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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 May 12, 2016.

Because Mark McDowall sadly left PomBase yesterday, there will be a longer than usual wait for the next update. Many thanks to Mark for getting this update finished in his last few days with us, and thanks to you for your patience until next time.

As usual, please don't hesitate to alert us of any other problems with the new search features, the 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 updated the data available on the PomBase web site. The data now includes manual curation through January 25, 2016.

The genome browser now includes variation data from natural S. pombe isolates, published in:

Jeffares DC et al. 2015. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet. 47(3): 235-241. doi:10.1038/ng.3215 PMID:25665008

To view the variation data, enable one or more of the tracks under "Variation". Help is available for enabling tracks (http://www.pombase.org/faqs/how-can-i-show-or-hide-tracks-genome-browser) and for the variation data (http://www.pombase.org/faqs/can-i-view-variation-data-pombase).

We have added graphical views of quantitative gene expression data, which show the expression level of a gene in the context of all genes (violin plots).

Some new files are now available from the PomBase FTP site, and are linked from pages in the Download Datasets area:

- Non-coding RNA sequence feature coordinates (available via the Data Mappings page);
- Protein features, such as domains and family assignments (available via the Protein Datasets page);
- Protein modification annotations (also in Protein Datasets).

Several genes have been merged or deleted, as summarised on the New and Removed Genes page (http://www.pombase.org/status/new-and-removed-genes ; scroll to the bottom of each table to see the most recent entries).

Note: Ontology graph views are no longer available in the genome browser, so links have been removed from the GO, FYPO, and modification tables on the gene pages. For GO and FYPO, links to external ontology browsers that offer graphical views are available on the Ontology Term pages (see http://www.pombase.org/documentation/ontology-term-page).

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

Sincerely yours,
The PomBase StaffDear pombe researchers,
In the Ensembl genome browser, click the "Configure this page" button in the left-hand bar. A pop-up box will appear. Note that this box has several tabs along its top, and the exact selection of tabs and configuration options depends on whether you are configuring the "Location", "Gene", ...
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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 September 6, 2015. Community curation now covers over 305 papers.

NOTE: As part of this update, we have corrected errors in the viability summary file (FYPOviability.tsv; see http://www.pombase.org/downloads/phenotype-annotations) that resulted from 
incorrect handling of the new multi-allele phenotype data. If you downloaded the FYPOviability.tsv file that accompanied the previous PomBase update (announced Sept. 8th), please replace it with the updated file at once.

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
Full phenotype annotations. Phenotype annotations (link downloads gzipped file from PomBase ftp) for alleles of S. pombe genes are manually curated from the literature using Fission Yeast Phenotype Ontology (FYPO) terms. Note: this file contains annotations for single allele phenotypes (single ...
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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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We have now updated the PomBase website. The data now includes manual curations through April 12, 2016.
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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 March 9, 2016.

IMPORTANT: We have corrected a problem that made erroneous interaction data and literature appear on some gene pages. Please check the pages for your favourite genes to ensure that all is well.

The gene pages now include interaction data from the Vo et al. proteome-wide study (curated by BioGRID and imported into PomBase):

http://europepmc.org/abstract/med/26771498

The genome browser now includes transcriptome data published in Eser et al (2016):

http://europepmc.org/abstract/med/26883383

There is an outstanding issue with the Variant Effect Predictor (VEP) that we expect to be resolved early next week.

We've also made a few other small improvements to displays and search behavior. As usual, please don't hesitate to alert us of any other problems with the new search features, the 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 updated the data available on the PomBase web site. The data now includes manual curation through November 9, 2015. Community curation now covers over 340 papers.

We have introduced a few new features to the Advanced Search:
- There are now two query reuse options: you can store a query in your web browser cache, or download a JSON file that can be uploaded later to re-run.
- You can now query for genes that interact genetically or physically with a specified gene.
- The FYPO query now offers some allele options: you can choose nulls (deletions or disruptions), wild-type overexpression, or all alleles. The search results will include any genes that have an allele that matches the allele criteria and the chosen phenotype.

As usual, please don't hesitate to alert us of any other problems with the new search features, the 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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This Primer introduces S. pombe by describing the yeast itself, providing a brief description of the origins of fission yeast research, and illustrating some genetic and bioinformatics tools used to study protein function in fission yeast.
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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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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.
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