A, Lu Z, Wang X, Cohen A, Fluck J, Ruch P . Overview of BioCreative II gene normalization. Genome Biol. 2008; 9 Suppl 2:S3. PMC: 2559987. DOI: 10.1186/gb-2008-9-s2-s3. View