Citing PomBase

To cite S. pombe genome data and annotation, please use:

Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG.
PomBase: a comprehensive online resource for fission yeast.
Nucleic Acids Res. 2012 Jan;40(Database issue):D695-9. Epub 2011 Oct 28.

PMID:22039153 DOI: 10.1093/nar/gkr853

You may also wish to cite the most recent PomBase NAR Database Issue paper:

McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V.
PomBase 2015: updates to the fission yeast database.
Nucleic Acids Res. 2015 Jan;43(Database issue):D665-61. Epub 2014 Oct 31.

PMID:25361970 DOI:10.1093/nar/gku1040

Genome Sequence

To cite the S. pombe genome sequence, use:

Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, et al.
The genome sequence of Schizosaccharomyces pombe.
Nature. 2002 Feb 21;415(6874):871-80. Erratum in: Nature 2003 Jan 2;421(6918):94. Cerrutti L [corrected to Cerutti L].

PMID:11859360

Full text at Nature

GO Annotations

To cite the S. pombe Gene Ontology annotation data, use the 2012 NAR Database Issue paper noted above.

(Note that GO annotation for S. pombe has also been previously published, but we now recommend the 2012 NAR paper as it is more up-to-date. Aslett M, Wood V. Gene Ontology annotation status of the fission yeast genome: preliminary coverage approaches 100%. Yeast 2006 Oct 15;23(13):913-9. Erratum in Yeast 2007 May;24(5):457. PMID:17072883)

Phenotype Ontology and Annotations

To cite the Fission Yeast Phenotype Ontology (FYPO) and/or S. pombe FYPO annotation data, use:

Harris MA, Lock A, Bähler J, Oliver SG, Wood V.
FYPO: The Fission Yeast Phenotype Ontology.
Bioinformatics. 2013 Jul 1;29(13):1671-8. doi: 10.1093/bioinformatics/btt266. Epub 2013 May 8.

PMID:23658422

Full text at Bioinformatics: HTML or PDF

Canto

To cite the online curaton tool Canto, use:

Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V.
Canto: An online tool for community literature curation.
Bioinformatics. 2014 Jun 15;30(12):1791-2. Epub 2014 Feb 25.

PMID:24574118 DOI: 10.1093/bioinformatics/btu103

Manually Curated Orthologs

To cite the manually curated S. cerevisiae or human orthologs (displayed on gene pages or downloaded), use the NAR database paper as noted above. Note that the manually curated orthologs use several data sources including Compara, but are distinct from the Compara results themselves.

Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG.
PomBase: a comprehensive online resource for fission yeast.
Nucleic Acids Res. 2012 Jan;40(Database issue):D695-9. Epub 2011 Oct 28.

PMID:22039153

Full text at NAR

Genome Browser

To cite the S. pombe genome browser, use:

Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E.
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Nucleic Acids Res. 2012 Jan;40(Database issue):D91-7. Epub 2011 Nov 8.

PMID:22067447

Full text at NAR

Compara

Note that the manually curated S. cerevisiae and human orthologs (displayed on gene pages or downloadable) use several data sources in addition to Compara, and are therefore distinct from the Compara data. To cite the S. pombe Compara data, use:

Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E.
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Genome Res 2009 Feb;19(2):327-35. Epub 2008 Nov 24.

PMID:19029536

Full text at Genome Research