FLUTE: Fast and Reliable Knowledge Retrieval from Biomedical Literature

Overview

Journal Database (Oxford)

Specialty Biology

Date 2020 Aug 8

PMID 32761077

Citations 5

Authors

Emilee Holtzapple

Cheryl A Telmer

Natasa Miskov-Zivanov

Affiliations

Soon will be listed here.

Abstract

State-of-the-art machine reading methods extract, in hours, hundreds of thousands of events from the biomedical literature. However, many of the extracted biomolecular interactions are incorrect or not relevant for computational modeling of a system of interest. Therefore, rapid, automated methods are required to filter and select accurate and useful information. The FiLter for Understanding True Events (FLUTE) tool uses public protein interaction databases to filter interactions that have been extracted by machines from databases such as PubMed and score them for accuracy. Confidence in the interactions allows for rapid and accurate model assembly. As our results show, FLUTE can reliably determine the confidence in the biomolecular interactions extracted by fast machine readers and at the same time provide a speedup in interaction filtering by three orders of magnitude. Database URL: https://bitbucket.org/biodesignlab/flute.

Citing Articles

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Using computable knowledge mined from the literature to elucidate confounders for EHR-based pharmacovigilance.

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References

Sayed K, Bocan K, Miskov-Zivanov N . Automated Extension of Cell Signaling Models with Genetic Algorithm. Annu Int Conf IEEE Eng Med Biol Soc. 2018; 2018:5030-5033. DOI: 10.1109/EMBC.2018.8513431. View

Joshi-Tope G, Gillespie M, Vastrik I, DEustachio P, Schmidt E, de Bono B . Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2004; 33(Database issue):D428-32. PMC: 540026. DOI: 10.1093/nar/gki072. View

Hornbeck P, Zhang B, Murray B, Kornhauser J, Latham V, Skrzypek E . PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 2014; 43(Database issue):D512-20. PMC: 4383998. DOI: 10.1093/nar/gku1267. View

Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J . STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2014; 43(Database issue):D447-52. PMC: 4383874. DOI: 10.1093/nar/gku1003. View

Hunter S, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D . InterPro: the integrative protein signature database. Nucleic Acids Res. 2008; 37(Database issue):D211-5. PMC: 2686546. DOI: 10.1093/nar/gkn785. View

von Mering C, Jensen L, Snel B, Hooper S, Krupp M, Foglierini M . STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 2004; 33(Database issue):D433-7. PMC: 539959. DOI: 10.1093/nar/gki005. View

Wieneke A, Bowles E, Cronkite D, Wernli K, Gao H, Carrell D . Validation of natural language processing to extract breast cancer pathology procedures and results. J Pathol Inform. 2015; 6:38. PMC: 4485196. DOI: 10.4103/2153-3539.159215. View

Hawse W, Sheehan R, Miskov-Zivanov N, Menk A, Kane L, Faeder J . Cutting Edge: Differential Regulation of PTEN by TCR, Akt, and FoxO1 Controls CD4+ T Cell Fate Decisions. J Immunol. 2015; 194(10):4615-9. PMC: 4418530. DOI: 10.4049/jimmunol.1402554. View

Zhang Q, Wu L, Zhang T, Han Y, Lin X . Autophagy-mediated HMGB1 release promotes gastric cancer cell survival via RAGE activation of extracellular signal-regulated kinases 1/2. Oncol Rep. 2015; 33(4):1630-8. PMC: 4358082. DOI: 10.3892/or.2015.3782. View

10.

Oughtred R, Stark C, Breitkreutz B, Rust J, Boucher L, Chang C . The BioGRID interaction database: 2019 update. Nucleic Acids Res. 2018; 47(D1):D529-D541. PMC: 6324058. DOI: 10.1093/nar/gky1079. View

11.

Finn R, Coggill P, Eberhardt R, Eddy S, Mistry J, Mitchell A . The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2015; 44(D1):D279-85. PMC: 4702930. DOI: 10.1093/nar/gkv1344. View

12.

Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V . NDEx, the Network Data Exchange. Cell Syst. 2015; 1(4):302-305. PMC: 4649937. DOI: 10.1016/j.cels.2015.10.001. View

13.

Peng Q, Lin K, Chang T, Zou L, Xing P, Shen Y . Identification of genomic expression differences between right-sided and left-sided colon cancer based on bioinformatics analysis. Onco Targets Ther. 2018; 11:609-618. PMC: 5797455. DOI: 10.2147/OTT.S154207. View

14.

Kim S, Thiessen P, Bolton E, Chen J, Fu G, Gindulyte A . PubChem Substance and Compound databases. Nucleic Acids Res. 2015; 44(D1):D1202-13. PMC: 4702940. DOI: 10.1093/nar/gkv951. View

15.

Zerva C, Batista-Navarro R, Day P, Ananiadou S . Using uncertainty to link and rank evidence from biomedical literature for model curation. Bioinformatics. 2017; 33(23):3784-3792. PMC: 5860317. DOI: 10.1093/bioinformatics/btx466. View

16.

Bjorne J, Ginter F, Pyysalo S, Tsujii J, Salakoski T . Complex event extraction at PubMed scale. Bioinformatics. 2010; 26(12):i382-90. PMC: 2881365. DOI: 10.1093/bioinformatics/btq180. View

17.

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

18.

Gyori B, Bachman J, Subramanian K, Muhlich J, Galescu L, Sorger P . From word models to executable models of signaling networks using automated assembly. Mol Syst Biol. 2017; 13(11):954. PMC: 5731347. DOI: 10.15252/msb.20177651. View

19.

. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2016; 45(D1):D158-D169. PMC: 5210571. DOI: 10.1093/nar/gkw1099. View

20.

Kummer K, Kalpachidou T, Kress M, Langeslag M . Signatures of Altered Gene Expression in Dorsal Root Ganglia of a Fabry Disease Mouse Model. Front Mol Neurosci. 2018; 10:449. PMC: 5788883. DOI: 10.3389/fnmol.2017.00449. View