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Results: 1 to 20 of 87

1.

The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process.

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

Genome Biol. 2009;10(5):R58. doi: 10.1186/gb-2009-10-5-r58. Epub 2009 May 29.

PMID:
19480664
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

KA-SB: from data integration to large scale reasoning.

Roldán-García Mdel M, Navas-Delgado I, Kerzazi A, Chniber O, Molina-Castro J, Aldana-Montes JF.

BMC Bioinformatics. 2009 Oct 1;10 Suppl 10:S5. doi: 10.1186/1471-2105-10-S10-S5.

PMID:
19796402
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

The cell cycle DB: a systems biology approach to cell cycle analysis.

Alfieri R, Merelli I, Mosca E, Milanesi L.

Nucleic Acids Res. 2008 Jan;36(Database issue):D641-5. Epub 2007 Dec 26.

PMID:
18160409
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

CelOWS: an ontology based framework for the provision of semantic web services related to biological models.

Matos EE, Campos F, Braga R, Palazzi D.

J Biomed Inform. 2010 Feb;43(1):125-36. doi: 10.1016/j.jbi.2009.08.008. Epub 2009 Aug 18.

PMID:
19695346
[PubMed - indexed for MEDLINE]
Free Article
5.

FYPO: the fission yeast phenotype ontology.

Harris MA, Lock A, Bähler J, Oliver SG, Wood V.

Bioinformatics. 2013 Jul 1;29(13):1671-8. doi: 10.1093/bioinformatics/btt266. Epub 2013 May 8.

PMID:
23658422
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
18460183
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The semantic metadatabase (SEMEDA): ontology based integration of federated molecular biological data sources.

Köhler J, Schulze-Kremer S.

In Silico Biol. 2002;2(3):219-31.

PMID:
12542408
[PubMed - indexed for MEDLINE]
8.

PhenoGO: an integrated resource for the multiscale mining of clinical and biological data.

Sam LT, Mendonça EA, Li J, Blake J, Friedman C, Lussier YA.

BMC Bioinformatics. 2009 Feb 5;10 Suppl 2:S8. doi: 10.1186/1471-2105-10-S2-S8.

PMID:
19208196
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

An ontology for collaborative construction and analysis of cellular pathways.

Demir E, Babur O, Dogrusoz U, Gursoy A, Ayaz A, Gulesir G, Nisanci G, Cetin-Atalay R.

Bioinformatics. 2004 Feb 12;20(3):349-56.

PMID:
14960461
[PubMed - indexed for MEDLINE]
Free Article
10.

The Gene Ontology in 2010: extensions and refinements.

Gene Ontology Consortium.

Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. Epub 2009 Nov 17.

PMID:
19920128
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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. Epub 2011 Apr 5.

PMID:
21471019
[PubMed - indexed for MEDLINE]
Free Article
12.

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.

PMID:
19796395
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM.

Nucleic Acids Res. 2002 Jan 1;30(1):69-72.

PMID:
11752257
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Data integration and visualization system for enabling conceptual biology.

Gopalacharyulu PV, Lindfors E, Bounsaythip C, Kivioja T, Yetukuri L, Hollmén J, Oresic M.

Bioinformatics. 2005 Jun;21 Suppl 1:i177-85.

PMID:
15961455
[PubMed - indexed for MEDLINE]
Free Article
15.

DynGO: a tool for visualizing and mining of Gene Ontology and its associations.

Liu H, Hu ZZ, Wu CH.

BMC Bioinformatics. 2005 Aug 9;6:201.

PMID:
16091147
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Building a bioinformatics ontology using OIL.

Stevens R, Goble C, Horrocks I, Bechhofer S.

IEEE Trans Inf Technol Biomed. 2002 Jun;6(2):135-41.

PMID:
12075668
[PubMed - indexed for MEDLINE]
17.

NeXO Web: the NeXO ontology database and visualization platform.

Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1269-74. doi: 10.1093/nar/gkt1192. Epub 2013 Nov 23.

PMID:
24271398
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D311-4.

PMID:
14681421
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Ontology annotation: mapping genomic regions to biological function.

Thomas PD, Mi H, Lewis S.

Curr Opin Chem Biol. 2007 Feb;11(1):4-11. Epub 2007 Jan 5. Review.

PMID:
17208035
[PubMed - indexed for MEDLINE]
20.

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results.

Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS.

Nucleic Acids Res. 2010 Jan;38(Database issue):D699-702. doi: 10.1093/nar/gkp1044. Epub 2009 Nov 24.

PMID:
19934261
[PubMed - indexed for MEDLINE]
Free PMC Article

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