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Items: 1 to 20 of 310


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.


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.


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.


Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.

Jupp S, Stevens R, Hoehndorf R.

J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S3. doi: 10.1186/2041-1480-3-S1-S3.


BioGateway: a semantic systems biology tool for the life sciences.

Antezana E, Blondé W, Egaña M, Rutherford A, Stevens R, De Baets B, Mironov V, Kuiper M.

BMC Bioinformatics. 2009 Oct 1;10 Suppl 10:S11. doi: 10.1186/1471-2105-10-S10-S11.


Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology.

Aranguren ME, Antezana E, Kuiper M, Stevens R.

BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S1. doi: 10.1186/1471-2105-9-S5-S1.


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.


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.


Regular paths in SparQL: querying the NCI Thesaurus.

Detwiler LT, Suciu D, Brinkley JF.

AMIA Annu Symp Proc. 2008 Nov 6:161-5.


Knowledge-level querying of temporal patterns in clinical research systems.

O'Connor MJ, Shankar RD, Parrish DB, Das AK.

Stud Health Technol Inform. 2007;129(Pt 1):311-5.


Semi-automated ontology generation within OBO-Edit.

Wächter T, Schroeder M.

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


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.


What's in a code? Towards a formal account of the relation of ontologies and coding systems.

Rector AL.

Stud Health Technol Inform. 2007;129(Pt 1):730-4.


Spatial location and its relevance for terminological inferences in bio-ontologies.

Schulz S, Markó K, Hahn U.

BMC Bioinformatics. 2007 Apr 20;8:134.


Dynamic sub-ontology evolution for traditional Chinese medicine web ontology.

Mao Y, Wu Z, Tian W, Jiang X, Cheung WK.

J Biomed Inform. 2008 Oct;41(5):790-805. doi: 10.1016/j.jbi.2008.05.008.


New concepts for building vocabulary for cell image ontologies.

Plant AL, Elliott JT, Bhat TN.

BMC Bioinformatics. 2011 Dec 21;12:487. doi: 10.1186/1471-2105-12-487.


Improving ontologies by automatic reasoning and evaluation of logical definitions.

Köhler S, Bauer S, Mungall CJ, Carletti G, Smith CL, Schofield P, Gkoutos GV, Robinson PN.

BMC Bioinformatics. 2011 Oct 27;12:418. doi: 10.1186/1471-2105-12-418.


Aber-OWL: a framework for ontology-based data access in biology.

Hoehndorf R, Slater L, Schofield PN, Gkoutos GV.

BMC Bioinformatics. 2015 Jan 28;16:26. doi: 10.1186/s12859-015-0456-9.

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