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Items: 1 to 20 of 106

1.

A strategy for building neuroanatomy ontologies.

Osumi-Sutherland D, Reeve S, Mungall CJ, Neuhaus F, Ruttenberg A, Jefferis GS, Armstrong JD.

Bioinformatics. 2012 May 1;28(9):1262-9. doi: 10.1093/bioinformatics/bts113. Erratum in: Bioinformatics. 2012 Aug 1;28(15):2091.

2.

Relations as patterns: bridging the gap between OBO and OWL.

Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, Herre H.

BMC Bioinformatics. 2010 Aug 31;11:441. doi: 10.1186/1471-2105-11-441.

3.

The Virtual Fly Brain browser and query interface.

Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA, Armstrong JD.

Bioinformatics. 2012 Feb 1;28(3):411-5. doi: 10.1093/bioinformatics/btr677.

4.

Unintended consequences of existential quantifications in biomedical ontologies.

Boeker M, Tudose I, Hastings J, Schober D, Schulz S.

BMC Bioinformatics. 2011 Nov 24;12:456. doi: 10.1186/1471-2105-12-456.

5.

Semi-automated ontology generation within OBO-Edit.

Wächter T, Schroeder M.

Bioinformatics. 2010 Jun 15;26(12):i88-96. doi: 10.1093/bioinformatics/btq188.

6.

Reasoning with bio-ontologies: using relational closure rules to enable practical querying.

Blondé W, Mironov V, Venkatesan A, Antezana E, De Baets B, Kuiper M.

Bioinformatics. 2011 Jun 1;27(11):1562-8. doi: 10.1093/bioinformatics/btr164.

7.

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. doi: 10.1093/nar/gkr469.

8.

The neuron classification problem.

Bota M, Swanson LW.

Brain Res Rev. 2007 Nov;56(1):79-88. Review.

9.

OntoQuery: easy-to-use web-based OWL querying.

Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C.

Bioinformatics. 2013 Nov 15;29(22):2955-7. doi: 10.1093/bioinformatics/btt514.

10.

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ.

J Biomed Semantics. 2014 May 19;5:21. doi: 10.1186/2041-1480-5-21.

11.

A common layer of interoperability for biomedical ontologies based on OWL EL.

Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV.

Bioinformatics. 2011 Apr 1;27(7):1001-8. doi: 10.1093/bioinformatics/btr058.

12.

From frames to OWL2: Converting the Foundational Model of Anatomy.

Detwiler LT, Mejino JL, Brinkley JF.

Artif Intell Med. 2016 May;69:12-21. doi: 10.1016/j.artmed.2016.04.003.

PMID:
27235801
13.

BioPortal: ontologies and integrated data resources at the click of a mouse.

Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W170-3. doi: 10.1093/nar/gkp440.

14.

ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.

Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S8. doi: 10.1186/1471-2105-11-S12-S8.

15.

The Virtual Insect Brain protocol: creating and comparing standardized neuroanatomy.

Jenett A, Schindelin JE, Heisenberg M.

BMC Bioinformatics. 2006 Dec 29;7:544.

16.

Ontology for vector surveillance and management.

Lozano-Fuentes S, Bandyopadhyay A, Cowell LG, Goldfain A, Eisen L.

J Med Entomol. 2013 Jan;50(1):1-14.

17.

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.

18.

The Drosophila phenotype ontology.

Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV.

J Biomed Semantics. 2013 Oct 18;4(1):30. doi: 10.1186/2041-1480-4-30.

19.

The environment ontology: contextualising biological and biomedical entities.

Buttigieg PL, Morrison N, Smith B, Mungall CJ, Lewis SE; ENVO Consortium..

J Biomed Semantics. 2013 Dec 11;4(1):43. doi: 10.1186/2041-1480-4-43.

20.

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

Côté RG, Jones P, Apweiler R, Hermjakob H.

BMC Bioinformatics. 2006 Feb 28;7:97.

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