News

Thursday, 20th Oct, 2016

We have updated the data available on the PomBase web site to include manual curation through September 11, 2016.

Tuesday, 28th Jun, 2016

In response to planned cuts to database funding, leading model organism researchers have prepared an open letter to NIH Director Dr. Francis Collins to demonstrate support for the independent community-focused databases that are essential to their work. Although PomBase is not directly funded by NIH, we collaborate extensively with those that are, including the GO Consortium and several model organism databases.

The Genetics Society of America website where the letter can be viewed and signed is at http://www.genetics-gsa.org/MODsupport

Please sign the letter to add your voice in support of the databases that help make your research possible. For more information, we recommend an email that Mike Cherry sent to the GO-Friends mailing list, archived at https://mailman.stanford.edu/pipermail/go-friends/2016-June/002355.html

Thursday, 16th Jun, 2016

Several of the PomBase staff, joined by our advisor Sir Paul Nurse, have published a Comment in BMC Biology briefly describing the importance of model organism databases to the success of modern biomedical research:

Oliver SG, Lock A, Harris MA, Nurse P, Wood V. 2016. Model organism databases: essential resources that need the support of both funders and users.
BMC Biol. 2016 14(1): 49. doi: 10.1186/s12915-016-0276-z. PMID:27334346

Wednesday, 1st Jun, 2016

We have updated the data available on the PomBase web site to include manual curation through May 12, 2016.

Tuesday, 10th May, 2016

We have updated the data available on the PomBase web site to include manual curation through April 8, 2016.

Tuesday, 12th Apr, 2016

We have updated the data available on the PomBase web site to include manual curation through March 9, 2016.

Important: We have corrected a problem that made erroneous interaction data and literature appear on some gene pages.

The gene pages now include interaction data from the Vo et al. proteome-wide study (curated by BioGRID and imported into PomBase):
Vo TV et al. 2016. A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human. Cell 164(1-2): 310-23. doi: 10.1016/j.cell.2015.11.037 PMID:26771498.

The genome browser now includes transcriptome data published in:

Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S, Cramer P, Gagneur J. 2016. Determinants of RNA metabolism in the Schizosaccharomyces pombe genome. Mol Syst Biol. 12(2): 857. doi: 10.15252/msb.20156526 PMID:26883383.

Friday, 12th Feb, 2016

We have updated the data available on the PomBase web site to include manual curation through January 25, 2016.
The genome browser includes variation data, in tracks under "Variation", 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

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).

The New and Removed Genes page has been updated to reflect recent deletions and merges.

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.

Thursday, 3rd Dec, 2015

We have updated the data available on the PomBase web site to include manual curation through November 9, 2015, including 340 community-curated publications.

Thursday, 3rd Dec, 2015

We have introduced new features to the Advanced Search:

  • There are now two query reuse options: 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 options to 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.
Tuesday, 20th Oct, 2015

A new genetics primer, aimed at researchers interested in using fission yeast as a model system, has recently been published. The primer includes a brief history of fission yeast research, an introduction to available genetic tools, and the use of PomBase for data analysis

Hoffman CS, Wood V, Fantes PA. (2015) An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System. Genetics 201:403-423. PMID:26447128 DOI:10.1534/genetics.115.181503

Tuesday, 29th Sep, 2015

We have updated the data available on the PomBase web site to include manual curation through September 6, 2015.

Errors in the previous FYPOviability.tsv file have been corrected, and we recommend that all users update this file, especially those who downloaded it earlier in September 2015.

Friday, 4th Sep, 2015

We have updated the data available on the PomBase web site to include manual curation through August 13, 2015, including 300 community-curated publications.

PomBase gene pages now include multi-allele phenotype annotations (i.e. phenotypes of double mutants, triple mutants, etc.). New sub-sections of the gene pages display multi-allele phenotypes at the population and individual cell level, paralleling the organisation of the single allele phenotype display. Compact and full views are available; both show phenotypes with the relevant genotypes and the alleles that make them up, and the full view adds details for evidence, expression, conditions, and references.

The genome browser now includes data tracks for two more publications:

DNA polymerase usage from:
Daigaku Y, Keszthelyi A, Müller CA, Miyabe I, Brooks T, Retkute R, Hubank M, Nieduszynski CA, Carr AM. 2015. A global profile of replicative polymerase usage. Nat Struct Mol Biol. 2015 Mar;22(3):192-8. doi: 10.1038/nsmb.2962 PMID:25664722

Promoters and transcription start sites from:
Li H, Hou J, Bai L, Hu C, Tong P, Kang Y, Zhao X, Shao Z. 2015. Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE. RNA Biol. 2015;12(5):525-37. doi: 10.1080/15476286.2015.1022704 PMID:25747261

Codon adaptation index (CAI) values are now included in the Protein Properties section of the gene pages and in the downloadable PeptideStats.tsv file. A file of amino acid composition data is also available from the FTP site and the Protein Datasets page.

The gene page section that was formerly misnamed "species distribution" is now called "taxonomic conservation".

Wednesday, 17th Jun, 2015

We have updated the data available on the PomBase web site to include manual curation through May 26, 2015, including 270 community-curated publications. See you at Pombe 2015 in Kobe!

Wednesday, 27th May, 2015

We have updated the data available on the PomBase web site to include manual curation through May 8, 2015, including 265 community-curated publications.

Wednesday, 27th May, 2015

Canto, PomBase's literature curation tool, will be unavailable for approximately 3 weeks starting at 12:00 midnight UK time (BST) tonight, 27 May 2015, while we deploy an upgraded version.

The upgraded Canto will feature an entirely new interface for annotating multi-allele phenotypes and the corresponding genotypes, as well as improved workflows for single-allele phenotypes, GO, etc. All existing annotations will be retained, and users can resume curation using the new and improved features in any unfinished sessions when Canto is back online.

We will announce when the new version of Canto is released to the public.

Friday, 24th Apr, 2015

Applications are now being accepted for fellowships to provide financial support for students and postdocs attending the 8th International Fission Yeast Meeting in Kobe, Japan. To apply, follow the instructions sent to the pombase mailing list. The deadline is may 17, 2015 (same as the registration deadline).

Monday, 20th Apr, 2015

We have updated the data available on the PomBase web site to include manual curation through April 7, 2015, including 260 community-curated publications.The Advanced Search now supports queries for proteins with a specified number of transmembrane domains.

Monday, 20th Apr, 2015

The abstract submission deadline for the 8th International Fission Yeast Meeting in Kobe, Japan has been extended until midnight Friday, April 24 for posters only. Registration is open until May 17.

Friday, 10th Apr, 2015

Abstracts are due on Sunday, April 19, 2015 for the 8th International Fission Yeast Meeting in Kobe, Japan. Registration will remain open until May 17, but the abstract submission deadline cannot be extended.

Tuesday, 24th Mar, 2015

We have updated the data available on the PomBase web site to include manual curation through March7, 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.

Friday, 27th Feb, 2015

Registration for Pombe 2015: 8th International Fission Yeast Meeting is now open at the conference web site, https://amarys-jtb.jp/web/Pombe2015/index.html

The registration deadline is 17 May 2015.

Thanks to Yasushi Hiraoka for this item.

Tuesday, 17th Feb, 2015

We have updated the data available on the PomBase web site to include manual curation through February 2, 2015, including 245 community-curated publications. On the gene pages, the interaction tables now provides a bit of descriptive text for each annotation, indicating the nature and direction of the interaction.

Tuesday, 27th Jan, 2015

We have updated the data available on the PomBase web site to include manual curation through January 12, 2015, including 240 community-curated publications. The gene page Phenotype section now features a compact default display. A downloadable "viability summary" data file is now available. The PomBase BLAST server has incorporated interface changes made Ensembl-wide.

Thursday, 11th Dec, 2014

PomBase has implemented network visualisations for fission yeast in esyN, using data curated by BioGRID and PomBase. esyN is a web-based tool for building, sharing, and viewing network data developed by Dan Bean and Giorgio Favrin in the Cambridge Systems Biology Centre, University of Cambridge, UK.

On gene pages, we have links to gene-specific interaction networks in esyN in the table headers of the Interactions sections:

  • The Genetic Interactions section links to all interactions centred on the gene and curated in BioGRID
  • The Physical interactions section has links to two datasets:

We also have esyN links on the GO Slim page and on ontology term pages for GO Slim biological process terms. Each GO Slim term links to the HCPIN physical interaction network in esyN (for example, see the "regulation of mitotic cell cycle" network).

Thursday, 11th Dec, 2014

To make the Gene Ontology (GO) annotations easier to read on PomBase gene pages, we have introduced a new, streamlined display that presents just the essentials. The summary shows the term name (hyperlinked to the ontology term page), the count of genes annotated to the term, and any annotation extensions. All of the previously visible annotation details are still available -- simply click the "Summary" button to switch to the "Full" view. Or click the "+" and "-" icons to expand or collapse the annotation to a single term.
 
In addition, the top of the Biological Process table now lists any GO slim terms applicable to the gene.

Thursday, 13th Nov, 2014

We have updated the data available on the PomBase web site to include manual curation through October 27, 2014, including 225 community-curated publications. The gene page Phenotype section 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. 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. doi: 10.1016/j.devcel.2014.09.005 PMID:25373780. Links to the accompanying SYSGRO resource have been added to the External References section of the gene pages.

The genome browser now includes tracks for intron branch point data from:

Bitton DA, Rallis C, Jeffares DC, Smith GC, Chen YY, Codlin S, Marguerat  S, Bähler J. LaSSO, a strategy for genome-wide mapping of intronic  lariats and branch points using RNA-seq. Genome Res. 2014 Jul;24(7):1169-79. doi: 10.1101/gr.166819.113 PMID: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. The FYPO search now uses has_part, has_output, and output_of as well as is_a and part_of. The Phenotype section now includes a highlighted sub-header that indicates whether a deletion mutant is viable or inviable. A file of protein complex subunits is available for download, and numerous smaller improvements have been made in the gene pages and static pages.

Wednesday, 17th Sep, 2014

We have updated the data available on the PomBase web site to include manual curation through August 30, 2014. Community curation now covers over 200 papers.

Tuesday, 19th Aug, 2014

We have updated the data available on the PomBase web site to include manual curation through August 8, 2014. Community curation now covers over 190 papers. Gene pages now include links to the S. pombe PeptideAtlas, a database of peptides identified in tandem mass spectrometry proteomics experiments.

Friday, 18th Jul, 2014

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

Wednesday, 9th Jul, 2014

We have updated the data available on the PomBase web site. The data now includes manual curation through June 6, 2014. In other improvements, a downloadable file of intron sequence data (FASTA format) is now available, and phenotypes are now included in the Target Of section on gene pages.

The gene pages also 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
Monday, 30th Jun, 2014

PomBase was an early adopter of annotation extensions, which add spatial, temporal, or substrate/target details to GO annotations. The GO Consortium has now published a paper describing its implementation of annotation extensions, in which PomBase examples and its gene page display figure prominently:

Huntley, R.P. et al. (2014) A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics 2014, 15:155. doi:10.1186/1471-2105-15-155 PMID:24885854

Friday, 16th May, 2014

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) 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

Friday, 21st Mar, 2014

Data on the PomBase web site now includes manual curation through February 24, 2014. Human orthologs that went missing from gene pages have been restored, and other small improvements have been made to gene pages. Community curation now covers over 130 publications.

Friday, 21st Feb, 2014

We have once again updated the data available on the PomBase web site. The data now includes manual curation through January 10, 2014, and covers over 100 papers that have been curated in Canto by community members. We again thank all who have contributed curation via Canto.

We have made some improvements to the gene pages. Highlights:

  • The Sequence section now has links to NCBI BLAST as well as Ensembl BLAST.
  • The External References section now links to the Pomb(A) polyadenylation viewer.

In the genome browser, new data tracks are now available for data from these publications:

  • Rhind N, [and many more]. 2011. Comparative functional genomics of the fission yeasts. Science 332(6032):930-6. doi: 10.1126/science.1203357. PMID:21511999
  • Schlackow M, Marguerat S, Proudfoot NJ, Bähler J, Erban R, Gullerova M. 2013. Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe. RNA. 19(12):1617-31. doi:10.1261/rna.040675.113. PMID:24152550
  • Soriano I, Quintales L, Antequera F. 2013. Clustered regulatory elements at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe. BMC Genomics. 14:813. doi:10.1186/1471-2164-14-813. PMID:24256300 (partial data;  remainder coming in the next update)
  • Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N. 2012. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol. 13(4):R27. doi:10.1186/gb-2012-13-4-r27. PMID:22531001

Now that more data tracks are available, we have added some categories to the track configuration section to improve organization. Additional documentation is in preparation, and will be announced here when available.

Genome sequences for additional Schizosaccharomyces species (S. japonicus, S. octosporus, and S. cryophilus) have recently become available in Ensembl Fungi, and the PomBase genome browser now includes comparative genomics data, with a view of region comparisons between each new genome and S. pombe.

Thursday, 20th Feb, 2014

We are about to release a data update for PomBase. Please note that there is still a problem with the human orthologs, as originally described on this list in mid-December (see archived message at http://listserver.ebi.ac.uk/pipermail/pombelist/2013/003926.html). We will correct this problem in the next PomBase release, and apologise for any inconvenience in the meantime.

Monday, 9th Dec, 2013

We have updated the data available on the PomBase web site to include manual curation through November 11, 2013. We now have future meetings available as a calendar or a list. The FAQ and some documentation pages have also been updated.

Monday, 25th Nov, 2013

A series of mini-reviews, which were invited in association with the International Fission Yeast Meeting in London, have now been published in Biochemical Society Transactions: http://www.biochemsoctrans.org/bst/041/6/default.htm#c

(Thanks to Jürg Bahler for this item)

Thursday, 21st Nov, 2013

The 2013 PomBase user survey closed at the end of October, and the results are available here. Some highlights have been sent to the pombe mailing list. Many thanks to all who completed the survey.

Monday, 28th Oct, 2013

With the October 2013 update, gene pages now include "Target Of" annotations, which describe genes that affect the gene of interest. These annotations are essentially the reciprocal of ontology annotation extensions. Each "Target Of" annotation includes a relationship that indicates how the genes are connected, the name and product of the second gene, and a reference. Genes listed under "Target Of" may include upstream regulators or enzymes that modify the product of the gene of interest. For example, the "Target Of" annotations for cdc2 indicate that it is a substrate of, and regulated by, the kinase Wee1 and the phosphatase Cdc25 (among others). At present, "Target Of" data includes annotations derived from GO annotation extensions. We will soon extend it to include data from phenotype annotation extensions.

Tuesday, 22nd Oct, 2013

The PomBase web site has been updated and now includes manually curated data through October 6, 2013. The number of community-curated papers continues to increase, ensuring that PomBase gene pages contain complete and up-to-date information. We are also pleased to announce that data tracks are now available in the genome browser for data from these two publications:

  • Woolcock KJ, Gaidatzis D, Punga T, Bühler M. 2010. Dicer associates with chromatin to repress genome activity in Schizosaccharomyces pombe. Nat Struct Mol Biol. 2011 Jan;18(1):94-9. doi: 10.1038/nsmb.1935 PMID:21151114
  • Mata J. 2013. Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation. RNA Biol. 2013 Aug 1;10(8):1407-14. doi: 10.4161/rna.25758 PMID:23900342
Thursday, 19th Sep, 2013

To guide current and future development, PomBase is now conducting a user survey, where we invite the fission yeast research community and any other PomBase users to evaluate the resources provided so far and comment on future priorities. The survey should take about 10 minutes to complete. Thank you for your participation!

https://www.surveymonkey.com/s/NDM2BQX

Monday, 16th Sep, 2013

We have once again updated the data available on the PomBase web site. The data now includes manual curation through August 11, 2013. We are particularly pleased to note that this update includes annotations from several dozen papers curated by the S. pombe community. Many thanks to all who have done, or are doing, paper curation in Canto.

We also have an updated version of the S. pombe/human ortholog table available upon request.

Monday, 19th Aug, 2013

At the pombe 2013 meeting in London, PomBase staff received numerous requests display various published data, such as gene expression, histone modifications, etc. in the genome browser. To provide this, we now invite pombe researchers to send data: If you have published any high-throughput experiments that produced data  that can be associated with genome sequence coordinates, and thereby displayed as tracks on the PomBase genome browser, please fill out the HTP Data Submission Form. We can also accept large sets of phenotype data via the Phenotype Data Submission Form. If you have any problems or questions, contact us via the PomBase Helpdesk at any time.

Tuesday, 30th Jul, 2013

To complement the mailing list and twitter (@PomBase) it is now possible to follow the activities of PomBase and interact with other members of the pombe community via the new LinkedIn Group and Google+.

Links to these are also available from the front page of the PomBase.org site.

Monday, 22nd Jul, 2013

The pombe community mailing list, pombelist, has migrated from the Wellcome Trust Sanger Institute and is now hosted by EBI. The new address is pombelist@ebi.ac.uk (please note that the old address no longer works, and will generate an automatic notification including the new address). The link to subscribe has also been updated, and the entire archive is available at the new location.

Friday, 19th Jul, 2013

We'd like to highlight a few improvements we've just made to the PomBase website. Most of the changes affect the gene pages:

  • The basic information display at the top of each gene page is more compact.
  • For ontology annotations, the number of genes annotated is now shown, in a column labeled "Count" (also, changes behind the scenes involving this data mean that pages should load faster).
  • Annotation extensions for GO are displayed using human-friendly text instead of internal "relation" labels.
  • The Quick Links box can now be collapsed and expanded by clicking its header.
  • Display of modification annotations using PSI-MOD is improved.

In addition, the Motif Search output now includes standard gene names and product descriptions. As we noted in a separate message, CDS coordinate files are once again available from the Downloads, with accurate and up-to-date data.

Monday, 24th Jun, 2013

At the pombe 2013 conference in London, PomBase officially launched its community curation initiative, which allows researchers to contribute publication-based annotations directly to the database. PomBase curators invite lab heads by individual email to curate newly published papers, providing links to the online curation system and its documentation. Researchers can also initiate curation of any older fission yeast publication in PubMed. Community curation uses the open-source online tool Canto.

Friday, 21st Jun, 2013

PomBase data now includes manual curation through June 9, 2013, and represents complete annotation for 664 publications (as well as partial curation of many more). A highlight of this month's literature curation update is the addition of over 9400 phenotype annotations, representing about 95% of the phenotype data from the recently published genome-wide study of cell cycle and cell morphology (Hayles et al. Open Biology May 2013; PMID:23697806). We have also improved the display of allele details for phenotype annotations. Other changes include better support for gene synonyms in the simple search, regular updates to the UTR data files, and a number of minor adjustments to external links in the annotation data tables and the external references section.

Tuesday, 21st May, 2013

We have updated the data available on the PomBase web site. The data now includes manual curation through 13 May, 2013.

Tuesday, 14th May, 2013

As of 14 May 2013, the old GeneDB database for S. pombe is no longer available. This resource consisted of static web pages, was not updated after March 2012, and not supported by an underlying relational database. The PomBase site fully supersedes GeneDB S. pombe, and provides improved infrastructure that will meet the current and future needs of the fission yeast community. Please e-mail the helpdesk if you cannot find a replacement for any GeneDB functionality in PomBase.

Wednesday, 8th May, 2013

We have extended the Gene Expression section of each gene page to support the display of quantitative expression data, and are now showing data from two publications:

  • Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, BählerJ. 2012. "Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells." Cell 151:671-683.
  • Wu JQ, Pollard TD. 2005. "Counting cytokinesis proteins globally and locally in fission yeast." Science 310:310-314.

We will also soon refine the display of the new expression data, and can add more datasets upon request. We thank Sam Marguerat for preparing the data from both papers for inclusion in PomBase.

We have also updated the PomBase site to include manual curation through April 4, 2013, and we have updated the "all gene names" file on the PomBase ftp site. The new file is available at
ftp://ftp.ebi.ac.uk/pub/databases/pombase/pombe/Mappings/allNames.tsv

Friday, 12th Apr, 2013

Carl Singer, who was an integral part of the yeast research community for many years, passed away on February 8, 2013. Throughout his career, Carl supported yeast research both with his engineering expertise and with his good cheer. In tribute to Carl, the Singer family has now set up The Carl Singer Foundation, a charitable foundation dedicated to supporting scientific education in the field of yeast genetics. Questions about the foundation may be directed to Harry Singer at harry [at] thecarlsingerfoundation.org.

Carl’s family would be happy to receive memories of Carl’s life at regards [at] singerinstruments.com.

H/T SGD

Wednesday, 3rd Apr, 2013
Dear Pombe Fans,

Please remember the imminent deadline (Monday 8th April) to register and submit abstracts for Pombe 2013: http://events.embo.org/13-pombe

Abstracts are also required from all who have already been invited to talk.
And do book your accommodation if you haven't yet done so.

More details are in previous email forwarded below.

Cheers,
-Jürg & Jacky


From: On Behalf Of Bahler, Jurg
Sent: 18 March 2013 17:49
To: pombelist at sanger.ac.uk
Subject: [Pombelist] Pombe 2013: Accommodation, registration & abstracts

Dear Pombe Afficionados,

Only three weeks left to register and submit abstracts for Pombe 2013, by Monday 8th April: http://events.embo.org/13-pombe
Speakers for 10 plenary talks and all workshop talks will be selected from abstracts, and there will be attractive poster prizes.
Payment is only requested after registration, by 10th May.

Important: if you require accommodation, please do book this real soon now. Especially the most cost-effective student accommodation (comfortable, with private bathrooms) may not be available much longer, as it will be put on general sale shortly. Both hotels and student accommodation will sell out in June, so you have to arrange it now. Information on accommodation is available here: http://events.embo.org/13-pombe/application.html

We will provide a number of free registrations for which you can apply during online registration (a few of which are reserved for student members of The Genetics Society: you become eligible if you join them now). The meeting is also supported by the Biochemical Society, so if you are, or become, a member you can apply to them for student bursaries or, if you have been a member for at least 1 year, also for travel grants.

We highly appreciate all the generous contributions from our sponsors so far:
Platinum: EMBO
Gold: Biochemical Society, Genetics Society, Formedium, Sunrise Science Products, Singer Instruments, F1000Research, PomBase/Wellcome Trust
Silver: MDPI - Open Access Publishing, Hybrigenics, Infors, Life Technologies, Bioneer
Bronze: Nature Communications, m2p labs, Imsol, Open Biology

We look very much forward to welcoming you in London this June!

All the best,
-Jürg & Jacky
Tuesday, 2nd Apr, 2013

We have once again updated the data available on the PomBase web site. The data now includes manual curation through March 6, 2013.

We now expect to be able to update PomBase data every month, and will soon have an automated pipeline in place. We thank all of you for your patience during the long months when updates were infrequent.

You should also see a few small improvements in the site:

  • Ontology term pages now display the text definition for each term.
  • FASTA sequence retrieval should be quicker, and less likely to time out, for large gene lists.
  • There has been some tidying of the display of "extension" data for GO and phenotype annotations.

Last month we noted an intermittent problem with the "Reference" column display in the data tables. The occurrence of this problem should now be greatly reduced, so please let us know if you see it recurring.

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

Saturday, 2nd Mar, 2013

We have updated the data available on the PomBase web site. The data now includes manual curation through December 17, 2012, and reflects complete curation of an additional 70 papers.

We have also made some improvements "under the hood" that should make gene page loading much faster. Please let us know if you have any problems with gene pages loading slowly or incompletely, whether or not you have reported issues in the past.

We are aware that there is an intermittent problem with the "Reference" column display in the data tables -- sometimes a PubMed ID appears instead of an author name and year. This problem will be fixed as soon as possible. Please alert us if you notice anything else odd or wrong.

Wednesday, 7th Nov, 2012

We are pleased to announce that we have updated both data and web site features for PomBase.

Most importantly, we have added new data types, and upgraded the gene pages to display them.

We have also added more annotations of existing data types, bringing the web site content up to September 11, 2012. The new annotations include the first contributions to come in via the new community curation system, and we thank the researchers who are participating in the initial phase of community curation.

New annotation types:

  • Phenotype annotations now use the Fission Yeast Phenotype Ontology (FYPO), and include allele details, expression levels, and experimental conditions. With FYPO, more detailed phenotypes can be described, and links between terms for related phenotypes support improved phenotype searches.
  • Many GO annotations now include "annotation extensions" that provide additional specificity. For example, extensions may capture the substrate of a catalytic activity, the cell cycle phase during which a function or process occurs, or any of several other types of supporting information for the annotation. Annotation extensions are described in more detail below.

You can see these new data types on many gene pages, such as cdc2 or pka1.

New web site features:

  • Annotation display - Gene page GO and phenotype displays have been revamped to show new annotation types described above.
  • Ontology term pages - Each ontology term ID now links to pages with information about the term and lists of genes annotated to it.
  • Ontology graph links - GO and phenotype annotation sections now include links to graphical ontology displays in the genome browser.
  • Sequence highlighting - Sequence download now offers an option to show colour highlighting of regions such as UTRs, introns and exons.
  • Versions - Each gene page now shows the current data version in the format PomBase:x.y, where x is the Ensembl Genomes (EG) version, and y is the Chado version. The sequence, and sequence feature locations, remain stable within any EG version, whereas annotations change with each Chado update.
  • Protein family information is now included in the Protein Features gene page section.
  • The Protein Feature section includes a link to the Pfam entry for a protein.
  • Transcript source data (e.g. for UTR coordinates) is now displayed in the Transcript Features section.
  • A Documentation page contains links to relevant portions of the Ensembl Genomes documentation. (More documentation will be added over the coming months.)

What are annotation extensions?

Annotation extensions are a form of supporting data that can be added GO annotations (or other ontology annotations) to capture additional details not provided by the ontology term itself.

The information in GO annotation extensions encompasses several effector-target relationships, such as

  • localisation dependencies
  • substrates of functions, e.g. targets of a protein kinase -- see the has_substrate extensions on Cdc2's "protein serine/threonine kinase" (GO:0004674) annotations
  • activators and inhibitors
  • regulation targets of signalling pathways or transcription factors

Additional extensions describe spatial and temporal aspects of processes. For example, several S. pombe annotations now include extensions that indicate in which phase of the cell cycle a gene product is found in a cellular component or involved in a process -- see the pka1 annotations to "nucleus" (GO:0005634) and "cytoplasm" (GO:0005737).

You may also find the GO wiki page on annotation extensions informative, although it is primarily aimed at curators.

Annotation extensions can also be used with phenotype annotations. The most common usage of phenotype annotation extensions is to capture which gene, protein, etc. was used in an assay. For example, the sam5 (G441E) mutation of pka1 causes nuclear accumulation of Ste11. This is represented by annotation to the ontology term "nuclear protein accumulation" (FYPO:0000255), with the extension "assayed_using(PomBase:SPBC32C12.02)". Extensions can also indicate expressivity or penetrance for a phenotype.


Monday, 2nd Jul, 2012

We are pleased to announce that the PomBase web site, www.pombase.org, is now fully live; the preview phase has ended. The site has been updated with an assortment of new features, datatypes, and bug fixes.

More recent data, reflecting additions and changes through March 20, 2012, are now available on gene pages and in search results.

The updated site features a Gene List Search that provides behavior equivalent to GeneDB's List Download. You can now type or paste lists into the Gene Systematic IDs and Gene Names filters, and use the Query History to combine a gene list search with other search options. For convenience, there is a direct link to a search page pre-configured to accept a list of systematic IDs available in the Find menu, on the Find page, and here: http://www.pombase.org/spombe/query/builder?filter=12

The Advanced Search also now offers:

  • options to search GO, FYPO, and other ontologies by term name or ID;
  • autocomplete for ontology term name search;
  • ability to search for genes in a region, such as centromeres or telomeres;
  • improved organization of filter selections.

We have also fixed a Sequence Download error reported by some users, so that the "CDS", CDS + UTRs", and "CDS + UTRs + Introns" options now retrieve the correct sequences.

In addition, numerous minor improvements have been made. Please send any questions or comments on the PomBase web site to us at <helpdesk@pombase.org>.

Monday, 28th Nov, 2011

A preview of PomBase, the new model organism database for the fission yeast Schizosaccharomyces pombe, has been announced to the S. pombe community for testing and feedback. For more on PomBase, see the NAR Database Issue paper (PubMed abstract) or contact the PomBase staff.

Friday, 28th Oct, 2011

A paper describing PomBase has been published online will be included in the 2012 Database Issue of Nucleic Acids Research. Abstract and open access full text are available.

Friday, 22nd Apr, 2011

A paper describing the major findings of the Schizosaccharomyces Comparative Genome Project was published today in Science Express and reported changes are included in GeneDB.

Further details are described in the pombe mailing list posts:

Wednesday, 2nd Feb, 2011

Further information on the pombe mailing list.

Tuesday, 1st Feb, 2011

Further details are available on the pombe mailing list.

Sunday, 16th May, 2010

The analysis of the fission yeast deletion collection is now published online in Nature Biotechnology.

Monday, 1st Mar, 2010

Funding was awarded by the Wellcome Trust for a fission yeast Model Organism Database, PomBase.

Tuesday, 1st Dec, 2009

Fission yeast is one of the 12 key organisms of the reference genomes project. The goal of this project is to completely annotate twelve reference genomes so that those annotations may be used to effectively seed the automatic annotation efforts of other genome.

Sunday, 1st Nov, 2009

GeneDB (S. pombe) now uses the latest update to Pfam, release 24.0 and 88.5% of fission yeast proteins now contain a match to at least one Pfam domain (increased from 83% in version 23).

Thursday, 1st Oct, 2009

The fission yeast genome and annotation dataset is now available as part of Ensembl Fungi.

Tuesday, 1st Sep, 2009

GeneDB is now using Version 23 of the Pfam protein family database. A total of 4154 (83%) S. pombe proteins now have at least one Pfam domain or family assignment (compared to 76% for S. cerevisiae), the highest percentage coverage for any eukaryote.

Monday, 1st Dec, 2008

S. pombe GeneDB now includes "deep links" to the Biological General Repository for Interaction Datasets (BioGRID) interaction datasets from the 'Database Cross References' section of the individual Gene Pages.

Thursday, 1st May, 2008

Dynamic repertoire of the fission yeast transcriptome reveals: 94% of the genome is transcribed; extensive variation in different stages and conditions; global and condition-specific coupling between splicing efficiency and transcription; confirms the majority of introns; refines ~75 gene structures; identifies 453 new transcripts 26 of which were predicted to code for proteins.

Friday, 1st Feb, 2008

The h- mating type region has been provided by Xavier Marsellach and Lorena Aguilar.

Tuesday, 1st Jan, 2008

Baumann and Zakian labs identify elusive telomerase RNA (PMID:18157152 and PMID:18157149)

Monday, 1st Oct, 2007

Wellcome Trust Advanced Course 'Genome-wide approaches with fission yeast' held in Hinxton.

Friday, 1st Jun, 2007

4th International Fission Yeast Meeting held in Copenhagen.

Monday, 1st Jan, 2007

GeneDB representation of the fission yeast data moved from contigs to chromosomes. See the pombelist archive for details.

Sunday, 1st Oct, 2006

The October issue of the journal Yeast is a fission yeast special issue containing 13 articles and reviews commissioned as a result of the European Fission Yeast Meeting, which are FREE to download.

Monday, 1st May, 2006

The fission yeast database survey is now closed. You can view the survey results here.

Saturday, 18th Mar, 2006

The European Fission Yeast Meeting (16th-18th March 2006) and The Fission Yeast Bioinformatics workshop (15th - 16th Mar 2006) both took place at the Wellcome Trust Genome Campus in Hinxton (Cambridge, UK).

Thursday, 17th Nov, 2005

Comparative Genomics of Eukaryotic Microorganisms:
Eukaryotic Genome Evolution, Approaches with Yeasts and Fungi


This conference took place from 12th-17th November 2005 in Sant Feliu de Guixols, Spain. Full details can be found here.

Sunday, 13th Nov, 2005

Second East Coast Regional pombe Meeting

This meeting took place from November 11-13, 2005 in Miami Beach, Florida.

Wednesday, 1st Sep, 2004

A project to record published genetic and physical interactions is underway with Mike Tyers and the GRID group at Toronto.

Monday, 30th Aug, 2004

The meeting was held at UC San Diego on August 24-29, 2004.

Saturday, 1st May, 2004

This issue of Methods includes 11 papers for fission yeast protocols including DNA damage checkpoint assays, cell wall analysis, TAP, nuclear envelope integrity assays, GFP imaging, TS mutant creation and plasmid use and construction. See the Methods site or the Table of Contents (at PomBase) for details of the papers including PMIDs.

Saturday, 1st Nov, 2003

Correlations Between Gene Expression and Gene Conservation in Fission Yeast. Mata J, Bahler J. Genome Res. 2003 Nov 12 PMID:14613978

FELINES: a utility for extracting and examining EST-defined introns and exons. Drabenstot SD et al Nucleic Acids Res. 2003 Nov 15;31(22):e141. PMID:14602934

Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. Segurado M, De Luis A, Antequera F. EMBO Rep. 2003 Nov;4(11):1048-53. Epub 2003 Oct 17. PMID:14566325

Retrotransposons and their recognition of pol II promoters: a comprehensive survey... Bowen NJ et al Genome Res. 2003 Sep;13(9):1984-97. PMID:12952871

Monday, 1st Sep, 2003

Egel, R., Copenhagen, Denmark (Ed.) The Molecular Biology of Schizosaccharomyces pombe Genetics, Genomics and Beyond ISBN:3-540-00693-1

Saturday, 1st Mar, 2003

Decottignies A, Sanchez-Perez I, Nurse P Genome Res. 2003 Mar;13(3):399-406. PMID:12618370

Wednesday, 1st Jan, 2003

Chen D, Toone WM, Mata J, Lyne R, Burns G, Kivinen K, Brazma A, Jones N, Bähler J. Mol Biol Cell. 2003 Jan;14(1):214-29. PMID:12529438