From e90340a2e77d4c36c0ee00bac22649c9bf204049 Mon Sep 17 00:00:00 2001 From: Kim Rutherford Date: Thu, 27 Jul 2023 19:56:08 +1200 Subject: [PATCH] Update docs components --- src/app/config/doc-config.json | 2 + src/app/config/docs.json | 14 +- .../documentation/docs/docs.component.html | 448 ++++++------------ .../recent-news/recent-news.component.html | 54 ++- 4 files changed, 192 insertions(+), 326 deletions(-) diff --git a/src/app/config/doc-config.json b/src/app/config/doc-config.json index eed0afeb..325b7124 100644 --- a/src/app/config/doc-config.json +++ b/src/app/config/doc-config.json @@ -56,6 +56,7 @@ "documentation/gene-page-modifications" : "Gene page: Modifications", "documentation/gene-page-phenotypes" : "Gene page: Phenotypes", "documentation/gene-page-protein-features" : "Gene page: Protein domains and properties", + "documentation/gene-page-protein-features-widget" : "Gene page: Protein feature widget", "documentation/gene-page-sequence" : "Gene page: Sequence", "documentation/gene-page-target" : "Gene page: Target of", "documentation/gene-page-transcript" : "Gene page: Transcript", @@ -462,6 +463,7 @@ "news/2023-02-22-pdb-structures-gene-pages" : "Experimental structures from PDB on gene pages", "news/2023-04-26-merging-nonsense-alleles" : "Curation update - \"nonsense mutation\" merged into \"partial amino acid deletion\"", "news/2023-06-19-rhea-reaction-diagrams" : "Reaction diagrams on term pages", + "news/2023-07-27-protein-feature-viewer" : "Protein feature viewer added to gene pages", "news/index" : "News archive", "status" : "Genome Status", "status/centromeres" : "Centromeres", diff --git a/src/app/config/docs.json b/src/app/config/docs.json index c0107cc9..42fd7af2 100644 --- a/src/app/config/docs.json +++ b/src/app/config/docs.json @@ -229,6 +229,11 @@ "heading" : "Gene page: Protein domains and properties", "id" : "documentation/gene-page-protein-features" }, + { + "content" : "\n\nThis widget shows a visual summary of protein features for the current gene. Hover over an allele, partial deletion, modification or Pfam domain to see more details. Hover over the track name for a brief description of the track.\n\n[pap1 gene page protein features widget]\n\nAvailable tracks\n\n- Sequence the amino acid sequence - zoom in to see individual residues\n- AA substitution positions positions where there are one or more amino acid substitutions\n- AA substitution alleles curated amino acid substitution alleles (available only in the full view)\n- Partial deletions curated alleles with partial amino acid deletions (full view only)\n- Modifications curated modified residues\n- Pfam families Pfam protein familes from InterPro\n- TM domains Trans-membrane domains calculated with TMHMM (Krogh et al. 2001)\n- Disordered regions Disordered regions from Pfam version 34.0 (El-Gebali et al. 2019)\n- Low complexity Low complexity regions from Pfam\n- Coiled coils Coiled coil regions from Pfam\n\nMutant display\n\nSingle residue alleles are shown as vertical lines (or rectangles if zoomed in). Alleles with multiple mutated residues (eg. “cdc15-E30K,E152K”) are connected with dashed lines.\n\nPartial deletions\n\nThe solid blue rectangles display the retained amino acids, dashed display the deleted regions.\n\nFull/detailed protein feature view\n\nFollow the “View all protein features …” link for a detailed view on the dedicated protein features page that includes the details of the individual amino acid substitution allele changes and “Partial deletions” tracks:\n\n[pap1 protein features page]\n\nThanks to the team at RCSB PDB for providing the Open Source software used to implement this feature.\n", + "heading" : "Gene page: Protein feature widget", + "id" : "documentation/gene-page-protein-features-widget" + }, { "content" : "\n\nThe Sequence section of a gene page provides a widget to download DNA sequences for any gene, and amino acid sequences for protein-coding genes, as well as links to send sequences to BLAST. For protein-coding genes, the predicted amino acid sequence is displayed by default:\n\n[peptide sequence section]\n\n1. If two or more transcripts are annotated for a gene, the primary transcript is shown by default. Use the selector to switch between transcript isoforms.\n\n2. Toggle to show the amino acid sequence for protein-coding genes (not available for non-coding RNA genes, which always show nucleotide sequence).\n\n3. Button to save the displayed sequence to a file, with the following options:\n\n- Displayed Sequence as FASTA\n - Genome region as GenBank: This feature downloads the genome region, in GenBank format. The file always includes the introns, exons and UTRs. You can include extra upstream or downstream sequences, if the “Show nucleotide sequence” is toggled but other settings are ignored. Files can be opened in sequence viewers (Snapgene, Ape, Benchling…) and contain the sequence feature annotations (CDS with labelled introns, translated sequence, UTRs, etc.).\n - Genome region as EMBL: Same as previous one, but in EMBL format.\n\n4. Links to send the displayed sequence to BLAST at NCBI or Ensembl.\n\n5. The peptide sequence header shows the transcript ID and the protein length.\n\nFor non-coding RNA genes, and for protein-coding genes with “Show nucleotide sequence” selected, more options are available:\n\n[DNA sequence section]\n\n1. Transcript selector (as above)\n\n2. Toggle to show the amino acid sequence (not available for non-coding RNA genes).\n\n3. Controls to add UTRs, introns, or flanking sequences to the displayed sequence. For upstream or downstream sequence, use the up/down control to increment by one base, or type or paste a number in the box.\n\n4. Link to save the displayed sequence to a file.\n\n5. Links to send the displayed sequence to BLAST at NCBI or Ensembl. DNA sequences link to BLASTN by default.\n\n6. The nucleotide sequence header shows the transcript ID and indicates what is included.\n\nWhen the “Show translation” option is selected, irrelevant controls are hidden and BLASTP links are shown:\n\n[sequence section showing translation]\n", "heading" : "Gene page: Sequence", @@ -540,7 +545,7 @@ "id" : "faq/can-i-search-gene-list-and-retrieve-results-same-order-as-input-list" }, { - "content" : "\n\nYes, use the “Taxonomic conservation” query in the advanced search.\n\nExample query: ``\n", + "content" : "\n\nYes, use the “Taxonomic conservation” query in the “Orthologs and conservation” menu of the advanced search.\n\nExample query: ``\n", "heading" : "Can I search for genes based on conservation in different taxa?", "id" : "faq/can-i-search-genes-based-on-conservation-different-taxa" }, @@ -2230,7 +2235,12 @@ "id" : "news/2023-06-19-rhea-reaction-diagrams" }, { - "content" : "\n\nReaction diagrams on term pages\n\n2023-06-19\n\nWhere available, we now show the reaction diagram from Rhea on GO function term pages. This feature is possible thanks to the great work of Rhea.\n\nSee the GO:0003849 term page for an example.\n\n[]\n\nCuration update - “nonsense mutation” merged into “partial amino acid deletion”\n\n2023-04-26\n\nWe have decided to merge the allele type “nonsense mutation” into “partial amino acid deletion”. This has mainly been driven by the fact that allele types that combine different variants require new types, such as “amino_acid_deletion_and_mutation”, “amino_acid_insertion_and_deletion”, etc. Otherwise, we would have ended up with many more types, and at the gene product level (which is what we describe in PomBase in phenotype interactions), both truncations are equivalent. In the next update, this allele type will not be available in Canto.\n\nIn any case, even if two alleles produce the same truncation, such as ase1-D13* or ase1Δ(13-731), they would still have separate entries in PomBase, and they may have different phenotypes. We are only assigning them the same allele type.\n\nIf for your analysis you need to make a distinction between the two using our allele dataset allele dataset, you can always check the “Allele description” field for the presence of the “*” character to tell whether an allele includes a nonsense mutation.\n\nExperimental structures from PDB on gene pages\n\n2023-02-22\n\nThe experimental protein structures from PDB are now embedded on the PomBase gene pages using Mol*. For example: lsm7/SPCC285.12 gene page\n\nIf you select the “PDB structures” view on a gene page, experimental structures will set as your default. AlphaFold predictions will be shown for genes where an experimental structure are not available.\n\nWe now also display the structures on the associated publication page. For example: PMID:31010807 Garg et al.\n\nTo help locate proteins with experimental protein structures (currently 375), we have added a new query option to the “Advanced search”, currently under “commonly used queries”: “Proteins with PDB structures”\n\n[PDB structures on the lsm7 gene page]\n\nAlphaFold protein structure on gene pages\n\n2023-02-02\n\nAlphaFold protein structure are now embedded on the PomBase gene pages. We hope to embed the experimental structures from PDB in the near future.\n\n[Example from the mvp1 gene page]\n\nRevised canonical 5’ UTRs\n\n2023-01-24\n\nWe have revised the curated 5’UTRs using Transcription Start Sites (TSS) data (in vegetative growth/ minimal media) from the Cap Analysis of Gene Expression (CAGE) data provided by Thodberg et al. All new gene structures were manually reviewed, around ~80 protein features had N-terminal coordinate revisions to align with TSS data.\n\nGlobal Core Biodata Resource status for PomBase\n\n2022-12-15\n\nWe are very pleased to announce that PomBase has been selected as one of the first Global Core Biodata Resource (GCBR) — a collection of 37 resources whose long term funding and sustainability is critical to life science and biomedical research worldwide. This accreditation recognizes PomBase as a primary knowledge base (adding value to data through expert curation) and as a crucial component of the research ecosystem. The candidate biodata resources were assessed against a series of rigorous criteria that included their scientific focus, the size and reach of their user communities, their quality of service, their governance, and their impact on global research.\n\nThank you to the entire community, especially the community curators who contribute regularly to our content, and our Scientific Advisory Board for their help and support.\n\nFor more information about the Global Biodata Coalition and PomBase’s new status, see the full press release.\n\nNext PombeTalks: Wednesday, December 14th\n\n2022-12-08\n\nThe next online PombeTalks will take place on Wednesday, December 14th. These talks are virtual seminars by and for the fission yeast community and friends.\n\n8:00 San Francisco; 11:00 NY; 16:00 London; 17:00 Paris; 20:30 Delhi, 23:00 Beijing; midnight Tokyo\n\nThis will be our last PombeTalks of 2022 before taking a winter break. The speaker will be:\n\n- Kristi E. Miller\n “The fission yeast cell size control system integrates pathways measuring cell surface area, volume and time”\n\nIt will be followed by some sum up/ feedback about PombeTalks from the organizing committee.\n\nSurvey\n\nPlease help us improve PombeTalks even more by taking this quick survey\n\nZoom details\n\nTopic: PombeTalksS308 Zoom Meeting\nDate: Dec 14th\nMeeting ID: 975 0331 6190\nPassword: will be sent the day of the meeting\n\nSlack\n\nFor more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nQuerying by RNA length in the Advanced Search tool\n\n2022-12-07\n\nYou can now query the RNA length of genes (spliced or unspliced) under the “Transcripts and exons” query grouping in the Advanced search.\n\nYou can also add RNA sequence length as a field in tables downloaded from the query builder.\n\n[RNA length queries are available under the “Transcripts and exons” tab]\n\nGenetic Interaction annotation model updated\n\n2022-11-29\n\nWe have recently implemented an improved way to annotate and display genetic interactions so they are linked to phenotype annotations and alleles.\n\nPreviously, our Genetic Interaction annotations only mentioned the interacting genes and the type of genetic interaction. For example, if a strain with genotype asp1-H397A has the phenotype decreased acid phosphatase activity affecting activity of pho1, but this phenotype is suppressed when rhn1 is deleted in that strain, we would annotate that the genes asp1 and rhn1 are part of a Phenotypic Suppression interaction.\n\n[GI old format]\n\nWe continue to display interactions in this format by default (showing only genes and interaction type), but if you expand the annotation, you can view the associated genotypes and phenotypes.\n\n[GI new format]\n\nIn the revised Canto interface, you can only annotate a genetic interaction from the double mutant phenotype annotation (by clicking on add.., as shown below).\n\n[GI annotation in Canto]\n\nOf course, genetic interactions predating this update are not linked to phenotypes or genotypes, but we are hoping to auto-annotate several of those. We will also prioritise for update any interactions where community curators have provided these details in an annotation comment. Finally, a big shoutout to Ana Sanchez and Angad Garg from the Shuman lab, for testing the new interface in numerous recently curated publications. The examples provided here are from Sanchez et al. 2019. Go read it and see the annotations in PomBase.\n\nBest, The PomBase team\n\nNext pombeTalks: Wednesday, November 16th\n\n2022-11-11\n\nThe next online pombeTalks will take place on Wednesday, November 16th. These talks are virtual seminars by and for the fission yeast community and friends.\n\nNote that this session will happen earlier at:\nmidnight San Francisco; 03:00 NY; 08:00 London; 09:00 Paris; 13:30 Delhi, 16:00 Beijing; 17:00 Tokyo\n\nTalks this session:\n\n- Wenfan Wei, University of Science and Technology of China\n “The Cdc42 GAP Rga6 promotes monopolar outgrowth of spores”\n\n- Gaowen Liu, Shenzhen Institute of Synthetic Biology\n “Fusion eciency evolution to the deletion of an essential mating gene Prm1”\n\nZoom details\n\nTopic: PombeTalks S03E07 Zoom Meeting\nDate: Nov 16, 2022\nTime: midnight San Francisco; 03:00 NY; 08:00 London; 09:00 Paris; 13:30 Delhi, 16:00 Beijing; 17:00 Tokyo\nMeeting ID: 932 8857 4852\nPassword: will be sent the day of the meeting\n\nSlack\n\nFor more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nUsing AlphaFold models to discover distant human and budding yeast homologues\n\n2022-10-14\n\nWe collaborated with the Pfam group at the EBI to evaluate predictions generated from AlphaFold reciprocal best structure hits to identify potential distant orthologs. The Reciprocal Best Structure Hits (RBSH) approach provided 11 novel human homologues, including Pho86 -> NAT8 (ER acetyltransferase), Mug174 -> COIL (Coilin), Ach1 -> OXCT1 (succinyl-CoA:3-ketoacid coenzyme A transferase), SPAC1952.08c -> CREG1, imt1 -> A4GALT (Lactosylceramide 4-alpha-galactosyltransferase), Rtc5 -> MEAK7 (MTOR associated protein). A further 41 novel orthologs were predicted between S. pombe and S. cerevisiae which had fallen under the radar for all other methods used at PomBase. Most of the novel connections provided additional functional information, or supported existing knowledge for poorly characterised proteins. See supporting data tables S4 and S5 for the complete list of predictions included in PomBase. Article.\n\nNext pombeTalks: Wednesday, October 19th\n\n2022-10-13\n\nThe next online pombeTalks will take place on Wednesday, October 19th. These talks are virtual seminars by and for the fission yeast community and friends.\n\n8:00 San Francisco / 11:00 NY / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / midnight Tokyo\n\nTalks this session:\n\n- Cecilia D’Alessio, University of Buenos Aires and CONICET\n “N-Glycosylation and glycoprotein folding in fission yeasts, a model to study human congenital disorders of glycosylation”\n\n- Jason Tanny, McGill University, Montreal\n “A novel transcriptional mechanism regulating the cellular response to replication stress”\n\nZoom details\n\nTopic: PombeTalks S03E06 Zoom Meeting\nTime: Oct 19, 2022 05:00 PM Paris\nMeeting ID: 933 7072 6178\nPassword: will be sent the day of the meeting\n\nSlack\n\nFor more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nNew to fission yeast? check out our quick start guide for new users\n\n2022-10-13\n\nWe have added a new page providing useful information for new fission yeast researchers:\nGetting started with S.pombe and PomBase\n\nIncludes details of how to join the community mailing list and the Slack channel, links to useful tools and resources, information about fission yeast as a model organism, an overview of PomBase and more.\n\n77 new disease gene associations\n\n2022-09-16\n\nWe have added 77 new disease-gene associations for 71 fission yeast human gene orthologs. These were identified using “PombeMine” to identify the disease genes curated by OMIM not annotated with an existing MONDO mapping. The number of human disease gene associations is currently 1471. Disease genes can be browsed via the disease slim set or from the MONDO root node term.\n\nPombeMine: an InterMine instance for S. pombe\n\n2022-09-16\n\nAs part of an Elixir funded collaboration with the InterMine team we have created PombeMine. Gene lists can be sent directly from PomBase query results pages directly to Intermine (under the “export” tab), providing direct (2 click) access to GO and phenotype enrichment tools.\n\nNext pombeTalks: Wednesday, September 21st\n\n2022-09-15\n\nThe next online pombeTalks will take place on Wednesday, September 21st. These talks are virtual seminars by and for the fission yeast community and friends.\n\n8:00 San Francisco / 11:00 NY / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / midnight Tokyo\n\nTalks this session:\n\n- Manuel Lera Ramirez, PomBase / Tran Lab, Institute Curie “Microtubule rescue at midzone edges promotes overlap stability and prevents spindle collapse during anaphase B”\n\n- Hannah Opalko, Moseley lab, Dartmouth College “Mechanisms of spatial patterning of cell cycle regulator Cdr2”\n\nZoom details\n\nTopic: PombeTalks S03E05 Zoom Meeting\nTime: Sep 21, 2022 05:00 PM Paris\nMeeting ID: 985 8572 1420\nPassword: will be sent the day of the meeting\n\nSlack\n\nFor more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nProtein sequence changes\n\n2022-09-06\n\n78 protein have been shortened (at the N-term). This set includes 34 published proteins (Apl4, Brc1, Cdc48, Cdt1, Cho1, Cmb1, Cut2, Cut6, Cwf26, Dbr1, Dri1, Elo2, Eri1, Lsd2, Lys2, Med13, Naa38, Nup107, Nup82, Orc2, Pof10, Ppt1, Rec24, Rga2, Rmt3, Rns1, RRpn7, Sap145, Skb1, Snf5, Snt2, Spn3, Tpp2, Trm1, and Tup12). Allele description changes and modification position changes are pending.\n\nNext pombeTalks: Wednesday, August 17th\n\n2022-08-13\n\nThe next online pombeTalks will take place on Wednesday, August 17th. These talks are virtual seminars by and for the fission yeast community and friends.\n\n8:00 San Francisco / 11:00 NY / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / midnight Tokyo\n\nTalks this session:\n\n- Pranas Grigaitis, Vrije Universiteit Amsterdam\n “Prediction of metabolic strategies in Schizosaccharomyces pombe based on optimal resource allocation”\n- Abhishek Poddar, University of Toledo\n “Membrane stretching activates calcium-permeability of a putative channel Pkd2 during fission yeast cytokinesis”\n\nAs always, connection details will be sent the day of the talk. For more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nNext pombeTalks: Wednesday, July 20th\n\n2022-07-12\n\nThe next online pombeTalks will take place on Wednesday, July 20th. These talks are virtual seminars by and for the fission yeast community and friends.\n\n0:00 San Francisco / 3:00 New York / 8:00 London / 9:00 Paris / 12:30 Delhi / 15:00 Beijing / 16:00 Tokyo.\n\nTalks this session:\n\n- Leeba Ann Chacko, Ananthanarayanan Lab, University of New South Wales\n “Microtubules and mitochondria cooperate to ensure cell division symmetry, polarity and equipartitioning in fission yeast”\n- Dan Zhang, Temasek Life Sciences Laboratory, National University of Singapore\n “The cortical ER remodeling for actomyosin ring assembly”\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and pombeSlack one day in advance, so make sure you’ve signed up.\n\nPombeTalks Wednesday June 15th\n\n2022-06-14\n\nThe next online pombeTalks will take place on Wednesday June 15th. These are virtual seminars by and for the fission yeast community and friends.\n\n08:00 San Francisco / 11:00 New York / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / 00:00 Tokyo\n\nTalks this session:\n\n- Elliott Chapman, Bayne Lab, University of Edinburgh\n “Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus”\n- Fei Li, New York University\n “Phosphorylation-mediated Ccp1-Ndc80 switch at the N-terminus of CENP-T regulates kinetochore assembly in fission yeast”\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and pombeSlack one day in advance, so make sure you’ve signed up.\n\nAs before, questions will be posted to #pombetalks-qna on pombeSlack channel and recordings uploaded.\n\nPombeTalks May 18th\n\n2022-05-05\n\nThe next online pombeTalks will take place on May 18th. These are virtual seminars by and for the fission yeast community and friends.\n\n08:00 San Francisco / 11:00 New York / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / 00:00 Tokyo\n\nTalks this session:\n\n- Jennifer Porat, Bayfield Lab, York University: The methyl phosphate capping enzyme Bmc1/Bin3 is a stable component of the fission yeast telomerase holoenzyme\n- Ingrid Billault-Chaumartin, Martin Lab, UNIL: Fus1, the fusion focus formin\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nNew phenotype slim\n\n2022-04-13\n\nWe have added a phenotype slim overview to complement those provided for disease association, biological process, molecular function and cellular component annotation. The purpose of the phenotype slim is to provide subsets of commonly used ‘broad’ phenotypic classes or annotation subsets that can provide a useful starting point for accessing phenotype lists. The phenotype slim page provides links to ontology term pages, annotated genes, and to download files containing the slim terms and IDs.\n\nThe phenotype slim has also been added to the PomBase advanced search results panel “Slim with” menu. For example, you can query for all genes involved in a GO process, another phenotype, or any other list, and “slim” the results using the “Phenotype slim” option to view categories of phenotypes assigned to the list.\n\nMaking biological knowledge useful for humans and machines\n\n2022-04-04\n\nA GENETICS special issue featuring model organism database updates is published today. This issue features the recent PomBase and JaponicusDB publications and is accompanied by an editorial “Making biological knowledge useful for humans and machines” co-authored by Val Wood, Paul Sternberg and Howard Lipshitz.\n\n- Fission stories: using PomBase to understand Schizosaccharomyces pombe biology\n- JaponicusDB: rapid deployment of a model organism database for an emerging model species\n\nThe fission yeast community have now curated over 1000 publications\n\n2022-03-26\n\nWe would like to extend a huge “thank you” to the fission yeast community for curation contributions. The community have now curated 1008 publications providing 19,156 independent annotations, representing 25% of the curation from small-scale publications. In addition, another 80,000 annotations have been provided via the submission of HTP datasets.\n\nPlease contact us via the helpdesk if you would like to provide curation for your manuscript but don’t know how.\n\nLinks:\n\n- All community curated publications\n- Spotlights\n- Canto curation tool\n- HTP data and browser track submission\n\nNew human orthologs including 3 MRP complex subunits\n\n2022-03-23\n\nWe continue to identify distant human orthologs. Four new 1:1 human ortholog connections have been added to PomBase this week:\n\n- RNase MRP subunit Rmp1 = human NEPRO (family submitted to Pfam)\n- RNase P and RNase MRP subunit Pop23 = human RPP38 (members of the same Pfam clan)\n- RNase P and RNase MRP subunit Pop8 = human RPP14 (family submitted to Pfam)\n- glutamyl-tRNA amidotransferase complex subunit 3 (Gtf1) = human GATC\n\nHuman NEPRO is a poorly characterised protein linked to the disease Anauxetic dysplasia 3, and GATC is the causal gene for “combined oxidative phosphorylation deficiency 42”\n\nPomBase now uses InterPro Version 88.0\n\n2022-03-12\n\nPomBase now uses InterPro Version 88.0.\n\nFeatures include:\n\n- The addition of 39 InterPro entries (40,071 total entries)\n- Integration of 45 new methods from the PRINTS (1), SMART (1), Pfam (2), SUPERFAMILY (7), CATH-Gene3D (14), PANTHER (13), CDD (7) databases\n\nTOR and nutritional phosphoproteome dataset loaded\n\n2022-03-11\n\nWe have loaded the TOR and nutritional phosphoproteome dataset described in Halova et al. (9424 annotations). Many thanks to Janni Petersen for preparing the files.\n\nPublication page for PMID:33823663\n\nAn additional 5775 novel curated lncRNAs from Atkinson et al.\n\n2022-03-10\n\nWe have added an additional 5775 novel curated lncRNAs from Atkinson et al. to PomBase. We will refine the descriptions of these gene products to align with Sequence Ontology (SO) terms describing RNA features in the coming months.\n\nThanks to María Rodríguez-López for preparing the files.\n\nPublication page for PMID:29914874\n\nPomBase & JaponicusDB publications in the GENETICS MOD reports special issue\n\n2022-02-02\n\nPapers describing PomBase and JaponicusDB are now published (early online). These articles are part of a special issue of GENETICS devoted to model organism database (MOD) reports. The MOD papers will highlight the journal’s new section on Computational Resources, Software & Databases.\n\n- Fission stories: using PomBase to understand Schizosaccharomyces pombe biology\n- JaponicusDB: rapid deployment of a model organism database for an emerging model species\n\nImproved options for filtering annotations by cell cycle phase\n\n2021-12-19\n\nThe Gene Ontology annotation filter for “during” specific cell cycle phases is now included on the “Summary” view in addition to the “Details” view. Available phases have been extended to cover all phases used, and to provide\nuseful grouping terms. This filter is “ontology aware” (i.e. a search on interphase will also display G1/S/G2 phase annotation). The phase filter is most useful on pages that display increasing volume of phase-specific curation (such as cdc2). The revised phase filter options are also available in the gene expression section.\n\nThe phase filters are located at the top right of GO and gene expression annotation sections:\n\n[During filter]\n\nPomBase now uses InterPro Version 87.0\n\n2021-11-23\n\nPomBase now uses InterPro Version 87.0, which integrates:\n\n- 1,155 new InterPro entries\n- Update to Pfam 34.0\n- 1,256 new methods\n\nCoils, disorder, and more: new protein feature queries\n\n2021-10-18\n\nThe PomBase advanced search now allows you to find proteins that have coiled-coil regions, disordered regions, and low-complexity regions. The query-building interface also now organises query options more sensibly, and the documentation has been updated.\n\nPomBase & JaponicusDB preprints\n\n2021-09-27\n\nPapers describing PomBase and JaponicusDB will appear in an issue of GENETICS devoted to model organism database (MOD) reports. The MOD papers will highlight the journal’s new section on Computational Resources, Software & Databases.\n\nFollow the links to the PomBase preprint and JaponicusDB preprint, and watch for the full-fledged publications to appear in March 2022.\n\nJaponicusDB: a new fission yeast database\n\n2021-09-01\n\nWe are delighted to announce the official release of PomBase’s new sister: JaponicusDB is a new, curated model organism database for the fission yeast Schizosaccharomyces japonicus. JaponicusDB highlights include revised gene structures, distant ortholog detection, improved GO annotation, community literature curation, and reciprocal gene page links with PomBase, providing a familiar environment for all fission yeast researchers.\n\nThe S. japonicus community will maintain JaponicusDB from now on. Join the new mailing list, and follow @japonicusdb on Twitter.\n\nImproved gene-disease curation: over 1400 S. pombe genes\n\n2021-08-06\n\nPomBase disease gene curation associates disease descriptors with fission yeast orthologs of human disease-causing genes. We have added new gene–disease term connections, to bring the total to 1401 S. pombe genes. Disease associations now cover 27.3% of all fission yeast protein-coding genes, and almost 40% with human orthologs.\n\nPombeTalks August 4th\n\n2021-07-28\n\nThe next online PombeTalks will take place on Wednesday 4th August 2021, at 17:00 Central European Time. Speakers:\n\n- Tiffany Mak, Nurse lab, The Francis Crick Institute: The TOR-dependant phosphoproteome and regulation of cellular protein synthesis\n\n- Weifang Wu, Allshire lab, University of Edinburgh: Spatial organisation of the nucleus influences centromere identity\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nAfter these talks, PombeTalks will take a break for the rest of the summer, so watch this space, pombelist, or PombeSlack for updates. In the meantime, you can fill out this form at any time if you’re interested in speaking.\n\nAlphaFold links\n\n2021-07-28\n\nPomBase gene pages now have links to the AlphaFold Protein Structure Database, the collection of structures predicted by AI developed by DeepMind, hosted at EBI. Look in the “External references” section of your favorite gene page, or check out this example (pap1), or read more at the EBI AlphaFold home.\n\nPombeTalks July 21st\n\n2021-07-14\n\nThe next online PombeTalks will take place on Wednesday 21st July 2021, at 10:00 Central European Time / 17:00 Japan & Korea. Speakers:\n\n- Yoko Otsubo, Yamashita lab, National Institute for Basic Biology: Novel links between TORC1 and traditional non-coding RNA, tRNA\n\n- Jie Su, Nakagawa lab, Osaka University: Rad8-dependent PCNA ubiquitination at lysine 107 causes gross chromosomal rearrangements\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nKEGG pathway links\n\n2021-07-06\n\nPomBase gene pages now have links to pathway entries in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, as well as links to gene lists for each linked pathway (example: 2-Oxocarboxylic acid metabolism). The KEGG pathway links are the first entry in a new gene page section, “Molecular pathway”, dedicated to connecting genes in PomBase to depictions of biochemical and signaling pathways.\n\nPomBase now uses InterPro Version 86.0\n\n2021-06-30\n\nPomBase now uses InterPro Version 86.0, which integrates:\n\n- 299 new InterPro entries\n- An update to PROSITE patterns [2021_01] and PROSITE profiles [2021_01]\n- 454 new methods from the PROSITE profiles (39), SMART (2), Pfam (7), SUPERFAMILY (3), CATH-Gene3D (80), PANTHER (295), CDD (27), SFLD (1) databases.\n\nInterPro cites 52235 publications in PubMed. See the InterPro release notes for further information.\n\nPombeTalks July 7th\n\n2021-06-30\n\nThe next online PombeTalks will take place on Wednesday 7th July 2021, at 17:00 Central European Time. Speakers:\n\n- Debatrayee Sinha, Qian Chen lab, University of Toledo: Fission yeast polycystin Pkd2p promotes resumption of cell growth after cytokinesis\n\n- Joël Lemière, Fred Chang Lab, UCSF: The role of osmotic forces in nuclear size control\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks June 23rd\n\n2021-06-17\n\nThe next online PombeTalks will take place on Wednesday 23rd June 2021, at 17:00 Central European Time. Speakers:\n\n- Yi Wei, Grewal lab, NCI CCR, Bethesda: TOR targets an RNA processing network to regulate cell proliferation and sexual development\n\n- Nicholas Ader, LusKing Lab, Yale School of Medicine: I open at the close(d mitosis): Investigating post-mitotic nuclear envelope sealing in fission yeast\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nViolin plots for gene expression\n\n2021-06-15\n\nThe “Quantitative gene expression” section of PomBase gene pages now offers a display of violin plots to visualize where the gene appears in available expression datasets.\n\nViolin plots are also available to visualize sets of up to 150 genes in the advanced search results.\n\nAt present data from Marguerat S et al. (2012) and Carpy A et al. (2014) are included.\n\nPombeTalks June 9th\n\n2021-06-02\n\nThe next online PombeTalks will take place on Wednesday 9th June 2021, at 10:00 Central European Time / 17:00 Japan & Korea. Speakers:\n\n- Yusuke Toyoda, Saitoh lab, Kurume University: Nitrogen-dependent persistence of S. pombe Ght5 glucose transporter on the cell surface is effected by TORC2 inhibition of α-arrestin Aly3\n\n- Anupa T. Anil, Mishra lab, IISER Mohali: How does spliceosome capture branchpoint-distant 3’ splice site?\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks May 26th\n\n2021-05-20\n\nThe next online PombeTalks will take place on Wednesday 26th May 2021, at 17:00 Central European Time. Speakers:\n\n- Mélina Vaurs (Vincent Géli & Stéphane Coulon labs - Cancer Research Center, Marseille): Shelterin-dependent telomerase regulation differs between quiescent and vegetative cells\n\n- Arthur Molines (Fred Chang lab – UCSF): Physical properties of the cytoplasm modulate microtubule dynamics\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks May 12th\n\n2021-05-05\n\nThe next online PombeTalks will take place on Wednesday 12th May 2021, at 17:00 Central European Time. Speakers:\n\n- Sierra Cullati, Gould lab, Vanderbilt University: Autophosphorylation of the CK1 Kinase Domain Regulates Enzyme Activity and Substrate Specificity\n\n- Stephen Huisman, Brunner Lab, University of Zurich: Vip1, a temperature-dependent filament forming protein involved in cell length regulation\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nNew diploid genotype & phenotype display\n\n2021-04-29\n\nPomBase now includes pages for curated diploid genotypes, and displays phenotypes annotated to them on gene and publication pages. For more details see the documentation for phenotype annotations and genotype pages.\n\nPombeTalks April 28th\n\n2021-04-22\n\nThe next online PombeTalks will take place on Wednesday 28th April 2021, at 10:00 Central European Time / 17:00 Japan & Korea. Speakers:\n\n- Tomoyuki Fukuda, Niigata University Graduate School of Medical and Dental Sciences: Atg43 serves as a selective autophagy receptor to promote mitophagy\n\n- Xiao-Ran Zhang, NIBS, Beijing, China: An improved auxin-inducible degron system for fission yeast\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPomBase now uses InterPro Version 85.0\n\n2021-04-15\n\nPomBase now uses InterPro Version 85.0, which integrates:\n\n- 157 new InterPro entries\n- An update to CATH-Gene3D [4.3.0]\n- 333 new methods from the Pfam (3), SUPERFAMILY (11), CATH-Gene3D (168), PANTHER (88), CDD (62), SFLD (1) databases\n\nInterPro cites 51539 publications in PubMed. See the InterPro release notes for further information.\n\nPombeTalks April 14th\n\n2021-04-08\n\nThe next online PombeTalks will take place on Wednesday 14th April 2021, at 17:00 Central European Time:\n\n- Pabitra Parua,�Fisher�lab,�Icahn School of Medicine at Mount Sinai: Control of the RNA polymerase II transcription cycle by CDK-phosphatase switches\n\n- Ye Dee Tay, Sawin Lab,�University of�Edinburgh: Gef1: the first aider of Cdc42 polarity module during stress\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the new Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nNew genome browser data: GC content\n\n2021-03-31\n\nA data track showing the fraction of G/C bases in a region is now available in PomBase JBrowse, listed under “Base composition”. The track is generated using the gccontent plugin, and uses a default window of 100 bp.\n\nQualitative gene expression annotation in Canto\n\n2021-03-31\n\nCanto, PomBase’s online curation tool, now supports qualitative gene expression annotation. Two new annotation types are available to represent observations about the levels of RNA or protein observed in wild-type cells, and how they change over the cell cycle or in response to a stimulus. See the Canto documentation for more information. We have also updated the display of qualitative gene expression on PomBase gene and publication pages.\n\nNew protein feature display\n\n2021-03-30\n\nPomBase has released a new, interactive display for protein features on gene pages. The new view is clearer, with details for each feature available via mouseover as well as in the accompanying table.\n\nIn addition, PomBase now uses InterPro Version 84.0, which includes 205 new entries and integrates 252 new methods from the Pfam, PANTHER, and CDD databases. See the InterPro release notes for further information.\n\nPombeTalks March 31st\n\n2021-03-27\n\nThe next online PombeTalks will take place on Wednesday 31st March 2021, at 17:00 Central European Time:\n\n- Udo Onwubiko, Das lab, University of Tennessee: Cdc42 prevents early Rho1 activation during cytokinesis\n\n- Chunmin Shan, Jia lab, Columbia University: The INO80 complex regulates epigenetic inheritance of heterochromatin\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the new Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks March 17th - new time!\n\n2021-03-10\n\nThe new season of online PombeTalks for 2021 will begin on Wednesday 3rd March 2021, at a different time: 9:00 Central European Time / 17:00 Japan & Korea. Speakers:\n\n- Yasuto Murayama, National Institute of Genetics, Shizuoka: Biochemical analysis of the fission yeast structural maintenance of chromosomes complex\n\n- Ken Ishikawa, Kurume University, Kurume: dCas9-mediated CRISPRi for S. pombe\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the new Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks return March 3rd\n\n2021-02-24\n\nThe new season of online PombeTalks for 2021 will begin on Wednesday 3rd March 2021 at 17:00 Central European Time:\n\n- Maria Rodriguez Lopez, Bähler lab, UCL: Clr6 orchestrates transcriptional switches to regulate metabolism during oxidative stress\n\n- Olivia Muriel-Lopez, Martin lab, University of Lausanne: ’Ultrastructural plasma membrane asymmetries underlie cell-cell fusion in S. pombe*\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will resume its fortnightly schedule, so watch this space, pombelist, or PombeSlack for updates. As in the past, you are always welcome to fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPomBase identifier mapper now available\n\n2021-02-04\n\nWe have developed an identifier mapper that retrieves S. pombe gene systematic IDs and standard names for a selection of different input ID types. You can now find S. pombe genes using UniProt accessions, and retrieve manually curated orthologs for S. cerevisiae using standard gene names or ORF names, and for human using standard gene names or HGNC identifiers.\n\nTry the identifier mapper or check out the documentation.\n\nPomBase now uses InterPro Version 83.0\n\n2021-01-25\n\nPomBase now uses InterPro Version 83.0, which integrates:\n\n- 376 new InterPro entries\n- An update to HAMAP [2020_05], CDD [3.18]\n- 462 new methods from the SMART (2), TIGRFAMs (2), Pfam (3), PANTHER (140), HAMAP (19), CDD (286), SFLD (10) databases\n\nInterPro cites 50487 publications in PubMed. See the InterPro release notes for further information.\n\nFirst S. pombe microPublication goes live\n\n2021-01-07\n\nThe first fission yeast microPublication has now been published:\n\nNafees Ahamad, Simmi Anjum, Shakil Ahmed\\ Pyrogallol induces oxidative stress defects in the fission yeast S. pombe.\n\nCongratulations to the authors, and thanks to the microPublication team!\n\nPombeTalks November 25th\n\n2020-11-18\n\nThe last online PombeTalks for 2020 will take place on Wednesday 25th November 2020 at 17:00 Central European Time:\n\n- I-Ju Lee, David Pellman’s Lab, Dana-Farber Cancer Institute: Factors promoting nuclear envelope assembly independent of the canonical ESCRT pathway\n\n- Ulrike Endesfelder, Carnegie Mellon University: TBC\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nAfter these talks, PombeTalks will take a well-earned break, and return in early 2021. The schedule is available, and you are always welcome to fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks November 11th\n\n2020-11-04\n\nThe next online PombeTalks will take place on Wednesday 11th November 2020 at 17:00 Central European Time:\n\n- Farnaz Mansouri, Mark Bayfield lab (York University, Toronto): The uncharacterized S. pombe La-related protein 1 functions in translation and affects RNA abundance\n\n- Saz Basu, Paul Nurse lab (Francis Crick Institute, London): Unmasking the mitotic potential of G1/S Cyclin-CDK\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on November 25. PombeTalks will then take a break, and return in early 2021. The schedule is available, and you are always welcome to fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nGO annotations from PAINT\n\n2020-11-01\n\nPomBase now includes over 3000 GO annotations made using Phylogenetic Annotation and INference Tool (PAINT), developed by the GO Consortium to infer protein function in a phylogenetic context, supporting precise assertions as to when functions were gained and lost during evolution. PAINT annotations use the evidence code “inferred from biological aspect of ancestor” (IBA). PAINT curation is described in more detail in Gaudet et al. 2011.\n\nPombeTalks October 28th\n\n2020-10-24\n\nThe next online PombeTalks will take place on Wednesday 28th October 2020 at 17:00 Central European Time:\n\n- Omaya Dudin, EPFL, Switzerland: Cellularization of Ichthyosporean coenocytes\n\n- Bassem Al-Sady, UCSF, USA: Single cell analysis of the heterochromatin spreading reaction\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on November 11, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks October 14th\n\n2020-10-08\n\nThe next online PombeTalks will take place on Wednesday 14th October 2020 at 17:00 Central European Time:\n\n- Dimitrios Vavylonis, Lehigh University: Modeling fission yeast’s polarization pattern\n\n- Chloe Snider, Gould Lab, Vanderbilt University: Opposite surfaces of the Cdc15 F-BAR domain create a membrane platform that coordinates cytoskeletal and signaling components for cytokinesis\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on October 28, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks September 30th\n\n2020-09-23\n\nThe next online PombeTalks will take place on Wednesday 16th September 2020 at 17:00 Central European Time:\n\n- Alexander Lorenz, University of Aberdeen, UK: Meiotic recombination outcome in the face of genetic diversity\n\n- Veneta Gerganova, Martin Lab, UNIL, Switzerland: Patterning of membrane-associated proteins through membrane flows\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on October 14, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nNew genome browser datasets 2020-09-17\n\n2020-09-17\n\nTwo new datasets in are now available in PomBase JBrowse (links go to PomBase publication pages, which in turn link to the browser with the tracks enabled):\n\n- Meiotic DSBs from\n Fowler KR, Gutiérrez-Velasco S, Martín-Castellanos C, Smith GR. 2013.\n Protein determinants of meiotic DNA break hot spots.\n PMID:25747261 DOI: 10.1016/j.molcel.2013.01.008\n\nand\n\n- Time-lapse single-cell transcripts for dormancy breaking from\n Tsuyuzaki H, Hosokawa M, Arikawa K, Yoda T, Okada N, Takeyama H, Sato. 2020.\n Time-lapse single-cell transcriptomics reveals modulation of histone H3 for dormancy breaking in fission yeast.\n PMID:32152323 DOI: 10.1016/j.molcel.2013.01.008\n\nMore datasets are always welcome, so check out our instructions for submission.\n\nPombeTalks September 16th\n\n2020-09-14\n\nThe next online PombeTalks will take place on Wednesday 16th September 2020 at 17:00 Central European Time:\n\n- Susan Forsburg, University of Southern California: Visualizing replication stress\n\n- Sigurd Braun, Ludwig-Maximilians-Universität, München: Gene repression at the nuclear membrane: Multifaceted roles of Lem2\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on September 30, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nNew dataset: Hermes transposon insertions\n\n2020-09-11\n\nPomBase now hosts transposon integration data from Lee et al. 2020. Henry Levin explains the background and significance of the work:\n\n“Transposon Integration Sequencing is a genome wide method of mapping sequences that contribute to growth. High throughput sequencing of transposon integration sites in haploid cells with single insertions reveals which genes are dispensable. Once propagated, cultures exhibit a pronounced lack of insertions in genes necessary for growth. This method, originally developed to study bacteria is now used to characterize the genomes of several yeasts including S. pombe. In earlier work we used the transposon Hermes to identify genes of S. pombe required for growth (Guo et al., 2013, Genetics, PMID:23893486). We have now applied Hermes and Transposon Integration Sequencing to identify genes important for the formation of heterochromatin (Lee et al., 2020, Cell Reports, PMID:32101745). Insertion sites from eight independent cultures can be visualized from PomBase as custom tracks on Jbrowse. Four cultures were of cells with ura4 silenced by cen1 heterochromatin. The other four cultures were\nof a strain without ura4. By passaging the cultures in 5-FOA we selected against cells with defects in heterochromatin. Genes that contributed to the formation of heterochromatin exhibited fewer insertions in cells with the cen1 copy of ura4 relative to the strain lacking ura4. To distinguish genes critical for heterochromatin from genes that contribute to a lesser extent we passaged cultures in 5-FOA for 5 generations and for 80 generations. While viewing these integration sites can indicate whether genes of interest contribute to heterochromatin formation you can also examine insertions in the cultures lacking ura4 to gage whether specific genes or noncoding sequences make significant contributions to growth.”\n\nNew genome browser datasets 2020-09-08\n\n2020-09-08\n\nThree new datasets in are now available in PomBase JBrowse (links go to PomBase publication pages, which in turn link to the browser with the tracks enabled):\n\n- Transcription start sites from\n Li H, Hou J, Bai L, Hu C, Tong P, Kang Y, Zhao X, Shao Z. 2015.\n Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE.\n PMID:25747261 DOI:10.1080/15476286.2015.1022704\n\n- Transcript data from\n Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S, Cramer P, Gagneur J. 2016\n Determinants of RNA metabolism in the Schizosaccharomyces pombe genome.\n PMID:26883383 DOI:10.15252/msb.20156526\n\n- Transposon insertion sites from\n Lee SY, Hung S, Esnault C, Pathak R, Johnson KR, Bankole O, Yamashita A, Zhang H Levin HL.\n Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation.\n PMID:32101745 DOI:10.1016/j.celrep.2020.01.094\n\nSubmit your genome browser data\n\n2020-09-08\n\nWe have updated our HTP data submission procedure to make it easier for you to contribute your datasets for PomBase JBrowse:\n\nWe now provide spreadsheet templates in Excel and Open Document formats that gather the metadata we need to load and display your data. You can download a template from the documentation page on HTP data submission. Send completed spreadsheets to the PomBase helpdesk.\n\nPublished: GO Term Matrix for annotation QC\n\n2020-09-02\n\nIn collaboration with the GO Consortium, the PomBase team has published a report on the Term Matrix approach to GO annotation quality control. The article, out this week in Open Biology, describes biological processes that do, or don’t, share annotated gene products, and how we use co-annotation patterns to build rules to detect, correct, and prevent errors.\n\nPombeTalks September 2nd\n\n2020-09-01\n\nThe next online PombeTalks will take place on Wednesday 2nd September 2020 at 17:00 Central European Time:\n\n- François Bachand, USherbrooke, Canada: Proximity-dependent biotinylation assays in fission yeast and a tale about slow RNA polymerase II transcription\n\n- Scott Curran, Nurse Lab, The Crick Institute, UK: A quantitative and spatial analysis of the cell cycle control network\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on September 16, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\n11th Pombe meeting postponed to 2022\n\n2020-08-19\n\nDue to the ongoing Covid-19 pandemic, the 11th International Fission Yeast Meeting, due to take place in Hiroshima, Japan, has been postponed.\n\nThe new dates will be 12th (Sun -17th (Fri) June, 2022.\n\nPlease see the conference website and pombelist for further announcements.\n\nPombeTalks August 19th\n\n2020-08-12\n\nThe next online PombeTalks will take place on Wednesday 19th August 2020 at 17:00 Central European Time:\n\n- Joe Magliozzi, Moseley Lab, Dartmouth: Cell polarity kinases regulate RNA-binding protein Sts5 to control cell shape\n\n- Ramakanth Neeli, Minc Lab, Institute Jacques Monod: Mechanisms and Functions of Cell Wall Mechanosensing in Fission Yeast\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on September 2, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks August 5th\n\n2020-07-31\n\nThe next online PombeTalks will take place on Wednesday 5th August 2020 at 17:00 Central European Time:\n\n- Feng Li, Levin Lab NICHD/NIH, USA: Identification of an integrase-independent pathway of retrotransposition\n\n- Ivan Surovtsev, King lab, Yale University, USA: Liquid-liquid phase separation, heterochromatin domains and nuclear mechanics\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on August 19, and the summer schedule is available. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nFission yeast microPublications\n\n2020-07-22\n\nPomBase has recently joined microPublication.org, which “publishes brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative”, as a Partner Database. Fission yeast researchers can thus now make any results available to the community, even those that don’t fit neatly into traditional publications.\n\nVisit the microPublications website to learn more, to register and submit your data, or sign up to review. Send questions to the PomBase helpdesk.\n\nPombeTalks July 22nd\n\n2020-07-21\n\nThe next online PombeTalks will take place on Wednesday 22nd July 2020 at 17:00 Central European Time:\n\n- Prof. Dr. Ann Ehrenhofer-Murray, Institut für Biologie, Humboldt-Universität zu Berlin: Queuosine and m5c modification of RNA: Nutritional control of translation in S. pombe homestasis\n\n- Dr. Sarah Sabatinos, Department of Chemistry and Biology, Ryerson University: Long-term effects of surviving replication instability\n\n- PomBase microPublications announcement (Midori Harris)\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on August 5, and the summer schedule is available. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks July 8th\n\n2020-07-02\n\nThe next online PombeTalks will take place on Wednesday 8th July 2020 at 17:00 Central European Time:\n\n- Sahana Holla, Grewal lab, NIH: Positioning heterochromatin at the nuclear periphery promotes epigenetic inheritance\n\n- Nick Rhind, UMass Medical School: Cell size is controlled by size-dependent expression of mitotic activators\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on July 22nd, and the summer schedule is available. If you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nPombeTalks June 24th\n\n2020-06-19\n\nThe next online PombeTalks will take place on Wednesday 24th June 2020 at 17:00 Central European Time:\n\n- Sito Torres-Garcia, Allshire lab, University of Edinburgh: Epigenetic gene silencing by heterochromatin primes fungal resistance\n\n- Julie Rich-Robinson, Das lab, University of Tennessee: Cell-cycle-dependent cues temporally regulate Cdc42 activity at growth sites in fission yeast\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up.\n\nA schedule is now available for the rest of the summer, including the next talks on July 8th. If you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nEditable PomBase query names\n\n2020-06-11\n\nEntries in the PomBase advanced search query history now show brief, user-editable query descriptions, and a toggle to show or hide additional details.\n\nPombeTalks POSTPONED to June 17th\n\n2020-06-05\n\nPlease note that the next online PombeTalks will take place one week later than originally planned, to support the STEM Strike for Black Lives on 10th June.\n\nIn the meantime, please complete this brief survey of the audience.\n\nOn Wednesday 17th June 2020 at 17:00 Central European Time, the speakers will be:\n\n- Gautam Dey, Baum lab, UCL / EMBL Heidelberg: Closed mitosis requires local disassembly of the nuclear envelope\n\n- Meredith Betterton, UC Boulder: Computational modeling of fission yeast mitosis: what we can learn about pombe from computer simulations\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. The next two sessions will b on June 27 and July 8. If you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nPombeTalks May 27th\n\n2020-05-21\n\nThe next online PombeTalks will take place on Wednesday 27 May 2020 at 17:00 Central European Time. This time, in addition to the usual pair of research talks, our own Val Wood will show a few of PomBase’s lesser-known features.\n\n- Angad Garg, Stewart Schuman’s lab, Memorial Sloan Kettering Cancer Center: Long non-coding RNA control of phosphate homeostasis\n\n- José López Hernández, Sarah Zander’s lab, Stowers Institute for Medical Research: Diverse mating strategies in S. pombe affect the spread of wtf meiotic drivers\n\n- Val Wood, PomBase: Hidden corners of PomBase: Ten features you might not have seen\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also mark your calendars for the next two sessions on and June 10 and 24, and if you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nNew fission yeast GO slims\n\n2020-05-20\n\nTo complement the overview provided by the fission yeast GO biological process slim, we have created GO slims for the molecular function and cellular component branches of GO. Each slim page provides links to ontology term pages, annotated genes, and to download files containing the slim terms and IDs.\n\nNew ontology slimming options for advanced search results\n\n2020-05-20\n\nThe PomBase advanced search results panel now allows you to retrieve annotations to any of the fission yeast GO slims or the Mondo disease slim for genes in the results list. For example, you can query for all genes involved in a process and slim the resulting list by molecular function or disease association.\n\nPomBase adopts MONDO for disease gene curation\n\n2020-05-18\n\nPomBase has switched from the Disease Ontology (DO) to the Monarch Initiative’s Mondo Disease Ontology (Mondo) for disease gene curation. Mondo covers the same set of disease descriptions as DO, but has a richer hierarchical structure that classifies more specific descriptions into broad categories (e.g. anemia, cancer, kidney disease) suitable for a disease “slim” term set.\n\nPomBase curators are collaborating with Mondo to improve its disease classification, especially in areas that will support inferences that improve fission yeast disease annotation coverage in the new PomBase Mondo slim. The new disease slim is a work in progress, so if there is a particular disease grouping that you would find useful, please let us know.\n\nImproved gene-disease curation\n\n2020-05-18\n\nPomBase disease gene curation associates disease descriptors with fission yeast orthologs of human disease-causing genes. We have now increased coverage by adding new gene–disease term connections, with 3954 individual annotations to 1195 genes (up from 2588 and 905 respectively in January 2019). Disease associations now cover 24.5% of all fission yeast protein-coding genes, and over one third of those with human orthologs.\n\nPublished: Community curation in PomBase\n\n2020-05-11\n\nThe PomBase team has published an overview of our experience with community curation for fission yeast. In the article, out this week in Database, we reflect on the factors that have made our community’s remarkable, standard-setting achievements possible, and on the benefits we and PomBase users derive from this effort. We highlight the collaboration between authors and professional curators that arises via community curation, and how annotation quality improves as a result.\n\nWatch for invitations to curate your new papers, or see our community curation page for more information.\n\nPombeTalks May 13th\n\n2020-05-07\n\nThe next online PombeTalks will take place on Wednesday 13 May 2020 at 17:00 Central European Time. Speakers:\n\n- Sarah Lambert, Institut Curie, Paris, France: Resolution of replication stress in space and time for maintaining genome stability\n\n- Cornelia Kilchert, Justus-Liebig-University, Giessen, Germany: RNA-binding proteins in fission yeast - a global perspective\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also mark your calendars for the next two sessions on May 27 and June 10, and if you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nChromatin silencing ontology & annotation overhaul\n\n2020-05-07\n\nPomBase curators have collaborated with the GO Consortium to improve the representation of chromatin silencing and the underlying heterochromatin organization processes in the GO biological process ontology and annotations.\n\nNotably, “chromatin silencing” terms have been removed from GO on the grounds that they conflated various heterochromatin assembly, formation, and maintenance pathways with processes that affect chromatin-mediated repression more indirectly (e.g. tethering to the nuclear envelope). Chromatin silencing is a phenotype resulting from the cumulative effects of these processes, and the Fission Yeast Phenotype Ontology (FYPO) accordingly retains a full suite of “chromatin silencing” terms.\n\nAnnotations using the GO chromatin silencing terms were reviewed, and either removed or reannotated based on what could be inferred from the phenotypes, resulting in a substantially revised set of heterochromatin assembly annotations. Further work is required, so please send us any corrections.\n\nPomBase now uses InterPro Version 79.0\n\n2020-05-05\n\nPomBase now uses InterPro Version 79.0, which integrates:\n\n- 128 new InterPro entries\n- An update to PIRSF [3.10]\n- 151 new methods from the SUPERFAMILY (4), CATH-Gene3D (6), PIRSF (9), PANTHER (106), and CDD (26) databases.\n\nInterPro cites 48466 publications in PubMed. See the InterPro release notes for further information.\n\nMitochondrial genome update\n\n2020-05-01\n\nThe mitochondrial genome sequence in PomBase has been updated to reflect corrections made in Tao et al. (2019) “Intraspecific Diversity of Fission Yeast Mitochondrial Genomes”.\n\nMidori Harris receives 2020 Biocuration Career Award\n\n2020-04-28\n\nMidori Harris, ontology developer and curator at PomBase, has been awarded the 2020 Biocuration Career Award.\n\nCongratulations to Midori and a huge thanks for all that you do for PomBase.\n\nPombeTalks start on April 29th\n\n2020-04-22\n\nThe first in the new series of online PombeTalks will take place on Wednesday 29 April 2020 at 17:00 Central European Time. Speakers:\n\n- Aleksandar Vjeṧtica, Sophie Martin’s lab, University of Lausanne: Cycling for reproductive fidelity: Coupling the cell cycle and re-fertilisation blocks ensures ploidy maintenance during sexual lifecycle\n\n- Haitong Hou, Julia Cooper’s lab, NCI & University of Colorado: Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also mark your calendars for the next two sessions on May 13 and May 27, and if you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nAnGeLi update\n\n2020-03-23\n\nAnGeLi (developed by Danny Bitton) is a tool that allows you to perform enrichments over gene lists.\n\nAnGeLi has recently been updated to provide 9320 lists, including ontology-based annotations from PomBase (as of 2020-03-04) as well as many additional datasets from the Bähler laboratory.\n\nNew search result download options\n\n2020-03-23\n\nThe PomBase Advanced search has added new options to the data you can download for your query results:\n\n- All physical interactors of a gene product\n- Deletion viability\n- Protein length\n\nPomBase now uses InterPro Version 77.0\n\n2020-03-01\n\nPomBase now uses InterPro Version 77.0, which integrates 145 new methods from the CATH-Gene3D (134), and SUPERFAMILY (11) databases. InterPro cites 59894 publications in PubMed. See the InterPro release notes for further information.\n\nCommunity curation response rate reaches 50%\n\n2020-02-28\n\n789/1587 publications assigned to community members for curation are finished. A big thank you to everyone who has participated so far. For more details, and all our curation metrics, see https://curation.pombase.org/pombe/stats/annotation\n\nA quarter of a million annotations\n\n2020-02-20\n\nPomBase recently reached 250,000 annotations to controlled vocabularies and ontologies. The majority (over 90%) are assigned manually from fission yeast experimental data derived from 3776 publications, most of which report low-throughput, hypothesis-driven experiments.\n\nYou can query and combine any of these data types in the Advanced search.\n\nThank you to everyone who contributed to this significant achievement through community curation.\n\nQuery phenotypes for conditions\n\n2020-02-05\n\nThe PomBase advanced search Advanced search now supports using experimental conditions as search criteria for phenotype annotations. For example, you can now query for genes that show abnormal chromosome segregation mutant phenotypes specifically at high or low temperatures. The search uses the same condition descriptors as Canto and the PomBase web pages.\n\nNote that phenotype queries that have condition constraints can be combined, but pay careful attention to the annotations for the results. Future work will add support for querying for multiple conditions on the same annotation, and for specifying conditions to exclude from results.\n\nLevures, Modèles et Outils 14th International Conference\n\n2020-02-04\n\nThe 14th edition of the “Levures, Modèles et Outils” meeting (LMO14) will be held in July 9-11, 2020, at the University of Strasbourg in France. Registration is open February 3rd to June 30th, and abstracts can be submitted from February 3rd to April 10th. Authors will be notified in early May and the final program will be available in early June.\n\nThe sessions will be diverse and present the latest findings using yeast as a model organism on the following topics:\n\n1. Cell biology, cell cycle, cytoskeleton\n2. Gene expression regulation\n3. Population, functional and evolutionary genomics\n4. Replication, repair and recombination\n5. Transport, sensing and signaling\n6. Pathogenic yeast and filamentous fungi\n7. Tools, resources and databases\n8. New technologies, yeast and industry\n\nPomBase is now an ELIXIR Node Service\n\n2020-01-17\n\nPomBase has been awarded Node Service status by the UK node of ELIXIR. ELIXIR-UK Node Services support the bioinformatics and broader biological research communities by providing training and resources that help researchers to find and share data, exchange expertise, and agree on best practices at national, European and international levels. The review panel describes PomBase as a “mature, leading model organism database which is popular, unique, well used, and has a strong user community.”\n\nNew vectors for simple, reliable S. pombe molecular biology\n\n2020-01-07\n\nTo enable fission yeast researchers to manipulate S. pombe molecular biology reproducibly and easily, Aleks Vještica and Magdalena Marek in Sophie Martin’s lab have designed and constructed a series of simple, fully characterized plasmids.\n\nThe Stable Integration Vector (SIV) series provides a highly modular toolbox to introduce heterologous sequences more stably was possible with than previously available vectors. The toolkit includes antibiotic resistance markers, promoters, fluorescent tags, and terminators, as well as large set of ready-to-use fluorescent probes to mark organelles and visualize cellular processes.\n\nThe work is published in the Journal of Cell Science, and a PomBase publication page is available.\n\nUnique permanent URLs for search results\n\n2019-11-28\n\nAll result pages from the Advanced search now have a unique permanent URL that can be bookmarked and shared with your colleagues.\n\nThe QuiLT and GO slim pages also now have permanent URLs.\n\nBrowser tracks now loadable from publication pages\n\n2019-10-16\n\nData tracks from datasets hosted in the PomBase genome browser can now be browsed and loaded from their respective publication pages. For an example, see Atkinson et al. (2018). Data tracks are now also downloadable from the publication pages.\n\nNew PomBase funding from the Wellcome Trust\n\n2019-10-07\n\nWe are pleased to announce that the recent PomBase application for continued Wellcome Trust funding was successful. Although the grant was not fully funded, we are confident that we can cover the shortfall by small grants for stand-alone projects and collaborations. We would like to thank the pombe community for their support with the application, and the Wellcome Trust for their continued funding. We look forward to supporting your research until 2025 (and beyond).\n\nPomBase now uses InterPro Version 76.0\n\n2019-10-06\n\nPomBase now uses InterPro Version 76.0, which integrates 277 new methods from the CATH-Gene3D (1), PANTHER (178) and CDD (98) databases. InterPro cites 59846 publications in PubMed. See the InterPro release notes for further information.\n\nReplication origin data loaded into JBrowse\n\n2019-08-30\n\nWe have loaded data from: Segurado et al. (2003) “A+T-rich islands”, Hayashi et al. (2007) “Pre-replicative complex localization; early and late firing origins”, and Mickle et al. (2007) “Replication origins with functional classification”.\n\nTo view the tracks, either follow the hyperlinks above to the respective PomBase publication pages, and click on the “view” link after “Datasets from this publication are available in the PomBase JBrowse genome browser”, or go directly to the browser and click on the “select tracks” button to find the tracks manually.\n\nFor anyone new to JBrowse we have a quick start guide.\n\nJoin the conversations on Slack\n\n2019-07-19\n\nThe vibrant fission yeast community now has a Slack channel. Slack provides a forum for the research community. Follow conversations you care about, message colleagues privately, or in groups, ask questions, post responses. All archived and searchable.\n\n- See the PombeSlack flyer for more information, including how to join.\n\n“Fitness Landscape of the Fission Yeast Genome” dataset loaded into JBrowse\n\n2019-07-11\n\nWe have loaded the Grech et al. (2019) “Fitness Landscape of the Fission Yeast Genome” dataset into JBrowse. In this study, transposon mutagenesis libraries were created to map transposon insertion sites in the S. pombe genome. From this data, functional elements of the genome were inferred. The tracks from this study can be loaded by a single click from the linked publication page above\n\nThanks Dan Jeffares for sending us the data.\n\nFor anyone new to JBrowse we have a quick start guide.\n\ntRNA metabolism GO annotation update\n\n2019-05-19\n\nThe process of tRNA metabolism, and the associated molecular functions have recently been reviewed.\n\n- “tRNA metabolic process” annotation\n- genes for “tRNA metabolic process”\n\nPlease let us know if the annotation can be further improved.\n\nCustomisable FASTA download\n\n2019-04-18\n\nYou can now download nucleotide or peptide sequences for genes in Advanced search results in FASTA format, and customise what is included in the FASTA headers (e.g. gene names, product descriptions, sequence coordinates, or various IDs can be included).\n\nNew homology modelling and ortholog links on gene pages\n\n2019-04-18\n\nWe have added new external links to PomBase gene pages for structure and ortholog predictions:\n\n- Protein-specific links to SWISS-MODEL, a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, lead to a SWISS-MODEL Repository page for each sequence and present results. If no structure or model is available, you can either trigger adding an entry to the repository with a single click or easily interactively search for templates and build models in your own SWISS-MODEL workspace.\n\n- Ensembl Fungi Compara and Ensembl Pan-taxonomic Compara links lead to orthology predictions from the Ensembl Compara pipeline for fungi and all species, respectively.\n\n- PANTHER links retrieve gene information, classification, and predicted orthologs.\n\nPomBase InterPro Update\n\n2019-04-17\n\nPomBase now uses InterPro Version 73.0, which integrates 1,531 new methods from the CATH-Gene3D (122), CDD (330), PANTHER (1075), Pfam (2), PROSITE profiles (1) and TIGRFAMs (1) databases, and covers 81.2% of UniProt Knowledgebase release 2019_02.\n\nSee the news item at InterPro for additional information, including release notes.\n\nS. pombe included in Gene Info browser extension\n\n2019-04-16\n\nS. pombe gene information is now included in the Gene Info extension (GIX) for the Chrome and Firefox web browsers. GIX allows you to retrieve information about a gene product directly on any webpage simply by double clicking an official gene name, synonym or supported accession. Searching or double-clicking on text terms retrieves gene function annotation, GO terms, external database links, and interaction data drawn from BioGRID and IntAct. Retrieved gene names are automatically hyperlinked for rapid recursive searches.\n\nGeneInfo is fully open source, available online at GitHub. Tutorial videos, a step-by-step guide, and download links for Firefox Add-ons and the Chrome web storeare available online. GeneInfo was developed by James Knight in the Gingras Lab at the Lunenfeld-Tanenbaum Research Institute in Toronto, Canada.\n\nIntegrated motif search\n\n2019-03-19\n\nThe PomBase motif search has been fully integrated into the website, and allows users to find protein motifs and send them directly to the PomBase advanced search.\n\nICYGMB 2019 - registration open\n\n2019-03-13\n\nRegistration is now open for the 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB), which returns to Gothenburg, Sweden, August 18-22, 2019.\n\nYeast2019 is the meeting of the international yeast research community where the latest, and even unpublished results are exchanged, and new projects, alliances, and collaborations are founded. Featuring 55 confirmed speakers including keynote lectures by Susan Gasser, Roger Kornberg and Frederick Roth, this conference will contain important news and information for all yeast researchers. A do-not-miss-event.\n\nGO slim for any S. pombe gene list\n\n2019-03-05\n\nPomBase’s advanced search now allows you to retrieve GO slim annotations for any set of search results. To find GO slim annotations for your own list of S. pombe genes, use the advanced search “Gene names and IDs” option, and then use the “Slim” button on the search results page.\n\nSee the fission yeast GO slim page and the advanced search documentation for more information.\n\nSouth Eastern Regional Yeast Meeting (SERYM) - registration open\n\n2019-03-04\n\nRegistration is now open for the 26th annual South Eastern Regional Yeast Meeting (SERYM), which will be held April 12-14, 2019, in Atlanta, GA, USA.\n\nFission yeast’s own Susan Forsburg is the keynote speaker. The meeting brings together researchers who use any type of yeast as a model system, covering diverse, interdisciplinary topics from strategies for treatment of fungal disease to modeling human disease in yeast.\n\nIcon: SERYM 2019\n\nInternational Cell Cycle meeting - registration open\n\n2019-02-27\n\nRegistration is now open for the Inaugural Trieste Cell Cycle Meeting, which will be held June 3-6, 2019, in Trieste, Italy.\n\nThis is the first of a planned series of biennial cell cycle meetings that will take place in Europe, and will alternate with the Salk Cell Cycle meetings held on the US west coast.\n\nOrganisers Rob de Bruin, Snezhana Oliferenko, Rosella Visintin and Peter Thorpe hope to see you there!\n\nIcon derived from meeting image; credit: Chantal Roubinet, Baum lab\n\nPublished: Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?\n\n2019-02-20\n\nOur analysis of conserved unknown proteins has now been published in Open Biology. In it, PomBase curators consider the challenges and opportunities that conserved, but persistently unstudied, proteins pose for diverse areas of basic and applied biology. We develop metrics to define unknown lists, provide unknown inventories for human and yeast, and classify S. pombe unknowns by numerous orthogonal attributes, all with a view to drawing attention to the unknowns to alleviate their neglect.\n\nPombe 2019 - registration open\n\n2019-02-15\n\nRegistration for the 10th International Fission Yeast Meeting is now open!\n\nThe conference will take place July 14-19, 2019, in Barcelona, Spain. Early registration closes on April 15th — or when capacity is reached. Please see the conference website for more information, including registration final deadline and costs (some travel grants are available), abstract submission, programme, accommodation, and logistics.\n\nVal Wood wins Biocuration society award\n\n2019-02-12\n\nCongratulations to PomBase project leader Val Wood, who has received the 2019 Exceptional Contributions to Biocuration Award from the International Society for Biocuration. Read more at the ISB site\n\nImproved disease association dataset released\n\n2019-01-09\n\nWe are pleased to announce the release of our improved human disease mappings dataset. This dataset connects human disease causing genes to their S. pombe orthologs.\n\nDiseases are now mapped to the Disease Ontology (DO) and the dataset has been extended by data from Malacards. All disease associations can be accessed from the top level disease page. A disease slim has been created to facilitate browsing of disease categories. Currently, 907 S. pombe genes are associated with disease (up from 610 in the original dataset). This number is due to increase as mappings are still in progress.\n\nMany thanks to DO and Malacards for help in improving this annotation set. Icon courtesy of Julie McMurry.\n\nMitochondrial GO annotation update\n\n2018-12-17\n\nResponding to increasing interest in mitochondrial biology, especially relating to ageing, neurogenerative diseases, and processes at the ER-mitochondrion interface, we have reviewed S. pombe mitochondrial GO annotations. Although there is still relatively little fission yeast-derived experimental data in this area, we have refined many inferred annotations for mitochondrial complexes and sub-components as well as some for processes.\n\nYou can see all 753 S. pombe mitochondrial annotations on the ontology term page for mitochondrion (GO:0005739).\n\nIcon courtesy of Reactome.\n\nNew nucleosome occupancy maps loaded\n\n2018-12-03\n\nWe have loaded the nucleosome occupancy maps as described in González et al. (2016) PMID: 27662899. This dataset was generated using the paired-end sequencing protocol of Illumina and thus those maps are of higher resolution than those made with single-end (SE) sequencing hosted in the browser since before.\n\nHere is a link that loads the tracks in PomBase JBrowse. And here is a link to our JBrowse quickstart guide.\n\nMany thanks to Paco Antequera for sending us the bigwig files! If you would like us to load any datasets then please get in touch.\n\nSee your genes in a QuiLT\n\n2018-11-21\n\nPomBase now offers a new way to display gene lists graphically based on multiple orthogonal annotation types — the Quick Little Tool (QuiLT) for visualisation.\n\nInspired by our recent analysis of conserved unstudied proteins (see figures 4 and S1 in the manuscript at bioRxiv), QuiLT allows you to create a similar figure for any gene list you create or import using the advanced search. To use QuiLT, follow the link to your search results, then click the “Visualise” button. QuiLT visualisation is also available from the PomBase pages that list genes annotated to an ontology term, and on the Priority unstudied genes page.\n\nTo see the Unknowns dataset in QuiLT, visit the unknowns results page and click “Visualise”.\n\nThe QuiLT display is interactive, and you can:\n\n- Highlight subsets of the list, and filter the display\n- Toggle annotation types on and off\n- Reorder the list to focus on features of most interest\n- Download the image\n\nSee the QuiLT documentation for more information, and contact the curators if you have comments, questions or suggestions.\n\nMany thanks to our star (and only) programmer, Kim Rutherford, for developing QuiLT.\n\nFission yeast transmembrane transport overhaul\n\n2018-11-20\n\nThe Gene Ontology “transmembrane transport” branch has recently been substantially revised. In line with these revisions, PomBase has standardised gene product descriptions for transporters, and overhauled GO annotations to be as complete and comprehensive as possible based on current knowledge.\n\nIcon courtesy of Reactome.\n\nHidden in plain sight: What remains to be discovered in the eukaryotic proteome?\n\n2018-11-17\n\nIn a new publication, PomBase curators consider the challenges and opportunities that conserved, but persistently unstudied, proteins pose for diverse areas of basic and applied biology. To draw attention to these proteins, we develop metrics to define unknown lists, provide unknown inventories for human and yeast, classify S. pombe unknowns by numerous orthogonal attributes, and speculate about reasons for their neglect.\n\nA pre-publication manuscript is available at bioRxiv.\n\nPomBase in your pocket\n\n2018-11-14\n\nOur usage statistics informed us that over 20% of devices accessing PomBase are smartphones or tablets. We therefore spent some time optimizing the display for small screens. We hope that you will continue to enjoy PomBase on the go!\n\nCelebrating 20 years of GO\n\n2018-11-08\n\nPomBase curators are major contributors to the Gene Ontology (GO) project — ontology content, annotations, and QC procedures — and co-authors on the new GO NAR Database Issue paper.\n\nWe recommend citing the GO and PomBase NAR papers when you use GO data in your analyses.\n\nRNA central and PomBase\n\n2018-11-06\n\nRNAcentral is a comprehensive database of non-coding RNA sequences. PomBase is an RNAcentral Consortium member, and all of the curated non-coding RNAs from PomBase will be available in RNAcentral soon. For more information, see their recent NAR Database Issue paper, as well as current search results for S. pombe RNAs.\n\nNew PomBase genomic region graphics\n\n2018-10-23\n\nPomBase gene pages now use interactive graphics from PomBase JBrowse to depict the genomic region around the gene. Drag to scroll left and right, double-click to zoom in, shift-double-click to zoom out, and click a feature to see details in a popup. The “Full-screen view” link in the corner opens the fully functional JBrowse in a new tab or window. Reloading a gene page restores the display to the default location and zoom level.\n\nPomBase NAR Database Issue\n\n2018-10-15\n\nOur NAR database update “PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information” is now available. We have updated the Citing PomBase to recommend citing this new paper. Thank you all for guiding the development of the new, improved PomBase, and for your continued usage, curation contributions, and suggestions!\n\nFungal Pathogen Genomics Course 2019 - registration open\n\n2018-10-10\n\nRegistration for the 2019 Fungal Pathogen Genomics Course is now open. The course is hosted by Wellcome Genome Advanced Courses and Scientific Conferences, and will take place May 7-12, 2019, at the Wellcome Genome Campus, Hinxton, UK. Course content provides hands-on training on how to: - Take advantage of unique tools offered by FungiDB, EnsemblFungi, PomBase, SGD/CGD, and MycoCosm/JGI; - Develop testable hypotheses; - Investigate transcriptomics, proteomics and genomics datasets across multiple databases and different user interfaces. Please see the course website for more information, including how to apply, costs (limited bursaries are available), programme, and logistics.\n\nTranscript tracks from Atkinson et al. (2018) loaded\n\n2018-10-06\n\nWe are very pleased to announce that we have loaded the transcript tracks from Atkinson et al. (2018) into the PomBase JBrowse genome browser. For a brief introduction to getting started with PomBase JBrowse, please see our documentation page. If you have published data that you would like to see hosted, please get in touch.\n\npombelist changes\n\n2018-08-31\n\nThe pombe community mailing list, “pombelist”, is now hosted by the University of Cambridge. The new address for posting messages is pombelist@pombase.org. The link to subscribe has also changed.\n\nNew genome browser tracks\n\n2018-05-28\n\nWe are very pleased to announce that we have loaded a number of new datasets into the PomBase [JBrowse genome browser (https://www.pombase.org/jbrowse/). These include:\n\n- Thodberg et al. (2018) - CAGE-defined transcription start sites across 5 different conditions\n- Yadav et al. (2012) - G(x) scores specifying the amount of free energy needed to melt base pairs in the DNA duplex at different genomic locations\n- A PomBase-generated dataset of promoter elements across the genome (computational matching of the consensus promoter sequences to the reference DNA sequence)\n- Intron branch points from Bitton et al. (2014) which was also available in the Ensembl browser.\n\nFor anyone wanting a quick introduction to our genome browser, Antonia Lock has written “Getting started with PomBase JBrowse”, a basic guide that covers loading tracks, navigating the browser, what metadata we provide, and more.\n\nNew book chapter about PomBase\n\n2018-05-22\n\nPomBase has a new book chapter in Eukaryotic Genomic Databases (Methods and Protocols). This chapter provides insight into the curation philosophy and data organization at PomBase, and provides a guide to using PomBase tailored for infrequent visitors and anyone considering extending their research to include S. pombe. The chapter is free to download courtesy of the Wellcome Trust.\n\nPomBase releases JBrowse\n\n2018-04-16\n\nPomBase has now implemented JBrowse, from the GMOD project, as its genome browser. The new browser offers a number of improvements over the old:\n\n- Quick, responsive scrolling and zooming\n- Simple track selection interface\n- Intuitive controls\n- Simplified data submission pipeline behind the scenes\n- More informative track metadata\n\nIn memory of André Goffeau\n\n2018-04-05\n\nSadly, PomBase staff and the fission yeast community note the death of André Goffeau on April 2, 2018. In addition to initiating and coordinating the sequencing of the budding yeast genome, Prof. Goffeau will be remembered for his contributions to the fission yeast genome project and for his knowledge, leadership, and friendship.\n\nCongratulations to GSA award winners\n\n2017-11-24\n\nThe Genetics Society of America (GSA) has announced two award winners familiar to the model organism database world:\n\n- Ira Herskowitz Award: Mike Cherry, Stanford University\n- Lifetime Achievement Award: Steve Oliver, University of Cambridge\n\nThe awards will be presented at the next Yeast Genetics Meeting, at Stanford University in August 2018. Congratulations and thanks to Mike and Steve!\n\nNew, improved PomBase goes live\n\n2017-10-24\n\nThe new PomBase web site, which has been under development during 2017, has been released. The new site features:\n\n- Nightly data updates\n- New publication pages\n- New genotype pages\n- Improved ontology term pages\n- Improved summary views for annotation displays\n- Phenotype annotation display filtering\n- Faster querying in the advanced search\n- Front page research and community curation highlights\n- Streamlined back-end data storage and retrieval\n\nWe thank the members of the fission yeast research community who have followed its progress via the preview site, and welcome feedback from all users.\n\n9th International Fission Yeast Meeting - early registration closes soon\n\n2016-12-11\n\nReminder: early registration for the 9th International Fission Yeast Meeting in Banff closes Dec. 31, 2016. Please see the conference website at www.pombe2017.com for details.\n\n9th International Fission Yeast Meeting registration open\n\n2016-10-31\n\nRegistration for the 9th International Fission Yeast Meeting is now open. The meeting will be held in Banff, Canada from May 14-19, 2017. Early registration closes Dec 1, 2016! Please see our website at www.pombe2017.com for details. We look forward to seeing you in Banff!\n- Conference Organizers: Dallan Young, Gordon Chua, Paul Young\n\nPomBase data update 2016-10-19\n\n2016-10-19\n\nWe have updated the data available on the PomBase web site to include manual curation through September 11, 2016.\n\nShow your support for database funding\n\n2016-06-27\n\nIn 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.\nThe Genetics Society of America website where the letter can be viewed and signed is at http://www.genetics-gsa.org/MODsupport\nPlease 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\n\nOur model organism database commentary\n\n2016-06-15\n\nSeveral 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:\nOliver SG, Lock A, Harris MA, Nurse P, Wood V. 2016. Model organism databases: essential resources that need the support of both funders and users.\nBMC Biol. 2016 14(1): 49. doi: 10.1186/s12915-016-0276-z. PMID:27334346\n\nPomBase data update 2016-05-31\n\n2016-05-31\n\nWe have updated the data available on the PomBase web site to include manual curation through May 12, 2016.\n\nPomBase data update 2016-05-09\n\n2016-05-09\n\nWe have updated the data available on the PomBase web site to include manual curation through April 8, 2016.\n\nPomBase data update 2016-04-11\n\n2016-04-11\n\nWe have updated the data available on the PomBase web site to include manual curation through March 9, 2016.\n\nImportant: We have corrected a problem that made erroneous interaction data and literature appear on some gene pages.\n\nThe gene pages now include interaction data from the Vo et al. proteome-wide study (curated by BioGRID and imported into PomBase):\nVo 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.\n\nThe genome browser now includes transcriptome data published in:\nEser 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.\n\nPomBase data update 2016-02-11\n\n2016-02-11\n\nWe have updated the data available on the PomBase web site to include manual curation through January 25, 2016.\nThe genome browser includes variation data, in tracks under “Variation”, from natural S. pombe isolates, published in:\nJeffares 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\n\nNew files are now available from the PomBase FTP site, and are linked from pages in the Download Datasets area:\n\n- Non-coding RNA sequence feature coordinates (available via the Data Mappings page);\n- Protein features, such as domains and family assignments (available via the Protein Datasets page);\n- Protein modification annotations (also in Protein Datasets).\n\nThe New and Removed Genes page has been updated to reflect recent deletions and merges.\nNote: 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.\n\nPomBase data update 2015-12-02\n\n2015-12-02\n\nWe have updated the data available on the PomBase web site to include manual curation through November 9, 2015, including 340 community-curated publications.\n\nNew Advanced Search features\n\n2015-12-02\n\nWe have introduced new features to the Advanced Search:\n\n- 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.\n- You can now query for genes that interact genetically or physically with a specified gene.\n- 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.\n\nNew genetics primer for fission yeast\n\n2015-10-19\n\nA 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\n\nHoffman 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\n\nPomBase data update; viability summary correction alert\n\n2015-09-28\n\nWe have updated the data available on the PomBase web site to include manual curation through September 6, 2015.\n\nErrors 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.\n\nPomBase data update with multi-allele phenotypes\n\n2015-09-03\n\nWe have updated the data available on the PomBase web site to include manual curation through August 13, 2015, including 300 community-curated publications.\n\nPomBase 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.\n\nThe genome browser now includes data tracks for two more publications:\nDNA polymerase usage from:\nDaigaku 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\nPromoters and transcription start sites from:\nLi 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\n\nCodon 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.\n\nThe gene page section that was formerly misnamed “species distribution” is now called “taxonomic conservation”.\n\nPomBase data update 2015-06-16\n\n2015-06-16\n\nWe 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!\n\nCanto downtime & new version\n\n2015-05-26\n\nCanto, 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.\nThe 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.\nWe will announce when the new version of Canto is released to the public.\n\nPomBase data update 2015-05-26\n\n2015-05-26\n\nWe have updated the data available on the PomBase web site to include manual curation through May 8, 2015, including 265 community-curated publications.\n\nPombe 2015 travel fellowships\n\n2015-04-23\n\nApplications 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).\n\nPomBase data update 2015-04-19\n\n2015-04-19\n\nWe 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.\n\nPombe 2015 poster abstract deadline extended\n\n2015-04-19\n\nThe 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.\n\nPombe 2015 abstract deadline approaching\n\n2015-04-09\n\nAbstracts 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.\n\nPomBase data update 2015-03-23\n\n2015-03-23\n\nWe 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.\n\nPombe 2015 registration now open\n\n2015-02-26\n\nRegistration for Pombe 2015: 8th International Fission Yeast Meeting is now open at the conference web site, https://amarys-jtb.jp/web/Pombe2015/index.html\n\nThe registration deadline is 17 May 2015.\n\nThanks to Yasushi Hiraoka for this item.\n\nPomBase data update 2015-02-16\n\n2015-02-16\n\nWe 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.\n\nPomBase data update 2015-01-26\n\n2015-01-26\n\nWe 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.\n\nNew compact GO annotation display\n\n2014-12-10\n\nTo 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.\n In addition, the top of the Biological Process table now lists any GO slim terms applicable to the gene.\n\nesyN network visualizations in PomBase\n\n2014-12-10\n\nPomBase 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.\nOn gene pages, we have links to gene-specific interaction networks in esyN in the table headers of the Interactions sections:\n\n- The Genetic Interactions section links to all interactions centred on the gene and curated in BioGRID\n- The Physical interactions section has links to two datasets:\n - All physical interactions curated in BioGRID for the gene\n - Interactions for the gene in the PomBase High Confidence Physical Interaction Network (HCPIN)\n\nWe 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).\n\nPomBase data update 2014-11-12\n\n2014-11-12\n\nWe 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:\nGraml 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.\n\nThe genome browser now includes tracks for intron branch point data from:\n\nBitton 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.\n\nWe 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.\n\nPomBase data update 2014-09-16\n\n2014-09-16\n\nWe 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.\n\nPomBase data update 2014-08-18\n\n2014-08-18\n\nWe 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.\n\nPomBase data update 2014-07-17\n\n2014-07-17\n\nWe 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:\n\nKoch 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\nWe have also made corrections to some residue positions affected by sequence updates in one of the modification datasets we added last month:\n\nCarpy 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\n\nPomBase data update 2014-07-08\n\n2014-07-08\n\nWe 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.\n\nThe gene pages also now display protein modification data from two large-scale datasets:\n\n- 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\n- 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\n\nLink updated 2021-02-04\n\nGene Ontology publication on annotation extensions\n\n2014-06-29\n\nPomBase 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:\n\nHuntley, 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\n\nPomBase data update 2014-05-15\n\n2014-05-15\n\nWe 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.\n\nThank you to all who have done, or are doing, paper curation in Canto. Over 159 community-curated papers are now included in PomBase.\n\nThere 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.\n\nAs usual, please don’t hesitate to alert us of any other problems with data or site performance, or if you have any questions.\n\nSincerely yours,\nThe PomBase Staff\n\nPomBase data update 2014-03-20\n\n2014-03-20\n\nData 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.\n\nPomBase data update 2014-02-20\n\n2014-02-20\n\nWe 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.\n\nWe have made some improvements to the gene pages. Highlights:\n\n- The Sequence section now has links to NCBI BLAST as well as Ensembl BLAST.\n- The External References section now links to the Pomb(A) polyadenylation viewer.\n\nIn the genome browser, new data tracks are now available for data from these publications:\n\n- 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\n- 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\n- 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)\n- 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\n\nNow 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.\nGenome 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.\n\nHuman ortholog data correction coming next month\n\n2014-02-19\n\nWe 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.\n\nPomBase data update 2013-12-08\n\n2013-12-08\n\nWe 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.\n\n2021-08-18: Updated to remove out-of-date links (events are now listed only as news items).\n\n2013 meeting mini-reviews published\n\n2013-11-24\n\nA 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\n\n(Thanks to Jürg Bahler for this item)\n\nPomBase survey results available\n\n2013-11-20\n\nThe 2013 PomBase user survey closed at the end of October, and the results are available here (PDF at FTP site). Some highlights have been sent to the pombe mailing list. Many thanks to all who completed the survey.\n\nLink updated 2021-02-04\n\nNew “Target Of” gene page section\n\n2013-10-27\n\nWith 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.\n\nPomBase data update 2013-10-21\n\n2013-10-21\n\nThe 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:\n\n- 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\n- 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\n\nPomBase User Survey open\n\n2013-09-18\n\nTo 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!\n\nhttps://www.surveymonkey.com/s/NDM2BQX\n\nPomBase data update 2013-09-15\n\n2013-09-15\n\nWe 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.\nWe also have an updated version of the S. pombe/human ortholog table available upon request.\n\nSend HTP data to PomBase\n\n2013-08-18\n\nAt 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.\n\nConnecting With PomBase\n\n2013-07-29\n\nTo 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+.\n\nLinks to these are also available from the front page of the PomBase.org site.\n\npombelist has moved\n\n2013-07-21\n\nUpdate: This item dates from July 2013, and the links in it no longer work. \\ Please see the Fission Yeast Community page for the current mailing list link. \\ (2020-02-18)\n\nThe 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.\n\nPomBase website update\n\n2013-07-18\n\nWe’d like to highlight a few improvements we’ve just made to the PomBase website. Most of the changes affect the gene pages:\n\n- The basic information display at the top of each gene page is more compact.\n- 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).\n- Annotation extensions for GO are displayed using human-friendly text instead of internal “relation” labels.\n- The Quick Links box can now be collapsed and expanded by clicking its header.\n- Display of modification annotations using PSI-MOD is improved.\n\nIn 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.\n\nPomBase launches community curation\n\n2013-06-23\n\nAt 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.\n\nPomBase data update 2013-06-20\n\n2013-06-20\n\nPomBase 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.\n\nPomBase data update\n\n2013-05-20\n\nWe have updated the data available on the PomBase web site. The data now includes manual curation through 13 May, 2013.\n\nGeneDB S. pombe decommissioned\n\n2013-05-13\n\nAs 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.\n\nQuantitative gene expression data available in PomBase\n\n2013-05-07\n\nWe 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:\n\n- 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.\n- Wu JQ, Pollard TD. 2005. “Counting cytokinesis proteins globally and locally in fission yeast.” Science 310:310-314.\n\nWe 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.\n\nWe 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\nhttps://www.pombase.org/data/names_and_identifiers/gene_IDs_names.tsv\n\nLink updated 2021-02-04\n\nCarl Singer Foundation Established\n\n2013-04-11\n\nCarl 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.\nCarl’s family would be happy to receive memories of Carl’s life at regards [at] singerinstruments.com.\n\nH/T SGD\n\nPombe 2013: registration & abstracts by Mon 8th April\n\n2013-04-02\n\nDear Pombe Fans,\n Please remember the imminent deadline (Monday 8th April) to register and submit abstracts for Pombe 2013: http://events.embo.org/13-pombe\n Abstracts are also required from all who have already been invited to talk.\n And do book your accommodation if you haven't yet done so.\n More details are in previous email forwarded below.\n Cheers,\n -Jürg & Jacky\n From: On Behalf Of Bahler, Jurg\n Sent: 18 March 2013 17:49\n To: pombelist at sanger.ac.uk\n Subject: [Pombelist] Pombe 2013: Accommodation, registration & abstracts\n Dear Pombe Afficionados,\n Only three weeks left to register and submit abstracts for Pombe 2013, by Monday 8th April: http://events.embo.org/13-pombe\n Speakers for 10 plenary talks and all workshop talks will be selected from abstracts, and there will be attractive poster prizes.\n Payment is only requested after registration, by 10th May.\n 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\n 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.\n We highly appreciate all the generous contributions from our sponsors so far:\n Platinum: EMBO\n Gold: Biochemical Society, Genetics Society, Formedium, Sunrise Science Products, Singer Instruments, F1000Research, PomBase/Wellcome Trust\n Silver: MDPI - Open Access Publishing, Hybrigenics, Infors, Life Technologies, Bioneer\n Bronze: Nature Communications, m2p labs, Imsol, Open Biology\n We look very much forward to welcoming you in London this June!\n All the best,\n -Jürg & Jacky\n\nData update on PomBase web site\n\n2013-04-01\n\nWe have once again updated the data available on the PomBase web site. The data now includes manual curation through March 6, 2013.\nWe 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.\nYou should also see a few small improvements in the site:\n\n- Ontology term pages now display the text definition for each term.\n- FASTA sequence retrieval should be quicker, and less likely to time out, for large gene lists.\n- There has been some tidying of the display of “extension” data for GO and phenotype annotations.\n\nLast 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.\nAs usual, please don’t hesitate to alert us of any other problems with data or site performance, or if you have any questions.\n\nSpeed improvements and new data on PomBase web site\n\n2013-03-01\n\nWe 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.\nWe 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.\nWe 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.\n\nNew data and new features on PomBase web site\n\n2012-11-06\n\nWe are pleased to announce that we have updated both data and web site features for PomBase.\n\nMost importantly, we have added new data types, and upgraded the gene pages to display them.\n\nWe 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.\n\nNew annotation types:\n\n- 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.\n- 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.\n\nYou can see these new data types on many gene pages, such as cdc2 or pka1.\n\nNew web site features:\n\n- Annotation display - Gene page GO and phenotype displays have been revamped to show new annotation types described above.\n- Ontology term pages - Each ontology term ID now links to pages with information about the term and lists of genes annotated to it.\n- Ontology graph links - GO and phenotype annotation sections now include links to graphical ontology displays in the genome browser.\n- Sequence highlighting - Sequence download now offers an option to show colour highlighting of regions such as UTRs, introns and exons.\n- 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.\n- Protein family information is now included in the Protein Features gene page section.\n- The Protein Feature section includes a link to the Pfam entry for a protein.\n- Transcript source data (e.g. for UTR coordinates) is now displayed in the Transcript Features section.\n- A Documentation page contains links to relevant portions of the Ensembl Genomes documentation. (More documentation will be added over the coming months.)\n\nWhat are annotation extensions?\n\nAnnotation 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.\n\nThe information in GO annotation extensions encompasses several effector-target relationships, such as\n\n- localisation dependencies\n- 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\n- activators and inhibitors\n- regulation targets of signalling pathways or transcription factors\n\nAdditional 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).\n\nYou may also find the GO wiki page on annotation extensions informative, although it is primarily aimed at curators.\n\nAnnotation 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.\n\nPomBase web site fully live\n\n2012-07-01\n\nNote (2023-06-09): This is an archived news item about PomBase V1. See the documentation page to learn new Advanced search in PomBase V2.\n\nWe 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.\n\nMore recent data, reflecting additions and changes through March 20, 2012, are now available on gene pages and in search results.\n\nThe 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\n\nThe Advanced Search also now offers:\n\n- options to search GO, FYPO, and other ontologies by term name or ID;\n- autocomplete for ontology term name search;\n- ability to search for genes in a region, such as centromeres or telomeres;\n- improved organization of filter selections.\n\nWe 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.\nIn addition, numerous minor improvements have been made. Please send any questions or comments on the PomBase web site to us at .\n\nPomBase preview launch\n\n2011-11-27\n\nA 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.\n\nPomBase NAR paper published online\n\n2011-10-27\n\nA 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.\n\nGeneDB (S. pombe) now uses the latest release of the Pfam protein family database(25.0).\n\n2011-04-28\n\nSchizosaccharomyces Comparative Genome Paper Published\n\n2011-04-21\n\nA paper describing the major findings of the Schizosaccharomyces Comparative Genome Project was published today in Science Express and reported changes are included in GeneDB.\n\nFurther details are described in the pombe mailing list posts:\n\n- Schizosaccharomyces Comparative Genome Paper Published\n- Import of the fission yeast revisions from the Broad Institute comparative genome paper into GeneDB.\n\nGenome reappraisal reveals new genes and revised gene structures\n\n2011-02-01\n\nFurther information on the pombe mailing list.\n\nAnnotated transcription start and termination sites for fission yeast\n\n2011-01-31\n\nFurther details are available on the pombe mailing list.\n\nAnalysis of Fission Yeast Deletion Publication\n\n2010-05-15\n\nThe analysis of the fission yeast deletion collection is now published online in Nature Biotechnology.\n\nFunding for PomBase\n\n2010-02-28\n\nFunding was awarded by the Wellcome Trust for a fission yeast Model Organism Database, PomBase.\n\nFission yeast is one of the 12 key organisms of the reference genomes project\n\n2009-11-30\n\nFission 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.\n\nGeneDB (S. pombe) now uses the latest update to Pfam, release 24.0\n\n2009-10-31\n\nGeneDB (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).\n\nFission yeast in Ensembl Fungi\n\n2009-09-30\n\nThe fission yeast genome and annotation dataset is now available as part of Ensembl Fungi.\n\nGeneDB is now using Version 23 of the Pfam protein family database.\n\n2009-08-31\n\nGeneDB 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.\n\nS. pombe GeneDB now includes “deep links” to the Biological General Repository for Interaction Datasets (BioGRID)\n\n2008-11-30\n\nS. 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.\n\nGlobal sequence and chip study examines eukaryotic transcription\n\n2008-04-30\n\nDynamic 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.\n\nThe h- mating type region has been provided\n\n2008-01-31\n\nThe h- mating type region has been provided by Xavier Marsellach and Lorena Aguilar.\n\nBaumann and Zakian labs identify telomerase RNA\n\n2007-12-31\n\nBaumann and Zakian labs identify elusive telomerase RNA (PMID:18157152 and PMID:18157149)\n\nWellcome Trust Advanced Course ’Genome-wide approaches with fission yeast\n\n2007-09-30\n\nWellcome Trust Advanced Course ‘Genome-wide approaches with fission yeast’ held in Hinxton.\n\n4th International Fission Yeast Meeting\n\n2007-05-31\n\n4th International Fission Yeast Meeting held in Copenhagen.\n\nGeneDB representation of the fission yeast data moved from contigs to chromosomes\n\n2006-12-31\n\nGeneDB representation of the fission yeast data moved from contigs to chromosomes. See the pombelist archive for details.\n\nYeast Special Issue from the 2006 European Fission Yeast Meeting\n\n2006-09-30\n\nThe 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.\n\nThe first fission yeast whole proteome localization study is now published\n\n2006-06-30\n\nThe first fission yeast whole proteome localization study is now published: Matsuyama A. et al (2006): ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat Biotech 24, 841-7.\n Fission yeast database survey\n\n2006-04-30\n\nThe fission yeast database survey is now closed. You can view the survey results here.\n\nEuropean Fission Yeast Meeting\n\n2006-03-17\n\nThe 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).\n\nComparative Genomics of Eukaryotic Microorganisms\n\n2005-11-16\n\nComparative Genomics of Eukaryotic Microorganisms:\nEukaryotic Genome Evolution, Approaches with Yeasts and Fungi\n\nThis conference took place from 12th-17th November 2005 in Sant Feliu de Guixols, Spain. Full details can be found here.\n\nSecond East Coast Regional pombe Meeting\n\n2005-11-12\n\nSecond East Coast Regional pombe Meeting\nThis meeting took place from November 11-13, 2005 in Miami Beach, Florida.\n\nGeneral Repository for Interaction Datasets\n\n2004-08-31\n\nA project to record published genetic and physical interactions is underway with Mike Tyers and the GRID group at Toronto.\n\nThe Third International Fission Yeast Meeting\n\n2004-08-29\n\nThe meeting was held at UC San Diego on August 24-29, 2004.\n\nMethods Volume 33 Issue 3\n\n2004-04-30\n\nThis 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 for details of the papers including PMIDs.\n\n2021-08-18: Updated to remove out-of-date link.\n\nRecent Genome wide surveys\n\n2003-10-31\n\nCorrelations Between Gene Expression and Gene Conservation in Fission Yeast. Mata J, Bahler J. Genome Res. 2003 Nov 12 PMID:14613978\nFELINES: 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\nGenome-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\nRetrotransposons and their recognition of pol II promoters: a comprehensive survey… Bowen NJ et al Genome Res. 2003 Sep;13(9):1984-97. PMID:12952871\n\nThe ‘new’ fission yeast book is now published\n\n2003-08-31\n\nEgel, R., Copenhagen, Denmark (Ed.) The Molecular Biology of Schizosaccharomyces pombe Genetics, Genomics and Beyond ISBN:3-540-00693-1\n\nSchizosaccharomyces pombe Essential Genes: A pilot Study\n\n2003-02-28\n\nDecottignies A, Sanchez-Perez I, Nurse P Genome Res. 2003 Mar;13(3):399-406. PMID:12618370\n\nGlobal transcriptional responses of fission yeast to environmental stress\n\n2002-12-31\n\nChen 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\n", + "content" : "\n\nPomBase gene pages now include a protein feature widget. This tool shows protein features in the context of amino acid sequence. It includes:\n\n- amino acid substitution positions\n- Pfam domains\n- protein modifications\n- protein properties: low complexity regions, disordered regions, coiled coil regions and predicted trans-membrane domains\n\nHover over features for more information, such as allele descriptions and Pfam domain IDs.\n\n[Protein feature viewer widget - cdc15 gene page]\n\nFollow the “View all protein features …” link for a detailed view on the dedicated protein features page that includes:\n\n- details of the individual amino acid substitution allele changes\n- partial amino acid deletions\n\n[Protein feature viewer details page for cdc15]\n\nThanks to the team at RCSB PDB for providing the Open Source software used to implement this feature.\n", + "heading" : "Protein feature viewer added to gene pages", + "id" : "news/2023-07-27-protein-feature-viewer" + }, + { + "content" : "\n\nProtein feature viewer added to gene pages\n\n2023-07-27\n\nPomBase gene pages now include a protein feature widget. This tool shows protein features in the context of amino acid sequence. It includes:\n\n- amino acid substitution positions\n- Pfam domains\n- protein modifications\n- protein properties: low complexity regions, disordered regions, coiled coil regions and predicted trans-membrane domains\n\nHover over features for more information, such as allele descriptions and Pfam domain IDs.\n\n[Protein feature viewer widget - cdc15 gene page]\n\nFollow the “View all protein features …” link for a detailed view on the dedicated protein features page that includes:\n\n- details of the individual amino acid substitution allele changes\n- partial amino acid deletions\n\n[Protein feature viewer details page for cdc15]\n\nThanks to the team at RCSB PDB for providing the Open Source software used to implement this feature.\n\nReaction diagrams on term pages\n\n2023-06-19\n\nWhere available, we now show the reaction diagram from Rhea on GO function term pages. This feature is possible thanks to the great work of Rhea.\n\nSee the GO:0003849 term page for an example.\n\n[]\n\nCuration update - “nonsense mutation” merged into “partial amino acid deletion”\n\n2023-04-26\n\nWe have decided to merge the allele type “nonsense mutation” into “partial amino acid deletion”. This has mainly been driven by the fact that allele types that combine different variants require new types, such as “amino_acid_deletion_and_mutation”, “amino_acid_insertion_and_deletion”, etc. Otherwise, we would have ended up with many more types, and at the gene product level (which is what we describe in PomBase in phenotype interactions), both truncations are equivalent. In the next update, this allele type will not be available in Canto.\n\nIn any case, even if two alleles produce the same truncation, such as ase1-D13* or ase1Δ(13-731), they would still have separate entries in PomBase, and they may have different phenotypes. We are only assigning them the same allele type.\n\nIf for your analysis you need to make a distinction between the two using our allele dataset allele dataset, you can always check the “Allele description” field for the presence of the “*” character to tell whether an allele includes a nonsense mutation.\n\nExperimental structures from PDB on gene pages\n\n2023-02-22\n\nThe experimental protein structures from PDB are now embedded on the PomBase gene pages using Mol*. For example: lsm7/SPCC285.12 gene page\n\nIf you select the “PDB structures” view on a gene page, experimental structures will set as your default. AlphaFold predictions will be shown for genes where an experimental structure are not available.\n\nWe now also display the structures on the associated publication page. For example: PMID:31010807 Garg et al.\n\nTo help locate proteins with experimental protein structures (currently 375), we have added a new query option to the “Advanced search”, currently under “commonly used queries”: “Proteins with PDB structures”\n\n[PDB structures on the lsm7 gene page]\n\nAlphaFold protein structure on gene pages\n\n2023-02-02\n\nAlphaFold protein structure are now embedded on the PomBase gene pages. We hope to embed the experimental structures from PDB in the near future.\n\n[Example from the mvp1 gene page]\n\nRevised canonical 5’ UTRs\n\n2023-01-24\n\nWe have revised the curated 5’UTRs using Transcription Start Sites (TSS) data (in vegetative growth/ minimal media) from the Cap Analysis of Gene Expression (CAGE) data provided by Thodberg et al. All new gene structures were manually reviewed, around ~80 protein features had N-terminal coordinate revisions to align with TSS data.\n\nGlobal Core Biodata Resource status for PomBase\n\n2022-12-15\n\nWe are very pleased to announce that PomBase has been selected as one of the first Global Core Biodata Resource (GCBR) — a collection of 37 resources whose long term funding and sustainability is critical to life science and biomedical research worldwide. This accreditation recognizes PomBase as a primary knowledge base (adding value to data through expert curation) and as a crucial component of the research ecosystem. The candidate biodata resources were assessed against a series of rigorous criteria that included their scientific focus, the size and reach of their user communities, their quality of service, their governance, and their impact on global research.\n\nThank you to the entire community, especially the community curators who contribute regularly to our content, and our Scientific Advisory Board for their help and support.\n\nFor more information about the Global Biodata Coalition and PomBase’s new status, see the full press release.\n\nNext PombeTalks: Wednesday, December 14th\n\n2022-12-08\n\nThe next online PombeTalks will take place on Wednesday, December 14th. These talks are virtual seminars by and for the fission yeast community and friends.\n\n8:00 San Francisco; 11:00 NY; 16:00 London; 17:00 Paris; 20:30 Delhi, 23:00 Beijing; midnight Tokyo\n\nThis will be our last PombeTalks of 2022 before taking a winter break. The speaker will be:\n\n- Kristi E. Miller\n “The fission yeast cell size control system integrates pathways measuring cell surface area, volume and time”\n\nIt will be followed by some sum up/ feedback about PombeTalks from the organizing committee.\n\nSurvey\n\nPlease help us improve PombeTalks even more by taking this quick survey\n\nZoom details\n\nTopic: PombeTalksS308 Zoom Meeting\nDate: Dec 14th\nMeeting ID: 975 0331 6190\nPassword: will be sent the day of the meeting\n\nSlack\n\nFor more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nQuerying by RNA length in the Advanced Search tool\n\n2022-12-07\n\nYou can now query the RNA length of genes (spliced or unspliced) under the “Transcripts and exons” query grouping in the Advanced search.\n\nYou can also add RNA sequence length as a field in tables downloaded from the query builder.\n\n[RNA length queries are available under the “Transcripts and exons” tab]\n\nGenetic Interaction annotation model updated\n\n2022-11-29\n\nWe have recently implemented an improved way to annotate and display genetic interactions so they are linked to phenotype annotations and alleles.\n\nPreviously, our Genetic Interaction annotations only mentioned the interacting genes and the type of genetic interaction. For example, if a strain with genotype asp1-H397A has the phenotype decreased acid phosphatase activity affecting activity of pho1, but this phenotype is suppressed when rhn1 is deleted in that strain, we would annotate that the genes asp1 and rhn1 are part of a Phenotypic Suppression interaction.\n\n[GI old format]\n\nWe continue to display interactions in this format by default (showing only genes and interaction type), but if you expand the annotation, you can view the associated genotypes and phenotypes.\n\n[GI new format]\n\nIn the revised Canto interface, you can only annotate a genetic interaction from the double mutant phenotype annotation (by clicking on add.., as shown below).\n\n[GI annotation in Canto]\n\nOf course, genetic interactions predating this update are not linked to phenotypes or genotypes, but we are hoping to auto-annotate several of those. We will also prioritise for update any interactions where community curators have provided these details in an annotation comment. Finally, a big shoutout to Ana Sanchez and Angad Garg from the Shuman lab, for testing the new interface in numerous recently curated publications. The examples provided here are from Sanchez et al. 2019. Go read it and see the annotations in PomBase.\n\nBest, The PomBase team\n\nNext pombeTalks: Wednesday, November 16th\n\n2022-11-11\n\nThe next online pombeTalks will take place on Wednesday, November 16th. These talks are virtual seminars by and for the fission yeast community and friends.\n\nNote that this session will happen earlier at:\nmidnight San Francisco; 03:00 NY; 08:00 London; 09:00 Paris; 13:30 Delhi, 16:00 Beijing; 17:00 Tokyo\n\nTalks this session:\n\n- Wenfan Wei, University of Science and Technology of China\n “The Cdc42 GAP Rga6 promotes monopolar outgrowth of spores”\n\n- Gaowen Liu, Shenzhen Institute of Synthetic Biology\n “Fusion eciency evolution to the deletion of an essential mating gene Prm1”\n\nZoom details\n\nTopic: PombeTalks S03E07 Zoom Meeting\nDate: Nov 16, 2022\nTime: midnight San Francisco; 03:00 NY; 08:00 London; 09:00 Paris; 13:30 Delhi, 16:00 Beijing; 17:00 Tokyo\nMeeting ID: 932 8857 4852\nPassword: will be sent the day of the meeting\n\nSlack\n\nFor more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nUsing AlphaFold models to discover distant human and budding yeast homologues\n\n2022-10-14\n\nWe collaborated with the Pfam group at the EBI to evaluate predictions generated from AlphaFold reciprocal best structure hits to identify potential distant orthologs. The Reciprocal Best Structure Hits (RBSH) approach provided 11 novel human homologues, including Pho86 -> NAT8 (ER acetyltransferase), Mug174 -> COIL (Coilin), Ach1 -> OXCT1 (succinyl-CoA:3-ketoacid coenzyme A transferase), SPAC1952.08c -> CREG1, imt1 -> A4GALT (Lactosylceramide 4-alpha-galactosyltransferase), Rtc5 -> MEAK7 (MTOR associated protein). A further 41 novel orthologs were predicted between S. pombe and S. cerevisiae which had fallen under the radar for all other methods used at PomBase. Most of the novel connections provided additional functional information, or supported existing knowledge for poorly characterised proteins. See supporting data tables S4 and S5 for the complete list of predictions included in PomBase. Article.\n\nNext pombeTalks: Wednesday, October 19th\n\n2022-10-13\n\nThe next online pombeTalks will take place on Wednesday, October 19th. These talks are virtual seminars by and for the fission yeast community and friends.\n\n8:00 San Francisco / 11:00 NY / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / midnight Tokyo\n\nTalks this session:\n\n- Cecilia D’Alessio, University of Buenos Aires and CONICET\n “N-Glycosylation and glycoprotein folding in fission yeasts, a model to study human congenital disorders of glycosylation”\n\n- Jason Tanny, McGill University, Montreal\n “A novel transcriptional mechanism regulating the cellular response to replication stress”\n\nZoom details\n\nTopic: PombeTalks S03E06 Zoom Meeting\nTime: Oct 19, 2022 05:00 PM Paris\nMeeting ID: 933 7072 6178\nPassword: will be sent the day of the meeting\n\nSlack\n\nFor more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nNew to fission yeast? check out our quick start guide for new users\n\n2022-10-13\n\nWe have added a new page providing useful information for new fission yeast researchers:\nGetting started with S.pombe and PomBase\n\nIncludes details of how to join the community mailing list and the Slack channel, links to useful tools and resources, information about fission yeast as a model organism, an overview of PomBase and more.\n\n77 new disease gene associations\n\n2022-09-16\n\nWe have added 77 new disease-gene associations for 71 fission yeast human gene orthologs. These were identified using “PombeMine” to identify the disease genes curated by OMIM not annotated with an existing MONDO mapping. The number of human disease gene associations is currently 1471. Disease genes can be browsed via the disease slim set or from the MONDO root node term.\n\nPombeMine: an InterMine instance for S. pombe\n\n2022-09-16\n\nAs part of an Elixir funded collaboration with the InterMine team we have created PombeMine. Gene lists can be sent directly from PomBase query results pages directly to Intermine (under the “export” tab), providing direct (2 click) access to GO and phenotype enrichment tools.\n\nNext pombeTalks: Wednesday, September 21st\n\n2022-09-15\n\nThe next online pombeTalks will take place on Wednesday, September 21st. These talks are virtual seminars by and for the fission yeast community and friends.\n\n8:00 San Francisco / 11:00 NY / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / midnight Tokyo\n\nTalks this session:\n\n- Manuel Lera Ramirez, PomBase / Tran Lab, Institute Curie “Microtubule rescue at midzone edges promotes overlap stability and prevents spindle collapse during anaphase B”\n\n- Hannah Opalko, Moseley lab, Dartmouth College “Mechanisms of spatial patterning of cell cycle regulator Cdr2”\n\nZoom details\n\nTopic: PombeTalks S03E05 Zoom Meeting\nTime: Sep 21, 2022 05:00 PM Paris\nMeeting ID: 985 8572 1420\nPassword: will be sent the day of the meeting\n\nSlack\n\nFor more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nProtein sequence changes\n\n2022-09-06\n\n78 protein have been shortened (at the N-term). This set includes 34 published proteins (Apl4, Brc1, Cdc48, Cdt1, Cho1, Cmb1, Cut2, Cut6, Cwf26, Dbr1, Dri1, Elo2, Eri1, Lsd2, Lys2, Med13, Naa38, Nup107, Nup82, Orc2, Pof10, Ppt1, Rec24, Rga2, Rmt3, Rns1, RRpn7, Sap145, Skb1, Snf5, Snt2, Spn3, Tpp2, Trm1, and Tup12). Allele description changes and modification position changes are pending.\n\nNext pombeTalks: Wednesday, August 17th\n\n2022-08-13\n\nThe next online pombeTalks will take place on Wednesday, August 17th. These talks are virtual seminars by and for the fission yeast community and friends.\n\n8:00 San Francisco / 11:00 NY / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / midnight Tokyo\n\nTalks this session:\n\n- Pranas Grigaitis, Vrije Universiteit Amsterdam\n “Prediction of metabolic strategies in Schizosaccharomyces pombe based on optimal resource allocation”\n- Abhishek Poddar, University of Toledo\n “Membrane stretching activates calcium-permeability of a putative channel Pkd2 during fission yeast cytokinesis”\n\nAs always, connection details will be sent the day of the talk. For more fission yeast related topics and recordings of the talks, join pombeSlack, where additional questions can also be posted on the #pombetalks-qna channel.\n\nNext pombeTalks: Wednesday, July 20th\n\n2022-07-12\n\nThe next online pombeTalks will take place on Wednesday, July 20th. These talks are virtual seminars by and for the fission yeast community and friends.\n\n0:00 San Francisco / 3:00 New York / 8:00 London / 9:00 Paris / 12:30 Delhi / 15:00 Beijing / 16:00 Tokyo.\n\nTalks this session:\n\n- Leeba Ann Chacko, Ananthanarayanan Lab, University of New South Wales\n “Microtubules and mitochondria cooperate to ensure cell division symmetry, polarity and equipartitioning in fission yeast”\n- Dan Zhang, Temasek Life Sciences Laboratory, National University of Singapore\n “The cortical ER remodeling for actomyosin ring assembly”\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and pombeSlack one day in advance, so make sure you’ve signed up.\n\nPombeTalks Wednesday June 15th\n\n2022-06-14\n\nThe next online pombeTalks will take place on Wednesday June 15th. These are virtual seminars by and for the fission yeast community and friends.\n\n08:00 San Francisco / 11:00 New York / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / 00:00 Tokyo\n\nTalks this session:\n\n- Elliott Chapman, Bayne Lab, University of Edinburgh\n “Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus”\n- Fei Li, New York University\n “Phosphorylation-mediated Ccp1-Ndc80 switch at the N-terminus of CENP-T regulates kinetochore assembly in fission yeast”\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and pombeSlack one day in advance, so make sure you’ve signed up.\n\nAs before, questions will be posted to #pombetalks-qna on pombeSlack channel and recordings uploaded.\n\nPombeTalks May 18th\n\n2022-05-05\n\nThe next online pombeTalks will take place on May 18th. These are virtual seminars by and for the fission yeast community and friends.\n\n08:00 San Francisco / 11:00 New York / 16:00 London / 17:00 Paris / 20:30 Delhi / 23:00 Beijing / 00:00 Tokyo\n\nTalks this session:\n\n- Jennifer Porat, Bayfield Lab, York University: The methyl phosphate capping enzyme Bmc1/Bin3 is a stable component of the fission yeast telomerase holoenzyme\n- Ingrid Billault-Chaumartin, Martin Lab, UNIL: Fus1, the fusion focus formin\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nNew phenotype slim\n\n2022-04-13\n\nWe have added a phenotype slim overview to complement those provided for disease association, biological process, molecular function and cellular component annotation. The purpose of the phenotype slim is to provide subsets of commonly used ‘broad’ phenotypic classes or annotation subsets that can provide a useful starting point for accessing phenotype lists. The phenotype slim page provides links to ontology term pages, annotated genes, and to download files containing the slim terms and IDs.\n\nThe phenotype slim has also been added to the PomBase advanced search results panel “Slim with” menu. For example, you can query for all genes involved in a GO process, another phenotype, or any other list, and “slim” the results using the “Phenotype slim” option to view categories of phenotypes assigned to the list.\n\nMaking biological knowledge useful for humans and machines\n\n2022-04-04\n\nA GENETICS special issue featuring model organism database updates is published today. This issue features the recent PomBase and JaponicusDB publications and is accompanied by an editorial “Making biological knowledge useful for humans and machines” co-authored by Val Wood, Paul Sternberg and Howard Lipshitz.\n\n- Fission stories: using PomBase to understand Schizosaccharomyces pombe biology\n- JaponicusDB: rapid deployment of a model organism database for an emerging model species\n\nThe fission yeast community have now curated over 1000 publications\n\n2022-03-26\n\nWe would like to extend a huge “thank you” to the fission yeast community for curation contributions. The community have now curated 1008 publications providing 19,156 independent annotations, representing 25% of the curation from small-scale publications. In addition, another 80,000 annotations have been provided via the submission of HTP datasets.\n\nPlease contact us via the helpdesk if you would like to provide curation for your manuscript but don’t know how.\n\nLinks:\n\n- All community curated publications\n- Spotlights\n- Canto curation tool\n- HTP data and browser track submission\n\nNew human orthologs including 3 MRP complex subunits\n\n2022-03-23\n\nWe continue to identify distant human orthologs. Four new 1:1 human ortholog connections have been added to PomBase this week:\n\n- RNase MRP subunit Rmp1 = human NEPRO (family submitted to Pfam)\n- RNase P and RNase MRP subunit Pop23 = human RPP38 (members of the same Pfam clan)\n- RNase P and RNase MRP subunit Pop8 = human RPP14 (family submitted to Pfam)\n- glutamyl-tRNA amidotransferase complex subunit 3 (Gtf1) = human GATC\n\nHuman NEPRO is a poorly characterised protein linked to the disease Anauxetic dysplasia 3, and GATC is the causal gene for “combined oxidative phosphorylation deficiency 42”\n\nPomBase now uses InterPro Version 88.0\n\n2022-03-12\n\nPomBase now uses InterPro Version 88.0.\n\nFeatures include:\n\n- The addition of 39 InterPro entries (40,071 total entries)\n- Integration of 45 new methods from the PRINTS (1), SMART (1), Pfam (2), SUPERFAMILY (7), CATH-Gene3D (14), PANTHER (13), CDD (7) databases\n\nTOR and nutritional phosphoproteome dataset loaded\n\n2022-03-11\n\nWe have loaded the TOR and nutritional phosphoproteome dataset described in Halova et al. (9424 annotations). Many thanks to Janni Petersen for preparing the files.\n\nPublication page for PMID:33823663\n\nAn additional 5775 novel curated lncRNAs from Atkinson et al.\n\n2022-03-10\n\nWe have added an additional 5775 novel curated lncRNAs from Atkinson et al. to PomBase. We will refine the descriptions of these gene products to align with Sequence Ontology (SO) terms describing RNA features in the coming months.\n\nThanks to María Rodríguez-López for preparing the files.\n\nPublication page for PMID:29914874\n\nPomBase & JaponicusDB publications in the GENETICS MOD reports special issue\n\n2022-02-02\n\nPapers describing PomBase and JaponicusDB are now published (early online). These articles are part of a special issue of GENETICS devoted to model organism database (MOD) reports. The MOD papers will highlight the journal’s new section on Computational Resources, Software & Databases.\n\n- Fission stories: using PomBase to understand Schizosaccharomyces pombe biology\n- JaponicusDB: rapid deployment of a model organism database for an emerging model species\n\nImproved options for filtering annotations by cell cycle phase\n\n2021-12-19\n\nThe Gene Ontology annotation filter for “during” specific cell cycle phases is now included on the “Summary” view in addition to the “Details” view. Available phases have been extended to cover all phases used, and to provide\nuseful grouping terms. This filter is “ontology aware” (i.e. a search on interphase will also display G1/S/G2 phase annotation). The phase filter is most useful on pages that display increasing volume of phase-specific curation (such as cdc2). The revised phase filter options are also available in the gene expression section.\n\nThe phase filters are located at the top right of GO and gene expression annotation sections:\n\n[During filter]\n\nPomBase now uses InterPro Version 87.0\n\n2021-11-23\n\nPomBase now uses InterPro Version 87.0, which integrates:\n\n- 1,155 new InterPro entries\n- Update to Pfam 34.0\n- 1,256 new methods\n\nCoils, disorder, and more: new protein feature queries\n\n2021-10-18\n\nThe PomBase advanced search now allows you to find proteins that have coiled-coil regions, disordered regions, and low-complexity regions. The query-building interface also now organises query options more sensibly, and the documentation has been updated.\n\nPomBase & JaponicusDB preprints\n\n2021-09-27\n\nPapers describing PomBase and JaponicusDB will appear in an issue of GENETICS devoted to model organism database (MOD) reports. The MOD papers will highlight the journal’s new section on Computational Resources, Software & Databases.\n\nFollow the links to the PomBase preprint and JaponicusDB preprint, and watch for the full-fledged publications to appear in March 2022.\n\nJaponicusDB: a new fission yeast database\n\n2021-09-01\n\nWe are delighted to announce the official release of PomBase’s new sister: JaponicusDB is a new, curated model organism database for the fission yeast Schizosaccharomyces japonicus. JaponicusDB highlights include revised gene structures, distant ortholog detection, improved GO annotation, community literature curation, and reciprocal gene page links with PomBase, providing a familiar environment for all fission yeast researchers.\n\nThe S. japonicus community will maintain JaponicusDB from now on. Join the new mailing list, and follow @japonicusdb on Twitter.\n\nImproved gene-disease curation: over 1400 S. pombe genes\n\n2021-08-06\n\nPomBase disease gene curation associates disease descriptors with fission yeast orthologs of human disease-causing genes. We have added new gene–disease term connections, to bring the total to 1401 S. pombe genes. Disease associations now cover 27.3% of all fission yeast protein-coding genes, and almost 40% with human orthologs.\n\nPombeTalks August 4th\n\n2021-07-28\n\nThe next online PombeTalks will take place on Wednesday 4th August 2021, at 17:00 Central European Time. Speakers:\n\n- Tiffany Mak, Nurse lab, The Francis Crick Institute: The TOR-dependant phosphoproteome and regulation of cellular protein synthesis\n\n- Weifang Wu, Allshire lab, University of Edinburgh: Spatial organisation of the nucleus influences centromere identity\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nAfter these talks, PombeTalks will take a break for the rest of the summer, so watch this space, pombelist, or PombeSlack for updates. In the meantime, you can fill out this form at any time if you’re interested in speaking.\n\nAlphaFold links\n\n2021-07-28\n\nPomBase gene pages now have links to the AlphaFold Protein Structure Database, the collection of structures predicted by AI developed by DeepMind, hosted at EBI. Look in the “External references” section of your favorite gene page, or check out this example (pap1), or read more at the EBI AlphaFold home.\n\nPombeTalks July 21st\n\n2021-07-14\n\nThe next online PombeTalks will take place on Wednesday 21st July 2021, at 10:00 Central European Time / 17:00 Japan & Korea. Speakers:\n\n- Yoko Otsubo, Yamashita lab, National Institute for Basic Biology: Novel links between TORC1 and traditional non-coding RNA, tRNA\n\n- Jie Su, Nakagawa lab, Osaka University: Rad8-dependent PCNA ubiquitination at lysine 107 causes gross chromosomal rearrangements\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nKEGG pathway links\n\n2021-07-06\n\nPomBase gene pages now have links to pathway entries in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, as well as links to gene lists for each linked pathway (example: 2-Oxocarboxylic acid metabolism). The KEGG pathway links are the first entry in a new gene page section, “Molecular pathway”, dedicated to connecting genes in PomBase to depictions of biochemical and signaling pathways.\n\nPomBase now uses InterPro Version 86.0\n\n2021-06-30\n\nPomBase now uses InterPro Version 86.0, which integrates:\n\n- 299 new InterPro entries\n- An update to PROSITE patterns [2021_01] and PROSITE profiles [2021_01]\n- 454 new methods from the PROSITE profiles (39), SMART (2), Pfam (7), SUPERFAMILY (3), CATH-Gene3D (80), PANTHER (295), CDD (27), SFLD (1) databases.\n\nInterPro cites 52235 publications in PubMed. See the InterPro release notes for further information.\n\nPombeTalks July 7th\n\n2021-06-30\n\nThe next online PombeTalks will take place on Wednesday 7th July 2021, at 17:00 Central European Time. Speakers:\n\n- Debatrayee Sinha, Qian Chen lab, University of Toledo: Fission yeast polycystin Pkd2p promotes resumption of cell growth after cytokinesis\n\n- Joël Lemière, Fred Chang Lab, UCSF: The role of osmotic forces in nuclear size control\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks June 23rd\n\n2021-06-17\n\nThe next online PombeTalks will take place on Wednesday 23rd June 2021, at 17:00 Central European Time. Speakers:\n\n- Yi Wei, Grewal lab, NCI CCR, Bethesda: TOR targets an RNA processing network to regulate cell proliferation and sexual development\n\n- Nicholas Ader, LusKing Lab, Yale School of Medicine: I open at the close(d mitosis): Investigating post-mitotic nuclear envelope sealing in fission yeast\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nViolin plots for gene expression\n\n2021-06-15\n\nThe “Quantitative gene expression” section of PomBase gene pages now offers a display of violin plots to visualize where the gene appears in available expression datasets.\n\nViolin plots are also available to visualize sets of up to 150 genes in the advanced search results.\n\nAt present data from Marguerat S et al. (2012) and Carpy A et al. (2014) are included.\n\nPombeTalks June 9th\n\n2021-06-02\n\nThe next online PombeTalks will take place on Wednesday 9th June 2021, at 10:00 Central European Time / 17:00 Japan & Korea. Speakers:\n\n- Yusuke Toyoda, Saitoh lab, Kurume University: Nitrogen-dependent persistence of S. pombe Ght5 glucose transporter on the cell surface is effected by TORC2 inhibition of α-arrestin Aly3\n\n- Anupa T. Anil, Mishra lab, IISER Mohali: How does spliceosome capture branchpoint-distant 3’ splice site?\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks May 26th\n\n2021-05-20\n\nThe next online PombeTalks will take place on Wednesday 26th May 2021, at 17:00 Central European Time. Speakers:\n\n- Mélina Vaurs (Vincent Géli & Stéphane Coulon labs - Cancer Research Center, Marseille): Shelterin-dependent telomerase regulation differs between quiescent and vegetative cells\n\n- Arthur Molines (Fred Chang lab – UCSF): Physical properties of the cytoplasm modulate microtubule dynamics\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks May 12th\n\n2021-05-05\n\nThe next online PombeTalks will take place on Wednesday 12th May 2021, at 17:00 Central European Time. Speakers:\n\n- Sierra Cullati, Gould lab, Vanderbilt University: Autophosphorylation of the CK1 Kinase Domain Regulates Enzyme Activity and Substrate Specificity\n\n- Stephen Huisman, Brunner Lab, University of Zurich: Vip1, a temperature-dependent filament forming protein involved in cell length regulation\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nNew diploid genotype & phenotype display\n\n2021-04-29\n\nPomBase now includes pages for curated diploid genotypes, and displays phenotypes annotated to them on gene and publication pages. For more details see the documentation for phenotype annotations and genotype pages.\n\nPombeTalks April 28th\n\n2021-04-22\n\nThe next online PombeTalks will take place on Wednesday 28th April 2021, at 10:00 Central European Time / 17:00 Japan & Korea. Speakers:\n\n- Tomoyuki Fukuda, Niigata University Graduate School of Medical and Dental Sciences: Atg43 serves as a selective autophagy receptor to promote mitophagy\n\n- Xiao-Ran Zhang, NIBS, Beijing, China: An improved auxin-inducible degron system for fission yeast\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPomBase now uses InterPro Version 85.0\n\n2021-04-15\n\nPomBase now uses InterPro Version 85.0, which integrates:\n\n- 157 new InterPro entries\n- An update to CATH-Gene3D [4.3.0]\n- 333 new methods from the Pfam (3), SUPERFAMILY (11), CATH-Gene3D (168), PANTHER (88), CDD (62), SFLD (1) databases\n\nInterPro cites 51539 publications in PubMed. See the InterPro release notes for further information.\n\nPombeTalks April 14th\n\n2021-04-08\n\nThe next online PombeTalks will take place on Wednesday 14th April 2021, at 17:00 Central European Time:\n\n- Pabitra Parua,�Fisher�lab,�Icahn School of Medicine at Mount Sinai: Control of the RNA polymerase II transcription cycle by CDK-phosphatase switches\n\n- Ye Dee Tay, Sawin Lab,�University of�Edinburgh: Gef1: the first aider of Cdc42 polarity module during stress\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the new Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nNew genome browser data: GC content\n\n2021-03-31\n\nA data track showing the fraction of G/C bases in a region is now available in PomBase JBrowse, listed under “Base composition”. The track is generated using the gccontent plugin, and uses a default window of 100 bp.\n\nQualitative gene expression annotation in Canto\n\n2021-03-31\n\nCanto, PomBase’s online curation tool, now supports qualitative gene expression annotation. Two new annotation types are available to represent observations about the levels of RNA or protein observed in wild-type cells, and how they change over the cell cycle or in response to a stimulus. See the Canto documentation for more information. We have also updated the display of qualitative gene expression on PomBase gene and publication pages.\n\nNew protein feature display\n\n2021-03-30\n\nPomBase has released a new, interactive display for protein features on gene pages. The new view is clearer, with details for each feature available via mouseover as well as in the accompanying table.\n\nIn addition, PomBase now uses InterPro Version 84.0, which includes 205 new entries and integrates 252 new methods from the Pfam, PANTHER, and CDD databases. See the InterPro release notes for further information.\n\nPombeTalks March 31st\n\n2021-03-27\n\nThe next online PombeTalks will take place on Wednesday 31st March 2021, at 17:00 Central European Time:\n\n- Udo Onwubiko, Das lab, University of Tennessee: Cdc42 prevents early Rho1 activation during cytokinesis\n\n- Chunmin Shan, Jia lab, Columbia University: The INO80 complex regulates epigenetic inheritance of heterochromatin\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the new Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks March 17th - new time!\n\n2021-03-10\n\nThe new season of online PombeTalks for 2021 will begin on Wednesday 3rd March 2021, at a different time: 9:00 Central European Time / 17:00 Japan & Korea. Speakers:\n\n- Yasuto Murayama, National Institute of Genetics, Shizuoka: Biochemical analysis of the fission yeast structural maintenance of chromosomes complex\n\n- Ken Ishikawa, Kurume University, Kurume: dCas9-mediated CRISPRi for S. pombe\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will continue with its fortnightly schedule, and every third session will take place at the new Asia-friendly time. Watch this space, pombelist, or PombeSlack for updates, and please fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks return March 3rd\n\n2021-02-24\n\nThe new season of online PombeTalks for 2021 will begin on Wednesday 3rd March 2021 at 17:00 Central European Time:\n\n- Maria Rodriguez Lopez, Bähler lab, UCL: Clr6 orchestrates transcriptional switches to regulate metabolism during oxidative stress\n\n- Olivia Muriel-Lopez, Martin lab, University of Lausanne: ’Ultrastructural plasma membrane asymmetries underlie cell-cell fusion in S. pombe*\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nPombeTalks will resume its fortnightly schedule, so watch this space, pombelist, or PombeSlack for updates. As in the past, you are always welcome to fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPomBase identifier mapper now available\n\n2021-02-04\n\nWe have developed an identifier mapper that retrieves S. pombe gene systematic IDs and standard names for a selection of different input ID types. You can now find S. pombe genes using UniProt accessions, and retrieve manually curated orthologs for S. cerevisiae using standard gene names or ORF names, and for human using standard gene names or HGNC identifiers.\n\nTry the identifier mapper or check out the documentation.\n\nPomBase now uses InterPro Version 83.0\n\n2021-01-25\n\nPomBase now uses InterPro Version 83.0, which integrates:\n\n- 376 new InterPro entries\n- An update to HAMAP [2020_05], CDD [3.18]\n- 462 new methods from the SMART (2), TIGRFAMs (2), Pfam (3), PANTHER (140), HAMAP (19), CDD (286), SFLD (10) databases\n\nInterPro cites 50487 publications in PubMed. See the InterPro release notes for further information.\n\nFirst S. pombe microPublication goes live\n\n2021-01-07\n\nThe first fission yeast microPublication has now been published:\n\nNafees Ahamad, Simmi Anjum, Shakil Ahmed\\ Pyrogallol induces oxidative stress defects in the fission yeast S. pombe.\n\nCongratulations to the authors, and thanks to the microPublication team!\n\nPombeTalks November 25th\n\n2020-11-18\n\nThe last online PombeTalks for 2020 will take place on Wednesday 25th November 2020 at 17:00 Central European Time:\n\n- I-Ju Lee, David Pellman’s Lab, Dana-Farber Cancer Institute: Factors promoting nuclear envelope assembly independent of the canonical ESCRT pathway\n\n- Ulrike Endesfelder, Carnegie Mellon University: TBC\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nAfter these talks, PombeTalks will take a well-earned break, and return in early 2021. The schedule is available, and you are always welcome to fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks November 11th\n\n2020-11-04\n\nThe next online PombeTalks will take place on Wednesday 11th November 2020 at 17:00 Central European Time:\n\n- Farnaz Mansouri, Mark Bayfield lab (York University, Toronto): The uncharacterized S. pombe La-related protein 1 functions in translation and affects RNA abundance\n\n- Saz Basu, Paul Nurse lab (Francis Crick Institute, London): Unmasking the mitotic potential of G1/S Cyclin-CDK\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on November 25. PombeTalks will then take a break, and return in early 2021. The schedule is available, and you are always welcome to fill out this form if you’re interested in speaking.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nGO annotations from PAINT\n\n2020-11-01\n\nPomBase now includes over 3000 GO annotations made using Phylogenetic Annotation and INference Tool (PAINT), developed by the GO Consortium to infer protein function in a phylogenetic context, supporting precise assertions as to when functions were gained and lost during evolution. PAINT annotations use the evidence code “inferred from biological aspect of ancestor” (IBA). PAINT curation is described in more detail in Gaudet et al. 2011.\n\nPombeTalks October 28th\n\n2020-10-24\n\nThe next online PombeTalks will take place on Wednesday 28th October 2020 at 17:00 Central European Time:\n\n- Omaya Dudin, EPFL, Switzerland: Cellularization of Ichthyosporean coenocytes\n\n- Bassem Al-Sady, UCSF, USA: Single cell analysis of the heterochromatin spreading reaction\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on November 11, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks October 14th\n\n2020-10-08\n\nThe next online PombeTalks will take place on Wednesday 14th October 2020 at 17:00 Central European Time:\n\n- Dimitrios Vavylonis, Lehigh University: Modeling fission yeast’s polarization pattern\n\n- Chloe Snider, Gould Lab, Vanderbilt University: Opposite surfaces of the Cdc15 F-BAR domain create a membrane platform that coordinates cytoskeletal and signaling components for cytokinesis\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on October 28, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks September 30th\n\n2020-09-23\n\nThe next online PombeTalks will take place on Wednesday 16th September 2020 at 17:00 Central European Time:\n\n- Alexander Lorenz, University of Aberdeen, UK: Meiotic recombination outcome in the face of genetic diversity\n\n- Veneta Gerganova, Martin Lab, UNIL, Switzerland: Patterning of membrane-associated proteins through membrane flows\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on October 14, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nNew genome browser datasets 2020-09-17\n\n2020-09-17\n\nTwo new datasets in are now available in PomBase JBrowse (links go to PomBase publication pages, which in turn link to the browser with the tracks enabled):\n\n- Meiotic DSBs from\n Fowler KR, Gutiérrez-Velasco S, Martín-Castellanos C, Smith GR. 2013.\n Protein determinants of meiotic DNA break hot spots.\n PMID:25747261 DOI: 10.1016/j.molcel.2013.01.008\n\nand\n\n- Time-lapse single-cell transcripts for dormancy breaking from\n Tsuyuzaki H, Hosokawa M, Arikawa K, Yoda T, Okada N, Takeyama H, Sato. 2020.\n Time-lapse single-cell transcriptomics reveals modulation of histone H3 for dormancy breaking in fission yeast.\n PMID:32152323 DOI: 10.1016/j.molcel.2013.01.008\n\nMore datasets are always welcome, so check out our instructions for submission.\n\nPombeTalks September 16th\n\n2020-09-14\n\nThe next online PombeTalks will take place on Wednesday 16th September 2020 at 17:00 Central European Time:\n\n- Susan Forsburg, University of Southern California: Visualizing replication stress\n\n- Sigurd Braun, Ludwig-Maximilians-Universität, München: Gene repression at the nuclear membrane: Multifaceted roles of Lem2\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on September 30, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nNew dataset: Hermes transposon insertions\n\n2020-09-11\n\nPomBase now hosts transposon integration data from Lee et al. 2020. Henry Levin explains the background and significance of the work:\n\n“Transposon Integration Sequencing is a genome wide method of mapping sequences that contribute to growth. High throughput sequencing of transposon integration sites in haploid cells with single insertions reveals which genes are dispensable. Once propagated, cultures exhibit a pronounced lack of insertions in genes necessary for growth. This method, originally developed to study bacteria is now used to characterize the genomes of several yeasts including S. pombe. In earlier work we used the transposon Hermes to identify genes of S. pombe required for growth (Guo et al., 2013, Genetics, PMID:23893486). We have now applied Hermes and Transposon Integration Sequencing to identify genes important for the formation of heterochromatin (Lee et al., 2020, Cell Reports, PMID:32101745). Insertion sites from eight independent cultures can be visualized from PomBase as custom tracks on Jbrowse. Four cultures were of cells with ura4 silenced by cen1 heterochromatin. The other four cultures were\nof a strain without ura4. By passaging the cultures in 5-FOA we selected against cells with defects in heterochromatin. Genes that contributed to the formation of heterochromatin exhibited fewer insertions in cells with the cen1 copy of ura4 relative to the strain lacking ura4. To distinguish genes critical for heterochromatin from genes that contribute to a lesser extent we passaged cultures in 5-FOA for 5 generations and for 80 generations. While viewing these integration sites can indicate whether genes of interest contribute to heterochromatin formation you can also examine insertions in the cultures lacking ura4 to gage whether specific genes or noncoding sequences make significant contributions to growth.”\n\nNew genome browser datasets 2020-09-08\n\n2020-09-08\n\nThree new datasets in are now available in PomBase JBrowse (links go to PomBase publication pages, which in turn link to the browser with the tracks enabled):\n\n- Transcription start sites from\n Li H, Hou J, Bai L, Hu C, Tong P, Kang Y, Zhao X, Shao Z. 2015.\n Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE.\n PMID:25747261 DOI:10.1080/15476286.2015.1022704\n\n- Transcript data from\n Eser P, Wachutka L, Maier KC, Demel C, Boroni M, Iyer S, Cramer P, Gagneur J. 2016\n Determinants of RNA metabolism in the Schizosaccharomyces pombe genome.\n PMID:26883383 DOI:10.15252/msb.20156526\n\n- Transposon insertion sites from\n Lee SY, Hung S, Esnault C, Pathak R, Johnson KR, Bankole O, Yamashita A, Zhang H Levin HL.\n Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation.\n PMID:32101745 DOI:10.1016/j.celrep.2020.01.094\n\nSubmit your genome browser data\n\n2020-09-08\n\nWe have updated our HTP data submission procedure to make it easier for you to contribute your datasets for PomBase JBrowse:\n\nWe now provide spreadsheet templates in Excel and Open Document formats that gather the metadata we need to load and display your data. You can download a template from the documentation page on HTP data submission. Send completed spreadsheets to the PomBase helpdesk.\n\nPublished: GO Term Matrix for annotation QC\n\n2020-09-02\n\nIn collaboration with the GO Consortium, the PomBase team has published a report on the Term Matrix approach to GO annotation quality control. The article, out this week in Open Biology, describes biological processes that do, or don’t, share annotated gene products, and how we use co-annotation patterns to build rules to detect, correct, and prevent errors.\n\nPombeTalks September 2nd\n\n2020-09-01\n\nThe next online PombeTalks will take place on Wednesday 2nd September 2020 at 17:00 Central European Time:\n\n- François Bachand, USherbrooke, Canada: Proximity-dependent biotinylation assays in fission yeast and a tale about slow RNA polymerase II transcription\n\n- Scott Curran, Nurse Lab, The Crick Institute, UK: A quantitative and spatial analysis of the cell cycle control network\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on September 16, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\n11th Pombe meeting postponed to 2022\n\n2020-08-19\n\nDue to the ongoing Covid-19 pandemic, the 11th International Fission Yeast Meeting, due to take place in Hiroshima, Japan, has been postponed.\n\nThe new dates will be 12th (Sun -17th (Fri) June, 2022.\n\nPlease see the conference website and pombelist for further announcements.\n\nPombeTalks August 19th\n\n2020-08-12\n\nThe next online PombeTalks will take place on Wednesday 19th August 2020 at 17:00 Central European Time:\n\n- Joe Magliozzi, Moseley Lab, Dartmouth: Cell polarity kinases regulate RNA-binding protein Sts5 to control cell shape\n\n- Ramakanth Neeli, Minc Lab, Institute Jacques Monod: Mechanisms and Functions of Cell Wall Mechanosensing in Fission Yeast\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on September 2, and the schedule is available for the next few weeks. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks August 5th\n\n2020-07-31\n\nThe next online PombeTalks will take place on Wednesday 5th August 2020 at 17:00 Central European Time:\n\n- Feng Li, Levin Lab NICHD/NIH, USA: Identification of an integrase-independent pathway of retrotransposition\n\n- Ivan Surovtsev, King lab, Yale University, USA: Liquid-liquid phase separation, heterochromatin domains and nuclear mechanics\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on August 19, and the summer schedule is available. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nFission yeast microPublications\n\n2020-07-22\n\nPomBase has recently joined microPublication.org, which “publishes brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative”, as a Partner Database. Fission yeast researchers can thus now make any results available to the community, even those that don’t fit neatly into traditional publications.\n\nVisit the microPublications website to learn more, to register and submit your data, or sign up to review. Send questions to the PomBase helpdesk.\n\nPombeTalks July 22nd\n\n2020-07-21\n\nThe next online PombeTalks will take place on Wednesday 22nd July 2020 at 17:00 Central European Time:\n\n- Prof. Dr. Ann Ehrenhofer-Murray, Institut für Biologie, Humboldt-Universität zu Berlin: Queuosine and m5c modification of RNA: Nutritional control of translation in S. pombe homestasis\n\n- Dr. Sarah Sabatinos, Department of Chemistry and Biology, Ryerson University: Long-term effects of surviving replication instability\n\n- PomBase microPublications announcement (Midori Harris)\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on August 5, and the summer schedule is available. If you’re interested in speaking, please fill out this form.\n\nThanks to the PombeTalks team for organizing. See you online!\n\nPombeTalks July 8th\n\n2020-07-02\n\nThe next online PombeTalks will take place on Wednesday 8th July 2020 at 17:00 Central European Time:\n\n- Sahana Holla, Grewal lab, NIH: Positioning heterochromatin at the nuclear periphery promotes epigenetic inheritance\n\n- Nick Rhind, UMass Medical School: Cell size is controlled by size-dependent expression of mitotic activators\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also see PombeSlack for Q&A after the talks, and for recordings of previous sessions.\n\nThe next talks are on July 22nd, and the summer schedule is available. If you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nPombeTalks June 24th\n\n2020-06-19\n\nThe next online PombeTalks will take place on Wednesday 24th June 2020 at 17:00 Central European Time:\n\n- Sito Torres-Garcia, Allshire lab, University of Edinburgh: Epigenetic gene silencing by heterochromatin primes fungal resistance\n\n- Julie Rich-Robinson, Das lab, University of Tennessee: Cell-cycle-dependent cues temporally regulate Cdc42 activity at growth sites in fission yeast\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up.\n\nA schedule is now available for the rest of the summer, including the next talks on July 8th. If you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nEditable PomBase query names\n\n2020-06-11\n\nEntries in the PomBase advanced search query history now show brief, user-editable query descriptions, and a toggle to show or hide additional details.\n\nPombeTalks POSTPONED to June 17th\n\n2020-06-05\n\nPlease note that the next online PombeTalks will take place one week later than originally planned, to support the STEM Strike for Black Lives on 10th June.\n\nIn the meantime, please complete this brief survey of the audience.\n\nOn Wednesday 17th June 2020 at 17:00 Central European Time, the speakers will be:\n\n- Gautam Dey, Baum lab, UCL / EMBL Heidelberg: Closed mitosis requires local disassembly of the nuclear envelope\n\n- Meredith Betterton, UC Boulder: Computational modeling of fission yeast mitosis: what we can learn about pombe from computer simulations\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. The next two sessions will b on June 27 and July 8. If you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nPombeTalks May 27th\n\n2020-05-21\n\nThe next online PombeTalks will take place on Wednesday 27 May 2020 at 17:00 Central European Time. This time, in addition to the usual pair of research talks, our own Val Wood will show a few of PomBase’s lesser-known features.\n\n- Angad Garg, Stewart Schuman’s lab, Memorial Sloan Kettering Cancer Center: Long non-coding RNA control of phosphate homeostasis\n\n- José López Hernández, Sarah Zander’s lab, Stowers Institute for Medical Research: Diverse mating strategies in S. pombe affect the spread of wtf meiotic drivers\n\n- Val Wood, PomBase: Hidden corners of PomBase: Ten features you might not have seen\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also mark your calendars for the next two sessions on and June 10 and 24, and if you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nNew fission yeast GO slims\n\n2020-05-20\n\nTo complement the overview provided by the fission yeast GO biological process slim, we have created GO slims for the molecular function and cellular component branches of GO. Each slim page provides links to ontology term pages, annotated genes, and to download files containing the slim terms and IDs.\n\nNew ontology slimming options for advanced search results\n\n2020-05-20\n\nThe PomBase advanced search results panel now allows you to retrieve annotations to any of the fission yeast GO slims or the Mondo disease slim for genes in the results list. For example, you can query for all genes involved in a process and slim the resulting list by molecular function or disease association.\n\nPomBase adopts MONDO for disease gene curation\n\n2020-05-18\n\nPomBase has switched from the Disease Ontology (DO) to the Monarch Initiative’s Mondo Disease Ontology (Mondo) for disease gene curation. Mondo covers the same set of disease descriptions as DO, but has a richer hierarchical structure that classifies more specific descriptions into broad categories (e.g. anemia, cancer, kidney disease) suitable for a disease “slim” term set.\n\nPomBase curators are collaborating with Mondo to improve its disease classification, especially in areas that will support inferences that improve fission yeast disease annotation coverage in the new PomBase Mondo slim. The new disease slim is a work in progress, so if there is a particular disease grouping that you would find useful, please let us know.\n\nImproved gene-disease curation\n\n2020-05-18\n\nPomBase disease gene curation associates disease descriptors with fission yeast orthologs of human disease-causing genes. We have now increased coverage by adding new gene–disease term connections, with 3954 individual annotations to 1195 genes (up from 2588 and 905 respectively in January 2019). Disease associations now cover 24.5% of all fission yeast protein-coding genes, and over one third of those with human orthologs.\n\nPublished: Community curation in PomBase\n\n2020-05-11\n\nThe PomBase team has published an overview of our experience with community curation for fission yeast. In the article, out this week in Database, we reflect on the factors that have made our community’s remarkable, standard-setting achievements possible, and on the benefits we and PomBase users derive from this effort. We highlight the collaboration between authors and professional curators that arises via community curation, and how annotation quality improves as a result.\n\nWatch for invitations to curate your new papers, or see our community curation page for more information.\n\nPombeTalks May 13th\n\n2020-05-07\n\nThe next online PombeTalks will take place on Wednesday 13 May 2020 at 17:00 Central European Time. Speakers:\n\n- Sarah Lambert, Institut Curie, Paris, France: Resolution of replication stress in space and time for maintaining genome stability\n\n- Cornelia Kilchert, Justus-Liebig-University, Giessen, Germany: RNA-binding proteins in fission yeast - a global perspective\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also mark your calendars for the next two sessions on May 27 and June 10, and if you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nChromatin silencing ontology & annotation overhaul\n\n2020-05-07\n\nPomBase curators have collaborated with the GO Consortium to improve the representation of chromatin silencing and the underlying heterochromatin organization processes in the GO biological process ontology and annotations.\n\nNotably, “chromatin silencing” terms have been removed from GO on the grounds that they conflated various heterochromatin assembly, formation, and maintenance pathways with processes that affect chromatin-mediated repression more indirectly (e.g. tethering to the nuclear envelope). Chromatin silencing is a phenotype resulting from the cumulative effects of these processes, and the Fission Yeast Phenotype Ontology (FYPO) accordingly retains a full suite of “chromatin silencing” terms.\n\nAnnotations using the GO chromatin silencing terms were reviewed, and either removed or reannotated based on what could be inferred from the phenotypes, resulting in a substantially revised set of heterochromatin assembly annotations. Further work is required, so please send us any corrections.\n\nPomBase now uses InterPro Version 79.0\n\n2020-05-05\n\nPomBase now uses InterPro Version 79.0, which integrates:\n\n- 128 new InterPro entries\n- An update to PIRSF [3.10]\n- 151 new methods from the SUPERFAMILY (4), CATH-Gene3D (6), PIRSF (9), PANTHER (106), and CDD (26) databases.\n\nInterPro cites 48466 publications in PubMed. See the InterPro release notes for further information.\n\nMitochondrial genome update\n\n2020-05-01\n\nThe mitochondrial genome sequence in PomBase has been updated to reflect corrections made in Tao et al. (2019) “Intraspecific Diversity of Fission Yeast Mitochondrial Genomes”.\n\nMidori Harris receives 2020 Biocuration Career Award\n\n2020-04-28\n\nMidori Harris, ontology developer and curator at PomBase, has been awarded the 2020 Biocuration Career Award.\n\nCongratulations to Midori and a huge thanks for all that you do for PomBase.\n\nPombeTalks start on April 29th\n\n2020-04-22\n\nThe first in the new series of online PombeTalks will take place on Wednesday 29 April 2020 at 17:00 Central European Time. Speakers:\n\n- Aleksandar Vjeṧtica, Sophie Martin’s lab, University of Lausanne: Cycling for reproductive fidelity: Coupling the cell cycle and re-fertilisation blocks ensures ploidy maintenance during sexual lifecycle\n\n- Haitong Hou, Julia Cooper’s lab, NCI & University of Colorado: Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8\n\nTalks will be streamed live via Zoom. The link will be circulated via pombelist and PombeSlack one day in advance, so make sure you’ve signed up. Also mark your calendars for the next two sessions on May 13 and May 27, and if you’re interested in speaking, please fill out this form.\n\nThanks to Gautam Dey and the rest of the PombeTalks team for organizing. See you online!\n\nAnGeLi update\n\n2020-03-23\n\nAnGeLi (developed by Danny Bitton) is a tool that allows you to perform enrichments over gene lists.\n\nAnGeLi has recently been updated to provide 9320 lists, including ontology-based annotations from PomBase (as of 2020-03-04) as well as many additional datasets from the Bähler laboratory.\n\nNew search result download options\n\n2020-03-23\n\nThe PomBase Advanced search has added new options to the data you can download for your query results:\n\n- All physical interactors of a gene product\n- Deletion viability\n- Protein length\n\nPomBase now uses InterPro Version 77.0\n\n2020-03-01\n\nPomBase now uses InterPro Version 77.0, which integrates 145 new methods from the CATH-Gene3D (134), and SUPERFAMILY (11) databases. InterPro cites 59894 publications in PubMed. See the InterPro release notes for further information.\n\nCommunity curation response rate reaches 50%\n\n2020-02-28\n\n789/1587 publications assigned to community members for curation are finished. A big thank you to everyone who has participated so far. For more details, and all our curation metrics, see https://curation.pombase.org/pombe/stats/annotation\n\nA quarter of a million annotations\n\n2020-02-20\n\nPomBase recently reached 250,000 annotations to controlled vocabularies and ontologies. The majority (over 90%) are assigned manually from fission yeast experimental data derived from 3776 publications, most of which report low-throughput, hypothesis-driven experiments.\n\nYou can query and combine any of these data types in the Advanced search.\n\nThank you to everyone who contributed to this significant achievement through community curation.\n\nQuery phenotypes for conditions\n\n2020-02-05\n\nThe PomBase advanced search Advanced search now supports using experimental conditions as search criteria for phenotype annotations. For example, you can now query for genes that show abnormal chromosome segregation mutant phenotypes specifically at high or low temperatures. The search uses the same condition descriptors as Canto and the PomBase web pages.\n\nNote that phenotype queries that have condition constraints can be combined, but pay careful attention to the annotations for the results. Future work will add support for querying for multiple conditions on the same annotation, and for specifying conditions to exclude from results.\n\nLevures, Modèles et Outils 14th International Conference\n\n2020-02-04\n\nThe 14th edition of the “Levures, Modèles et Outils” meeting (LMO14) will be held in July 9-11, 2020, at the University of Strasbourg in France. Registration is open February 3rd to June 30th, and abstracts can be submitted from February 3rd to April 10th. Authors will be notified in early May and the final program will be available in early June.\n\nThe sessions will be diverse and present the latest findings using yeast as a model organism on the following topics:\n\n1. Cell biology, cell cycle, cytoskeleton\n2. Gene expression regulation\n3. Population, functional and evolutionary genomics\n4. Replication, repair and recombination\n5. Transport, sensing and signaling\n6. Pathogenic yeast and filamentous fungi\n7. Tools, resources and databases\n8. New technologies, yeast and industry\n\nPomBase is now an ELIXIR Node Service\n\n2020-01-17\n\nPomBase has been awarded Node Service status by the UK node of ELIXIR. ELIXIR-UK Node Services support the bioinformatics and broader biological research communities by providing training and resources that help researchers to find and share data, exchange expertise, and agree on best practices at national, European and international levels. The review panel describes PomBase as a “mature, leading model organism database which is popular, unique, well used, and has a strong user community.”\n\nNew vectors for simple, reliable S. pombe molecular biology\n\n2020-01-07\n\nTo enable fission yeast researchers to manipulate S. pombe molecular biology reproducibly and easily, Aleks Vještica and Magdalena Marek in Sophie Martin’s lab have designed and constructed a series of simple, fully characterized plasmids.\n\nThe Stable Integration Vector (SIV) series provides a highly modular toolbox to introduce heterologous sequences more stably was possible with than previously available vectors. The toolkit includes antibiotic resistance markers, promoters, fluorescent tags, and terminators, as well as large set of ready-to-use fluorescent probes to mark organelles and visualize cellular processes.\n\nThe work is published in the Journal of Cell Science, and a PomBase publication page is available.\n\nUnique permanent URLs for search results\n\n2019-11-28\n\nAll result pages from the Advanced search now have a unique permanent URL that can be bookmarked and shared with your colleagues.\n\nThe QuiLT and GO slim pages also now have permanent URLs.\n\nBrowser tracks now loadable from publication pages\n\n2019-10-16\n\nData tracks from datasets hosted in the PomBase genome browser can now be browsed and loaded from their respective publication pages. For an example, see Atkinson et al. (2018). Data tracks are now also downloadable from the publication pages.\n\nNew PomBase funding from the Wellcome Trust\n\n2019-10-07\n\nWe are pleased to announce that the recent PomBase application for continued Wellcome Trust funding was successful. Although the grant was not fully funded, we are confident that we can cover the shortfall by small grants for stand-alone projects and collaborations. We would like to thank the pombe community for their support with the application, and the Wellcome Trust for their continued funding. We look forward to supporting your research until 2025 (and beyond).\n\nPomBase now uses InterPro Version 76.0\n\n2019-10-06\n\nPomBase now uses InterPro Version 76.0, which integrates 277 new methods from the CATH-Gene3D (1), PANTHER (178) and CDD (98) databases. InterPro cites 59846 publications in PubMed. See the InterPro release notes for further information.\n\nReplication origin data loaded into JBrowse\n\n2019-08-30\n\nWe have loaded data from: Segurado et al. (2003) “A+T-rich islands”, Hayashi et al. (2007) “Pre-replicative complex localization; early and late firing origins”, and Mickle et al. (2007) “Replication origins with functional classification”.\n\nTo view the tracks, either follow the hyperlinks above to the respective PomBase publication pages, and click on the “view” link after “Datasets from this publication are available in the PomBase JBrowse genome browser”, or go directly to the browser and click on the “select tracks” button to find the tracks manually.\n\nFor anyone new to JBrowse we have a quick start guide.\n\nJoin the conversations on Slack\n\n2019-07-19\n\nThe vibrant fission yeast community now has a Slack channel. Slack provides a forum for the research community. Follow conversations you care about, message colleagues privately, or in groups, ask questions, post responses. All archived and searchable.\n\n- See the PombeSlack flyer for more information, including how to join.\n\n“Fitness Landscape of the Fission Yeast Genome” dataset loaded into JBrowse\n\n2019-07-11\n\nWe have loaded the Grech et al. (2019) “Fitness Landscape of the Fission Yeast Genome” dataset into JBrowse. In this study, transposon mutagenesis libraries were created to map transposon insertion sites in the S. pombe genome. From this data, functional elements of the genome were inferred. The tracks from this study can be loaded by a single click from the linked publication page above\n\nThanks Dan Jeffares for sending us the data.\n\nFor anyone new to JBrowse we have a quick start guide.\n\ntRNA metabolism GO annotation update\n\n2019-05-19\n\nThe process of tRNA metabolism, and the associated molecular functions have recently been reviewed.\n\n- “tRNA metabolic process” annotation\n- genes for “tRNA metabolic process”\n\nPlease let us know if the annotation can be further improved.\n\nCustomisable FASTA download\n\n2019-04-18\n\nYou can now download nucleotide or peptide sequences for genes in Advanced search results in FASTA format, and customise what is included in the FASTA headers (e.g. gene names, product descriptions, sequence coordinates, or various IDs can be included).\n\nNew homology modelling and ortholog links on gene pages\n\n2019-04-18\n\nWe have added new external links to PomBase gene pages for structure and ortholog predictions:\n\n- Protein-specific links to SWISS-MODEL, a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, lead to a SWISS-MODEL Repository page for each sequence and present results. If no structure or model is available, you can either trigger adding an entry to the repository with a single click or easily interactively search for templates and build models in your own SWISS-MODEL workspace.\n\n- Ensembl Fungi Compara and Ensembl Pan-taxonomic Compara links lead to orthology predictions from the Ensembl Compara pipeline for fungi and all species, respectively.\n\n- PANTHER links retrieve gene information, classification, and predicted orthologs.\n\nPomBase InterPro Update\n\n2019-04-17\n\nPomBase now uses InterPro Version 73.0, which integrates 1,531 new methods from the CATH-Gene3D (122), CDD (330), PANTHER (1075), Pfam (2), PROSITE profiles (1) and TIGRFAMs (1) databases, and covers 81.2% of UniProt Knowledgebase release 2019_02.\n\nSee the news item at InterPro for additional information, including release notes.\n\nS. pombe included in Gene Info browser extension\n\n2019-04-16\n\nS. pombe gene information is now included in the Gene Info extension (GIX) for the Chrome and Firefox web browsers. GIX allows you to retrieve information about a gene product directly on any webpage simply by double clicking an official gene name, synonym or supported accession. Searching or double-clicking on text terms retrieves gene function annotation, GO terms, external database links, and interaction data drawn from BioGRID and IntAct. Retrieved gene names are automatically hyperlinked for rapid recursive searches.\n\nGeneInfo is fully open source, available online at GitHub. Tutorial videos, a step-by-step guide, and download links for Firefox Add-ons and the Chrome web storeare available online. GeneInfo was developed by James Knight in the Gingras Lab at the Lunenfeld-Tanenbaum Research Institute in Toronto, Canada.\n\nIntegrated motif search\n\n2019-03-19\n\nThe PomBase motif search has been fully integrated into the website, and allows users to find protein motifs and send them directly to the PomBase advanced search.\n\nICYGMB 2019 - registration open\n\n2019-03-13\n\nRegistration is now open for the 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB), which returns to Gothenburg, Sweden, August 18-22, 2019.\n\nYeast2019 is the meeting of the international yeast research community where the latest, and even unpublished results are exchanged, and new projects, alliances, and collaborations are founded. Featuring 55 confirmed speakers including keynote lectures by Susan Gasser, Roger Kornberg and Frederick Roth, this conference will contain important news and information for all yeast researchers. A do-not-miss-event.\n\nGO slim for any S. pombe gene list\n\n2019-03-05\n\nPomBase’s advanced search now allows you to retrieve GO slim annotations for any set of search results. To find GO slim annotations for your own list of S. pombe genes, use the advanced search “Gene names and IDs” option, and then use the “Slim” button on the search results page.\n\nSee the fission yeast GO slim page and the advanced search documentation for more information.\n\nSouth Eastern Regional Yeast Meeting (SERYM) - registration open\n\n2019-03-04\n\nRegistration is now open for the 26th annual South Eastern Regional Yeast Meeting (SERYM), which will be held April 12-14, 2019, in Atlanta, GA, USA.\n\nFission yeast’s own Susan Forsburg is the keynote speaker. The meeting brings together researchers who use any type of yeast as a model system, covering diverse, interdisciplinary topics from strategies for treatment of fungal disease to modeling human disease in yeast.\n\nIcon: SERYM 2019\n\nInternational Cell Cycle meeting - registration open\n\n2019-02-27\n\nRegistration is now open for the Inaugural Trieste Cell Cycle Meeting, which will be held June 3-6, 2019, in Trieste, Italy.\n\nThis is the first of a planned series of biennial cell cycle meetings that will take place in Europe, and will alternate with the Salk Cell Cycle meetings held on the US west coast.\n\nOrganisers Rob de Bruin, Snezhana Oliferenko, Rosella Visintin and Peter Thorpe hope to see you there!\n\nIcon derived from meeting image; credit: Chantal Roubinet, Baum lab\n\nPublished: Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?\n\n2019-02-20\n\nOur analysis of conserved unknown proteins has now been published in Open Biology. In it, PomBase curators consider the challenges and opportunities that conserved, but persistently unstudied, proteins pose for diverse areas of basic and applied biology. We develop metrics to define unknown lists, provide unknown inventories for human and yeast, and classify S. pombe unknowns by numerous orthogonal attributes, all with a view to drawing attention to the unknowns to alleviate their neglect.\n\nPombe 2019 - registration open\n\n2019-02-15\n\nRegistration for the 10th International Fission Yeast Meeting is now open!\n\nThe conference will take place July 14-19, 2019, in Barcelona, Spain. Early registration closes on April 15th — or when capacity is reached. Please see the conference website for more information, including registration final deadline and costs (some travel grants are available), abstract submission, programme, accommodation, and logistics.\n\nVal Wood wins Biocuration society award\n\n2019-02-12\n\nCongratulations to PomBase project leader Val Wood, who has received the 2019 Exceptional Contributions to Biocuration Award from the International Society for Biocuration. Read more at the ISB site\n\nImproved disease association dataset released\n\n2019-01-09\n\nWe are pleased to announce the release of our improved human disease mappings dataset. This dataset connects human disease causing genes to their S. pombe orthologs.\n\nDiseases are now mapped to the Disease Ontology (DO) and the dataset has been extended by data from Malacards. All disease associations can be accessed from the top level disease page. A disease slim has been created to facilitate browsing of disease categories. Currently, 907 S. pombe genes are associated with disease (up from 610 in the original dataset). This number is due to increase as mappings are still in progress.\n\nMany thanks to DO and Malacards for help in improving this annotation set. Icon courtesy of Julie McMurry.\n\nMitochondrial GO annotation update\n\n2018-12-17\n\nResponding to increasing interest in mitochondrial biology, especially relating to ageing, neurogenerative diseases, and processes at the ER-mitochondrion interface, we have reviewed S. pombe mitochondrial GO annotations. Although there is still relatively little fission yeast-derived experimental data in this area, we have refined many inferred annotations for mitochondrial complexes and sub-components as well as some for processes.\n\nYou can see all 753 S. pombe mitochondrial annotations on the ontology term page for mitochondrion (GO:0005739).\n\nIcon courtesy of Reactome.\n\nNew nucleosome occupancy maps loaded\n\n2018-12-03\n\nWe have loaded the nucleosome occupancy maps as described in González et al. (2016) PMID: 27662899. This dataset was generated using the paired-end sequencing protocol of Illumina and thus those maps are of higher resolution than those made with single-end (SE) sequencing hosted in the browser since before.\n\nHere is a link that loads the tracks in PomBase JBrowse. And here is a link to our JBrowse quickstart guide.\n\nMany thanks to Paco Antequera for sending us the bigwig files! If you would like us to load any datasets then please get in touch.\n\nSee your genes in a QuiLT\n\n2018-11-21\n\nPomBase now offers a new way to display gene lists graphically based on multiple orthogonal annotation types — the Quick Little Tool (QuiLT) for visualisation.\n\nInspired by our recent analysis of conserved unstudied proteins (see figures 4 and S1 in the manuscript at bioRxiv), QuiLT allows you to create a similar figure for any gene list you create or import using the advanced search. To use QuiLT, follow the link to your search results, then click the “Visualise” button. QuiLT visualisation is also available from the PomBase pages that list genes annotated to an ontology term, and on the Priority unstudied genes page.\n\nTo see the Unknowns dataset in QuiLT, visit the unknowns results page and click “Visualise”.\n\nThe QuiLT display is interactive, and you can:\n\n- Highlight subsets of the list, and filter the display\n- Toggle annotation types on and off\n- Reorder the list to focus on features of most interest\n- Download the image\n\nSee the QuiLT documentation for more information, and contact the curators if you have comments, questions or suggestions.\n\nMany thanks to our star (and only) programmer, Kim Rutherford, for developing QuiLT.\n\nFission yeast transmembrane transport overhaul\n\n2018-11-20\n\nThe Gene Ontology “transmembrane transport” branch has recently been substantially revised. In line with these revisions, PomBase has standardised gene product descriptions for transporters, and overhauled GO annotations to be as complete and comprehensive as possible based on current knowledge.\n\nIcon courtesy of Reactome.\n\nHidden in plain sight: What remains to be discovered in the eukaryotic proteome?\n\n2018-11-17\n\nIn a new publication, PomBase curators consider the challenges and opportunities that conserved, but persistently unstudied, proteins pose for diverse areas of basic and applied biology. To draw attention to these proteins, we develop metrics to define unknown lists, provide unknown inventories for human and yeast, classify S. pombe unknowns by numerous orthogonal attributes, and speculate about reasons for their neglect.\n\nA pre-publication manuscript is available at bioRxiv.\n\nPomBase in your pocket\n\n2018-11-14\n\nOur usage statistics informed us that over 20% of devices accessing PomBase are smartphones or tablets. We therefore spent some time optimizing the display for small screens. We hope that you will continue to enjoy PomBase on the go!\n\nCelebrating 20 years of GO\n\n2018-11-08\n\nPomBase curators are major contributors to the Gene Ontology (GO) project — ontology content, annotations, and QC procedures — and co-authors on the new GO NAR Database Issue paper.\n\nWe recommend citing the GO and PomBase NAR papers when you use GO data in your analyses.\n\nRNA central and PomBase\n\n2018-11-06\n\nRNAcentral is a comprehensive database of non-coding RNA sequences. PomBase is an RNAcentral Consortium member, and all of the curated non-coding RNAs from PomBase will be available in RNAcentral soon. For more information, see their recent NAR Database Issue paper, as well as current search results for S. pombe RNAs.\n\nNew PomBase genomic region graphics\n\n2018-10-23\n\nPomBase gene pages now use interactive graphics from PomBase JBrowse to depict the genomic region around the gene. Drag to scroll left and right, double-click to zoom in, shift-double-click to zoom out, and click a feature to see details in a popup. The “Full-screen view” link in the corner opens the fully functional JBrowse in a new tab or window. Reloading a gene page restores the display to the default location and zoom level.\n\nPomBase NAR Database Issue\n\n2018-10-15\n\nOur NAR database update “PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information” is now available. We have updated the Citing PomBase to recommend citing this new paper. Thank you all for guiding the development of the new, improved PomBase, and for your continued usage, curation contributions, and suggestions!\n\nFungal Pathogen Genomics Course 2019 - registration open\n\n2018-10-10\n\nRegistration for the 2019 Fungal Pathogen Genomics Course is now open. The course is hosted by Wellcome Genome Advanced Courses and Scientific Conferences, and will take place May 7-12, 2019, at the Wellcome Genome Campus, Hinxton, UK. Course content provides hands-on training on how to: - Take advantage of unique tools offered by FungiDB, EnsemblFungi, PomBase, SGD/CGD, and MycoCosm/JGI; - Develop testable hypotheses; - Investigate transcriptomics, proteomics and genomics datasets across multiple databases and different user interfaces. Please see the course website for more information, including how to apply, costs (limited bursaries are available), programme, and logistics.\n\nTranscript tracks from Atkinson et al. (2018) loaded\n\n2018-10-06\n\nWe are very pleased to announce that we have loaded the transcript tracks from Atkinson et al. (2018) into the PomBase JBrowse genome browser. For a brief introduction to getting started with PomBase JBrowse, please see our documentation page. If you have published data that you would like to see hosted, please get in touch.\n\npombelist changes\n\n2018-08-31\n\nThe pombe community mailing list, “pombelist”, is now hosted by the University of Cambridge. The new address for posting messages is pombelist@pombase.org. The link to subscribe has also changed.\n\nNew genome browser tracks\n\n2018-05-28\n\nWe are very pleased to announce that we have loaded a number of new datasets into the PomBase [JBrowse genome browser (https://www.pombase.org/jbrowse/). These include:\n\n- Thodberg et al. (2018) - CAGE-defined transcription start sites across 5 different conditions\n- Yadav et al. (2012) - G(x) scores specifying the amount of free energy needed to melt base pairs in the DNA duplex at different genomic locations\n- A PomBase-generated dataset of promoter elements across the genome (computational matching of the consensus promoter sequences to the reference DNA sequence)\n- Intron branch points from Bitton et al. (2014) which was also available in the Ensembl browser.\n\nFor anyone wanting a quick introduction to our genome browser, Antonia Lock has written “Getting started with PomBase JBrowse”, a basic guide that covers loading tracks, navigating the browser, what metadata we provide, and more.\n\nNew book chapter about PomBase\n\n2018-05-22\n\nPomBase has a new book chapter in Eukaryotic Genomic Databases (Methods and Protocols). This chapter provides insight into the curation philosophy and data organization at PomBase, and provides a guide to using PomBase tailored for infrequent visitors and anyone considering extending their research to include S. pombe. The chapter is free to download courtesy of the Wellcome Trust.\n\nPomBase releases JBrowse\n\n2018-04-16\n\nPomBase has now implemented JBrowse, from the GMOD project, as its genome browser. The new browser offers a number of improvements over the old:\n\n- Quick, responsive scrolling and zooming\n- Simple track selection interface\n- Intuitive controls\n- Simplified data submission pipeline behind the scenes\n- More informative track metadata\n\nIn memory of André Goffeau\n\n2018-04-05\n\nSadly, PomBase staff and the fission yeast community note the death of André Goffeau on April 2, 2018. In addition to initiating and coordinating the sequencing of the budding yeast genome, Prof. Goffeau will be remembered for his contributions to the fission yeast genome project and for his knowledge, leadership, and friendship.\n\nCongratulations to GSA award winners\n\n2017-11-24\n\nThe Genetics Society of America (GSA) has announced two award winners familiar to the model organism database world:\n\n- Ira Herskowitz Award: Mike Cherry, Stanford University\n- Lifetime Achievement Award: Steve Oliver, University of Cambridge\n\nThe awards will be presented at the next Yeast Genetics Meeting, at Stanford University in August 2018. Congratulations and thanks to Mike and Steve!\n\nNew, improved PomBase goes live\n\n2017-10-24\n\nThe new PomBase web site, which has been under development during 2017, has been released. The new site features:\n\n- Nightly data updates\n- New publication pages\n- New genotype pages\n- Improved ontology term pages\n- Improved summary views for annotation displays\n- Phenotype annotation display filtering\n- Faster querying in the advanced search\n- Front page research and community curation highlights\n- Streamlined back-end data storage and retrieval\n\nWe thank the members of the fission yeast research community who have followed its progress via the preview site, and welcome feedback from all users.\n\n9th International Fission Yeast Meeting - early registration closes soon\n\n2016-12-11\n\nReminder: early registration for the 9th International Fission Yeast Meeting in Banff closes Dec. 31, 2016. Please see the conference website at www.pombe2017.com for details.\n\n9th International Fission Yeast Meeting registration open\n\n2016-10-31\n\nRegistration for the 9th International Fission Yeast Meeting is now open. The meeting will be held in Banff, Canada from May 14-19, 2017. Early registration closes Dec 1, 2016! Please see our website at www.pombe2017.com for details. We look forward to seeing you in Banff!\n- Conference Organizers: Dallan Young, Gordon Chua, Paul Young\n\nPomBase data update 2016-10-19\n\n2016-10-19\n\nWe have updated the data available on the PomBase web site to include manual curation through September 11, 2016.\n\nShow your support for database funding\n\n2016-06-27\n\nIn 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.\nThe Genetics Society of America website where the letter can be viewed and signed is at http://www.genetics-gsa.org/MODsupport\nPlease 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\n\nOur model organism database commentary\n\n2016-06-15\n\nSeveral 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:\nOliver SG, Lock A, Harris MA, Nurse P, Wood V. 2016. Model organism databases: essential resources that need the support of both funders and users.\nBMC Biol. 2016 14(1): 49. doi: 10.1186/s12915-016-0276-z. PMID:27334346\n\nPomBase data update 2016-05-31\n\n2016-05-31\n\nWe have updated the data available on the PomBase web site to include manual curation through May 12, 2016.\n\nPomBase data update 2016-05-09\n\n2016-05-09\n\nWe have updated the data available on the PomBase web site to include manual curation through April 8, 2016.\n\nPomBase data update 2016-04-11\n\n2016-04-11\n\nWe have updated the data available on the PomBase web site to include manual curation through March 9, 2016.\n\nImportant: We have corrected a problem that made erroneous interaction data and literature appear on some gene pages.\n\nThe gene pages now include interaction data from the Vo et al. proteome-wide study (curated by BioGRID and imported into PomBase):\nVo 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.\n\nThe genome browser now includes transcriptome data published in:\nEser 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.\n\nPomBase data update 2016-02-11\n\n2016-02-11\n\nWe have updated the data available on the PomBase web site to include manual curation through January 25, 2016.\nThe genome browser includes variation data, in tracks under “Variation”, from natural S. pombe isolates, published in:\nJeffares 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\n\nNew files are now available from the PomBase FTP site, and are linked from pages in the Download Datasets area:\n\n- Non-coding RNA sequence feature coordinates (available via the Data Mappings page);\n- Protein features, such as domains and family assignments (available via the Protein Datasets page);\n- Protein modification annotations (also in Protein Datasets).\n\nThe New and Removed Genes page has been updated to reflect recent deletions and merges.\nNote: 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.\n\nPomBase data update 2015-12-02\n\n2015-12-02\n\nWe have updated the data available on the PomBase web site to include manual curation through November 9, 2015, including 340 community-curated publications.\n\nNew Advanced Search features\n\n2015-12-02\n\nWe have introduced new features to the Advanced Search:\n\n- 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.\n- You can now query for genes that interact genetically or physically with a specified gene.\n- 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.\n\nNew genetics primer for fission yeast\n\n2015-10-19\n\nA 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\n\nHoffman 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\n\nPomBase data update; viability summary correction alert\n\n2015-09-28\n\nWe have updated the data available on the PomBase web site to include manual curation through September 6, 2015.\n\nErrors 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.\n\nPomBase data update with multi-allele phenotypes\n\n2015-09-03\n\nWe have updated the data available on the PomBase web site to include manual curation through August 13, 2015, including 300 community-curated publications.\n\nPomBase 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.\n\nThe genome browser now includes data tracks for two more publications:\nDNA polymerase usage from:\nDaigaku 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\nPromoters and transcription start sites from:\nLi 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\n\nCodon 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.\n\nThe gene page section that was formerly misnamed “species distribution” is now called “taxonomic conservation”.\n\nPomBase data update 2015-06-16\n\n2015-06-16\n\nWe 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!\n\nCanto downtime & new version\n\n2015-05-26\n\nCanto, 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.\nThe 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.\nWe will announce when the new version of Canto is released to the public.\n\nPomBase data update 2015-05-26\n\n2015-05-26\n\nWe have updated the data available on the PomBase web site to include manual curation through May 8, 2015, including 265 community-curated publications.\n\nPombe 2015 travel fellowships\n\n2015-04-23\n\nApplications 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).\n\nPomBase data update 2015-04-19\n\n2015-04-19\n\nWe 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.\n\nPombe 2015 poster abstract deadline extended\n\n2015-04-19\n\nThe 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.\n\nPombe 2015 abstract deadline approaching\n\n2015-04-09\n\nAbstracts 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.\n\nPomBase data update 2015-03-23\n\n2015-03-23\n\nWe 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.\n\nPombe 2015 registration now open\n\n2015-02-26\n\nRegistration for Pombe 2015: 8th International Fission Yeast Meeting is now open at the conference web site, https://amarys-jtb.jp/web/Pombe2015/index.html\n\nThe registration deadline is 17 May 2015.\n\nThanks to Yasushi Hiraoka for this item.\n\nPomBase data update 2015-02-16\n\n2015-02-16\n\nWe 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.\n\nPomBase data update 2015-01-26\n\n2015-01-26\n\nWe 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.\n\nNew compact GO annotation display\n\n2014-12-10\n\nTo 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.\n In addition, the top of the Biological Process table now lists any GO slim terms applicable to the gene.\n\nesyN network visualizations in PomBase\n\n2014-12-10\n\nPomBase 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.\nOn gene pages, we have links to gene-specific interaction networks in esyN in the table headers of the Interactions sections:\n\n- The Genetic Interactions section links to all interactions centred on the gene and curated in BioGRID\n- The Physical interactions section has links to two datasets:\n - All physical interactions curated in BioGRID for the gene\n - Interactions for the gene in the PomBase High Confidence Physical Interaction Network (HCPIN)\n\nWe 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).\n\nPomBase data update 2014-11-12\n\n2014-11-12\n\nWe 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:\nGraml 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.\n\nThe genome browser now includes tracks for intron branch point data from:\n\nBitton 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.\n\nWe 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.\n\nPomBase data update 2014-09-16\n\n2014-09-16\n\nWe 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.\n\nPomBase data update 2014-08-18\n\n2014-08-18\n\nWe 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.\n\nPomBase data update 2014-07-17\n\n2014-07-17\n\nWe 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:\n\nKoch 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\nWe have also made corrections to some residue positions affected by sequence updates in one of the modification datasets we added last month:\n\nCarpy 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\n\nPomBase data update 2014-07-08\n\n2014-07-08\n\nWe 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.\n\nThe gene pages also now display protein modification data from two large-scale datasets:\n\n- 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\n- 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\n\nLink updated 2021-02-04\n\nGene Ontology publication on annotation extensions\n\n2014-06-29\n\nPomBase 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:\n\nHuntley, 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\n\nPomBase data update 2014-05-15\n\n2014-05-15\n\nWe 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.\n\nThank you to all who have done, or are doing, paper curation in Canto. Over 159 community-curated papers are now included in PomBase.\n\nThere 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.\n\nAs usual, please don’t hesitate to alert us of any other problems with data or site performance, or if you have any questions.\n\nSincerely yours,\nThe PomBase Staff\n\nPomBase data update 2014-03-20\n\n2014-03-20\n\nData 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.\n\nPomBase data update 2014-02-20\n\n2014-02-20\n\nWe 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.\n\nWe have made some improvements to the gene pages. Highlights:\n\n- The Sequence section now has links to NCBI BLAST as well as Ensembl BLAST.\n- The External References section now links to the Pomb(A) polyadenylation viewer.\n\nIn the genome browser, new data tracks are now available for data from these publications:\n\n- 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\n- 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\n- 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)\n- 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\n\nNow 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.\nGenome 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.\n\nHuman ortholog data correction coming next month\n\n2014-02-19\n\nWe 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.\n\nPomBase data update 2013-12-08\n\n2013-12-08\n\nWe 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.\n\n2021-08-18: Updated to remove out-of-date links (events are now listed only as news items).\n\n2013 meeting mini-reviews published\n\n2013-11-24\n\nA 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\n\n(Thanks to Jürg Bahler for this item)\n\nPomBase survey results available\n\n2013-11-20\n\nThe 2013 PomBase user survey closed at the end of October, and the results are available here (PDF at FTP site). Some highlights have been sent to the pombe mailing list. Many thanks to all who completed the survey.\n\nLink updated 2021-02-04\n\nNew “Target Of” gene page section\n\n2013-10-27\n\nWith 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.\n\nPomBase data update 2013-10-21\n\n2013-10-21\n\nThe 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:\n\n- 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\n- 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\n\nPomBase User Survey open\n\n2013-09-18\n\nTo 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!\n\nhttps://www.surveymonkey.com/s/NDM2BQX\n\nPomBase data update 2013-09-15\n\n2013-09-15\n\nWe 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.\nWe also have an updated version of the S. pombe/human ortholog table available upon request.\n\nSend HTP data to PomBase\n\n2013-08-18\n\nAt 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.\n\nConnecting With PomBase\n\n2013-07-29\n\nTo 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+.\n\nLinks to these are also available from the front page of the PomBase.org site.\n\npombelist has moved\n\n2013-07-21\n\nUpdate: This item dates from July 2013, and the links in it no longer work. \\ Please see the Fission Yeast Community page for the current mailing list link. \\ (2020-02-18)\n\nThe 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.\n\nPomBase website update\n\n2013-07-18\n\nWe’d like to highlight a few improvements we’ve just made to the PomBase website. Most of the changes affect the gene pages:\n\n- The basic information display at the top of each gene page is more compact.\n- 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).\n- Annotation extensions for GO are displayed using human-friendly text instead of internal “relation” labels.\n- The Quick Links box can now be collapsed and expanded by clicking its header.\n- Display of modification annotations using PSI-MOD is improved.\n\nIn 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.\n\nPomBase launches community curation\n\n2013-06-23\n\nAt 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.\n\nPomBase data update 2013-06-20\n\n2013-06-20\n\nPomBase 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.\n\nPomBase data update\n\n2013-05-20\n\nWe have updated the data available on the PomBase web site. The data now includes manual curation through 13 May, 2013.\n\nGeneDB S. pombe decommissioned\n\n2013-05-13\n\nAs 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.\n\nQuantitative gene expression data available in PomBase\n\n2013-05-07\n\nWe 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:\n\n- 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.\n- Wu JQ, Pollard TD. 2005. “Counting cytokinesis proteins globally and locally in fission yeast.” Science 310:310-314.\n\nWe 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.\n\nWe 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\nhttps://www.pombase.org/data/names_and_identifiers/gene_IDs_names.tsv\n\nLink updated 2021-02-04\n\nCarl Singer Foundation Established\n\n2013-04-11\n\nCarl 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.\nCarl’s family would be happy to receive memories of Carl’s life at regards [at] singerinstruments.com.\n\nH/T SGD\n\nPombe 2013: registration & abstracts by Mon 8th April\n\n2013-04-02\n\nDear Pombe Fans,\n Please remember the imminent deadline (Monday 8th April) to register and submit abstracts for Pombe 2013: http://events.embo.org/13-pombe\n Abstracts are also required from all who have already been invited to talk.\n And do book your accommodation if you haven't yet done so.\n More details are in previous email forwarded below.\n Cheers,\n -Jürg & Jacky\n From: On Behalf Of Bahler, Jurg\n Sent: 18 March 2013 17:49\n To: pombelist at sanger.ac.uk\n Subject: [Pombelist] Pombe 2013: Accommodation, registration & abstracts\n Dear Pombe Afficionados,\n Only three weeks left to register and submit abstracts for Pombe 2013, by Monday 8th April: http://events.embo.org/13-pombe\n Speakers for 10 plenary talks and all workshop talks will be selected from abstracts, and there will be attractive poster prizes.\n Payment is only requested after registration, by 10th May.\n 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\n 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.\n We highly appreciate all the generous contributions from our sponsors so far:\n Platinum: EMBO\n Gold: Biochemical Society, Genetics Society, Formedium, Sunrise Science Products, Singer Instruments, F1000Research, PomBase/Wellcome Trust\n Silver: MDPI - Open Access Publishing, Hybrigenics, Infors, Life Technologies, Bioneer\n Bronze: Nature Communications, m2p labs, Imsol, Open Biology\n We look very much forward to welcoming you in London this June!\n All the best,\n -Jürg & Jacky\n\nData update on PomBase web site\n\n2013-04-01\n\nWe have once again updated the data available on the PomBase web site. The data now includes manual curation through March 6, 2013.\nWe 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.\nYou should also see a few small improvements in the site:\n\n- Ontology term pages now display the text definition for each term.\n- FASTA sequence retrieval should be quicker, and less likely to time out, for large gene lists.\n- There has been some tidying of the display of “extension” data for GO and phenotype annotations.\n\nLast 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.\nAs usual, please don’t hesitate to alert us of any other problems with data or site performance, or if you have any questions.\n\nSpeed improvements and new data on PomBase web site\n\n2013-03-01\n\nWe 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.\nWe 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.\nWe 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.\n\nNew data and new features on PomBase web site\n\n2012-11-06\n\nWe are pleased to announce that we have updated both data and web site features for PomBase.\n\nMost importantly, we have added new data types, and upgraded the gene pages to display them.\n\nWe 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.\n\nNew annotation types:\n\n- 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.\n- 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.\n\nYou can see these new data types on many gene pages, such as cdc2 or pka1.\n\nNew web site features:\n\n- Annotation display - Gene page GO and phenotype displays have been revamped to show new annotation types described above.\n- Ontology term pages - Each ontology term ID now links to pages with information about the term and lists of genes annotated to it.\n- Ontology graph links - GO and phenotype annotation sections now include links to graphical ontology displays in the genome browser.\n- Sequence highlighting - Sequence download now offers an option to show colour highlighting of regions such as UTRs, introns and exons.\n- 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.\n- Protein family information is now included in the Protein Features gene page section.\n- The Protein Feature section includes a link to the Pfam entry for a protein.\n- Transcript source data (e.g. for UTR coordinates) is now displayed in the Transcript Features section.\n- A Documentation page contains links to relevant portions of the Ensembl Genomes documentation. (More documentation will be added over the coming months.)\n\nWhat are annotation extensions?\n\nAnnotation 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.\n\nThe information in GO annotation extensions encompasses several effector-target relationships, such as\n\n- localisation dependencies\n- 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\n- activators and inhibitors\n- regulation targets of signalling pathways or transcription factors\n\nAdditional 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).\n\nYou may also find the GO wiki page on annotation extensions informative, although it is primarily aimed at curators.\n\nAnnotation 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.\n\nPomBase web site fully live\n\n2012-07-01\n\nNote (2023-06-09): This is an archived news item about PomBase V1. See the documentation page to learn new Advanced search in PomBase V2.\n\nWe 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.\n\nMore recent data, reflecting additions and changes through March 20, 2012, are now available on gene pages and in search results.\n\nThe 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\n\nThe Advanced Search also now offers:\n\n- options to search GO, FYPO, and other ontologies by term name or ID;\n- autocomplete for ontology term name search;\n- ability to search for genes in a region, such as centromeres or telomeres;\n- improved organization of filter selections.\n\nWe 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.\nIn addition, numerous minor improvements have been made. Please send any questions or comments on the PomBase web site to us at .\n\nPomBase preview launch\n\n2011-11-27\n\nA 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.\n\nPomBase NAR paper published online\n\n2011-10-27\n\nA 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.\n\nGeneDB (S. pombe) now uses the latest release of the Pfam protein family database(25.0).\n\n2011-04-28\n\nSchizosaccharomyces Comparative Genome Paper Published\n\n2011-04-21\n\nA paper describing the major findings of the Schizosaccharomyces Comparative Genome Project was published today in Science Express and reported changes are included in GeneDB.\n\nFurther details are described in the pombe mailing list posts:\n\n- Schizosaccharomyces Comparative Genome Paper Published\n- Import of the fission yeast revisions from the Broad Institute comparative genome paper into GeneDB.\n\nGenome reappraisal reveals new genes and revised gene structures\n\n2011-02-01\n\nFurther information on the pombe mailing list.\n\nAnnotated transcription start and termination sites for fission yeast\n\n2011-01-31\n\nFurther details are available on the pombe mailing list.\n\nAnalysis of Fission Yeast Deletion Publication\n\n2010-05-15\n\nThe analysis of the fission yeast deletion collection is now published online in Nature Biotechnology.\n\nFunding for PomBase\n\n2010-02-28\n\nFunding was awarded by the Wellcome Trust for a fission yeast Model Organism Database, PomBase.\n\nFission yeast is one of the 12 key organisms of the reference genomes project\n\n2009-11-30\n\nFission 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.\n\nGeneDB (S. pombe) now uses the latest update to Pfam, release 24.0\n\n2009-10-31\n\nGeneDB (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).\n\nFission yeast in Ensembl Fungi\n\n2009-09-30\n\nThe fission yeast genome and annotation dataset is now available as part of Ensembl Fungi.\n\nGeneDB is now using Version 23 of the Pfam protein family database.\n\n2009-08-31\n\nGeneDB 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.\n\nS. pombe GeneDB now includes “deep links” to the Biological General Repository for Interaction Datasets (BioGRID)\n\n2008-11-30\n\nS. 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.\n\nGlobal sequence and chip study examines eukaryotic transcription\n\n2008-04-30\n\nDynamic 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.\n\nThe h- mating type region has been provided\n\n2008-01-31\n\nThe h- mating type region has been provided by Xavier Marsellach and Lorena Aguilar.\n\nBaumann and Zakian labs identify telomerase RNA\n\n2007-12-31\n\nBaumann and Zakian labs identify elusive telomerase RNA (PMID:18157152 and PMID:18157149)\n\nWellcome Trust Advanced Course ’Genome-wide approaches with fission yeast\n\n2007-09-30\n\nWellcome Trust Advanced Course ‘Genome-wide approaches with fission yeast’ held in Hinxton.\n\n4th International Fission Yeast Meeting\n\n2007-05-31\n\n4th International Fission Yeast Meeting held in Copenhagen.\n\nGeneDB representation of the fission yeast data moved from contigs to chromosomes\n\n2006-12-31\n\nGeneDB representation of the fission yeast data moved from contigs to chromosomes. See the pombelist archive for details.\n\nYeast Special Issue from the 2006 European Fission Yeast Meeting\n\n2006-09-30\n\nThe 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.\n\nThe first fission yeast whole proteome localization study is now published\n\n2006-06-30\n\nThe first fission yeast whole proteome localization study is now published: Matsuyama A. et al (2006): ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe. Nat Biotech 24, 841-7.\n Fission yeast database survey\n\n2006-04-30\n\nThe fission yeast database survey is now closed. You can view the survey results here.\n\nEuropean Fission Yeast Meeting\n\n2006-03-17\n\nThe 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).\n\nComparative Genomics of Eukaryotic Microorganisms\n\n2005-11-16\n\nComparative Genomics of Eukaryotic Microorganisms:\nEukaryotic Genome Evolution, Approaches with Yeasts and Fungi\n\nThis conference took place from 12th-17th November 2005 in Sant Feliu de Guixols, Spain. Full details can be found here.\n\nSecond East Coast Regional pombe Meeting\n\n2005-11-12\n\nSecond East Coast Regional pombe Meeting\nThis meeting took place from November 11-13, 2005 in Miami Beach, Florida.\n\nGeneral Repository for Interaction Datasets\n\n2004-08-31\n\nA project to record published genetic and physical interactions is underway with Mike Tyers and the GRID group at Toronto.\n\nThe Third International Fission Yeast Meeting\n\n2004-08-29\n\nThe meeting was held at UC San Diego on August 24-29, 2004.\n\nMethods Volume 33 Issue 3\n\n2004-04-30\n\nThis 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 for details of the papers including PMIDs.\n\n2021-08-18: Updated to remove out-of-date link.\n\nRecent Genome wide surveys\n\n2003-10-31\n\nCorrelations Between Gene Expression and Gene Conservation in Fission Yeast. Mata J, Bahler J. Genome Res. 2003 Nov 12 PMID:14613978\nFELINES: 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\nGenome-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\nRetrotransposons and their recognition of pol II promoters: a comprehensive survey… Bowen NJ et al Genome Res. 2003 Sep;13(9):1984-97. PMID:12952871\n\nThe ‘new’ fission yeast book is now published\n\n2003-08-31\n\nEgel, R., Copenhagen, Denmark (Ed.) The Molecular Biology of Schizosaccharomyces pombe Genetics, Genomics and Beyond ISBN:3-540-00693-1\n\nSchizosaccharomyces pombe Essential Genes: A pilot Study\n\n2003-02-28\n\nDecottignies A, Sanchez-Perez I, Nurse P Genome Res. 2003 Mar;13(3):399-406. PMID:12618370\n\nGlobal transcriptional responses of fission yeast to environmental stress\n\n2002-12-31\n\nChen 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\n", "heading" : "News archive", "id" : "news/index" }, diff --git a/src/app/documentation/docs/docs.component.html b/src/app/documentation/docs/docs.component.html index 602d71fa..3925545f 100644 --- a/src/app/documentation/docs/docs.component.html +++ b/src/app/documentation/docs/docs.component.html @@ -5214,6 +5214,7 @@

Curated inventories

Orthology
Tools and resources
Using ontologies
+
@@ -5289,41 +5290,26 @@

Enabling data tracks

To show data tracks:

  1. Click on the “Select tracks” button in the top left corner.

    -
    -JBrowse top, with “select tracks” button highlighted - -
    2. +

    JBrowse top, with “select tracks” button highlighted

  2. Locate the track(s) of interest (see below), and then click the tickbox for any individual track to toggle it on/off, or use the tickbox in the header to enable/disable all of the listed tracks at once.

  3. Click the “Back to browser” button at the top.

  4. The tracks should now be displayed. For example, the sequence feature and DNA sequence tracks look like this:

    -
    -JBrowse display of pombe sequence and features - -
    5. +

    JBrowse display of pombe sequence and features

To hide a track, click the (X) button to the left of the track label, or go to the “Select tracks” page and clear its tickbox.

Drag and drop tracks to change the order in which they appear.

Changing the track scale

By default, the scale fits the range of the data being displayed in the current viewing window. The scale can be manually defined.

Click the downarrow to the right of the track label, and click on edit config:

-
-Jbrowse edit config - -
+

Jbrowse edit config

Change the scale by defining a max_score and/or a min score:

-
-JBrowse_max_score defined - -
+

JBrowse_max_score defined

The scale can be made consistent across tracks:

rescaled tracks jbrowse_rescaled.png

More wiggle track configuration option in the official JBrowse documentation

Locating data

Each entry in the left-hand column can be used to filter the track list. Filter criteria fall into several categories, corresponding to some of the track metadata (see below):

-
-JBrowse track selection interface - -
+

JBrowse track selection interface

As you select filters, the screen will update to show only relevant criteria on the left, and matching tracks on the right.

You can also search for names, keywords, etc. using the “Contains text” box.

Any applied filters, including text, can be cleared by clicking the red X button that appears next to a selected filter (in the search box or the left-hand column), or by using the “Clear All Filters” button.

@@ -5348,25 +5334,13 @@

Track metadata

The metadata can be viewed in two ways:

  1. In the track selector, tracks are listed with associated metadata on the right hand side:

    -
    -JBrowse track selector with metadata headers highlighted - -
    2. +

    JBrowse track selector with metadata headers highlighted

  2. In the browser, hover over a track label to display a down arrow:

    -
    -JBrowse track label - -
    +

    JBrowse track label

    Click the arrow, then click “About this track” in the dropdown menu:

    -
    -JBrowse track dropdown menu - -
    +

    JBrowse track dropdown menu

    The metadata and stats are displayed:

    -
    -JBrowse track metadata popup - -
    +

    JBrowse track metadata popup

    To dismiss the popup, click the ‘X’ in the upper right corner or the ‘OK’ button at the bottom.

@@ -5403,10 +5377,7 @@

Moving around

  • For more information on the chromosome selection options, see PomBase documentation on genome sequencing status, the mating type region, and rDNA.

  • In the uppermost bar, a red box indicates the size and position of the currently displayed region, in the context of the whole chromosome. Click in the bar or drag the red box to change position.

    -
    -JBrowse position bar - -
    • +

    JBrowse position bar

  • Use the arrows next to the bar with the box for chromosomal coordinates to move right or left in increments.

  • Drag or swipe (depending on device) in the main browser window to scroll.

    • @@ -5416,34 +5387,19 @@

    Zooming

  • Use the + and - buttons, or

  • In the main browser window, double-click to zoom in, and shift-double-click to zoom out, or

  • Use the narrow bar below the chromosomal coordinates:

    -
    -JBrowse region selection bar - -
    +

    JBrowse region selection bar

    Click and drag to highlight a region, then click within the highlighted region to zoom so the region fills the browser window:

    -
    -JBrowse zoom in on selected region - -
    • +

    JBrowse zoom in on selected region

    To see the DNA sequence, zoom in until it appears, first as color-coded blocks, and then labeled with letters.

    More S. pombe-specific information can be found in the Genome browser FAQ list.

    Exporting data

    To export the data for any track, hover over the track label to display a down arrow:

    -
    -JBrowse track label - -
    +

    JBrowse track label

    Click the arrow, then click “Save track data” in the dropdown menu:

    -
    -JBrowse track dropdown menu save data - -
    +

    JBrowse track dropdown menu save data

    In the popup, choose a data format. DNA sequence is provided in FASTA format. GFF3 is available for most tracks; other options depend on the data type. You can also edit the name of the file where the data will be saved.

    -
    -JBrowse track metadata popup - -
    +

    JBrowse track metadata popup

    Click ‘View’ to see how the data will appear in the saved file. To download the data file click ‘Save’ (available in the original popup or the ‘View’ panel). To dismiss the popup withous saving, click the ‘X’ in the upper right corner or the ‘Close’ button at the bottom.

    @@ -5487,45 +5443,24 @@

    Overview

    In the Search menu, choose Advanced (or bookmark https://www.pombase.org/query).

    In the Query panel (top), click one of the links in the list on the left to choose a query type (described below). Arrowheads indicate list entries that expand to offer two or more query types, organized in tabs. For each query, the interface guides your input.

    -
    -advanced search page with new query - -
    +

    advanced search page with new query

    In the History panel (bottom), queries are listed in reverse chronological order (most recently run first). Results are linked in the Count column; the link goes to a page that displays the gene name, systematic ID, and product description for matching genes. The Download button offers additional options, including nucleotide and (where applicable) protein sequence. To return to the search page, use the blue “<- Advanced search” button just above the result list, not your browser’s “Back” button.

    You can select queries in the list to combine or delete them. To combine queries, you must select two or more from the list, and then click one of the operator buttons:

    -
    -advanced search Boolean operator buttons - -
    +

    advanced search Boolean operator buttons

    Results are added to the history list:

    -
    -advanced search query history list - -
    +

    advanced search query history list

    Queries using the NOT operator default place the more recently run query first (newer NOT/Subtract older):

    -
    -advanced search page NOT operator dialog - -
    +

    advanced search page NOT operator dialog

    Click “Change direction” to switch the order. Click “Submit” to run the query.

    You can also move any query to the top of the history list by clicking its “Results” link, and then clicking the “<- Advanced search” button.

    Query results can remain available in the history list for several days. If changes in annotation cause results to change since a query was last run, an additional “Previous” column will be displayed in the history list, showing the out-of-date result count:

    -
    -advanced search page with out-of-date query - -
    +

    advanced search page with out-of-date query

    Click on the “Results” link to re-run the query and retrieve the up-to-date result.

    If the parameters for a query are not all visible in the history, a “[details]” toggle (1) to show or hide additional details will appear. You can also edit the name that appears in the history list (2). The name will be used as part of the description when the query is used in any combined query (which can, in turn, be given a new name).

    -
    -advanced search query name and details - -
    +

    advanced search query name and details

    Query results page

    Clicking on any up-to-date count in the “Results” column goes to a page that shows the count, query details, and a list of matching genes.

    -
    -advanced search results page - -
    +

    advanced search results page

    1. Return to the main Advanced search page (you can also use the browser “back” button)

    2. Click on a header to sort by the column

      3. @@ -5557,21 +5492,12 @@

      GO

      The Gene Ontology (GO) query retrieves gene products annotated to a GO term and to any of its child terms, following the is_a, part_of, regulates, positively_regulates,and negatively_regulates relationships in the ontology. You may also find it helpful to search or browse in QuickGO or AmiGO to find GO terms of interest. If one search does not seem to retrieve as many results as you expect, try again using a less specific term. Note: prior to the November 2014 PomBase release, the regulates relations were not followed, and PomBase GO search results therefore did not match those in AmiGO.

      Phenotype

      The phenotype (Fission Yeast Phenotype Ontology) query retrieves genes annotated to a FYPO term and to any of its child terms, following the is_a, part_of, output_of, has_output, and has_part relationships in the ontology. This query also offers additional context-dependent options. By default, the phenotype search retrieves genes from single-allele haploid and diploid genotypes annotated to the searched FYPO term:

      -
      -phenotype default search options - -
      +

      phenotype default search options

      You can alter the selected options to add genes from multi-allele genotypes, and/or to search specifically for haploids or diploids. See the gene page phenotype documentation and the genotype page documentation for more information.

      If you select single-locus haploids, expression level options are also available:

      -
      -phenotype search options for single-locus haploids - -
      +

      phenotype search options for single-locus haploids

      Different alleles of one gene may have different phenotypes, and one allele may give rise to different phenotypes under different experimental conditions. At present, you can retrieve annotations for all alleles of a gene, or use the “Expression level” options restrict the query to null alleles (covers deletions and any other sequence changes, such as most disruptions, that completely abolish expression of the gene) or overexpression of the wild type allele.

      -
      -phenotype condition search option - -
      +

      phenotype condition search option

      The “Constrain condition” option restricts the results to include only genes that have phenotype annotations including the specified condition. The search uses the same condition descriptors as Canto and the PomBase web pages. Start typing, then choose from the autocomplete options.

      Note that the results will include any gene that has phenotype annotations including the specified condition for any allele. Queries that include conditions can be combined using the AND, NOT, or OR operators like any other, but the result of any combination of phenotype queries will likely include annotations for different alleles. There may not be any individual annotation in which both/all of multiple conditions co-occur.

      The search does not yet support querying for multiple conditions on the same annotation, nor for queries that exclude a given condition; both are planned for future development.

      @@ -6210,10 +6136,7 @@

      Gene page: Disease associations

      The Disease association section lists disease descriptions from the Monarch Initiative’s Mondo Disease Ontology (Mondo) for fission yeast orthologs of human disease-causing genes.

      The summary view shows slim terms (see below) and the names of the most specific terms used to annotate the gene.

      The detailed view shows more information for each annotation, and may display additional terms:

      -
      -full gene page disease association annotation - -
      +

      full gene page disease association annotation

      1. Mondo slim terms applicable to the gene.

      2. The Mondo term ID and name, which link to a page with additional information, including the term definition, any synonyms, relationships to other Mondo terms, and annotations to the term or its descendants.

        3. @@ -6226,10 +6149,7 @@

        Gene page: Disease associations

        Gene page: Basic information

        At the top of each gene page is a set of basic information about the gene:

        -
        -top of gene page - -
        +

        top of gene page

        1. See the Gene Name Registry for more information about S. pombe gene names. Synonyms include all names other than the standard name that have been published for a gene, and thus are not guaranteed to be unique.
        2. Free text description of the gene product
          3. @@ -6252,10 +6172,7 @@

          Gene page: External references

          Gene page: Gene expression

          The Gene expression section of a gene page displays curated qualitative and quantitative information about the level and timing of the gene’s expression. In each subsection, a simple summary appears by default:

          -
          -gene page expression section, summary view - -
          +

          gene page expression section, summary view

          1. Qualitative descriptions are drawn from a small internal controlled vocabulary, with supporting extensions. Each description links to a list of all genes annotated to the same term.

          Click “Show details” to reveal additional information:

          -
          -gene page expression section, detail view - -
          +

          gene page expression section, detail view

          1. Qualitative expression details:
              @@ -6311,20 +6225,14 @@

              Gene page: Gene Ontology

          A gene product may be annotated to several GO terms from each of the three ontologies; mcm3, for instance, is annotated to single-stranded DNA helicase activity, ATP binding, and DNA replication origin binding (MFs), it acts in mitotic DNA replication initiation and negatively regulates the MCM helicase activity (BPs), and is found locations including the replication fork and the pre-replicative complex (CC).

          Each table includes ontology term details and supporting data. The GO annotation display on PomBase gene pages includes ontology term details and supporting data. The summary view shows just the essentials: The list of terms is filtered, using the ontology structure, so that it shows only the most specific terms used to annotate a genotype, and each unique combination of gene, GO term, and extension(s) is shown once:

          -
          -summary gene page GO annotations - -
          +

          summary gene page GO annotations

          1. The GO term name, which links to a page with additional information, including the term definition, any synonyms, relationships to other GO terms, and annotations to the term or its descendants. (See the PomBase ontology term page documentation and the GO documentation on the GO graph and Relations in GO for more information.)
          2. GO Slim terms applicable to the gene.
          3. GO annotations may have extensions to capture any of several types of additional detail. S. pombe genes link to PomBase gene pages, and ontology term names link to ontology term pages.

          The detailed view shows annotations to all GO terms, and includes more details for each annotation. It shows separate entries for repeat determinations of a given gene/term/extension combination (if supported by more than one line of evidence and/or reported in more than one paper), and annotations to terms hidden in the summary view:

          -
          -full gene page GO annotations - -
          +

          full gene page GO annotations

          1. The unique ID and name for a GO term, linked to an ontology term page as described above.

          2. An abbreviation (code) for the type of (see “Evidence codes” below) that supports the annotation. The evidence categories come from the set of evidence codes defined by the GO Consortium.

            3. @@ -6386,15 +6294,9 @@

            Gene page: Modifications

            The Modifications section lists protein modifications that have been manually curated, using terms from the PSI-MOD ontology, for protein-coding genes. PomBase will add RNA modifications to this section in the future, when relevant data are curated.

            Ontology Annotations for Protein Features

            The summary view shows only the names of the most specific terms used to annotate the gene:

            -
            -summary gene page modification ontology annotation - -
            +

            summary gene page modification ontology annotation

            The detailed view shows more information for each annotation, and may display additional terms:

            -
            -full gene page modification ontology annotation - -
            +

            full gene page modification ontology annotation

            1. Name and ID of the ontology term
            2. Modification annotations may have extensions (see below) to capture any of several types of additional detail. S. pombe genes link to PomBase gene pages, and GO term names link to PomBase ontology term summary pages.
              3. @@ -6415,10 +6317,7 @@

              Gene page: Phenotypes

              PomBase defines a phenotype as an observable characteristic, or set of characteristics, of an organism that results from the interaction of its genotype with a given environment. In PomBase, phenotypes are annotated using terms from the Fission Yeast Phenotype Ontology (FYPO). FYPO uses several existing ontologies from the Open Biological and Biomedical Ontologies (OBO) collection to construct formal definitions. Basic documentation for FYPO is available at the OBO Foundry, and further information is available on the FYPO wiki).

              In the phenotype annotation display on PomBase gene pages, the first item shown is a brief summary indicating whether cells with a null (deletion) allele of the gene are viable or inviable, or either depending on experimental conditions. Next, single-locus phenotypes are shown in two tables. The first table lists phenotypes observed at the population level, such as viability in culture, and the second shows cell-level phenotypes. Note that the viable/inviable population terms describe whether a gene is essential or not, and see the wiki FYPO Content and Structure documentation for more information on cell and population phenotypes. Finally, two more tables list population-level and cell-level multi-locus phenotypes, i.e. phenotypes associated with double mutants, triple mutants, etc, and the relevant genotype details. Diploid genotypes are included in the single- or multi-locus tables as appropriate.

              Each table includes ontology term details and supporting data. The summary view shows just the essentials: The list of terms is filtered, using the ontology structure, so that it shows only the most specific terms used to annotate a genotype, and each unique combination of gene, FYPO term, allele(s) and extension(s) is shown once. For single-allele phenotypes, the display includes:

              -
              -single-locus FYPO summary on gene page - -
              +

              single-locus FYPO summary on gene page

              1. The FYPO term name, which links to a page with additional information, including the term definition, any synonyms, relationships to other FYPO terms, and annotations to the term or its descendants. (See the ontology term page documentation for more.)
              2. Allele details, including a name (if one is used in the literature) and description (where known). Diploid genotypes specify both alleles for the locus, and are shown in bold. Mouse over the allele name to show the allele type, which indicates whether partial deletions or altered residues refer to amino acids or nucleotides, and expression level. If you can provide a description for any allele shown as “unknown”, please contact the PomBase curators.
                3. @@ -6426,21 +6325,12 @@

                Gene page: Phenotypes

                is shown as affecting substrate.
              3. The phenotype display can be filtered to show subsets of the total set of annotations. Two filters, for ploidy and ontology terms, are available in the summary or detailed view. If there are both haploid and diploid genotypes curated, the first filter defaults to “Haploid or Diploid” to show all genotypes. The term filter lists several broad phenotypic categories derived from high-level FYPO terms:
              -
              -FYPO annotation term filter - -
              +

              FYPO annotation term filter

              Choose one to restrict the annotation display to terms in the selected branch of FYPO. When term filtering is active, a message appears to indicate that not all annotations are shown:

              -
              -filtered annotation display message - -
              +

              filtered annotation display message

              Change the selection back to “No filter” to see annotations to all terms.

              The detailed single-locus phenotype view shows annotations to all FYPO terms, and includes more details for each annotation. It shows separate entries for repeat determinations of a given gene/term/allele/extension combination (if supported by more than one line of evidence and/or reported in more than one paper), and annotations to terms hidden in the summary view:

              -
              -Single-locus FYPO detailed view on gene page - -
              +

              Single-locus FYPO detailed view on gene page

              1. The unique ID and name for a term in the phenotype ontology. The ID links to a page with additional information, including the term definition, any synonyms, relationships to other FYPO terms, and annotations to the term or its descendants. (See the ontology term page documentation for more.)

              2. Allele details, including a name (if one is used in the literature) and description (where known). The column is headed “Genotypes” for consistency between the single- and multi-locus displays. Diploid genotypes specify both alleles for the locus, and are shown in bold. Each genotype name links to a page with full details (type, description, and expression) for its allele(s), links to gene pages, and a list of all phenotype annotations for the genotype. If you can provide a description for any allele shown as “unknown”, please contact the PomBase curators.

                3. @@ -6454,20 +6344,14 @@

                Gene page: Phenotypes

              Similar displays are used for multi-locus phenotypes. Unless otherwise noted below, all items are as described above for single-locus phenotype displays.

              The multi-locus summary shows FYPO terms and genotype descriptions:

              -
              -multi-locus FYPO summary view on gene page - -
              +

              multi-locus FYPO summary view on gene page

              1. The FYPO term name, which links to the page for the term.
              2. Genotype details, including a name (if one is used in the literature) and descriptions for the relevant alleles (where known). Mouse over any genotype name to show more allele details, or click to go to the genotype detail page. Multiple genotypes annotated to the same term are separated by commas. Diploid genotypes specify both alleles for each locus, and are shown in bold.
              3. Display filters for ploidy and FYPO terms (as described above for single-locus phenotypes).

              The detailed view includes:

              -
              -multi-locus FYPO full view on gene page - -
              +

              multi-locus FYPO full view on gene page

              1. The unique ID and name for a term in the phenotype ontology, with links to the FYPO term page.
              2. Genotype details, including a name (if one is used in the literature) and descriptions for the relevant alleles (where known). Mouse over any genotype name to show more allele details, or click to go to the genotype detail page. Multiple genotypes annotated to the same term are listed one per line. Diploid genotypes specify both alleles for each locus, and are shown in bold.
                3. @@ -6483,10 +6367,7 @@

                Gene page: Phenotypes

                Gene page: Protein domains and properties

                Gene pages for protein-coding genes have a section describing protein domains and properties. Also see the Modifications documentation.

                -
                -gene page protein features - -
                +

                gene page protein features

                1. The graphical view is interactive, and shows the positions of domains and other features. Mouse over any feature to highlight its entry in the table, and to see a pop-up with the feature ID, name, nad position.
                2. The table of protein families and domains is described in more detail below.
                  3. @@ -6495,10 +6376,7 @@

                  Gene page: Protein domains and
                3. Table of the protein’s physical properties

                Protein Families and Domains

                -
                -gene page protein domains - -
                +

                gene page protein domains

                1. Feature ID of this family or domain in the originating database. Where feasible, the ID links to the source database. Databases include Pfam, SMART, Prosite, Gene3D, SUPERFAMILY, TMHMM and Panther.
                2. Source database name
                  3. @@ -6514,14 +6392,38 @@

                  Protein Families and Domains

                Note that some of the listed features (e.g. transmembrane domains from TMHMM) are predictions. Consult the contributing databases for further information, or contact the PomBase curators if you notice any problems with annotated or predicted features.

                +
                +
                +

                Gene page: Protein feature widget

                +

                This widget shows a visual summary of protein features for the current gene. Hover over an allele, partial deletion, modification or Pfam domain to see more details. Hover over the track name for a brief description of the track.

                +

                pap1 gene page protein features widget

                +

                Available tracks

                +
                  +
                • Sequence the amino acid sequence - zoom in to see individual residues
                  • +
                • AA substitution positions positions where there are one or more amino acid substitutions
                  • +
                • AA substitution alleles curated amino acid substitution alleles (available only in the full view)
                  • +
                • Partial deletions curated alleles with partial amino acid deletions (full view only)
                  • +
                • Modifications curated modified residues
                  • +
                • Pfam families Pfam protein familes from InterPro
                  • +
                • TM domains Trans-membrane domains calculated with TMHMM (Krogh et al. 2001)
                  • +
                • Disordered regions Disordered regions from Pfam version 34.0 (El-Gebali et al. 2019)
                  • +
                • Low complexity Low complexity regions from Pfam
                  • +
                • Coiled coils Coiled coil regions from Pfam
                  • +
                +

                Mutant display

                +

                Single residue alleles are shown as vertical lines (or rectangles if zoomed in). Alleles with multiple mutated residues (eg. “cdc15-E30K,E152K”) are connected with dashed lines.

                +

                Partial deletions

                +

                The solid blue rectangles display the retained amino acids, dashed display the deleted regions.

                +

                Full/detailed protein feature view

                +

                Follow the “View all protein features …” link for a detailed view on the dedicated protein features page that includes the details of the individual amino acid substitution allele changes and “Partial deletions” tracks:

                +

                pap1 protein features page

                +

                Thanks to the team at RCSB PDB for providing the Open Source software used to implement this feature.

                +

                Gene page: Sequence

                The Sequence section of a gene page provides a widget to download DNA sequences for any gene, and amino acid sequences for protein-coding genes, as well as links to send sequences to BLAST. For protein-coding genes, the predicted amino acid sequence is displayed by default:

                -
                -peptide sequence section - -
                +

                peptide sequence section

                1. If two or more transcripts are annotated for a gene, the primary transcript is shown by default. Use the selector to switch between transcript isoforms.

                2. Toggle to show the amino acid sequence for protein-coding genes (not available for non-coding RNA genes, which always show nucleotide sequence).

                  3. @@ -6535,10 +6437,7 @@

                  Gene page: Sequence

                3. The peptide sequence header shows the transcript ID and the protein length.

                For non-coding RNA genes, and for protein-coding genes with “Show nucleotide sequence” selected, more options are available:

                -
                -DNA sequence section - -
                +

                DNA sequence section

                1. Transcript selector (as above)

                2. Toggle to show the amino acid sequence (not available for non-coding RNA genes).

                  3. @@ -6548,10 +6447,7 @@

                  Gene page: Sequence

                3. The nucleotide sequence header shows the transcript ID and indicates what is included.

                When the “Show translation” option is selected, irrelevant controls are hidden and BLASTP links are shown:

                -
                -sequence section showing translation - -
                +

                sequence section showing translation

                @@ -6570,15 +6466,9 @@

                Gene page: Target of

                Gene page: Transcript

                The Transcript section of a gene page shows the positions of introns and exons in each transcript. The default is a graphical view:

                -
                -Transcript section (default) - -
                +

                Transcript section (default)

                The default view shows one diagram per annotated transcript, with intron and exon positions hidden. Click “Show exon/intron/UTR positions” to display a table under each transcript diagram:

                -
                -Transcript section (expanded) - -
                +

                Transcript section (expanded)

                1. ID(s) and genomic location(s). The transcript systematic ID is the gene systematic ID with a suffix appended. The primary transcript suffix is “.1”, and any additional annotated transcript isoforms receive sequentially numbered suffixes.

                2. By default, intron and exon positions are shown in the table as genomic coordinates. When the “Show transcript coordinates” button is checked, positions in the table are numbered using the annotated transcription start site as 1.

                  3. @@ -6598,10 +6488,7 @@

                  Genetic and physical interactions

                  Reference: The paper cited to support the interaction

                  Additional fields for Genetic Interactions

                  Since November 2022, new or updated Genetic Interaction annotations are linked to phenotype annotations and alleles. We continue to display interactions in the old format by default (showing only genes and interaction type), but if you expand the annotation, you can view the associated genotypes and phenotypes.

                  -
                  -During filter - -
                  +

                  During filter

                  More on Genetic Interactions

                  The definitions of all genetic interactions can be found in the BioGRID wiki. It is worth reading these definitions, as the language often used in publications does not match the naming of genetic interactions. For example, in publications we can find “double deletion of gene X and Y rescues the defects cellular morphology caused by deletion of gene Y”. However, for BioGRID this is a phenotypic suppression not a rescue, since rescue is reserved for lethality or growth defect. The genetic interactions that are used in low throughput curation in PomBase are:

                    @@ -6620,10 +6507,7 @@

                    More on Genetic Interactions

                  When exporting the data to BioGrid, “Synthetic Phenotype” genetic interactions are exported as “Phenotypic Enhancement”, see this GitHub issue for details.

                  Below is a decision making tree to determine the type of genetic interaction from the phenotypes of the single and double mutant. “Interacting allele” refers to the allele that is not present in the single mutant:

                  -
                  -Decision making for genetic interactions - -
                  +

                  Decision making for genetic interactions

                  -

                  Yes, use the “Taxonomic conservation” query in the advanced search.

                  +

                  Yes, use the “Taxonomic conservation” query in the “Orthologs and conservation” menu of the advanced search.

                  Example query:

                @@ -9984,6 +9829,7 @@

                Contact Curators

                +
                Protein feature viewer added to gene pages
                Reaction diagrams on term pages
                Curation update - "nonsense mutation" merged into "partial amino acid deletion"
                Experimental structures from PDB on gene pages
                @@ -12212,20 +12058,11 @@

                Genetic Interaction annota

                We have recently implemented an improved way to annotate and display genetic interactions so they are linked to phenotype annotations and alleles.

                Previously, our Genetic Interaction annotations only mentioned the interacting genes and the type of genetic interaction. For example, if a strain with genotype asp1-H397A has the phenotype decreased acid phosphatase activity affecting activity of pho1, but this phenotype is suppressed when rhn1 is deleted in that strain, we would annotate that the genes asp1 and rhn1 are part of a Phenotypic Suppression interaction.

                -
                -GI old format - -
                +

                GI old format

                We continue to display interactions in this format by default (showing only genes and interaction type), but if you expand the annotation, you can view the associated genotypes and phenotypes.

                -
                -GI new format - -
                +

                GI new format

                In the revised Canto interface, you can only annotate a genetic interaction from the double mutant phenotype annotation (by clicking on add.., as shown below).

                -
                -GI annotation in Canto - -
                +

                GI annotation in Canto

                Of course, genetic interactions predating this update are not linked to phenotypes or genotypes, but we are hoping to auto-annotate several of those. We will also prioritise for update any interactions where community curators have provided these details in an annotation comment. Finally, a big shoutout to Ana Sanchez and Angad Garg from the Shuman lab, for testing the new interface in numerous recently curated publications. The examples provided here are from Sanchez et al. 2019. Go read it and see the annotations in PomBase.

                Best, The PomBase team

                @@ -12236,10 +12073,7 @@

                Querying by RNA length in t

                You can now query the RNA length of genes (spliced or unspliced) under the “Transcripts and exons” query grouping in the Advanced search.

                You can also add RNA sequence length as a field in tables downloaded from the query builder.

                -
                -RNA length queries are available under the “Transcripts and exons” tab - -
                +

                RNA length queries are available under the “Transcripts and exons” tab

                @@ -12285,10 +12119,7 @@

                AlphaFold protein structure o

                AlphaFold protein structure are now embedded on the PomBase gene pages. We hope to embed the experimental structures from PDB in the near future.

                -
                -Example from the mvp1 gene page - -
                +

                Example from the mvp1 gene page

                @@ -12299,10 +12130,7 @@

                Experimental structures from

                If you select the “PDB structures” view on a gene page, experimental structures will set as your default. AlphaFold predictions will be shown for genes where an experimental structure are not available.

                We now also display the structures on the associated publication page. For example: PMID:31010807 Garg et al.

                To help locate proteins with experimental protein structures (currently 375), we have added a new query option to the “Advanced search”, currently under “commonly used queries”: “Proteins with PDB structures”

                -
                -PDB structures on the lsm7 gene page - -
                +

                PDB structures on the lsm7 gene page

                @@ -12320,19 +12148,62 @@

                Reaction diagrams on term pages

                Where available, we now show the reaction diagram from Rhea on GO function term pages. This feature is possible thanks to the great work of Rhea.

                See the GO:0003849 term page for an example.

                -

                +

                + +
                +
                +

                Protein feature viewer added to gene pages

                + + +

                PomBase gene pages now include a protein feature widget. This tool shows protein features in the context of amino acid sequence. It includes:

                +
                  +
                • amino acid substitution positions
                  • +
                • Pfam domains
                  • +
                • protein modifications
                  • +
                • protein properties: low complexity regions, disordered regions, coiled coil regions and predicted trans-membrane domains
                  • +
                +

                Hover over features for more information, such as allele descriptions and Pfam domain IDs.

                +

                Protein feature viewer widget - cdc15 gene page

                +

                Follow the “View all protein features …” link for a detailed view on the dedicated protein features page that includes:

                +
                  +
                • details of the individual amino acid substitution allele changes
                  • +
                • partial amino acid deletions
                  • +
                +

                Protein feature viewer details page for cdc15

                +

                Thanks to the team at RCSB PDB for providing the Open Source software used to implement this feature.

                News archive

                +
                +

                +

                Protein feature viewer added to gene pages

                +

                2023-07-27

                +

                PomBase gene pages now include a protein feature widget. This tool shows protein features in the context of amino acid sequence. It includes:

                +
                  +
                • amino acid substitution positions
                  • +
                • Pfam domains
                  • +
                • protein modifications
                  • +
                • protein properties: low complexity regions, disordered regions, coiled coil regions and predicted trans-membrane domains
                  • +
                +

                Hover over features for more information, such as allele descriptions and Pfam domain IDs.

                +

                Protein feature viewer widget - cdc15 gene page

                +

                Follow the “View all protein features …” link for a detailed view on the dedicated protein features page that includes:

                +
                  +
                • details of the individual amino acid substitution allele changes
                  • +
                • partial amino acid deletions
                  • +
                +

                Protein feature viewer details page for cdc15

                +

                Thanks to the team at RCSB PDB for providing the Open Source software used to implement this feature.

                +

                Reaction diagrams on term pages

                2023-06-19

                Where available, we now show the reaction diagram from Rhea on GO function term pages. This feature is possible thanks to the great work of Rhea.

                See the GO:0003849 term page for an example.

                -

                +

                @@ -12350,20 +12221,14 @@

                Experimental structures from

                If you select the “PDB structures” view on a gene page, experimental structures will set as your default. AlphaFold predictions will be shown for genes where an experimental structure are not available.

                We now also display the structures on the associated publication page. For example: PMID:31010807 Garg et al.

                To help locate proteins with experimental protein structures (currently 375), we have added a new query option to the “Advanced search”, currently under “commonly used queries”: “Proteins with PDB structures”

                -
                -PDB structures on the lsm7 gene page - -
                +

                PDB structures on the lsm7 gene page

                AlphaFold protein structure on gene pages

                2023-02-02

                AlphaFold protein structure are now embedded on the PomBase gene pages. We hope to embed the experimental structures from PDB in the near future.

                -
                -Example from the mvp1 gene page - -
                +

                Example from the mvp1 gene page

                @@ -12407,10 +12272,7 @@

                Querying by RNA length in t

                2022-12-07

                You can now query the RNA length of genes (spliced or unspliced) under the “Transcripts and exons” query grouping in the Advanced search.

                You can also add RNA sequence length as a field in tables downloaded from the query builder.

                -
                -RNA length queries are available under the “Transcripts and exons” tab - -
                +

                RNA length queries are available under the “Transcripts and exons” tab

                @@ -12418,20 +12280,11 @@

                Genetic Interaction annota

                2022-11-29

                We have recently implemented an improved way to annotate and display genetic interactions so they are linked to phenotype annotations and alleles.

                Previously, our Genetic Interaction annotations only mentioned the interacting genes and the type of genetic interaction. For example, if a strain with genotype asp1-H397A has the phenotype decreased acid phosphatase activity affecting activity of pho1, but this phenotype is suppressed when rhn1 is deleted in that strain, we would annotate that the genes asp1 and rhn1 are part of a Phenotypic Suppression interaction.

                -
                -GI old format - -
                +

                GI old format

                We continue to display interactions in this format by default (showing only genes and interaction type), but if you expand the annotation, you can view the associated genotypes and phenotypes.

                -
                -GI new format - -
                +

                GI new format

                In the revised Canto interface, you can only annotate a genetic interaction from the double mutant phenotype annotation (by clicking on add.., as shown below).

                -
                -GI annotation in Canto - -
                +

                GI annotation in Canto

                Of course, genetic interactions predating this update are not linked to phenotypes or genotypes, but we are hoping to auto-annotate several of those. We will also prioritise for update any interactions where community curators have provided these details in an annotation comment. Finally, a big shoutout to Ana Sanchez and Angad Garg from the Shuman lab, for testing the new interface in numerous recently curated publications. The examples provided here are from Sanchez et al. 2019. Go read it and see the annotations in PomBase.

                Best, The PomBase team

                @@ -14446,10 +14299,7 @@

                Glo

                Centromeres

                Repeats are also shown in the diagram below. To see the repeat sequences, download and unzip the contiguated sequence files and view them in Artemis. (See this FAQ for more information.)

                -
                -Centromere map - -
                +

                Centromere map

                Notes:

                • Recent work by Chad Ellermeier and Gerry Smith suggests that there are only 4 +/- 1 copies of the 6760 bp repeat missing from chromosome 3

                  • diff --git a/src/app/recent-news/recent-news.component.html b/src/app/recent-news/recent-news.component.html index 3f09ec0b..d48e1c15 100644 --- a/src/app/recent-news/recent-news.component.html +++ b/src/app/recent-news/recent-news.component.html @@ -1,11 +1,33 @@
                  +

                  Protein feature viewer added to gene pages

                  +

                  2023-07-27

                  +

                  PomBase gene pages now include a protein feature widget. This tool shows protein features in the context of amino acid sequence. It includes:

                  +
                    +
                  • amino acid substitution positions
                    • +
                  • Pfam domains
                    • +
                  • protein modifications
                    • +
                  • protein properties: low complexity regions, disordered regions, coiled coil regions and predicted trans-membrane domains
                    • +
                  +

                  Hover over features for more information, such as allele descriptions and Pfam domain IDs.

                  +

                  Protein feature viewer widget - cdc15 gene page

                  +

                  Follow the “View all protein features …” link for a detailed view on the dedicated protein features page that includes:

                  +
                    +
                  • details of the individual amino acid substitution allele changes
                    • +
                  • partial amino acid deletions
                    • +
                  +

                  Protein feature viewer details page for cdc15

                  +

                  Thanks to the team at RCSB PDB for providing the Open Source software used to implement this feature.

                  + +
                  +
                  +

                  Reaction diagrams on term pages

                  2023-06-19

                  Where available, we now show the reaction diagram from Rhea on GO function term pages. This feature is possible thanks to the great work of Rhea.

                  See the GO:0003849 term page for an example.

                  -

                  +

                  @@ -25,10 +47,7 @@

                  Experimental str

                  If you select the “PDB structures” view on a gene page, experimental structures will set as your default. AlphaFold predictions will be shown for genes where an experimental structure are not available.

                  We now also display the structures on the associated publication page. For example: PMID:31010807 Garg et al.

                  To help locate proteins with experimental protein structures (currently 375), we have added a new query option to the “Advanced search”, currently under “commonly used queries”: “Proteins with PDB structures”

                  -
                  -PDB structures on the lsm7 gene page - -
                  +

                  PDB structures on the lsm7 gene page

                  @@ -36,10 +55,7 @@

                  Experimental str

                  AlphaFold protein structure on gene pages

                  2023-02-02

                  AlphaFold protein structure are now embedded on the PomBase gene pages. We hope to embed the experimental structures from PDB in the near future.

                  -
                  -Example from the mvp1 gene page - -
                  +

                  Example from the mvp1 gene page

                  @@ -64,10 +80,7 @@

                  Querying by

                  2022-12-07

                  You can now query the RNA length of genes (spliced or unspliced) under the “Transcripts and exons” query grouping in the Advanced search.

                  You can also add RNA sequence length as a field in tables downloaded from the query builder.

                  -
                  -RNA length queries are available under the “Transcripts and exons” tab - -
                  +

                  RNA length queries are available under the “Transcripts and exons” tab

                  @@ -76,20 +89,11 @@

                  Genetic Interactio

                  2022-11-29

                  We have recently implemented an improved way to annotate and display genetic interactions so they are linked to phenotype annotations and alleles.

                  Previously, our Genetic Interaction annotations only mentioned the interacting genes and the type of genetic interaction. For example, if a strain with genotype asp1-H397A has the phenotype decreased acid phosphatase activity affecting activity of pho1, but this phenotype is suppressed when rhn1 is deleted in that strain, we would annotate that the genes asp1 and rhn1 are part of a Phenotypic Suppression interaction.

                  -
                  -GI old format - -
                  +

                  GI old format

                  We continue to display interactions in this format by default (showing only genes and interaction type), but if you expand the annotation, you can view the associated genotypes and phenotypes.

                  -
                  -GI new format - -
                  +

                  GI new format

                  In the revised Canto interface, you can only annotate a genetic interaction from the double mutant phenotype annotation (by clicking on add.., as shown below).

                  -
                  -GI annotation in Canto - -
                  +

                  GI annotation in Canto

                  Of course, genetic interactions predating this update are not linked to phenotypes or genotypes, but we are hoping to auto-annotate several of those. We will also prioritise for update any interactions where community curators have provided these details in an annotation comment. Finally, a big shoutout to Ana Sanchez and Angad Garg from the Shuman lab, for testing the new interface in numerous recently curated publications. The examples provided here are from Sanchez et al. 2019. Go read it and see the annotations in PomBase.

                  Best, The PomBase team