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Results: 1 to 20 of 82

1.

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

Malone J, Brown A, Lister AL, Ison J, Hull D, Parkinson H, Stevens R.

J Biomed Semantics. 2014 Jun 2;5:25. doi: 10.1186/2041-1480-5-25. eCollection 2014.

PMID:
25068035
[PubMed]
Free PMC Article
2.

The EBI RDF platform: linked open data for the life sciences.

Jupp S, Malone J, Bolleman J, Brandizi M, Davies M, Garcia L, Gaulton A, Gehant S, Laibe C, Redaschi N, Wimalaratne SM, Martin M, Le Novère N, Parkinson H, Birney E, Jenkinson AM.

Bioinformatics. 2014 May 1;30(9):1338-9. doi: 10.1093/bioinformatics/btt765. Epub 2014 Jan 11.

PMID:
24413672
[PubMed - in process]
Free PMC Article
3.

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations.

Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1001-6. doi: 10.1093/nar/gkt1229. Epub 2013 Dec 6.

PMID:
24316577
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D926-32. doi: 10.1093/nar/gkt1270. Epub 2013 Dec 4.

PMID:
24304889
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Updates to BioSamples database at European Bioinformatics Institute.

Faulconbridge A, Burdett T, Brandizi M, Gostev M, Pereira R, Vasant D, Sarkans U, Brazma A, Parkinson H.

Nucleic Acids Res. 2014 Jan;42(Database issue):D50-2. doi: 10.1093/nar/gkt1081. Epub 2013 Nov 21.

PMID:
24265224
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data.

Koscielny G, Yaikhom G, Iyer V, Meehan TF, Morgan H, Atienza-Herrero J, Blake A, Chen CK, Easty R, Di Fenza A, Fiegel T, Grifiths M, Horne A, Karp NA, Kurbatova N, Mason JC, Matthews P, Oakley DJ, Qazi A, Regnart J, Retha A, Santos LA, Sneddon DJ, Warren J, Westerberg H, Wilson RJ, Melvin DG, Smedley D, Brown SD, Flicek P, Skarnes WC, Mallon AM, Parkinson H.

Nucleic Acids Res. 2014 Jan;42(Database issue):D802-9. doi: 10.1093/nar/gkt977. Epub 2013 Nov 4.

PMID:
24194600
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

ArrayExpress update--trends in database growth and links to data analysis tools.

Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U.

Nucleic Acids Res. 2013 Jan;41(Database issue):D987-90. doi: 10.1093/nar/gks1174. Epub 2012 Nov 27.

PMID:
23193272
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.

Mallon AM, Iyer V, Melvin D, Morgan H, Parkinson H, Brown SD, Flicek P, Skarnes WC.

Mamm Genome. 2012 Oct;23(9-10):641-52. doi: 10.1007/s00335-012-9428-9. Epub 2012 Sep 19.

PMID:
22991088
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Toxicity of methyl tertiary-butyl ether (MTBE) following exposure of Wistar Rats for 13 weeks or one year via drinking water.

Bermudez E, Willson G, Parkinson H, Dodd D.

J Appl Toxicol. 2012 Sep;32(9):687-706. doi: 10.1002/jat.1674. Epub 2011 Mar 24.

PMID:
22833177
[PubMed - indexed for MEDLINE]
10.

MageComet--web application for harmonizing existing large-scale experiment descriptions.

Xue V, Burdett T, Lukk M, Taylor J, Brazma A, Parkinson H.

Bioinformatics. 2012 May 15;28(10):1402-3. doi: 10.1093/bioinformatics/bts148. Epub 2012 Apr 2.

PMID:
22474121
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information.

Adamusiak T, Parkinson H, Muilu J, Roos E, van der Velde KJ, Thorisson GA, Byrne M, Pang C, Gollapudi S, Ferretti V, Hillege H, Brookes AJ, Swertz MA.

Hum Mutat. 2012 May;33(5):867-73. doi: 10.1002/humu.22070. Epub 2012 Apr 4.

PMID:
22416047
[PubMed - indexed for MEDLINE]
12.

Two-year drinking water carcinogenicity study of methyl tertiary-butyl ether (MTBE) in Wistar rats.

Dodd D, Willson G, Parkinson H, Bermudez E.

J Appl Toxicol. 2013 Jul;33(7):593-606. doi: 10.1002/jat.1776. Epub 2011 Dec 7.

PMID:
22161475
[PubMed - indexed for MEDLINE]
13.

The BioSample Database (BioSD) at the European Bioinformatics Institute.

Gostev M, Faulconbridge A, Brandizi M, Fernandez-Banet J, Sarkans U, Brazma A, Parkinson H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D64-70. doi: 10.1093/nar/gkr937. Epub 2011 Nov 16.

PMID:
22096232
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

Kapushesky M, Adamusiak T, Burdett T, Culhane A, Farne A, Filippov A, Holloway E, Klebanov A, Kryvych N, Kurbatova N, Kurnosov P, Malone J, Melnichuk O, Petryszak R, Pultsin N, Rustici G, Tikhonov A, Travillian RS, Williams E, Zorin A, Parkinson H, Brazma A.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1077-81. doi: 10.1093/nar/gkr913. Epub 2011 Nov 7.

PMID:
22064864
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Anatomy ontologies and potential users: bridging the gap.

Travillian RS, Adamusiak T, Burdett T, Gruenberger M, Hancock J, Mallon AM, Malone J, Schofield P, Parkinson H.

J Biomed Semantics. 2011 Aug 9;2 Suppl 4:S3. doi: 10.1186/2041-1480-2-S4-S3. Epub 2011 Aug 9.

PMID:
21995944
[PubMed]
Free PMC Article
16.

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA.

BMC Bioinformatics. 2011 May 29;12:218. doi: 10.1186/1471-2105-12-218.

PMID:
21619703
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Data standards for Omics data: the basis of data sharing and reuse.

Chervitz SA, Deutsch EW, Field D, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Stoeckert CJ Jr, Taylor CF, Taylor R, Ball CA.

Methods Mol Biol. 2011;719:31-69. doi: 10.1007/978-1-61779-027-0_2. Review.

PMID:
21370078
[PubMed - indexed for MEDLINE]
18.

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL.

Stand Genomic Sci. 2010 Dec 25;3(3):259-66. doi: 10.4056/sigs.147362.

PMID:
21304730
[PubMed]
Free PMC Article
19.

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.

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

PMID:
21210979
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Contributions of the EMERALD project to assessing and improving microarray data quality.

Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M.

Biotechniques. 2011 Jan;50(1):27-31. doi: 10.2144/000113591.

PMID:
21231919
[PubMed - indexed for MEDLINE]
Free Article

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