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Dear pombe researchers,

We have now released the new version of the online curation tool Canto.

The upgraded Canto features an entirely new interface for annotating multi-allele phenotypes and the corresponding genotypes, as well as improved workflows for single-allele phenotypes, GO, etc.

Several of you have recently curated papers using the improved interface to help ensure that it is ready for general use. Many thanks for your contributions!

All of your existing annotations have been retained, and you can resume curation using the new and improved features any time. We will send more invitations to authors of recent publications, but you are also welcome to try curating any of your papers even if you don't receive an email about a specific paper. Please let us know if you have any suggestions for further improvements.

We'll also have a PomBase data update ready for you early next week.

Sincerely yours,
The PomBase Staff
Once you have found your paper, you can curate GO, phenotypes, interactions and protein modifications -- or reassign the paper to a colleague for curation. See the help pages for more information. First time curator? Visit ... Find out about community curation and the types of data that can be ...
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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 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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Replication profiling data has been made available from the Daigaku et al (2015) paper [http://www.ncbi.nlm.nih.gov/pubmed/25664722]

There are 7 tracks available to view from the genome browser [http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Share/63e23abda98aa37e3b52521c41e76eca74119895]. These can be enabled by via the "Configure this page" button in the left hand menu.
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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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People
Have them in circles
18 people
Michael Paulini's profile photo
He Gu (Grace)'s profile photo
Dan Staines's profile photo
esyN's profile photo
Kim Rutherford's profile photo
Mikel Zaratiegui's profile photo
Dom Helmlinger's profile photo
prof prem raj pushpakaran's profile photo
Hideki Tanizawa'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.