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Dear pombe researchers,

We have once again updated the data available on the PomBase web site. The data now includes manual curation through May 26, 2015. Community curation now covers over 270 papers.

This is the last release before the Pombe 2015 conference. We hope to receive more of your data submissions and community literature curation after the meeting.

As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
Home · Find · Simple Search · Advanced Search · Gene List Search · Genome Regions · GO Slim Annotations · Fission Yeast Phenotype Ontology · Tools · Genome Browser · BLAST · Gene List Search · Motif Search · Clone Resources · Submit · Submit Gene Names · Curate a Paper · HTP Sequence-linked Data ...
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PomBase

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Dear pombe researchers,

We have once again updated the data available on the PomBase web site. The data now includes manual curation through April 7, 2015. Community curation now covers over 260 papers.

We have also added a feature to the Advanced Search that allows you to query for proteins with a specified number of transmembrane domains. To use it, select "Transmembrane Domains" unter the "Protein Filters" 
heading.

As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
PomBase maintains two sets of manually curated orthologs: fission yeast (S. pombe) and budding yeast (S. cerevisiae), and fission yeast and human. Both can be queried in the simple search -- for budding yeast, use an ORF name (e.g. YBR160W); for human, use an HGNC-approved gene name (e.g. NCAPG) ...
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PomBase

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Dear pombe researchers,

We have once again updated the data available on the PomBase web site. The data now includes manual curation through February 2, 2015. Community curation now covers over 245 papers.

The most notable change on the gene pages is that the interaction tables now provides a bit of descriptive text for each annotation, indicating the nature and direction of the interaction.

We have also made a few other small fixes and improvements to the gene pages and static web pages. As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
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PomBase

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Dear pombe researchers,

We have once again updated the data available on the PomBase web site. The data now includes manual curation through January 12, 2015. Community curation now covers over 240 papers.

On the gene pages, the phenotype (FYPO) annotation display now defaults to a compact view. As in the GO tables, display of full details can be toggled on and off.

The "viability summary" data shown at the top of the FYPO table is now also available as a downloadable file -- see the "Phenotype annotations" link on the Download Datasets page.

The BLAST server reflects interface changes made throughout Ensembrl, and is now less confusing and illegible (hint: to see results in the usual format, click the "download results" button). This work is ongoing as of this email, so please be patient!

As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
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PomBase

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Dear pombe researchers,

We have once again updated the data available on the PomBase web site. The data now includes manual curation through August 8, 2014. Community curation now covers over 190 papers.

The External References section of the gene pages now includes links to the S. pombe PeptideAtlas (home page https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=355) database of peptides identified in tandem mass spectrometry proteomics experiments.

We have also made a few small fixes and improvements to the gene pages and static web pages. As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
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PomBase

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Dear pombe researchers,

We have once again updated the data available on the PomBase web site. The data now includes manual curation through August 8, 2014. Community curation now covers over 190 papers.

The External References section of the gene pages now includes links to the S. pombe PeptideAtlas (home page https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=355) database of peptides identified in tandem mass spectrometry proteomics experiments.

We have also made a few small fixes and improvements to the gene pages and static web pages. As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
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PomBase

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Dear pombe researchers,

We have once again updated the data available on the PomBase web site. The data now includes manual curation through June 6, 2014.

A downloadable file of intron sequence data (FASTA format) is now available:

ftp://ftp.ebi.ac.uk/pub/databases/pombase/FASTA/introns.fa.gz

This file will be linked to the Intron Data web page in the next day or two.

The gene pages now display protein modification data from two large-scale datasets:

Wilson-Grady JT, Villén J, Gygi SP. 2008 .Phosphoproteome analysis of fission yeast. J Proteome Res. 2008 Mar;7(3):1088-97. doi: 10.1021/pr7006335. PMID:18257517

Carpy A, Krug K, Graf S, Koch A, Popic S, Hauf S, Macek B. 2014. Absolute proteome and phosphoproteome dynamics during the cell cycle of fission yeast. Mol Cell Proteomics. 2014 Apr 23. [Epub ahead of print] PMID:24763107 (Note that there will be a few corrections to residue positions in the
  next data update.)

The Target Of section now reports phenotypes of other genes that affect the gene on the page.

In the previous update, some annotation extensions using Sequence Ontology (SO) terms went missing; these have been restored to the gene page display.

Thanks again to all who have done, or are doing, paper curation in Canto. Over 170 community-curated papers are now included in PomBase.

As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
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PomBase

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Dear pombe researchers,

We have once again updated the data available on the PomBase web site. The data now includes manual curation through May 8, 2015. Community curation now covers over 265 papers.

We expect to make one more release before the Pombe 2015 conference.

As usual, please don't hesitate to alert us of any other problems with
data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
PomBase maintains two sets of manually curated orthologs: fission yeast (S. pombe) and budding yeast (S. cerevisiae), and fission yeast and human. Both can be queried in the simple search -- for budding yeast, use an ORF name (e.g. YBR160W); for human, use an HGNC-approved gene name (e.g. NCAPG) ...
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PomBase

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We have updated the data available on the PomBase.org web site to include manual curation through March 7, 2015, including 250 community-curated publications. The autocomplete feature of the Advanced Search ontology term filter has been improved with respect to response time and relevance of suggested terms. [Picture provided by Silke Hauf]
Home · Find · Simple Search · Advanced Search · Gene List Search · Genome Regions · GO Slim Annotations · Fission Yeast Phenotype Ontology · Tools · Genome Browser · BLAST · Gene List Search · Motif Search · Clone Resources · Submit · Submit Gene Names · Curate a Paper · HTP Sequence-linked Data ...
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PomBase

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Dear pombe researchers,

We have updated the data available on the PomBase web site. The data now represents manual curation through October 27, 2014, including 225 community-curated publications.

The Phenotype section of the gene pages now includes data from the high-throughput microscopy analysis of viable deletion mutants reported in:

Graml V, Studera X, Lawson JL, Chessel A, Geymonat M, Bortfeld-Miller M, Walter T, Wagstaff L, Piddini E, Carazo-Salas RE. 2014. A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression. Dev Cell. 2014 Oct 27;31(2):227-39. http://europepmc.org/abstract/MED/25373780.

Links to the accompanying SYSGRO resource have also been added to the External References section of the gene pages.

In the genome browser, we have added tracks for intron branch point data from:

Bitton DA, Rallis C, Jeffares DC, Smith GC, Chen YY, Codlin S, Marguerat S, Bählre J. 2014. LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq. Genome Res. 2014 Jul;24(7):1169-79. http://europepmc.org/abstract/MED/24709818.

We have greatly improved search results for GO and FYPO annotations: both now follow more relationship types within the ontology to retrieve genes annotated to a term. The PomBase GO search now includes the "regulates" relationships, so its search results are consistent with those in the GO Consortium's AmiGO browser. For example, a search for "cytokinesis" will include genes annotated to "regulation of cytokinesis" in both AmiGO and PomBase.

The FYPO search now uses "has_part", "has_output", and "output_of" as well as "is_a" and "part_of". For example, FYPO includes the relation inviable swollen elongated cell with enlarged nucleus (FYPO:0002083) has_part swollen cell (FYPO:0000025). Genes annotated to FYPO:0002083 will therefore be retrieved in a search for FYPO:0000025.

You can find more information on ontology relations and annotation propagation in the PomBase GO documentation, advanced search documentation, and pages linked there.

We have also made a few other adjustments to the PomBase pages. Notably, the gene page Phenotype section now includes a highlighted sub-header that indicates whether a deletion mutant is viable or inviable (or if viability depends on conditions).

In the Downloads section, a file of protein complex subunits is now available, and other files have been updated.

As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
Understanding cells as integrated systems requires that we systematically decipher how single genes affect multiple biological processes and how processes are functionally linked. Here, we used multiprocess phenotypic profiling, combining high-resolution 3D confocal microscopy and multiparametric image analysis, to simultaneously survey the fission yeast genome with respect to three key cellular processes: cell shape, microtubule organization, an...
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PomBase

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We have updated the data available on the PomBase web site to include manual curation through July 8, 2014. The gene pages also now display protein modification data from an additional large-scale dataset:

Koch A, Krug K, Pengelley S, Macek B, Hauf S. 2011. Mitotic substrates of the kinase aurora with roles in chromatin regulation identified through quantitative phosphoproteomics of fission yeast. Sci Signal. 4(179): rs6 doi: 10.1126/scisignal.2001588 PMID:21712547

We have also made corrections to some residue positions affected by sequence updates in one of the modification datasets we added last month:

Carpy A, Krug K, Graf S, Koch A, Popic S, Hauf S, Macek B. 2014. Absolute proteome and phosphoproteome dynamics during the cell cycle of fission yeast. Mol Cell Proteomics. 2014 Apr 23. [Epub ahead of print] PMID:24763107
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PomBase

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Dear pombe researchers,

We have updated the data available on the PomBase web site. The data now includes manual curation through April 28, 2014. Transcriptome data from Margeurat et al. (2012) [http://europepmc.org/abstract/MED/23101633] is now available as Ensembl Browser tracks.

Thank you to all who have done, or are doing, paper curation in Canto. Over 159 community-curated papers are now included in PomBase.

There are a number of routes to accelerate your data into PomBase, (either through community curation, or by supplying HTP  sequence, modification or phenotype data in one of our specified formats), see http://www.pombase.org/submit-data for more details.

As usual, please don't hesitate to alert us of any other problems with data or site performance, or if you have any questions.

Sincerely yours,
The PomBase Staff
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Have them in circles
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Bob Carroll's profile photo
Hideki Tanizawa's profile photo
Dan Staines's profile photo
prof prem raj pushpakaran's profile photo
esyN Blog's profile photo
qian chen's profile photo
Alba Saucedo Fuentes's profile photo
Kim Rutherford's profile photo
Mark McDowall's profile photo
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The scientific resource for fission yeast
Introduction
PomBase is a comprehensive database for the fission yeast Schizosaccharomycespombe, providing structural and functional annotation, literature curation and access to large-scale data sets.