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Items: 1 to 20 of 24

1.

The development of non-coding RNA ontology.

Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, de Silva N, Kasukurthi MV, Jha VK, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M.

Int J Data Min Bioinform. 2016;15(3):214-232.

2.

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D339-D346. doi: 10.1093/nar/gkw1075. Epub 2016 Nov 28.

3.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, Mungall C, Courtot M, Ruttenberg A, He Y.

Nucleic Acids Res. 2017 Jan 4;45(D1):D347-D352. doi: 10.1093/nar/gkw918. Epub 2016 Oct 12.

4.

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Diehl AD, Meehan TF, Bradford YM, Brush MH, Dahdul WM, Dougall DS, He Y, Osumi-Sutherland D, Ruttenberg A, Sarntivijai S, Van Slyke CE, Vasilevsky NA, Haendel MA, Blake JA, Mungall CJ.

J Biomed Semantics. 2016 Jul 4;7(1):44. doi: 10.1186/s13326-016-0088-7.

5.

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake JA, Eilbeck K, Natale DA, Lin Y, Wu B, Silva Nd, Wang X, Liu Z, Borchert GM, Tan M, Ruttenberg A.

J Biomed Semantics. 2016 May 10;7:25. doi: 10.1186/s13326-016-0064-2. eCollection 2016.

6.

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale DA, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M.

J Biomed Semantics. 2016 May 4;7:24. doi: 10.1186/s13326-016-0066-0. eCollection 2016.

7.

The Ontology for Biomedical Investigations.

Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.

PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016.

8.

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.

Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P.

PLoS One. 2015 Jun 18;10(6):e0131148. doi: 10.1371/journal.pone.0131148. eCollection 2015. No abstract available.

9.

Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P.

PLoS One. 2015 Apr 20;10(3):e0122978. doi: 10.1371/journal.pone.0122978. eCollection 2015. Erratum in: PLoS One. 2015;10(6):e0131148.

10.

Finding our way through phenotypes.

Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.

PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

11.

flowCL: ontology-based cell population labelling in flow cytometry.

Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR.

Bioinformatics. 2015 Apr 15;31(8):1337-9. doi: 10.1093/bioinformatics/btu807. Epub 2014 Dec 6.

12.

The logic of surveillance guidelines: an analysis of vaccine adverse event reports from an ontological perspective.

Courtot M, Brinkman RR, Ruttenberg A.

PLoS One. 2014 Mar 25;9(3):e92632. doi: 10.1371/journal.pone.0092632. eCollection 2014.

13.

The neurological disease ontology.

Jensen M, Cox AP, Chaudhry N, Ng M, Sule D, Duncan W, Ray P, Weinstock-Guttman B, Smith B, Ruttenberg A, Szigeti K, Diehl AD.

J Biomed Semantics. 2013 Dec 6;4(1):42. doi: 10.1186/2041-1480-4-42.

14.

An ontology-based method for secondary use of electronic dental record data.

Schleyer TK, Ruttenberg A, Duncan W, Haendel M, Torniai C, Acharya A, Song M, Thyvalikakath TP, Liu K, Hernandez P.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:234-8. eCollection 2013.

15.

Protein Ontology: a controlled structured network of protein entities.

Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D415-21. doi: 10.1093/nar/gkt1173. Epub 2013 Nov 21.

16.

The representation of protein complexes in the Protein Ontology (PRO).

Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D'Eustachio P, Smith B, Blake JA, Wu C.

BMC Bioinformatics. 2011 Sep 19;12:371. doi: 10.1186/1471-2105-12-371.

17.

Meeting Report: BioSharing at ISMB 2010.

Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A.

Stand Genomic Sci. 2010 Dec 4;3(3):254-8. doi: 10.4056/sigs/1403501.

18.

Ontology and the future of dental research informatics.

Smith B, Goldberg LJ, Ruttenberg A, Glick M.

J Am Dent Assoc. 2010 Oct;141(10):1173-5. No abstract available.

19.

Modeling biomedical experimental processes with OBI.

Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J; OBI consortium..

J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7. doi: 10.1186/2041-1480-1-S1-S7.

20.

OntoFox: web-based support for ontology reuse.

Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y.

BMC Res Notes. 2010 Jun 22;3:175. doi: 10.1186/1756-0500-3-175.

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