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Molecular
Function, Biological Process, Cellular Component, Phenotype, Genotype, Allele, Protein Modification, Gene Expression, Protein expression, Nucleotide Sequence, RNA sequence, Protein sequence, Genomics, Human Orthologs, Saccharomyces cerevisiae Orthlogs, Complementation, Disease
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204:
sequence and annotated features, together with a wide range of manually curated functional gene-specific data. The PomBase website was redeveloped in 2016 to provide users with a more fully integrated, better-performing service (described in ).
451:
Usage of PomBase as a research tool is explored in the "Eukaryotic
Genomic Databases" (Methods and Protocols) book chapter. Developments and updates are described in the NAR Database Issue papers. For a detailed overview of using
381:
To supplement the work of the small team of professional PomBase curators, fission yeast researchers contribute annotations directly to PomBase via an innovative community curation scheme, for which an online curation tool,
357:
provides an overview of the "biological role" of all "known" fission yeast genes - these are proteins that have either been experimentally characterized in fission yeast, or in another species and transferred by orthology.
668:
Montecchi-Palazzi, L; Beavis, R; Binz, PA; Chalkley, RJ; Cottrell, J; Creasy, D; Shofstahl, J; Seymour, SL; Garavelli, JS (August 2008). "The PSI-MOD community standard for representation of protein modification data".
221:
PomBase staff manually curate a wide variety of data types using both primary literature and bioinformatics sources, and numerous mechanisms are employed to ensure both syntactical and biological content validity.
315:
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Remarkably, nearly 20% of eukaryotic proteomes, from yeast to human, are uncharacterized in terms of the pathways and processes that these proteins participate in, making it one of the great
566:
Wood, V; Carbon, S; Harris, MA; Lock, A; Engel, SR; Hill, DP; Van Auken, K; Attrill, H; Feuermann, M; Gaudet, P; Lovering, RC; Poux, S; Rutherford, KM; Mungall, CJ (September 2020).
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Gene annotation can be viewed either at a gene-specific level (on the gene pages) or at a term-specific level (on the ontology term pages). This makes it possible to either:
365:. The role that these proteins play in biology, have not yet been discovered in any species. To aid research into these unknown proteins, PomBase maintains an inventory of
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519:"PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information"
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list represents the subset of uncharacterized fission yeast genes that are conserved to man, making it an especially high priority research target.
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Fission Yeast
Phenotype Ontology (FYPO), Used to associate phenotypes with alleles of genes, in comparison to the phenotype of the reference strain
1461:
814:"Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications"
386:, has been developed. Community curation is reviewed by PomBase staff, and this results in highly accurate, effectively co-curated, annotations.
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Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG (January 2012).
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Genome-wide datasets (including protein datasets, all annotations, manually curated ortholog lists etc) can be accessed from the
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Complementation data for where there is functional complementation between a fission yeast gene and a gene from another organism
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568:"Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns"
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McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V (January 2015).
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Lock, A; Rutherford, K; Harris, MA; Wood, V (2018). "PomBase: The
Scientific Resource for Fission Yeast".
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page. Datasets suitable for display in a genome browser and that have been loaded can be accessed via the
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Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
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Lock, A; Rutherford, K; Harris, MA; Hayles, J; Oliver, SG; Bähler, J; Wood, V (13 October 2018).
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Creative
Commons Attribution 4.0 International license, GNU General Public License, MIT License
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Antonia Lock, Midori A Harris, Manuel Lera-RamĂrez, Pascal Carme, Kim
Rutherford, Juan Mata,
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PomBase uses several biological ontologies to capture gene-specific information, including:
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Wood, V; Lock, A; Harris, MA; Rutherford, K; Bähler, J; Oliver, SG (28 February 2019).
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Microsoft
Research - University of Trento Centre for Computational and Systems Biology
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714:"Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?"
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functions, the cellular processes they participate in and where they localize
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Associations, Protein features, Physical
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Disease associations for when the human ortholog is known to cause disease
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Lock, A; Harris, MA; Rutherford, K; Hayles, J; Wood, V (1 January 2020).
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View all annotations created from a specific reference, for example
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Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V (June 2014).
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865:. Methods in Molecular Biology. Vol. 1757. pp. 49–68.
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Rutherford, Kim M.; Lera-RamĂrez, Manuel; Wood, Valerie (2024).
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An overview of data provided by PomBase and ways to access it.
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African
Society for Bioinformatics and Computational Biology
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914:"PomBase: a comprehensive online resource for fission yeast"
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Harris MA, Lock A, Bähler J, Oliver SG, Wood V (July 2013).
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Max Planck Institute of Molecular Cell Biology and Genetics
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Database: The Journal of Biological Databases and Curation
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1014:"An Ancient Yeast for Young Geneticists: A Primer on the
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International Nucleotide Sequence Database Collaboration
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Specific protein modification sites and when they occur
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964:"PomBase 2015: updates to the fission yeast database"
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View all annotations created for a gene, for example
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Metadata of datasets loaded into the genome browser
1142:, database of protein sequences grouping together
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328:(GO) - used to describe the enzymatic functions,
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1377:US National Center for Biotechnology Information
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269:Data regarding when specific genes are expressed
1462:International Society for Computational Biology
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1529:ISCB Africa ASBCB Conference on Bioinformatics
1012:Hoffman CS, Wood V, Fantes PA (October 2015).
1476:Institute of Genomics and Integrative Biology
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332:roles and cellular locations of gene products
294:View all genes annotated a term, for example
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619:"FYPO: The Fission Yeast Phenotype Ontology"
1540:Research in Computational Molecular Biology
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341:- used to describe DNA or protein features
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367:uncharacterized fission yeast proteins
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1354:European Molecular Biology Laboratory
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344:Protein modifications - using PSI-MOD
239:Phenotypes associated with different
16:Database on Schizosaccharomyces pombe
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171:Professionally and community curated
1482:Japanese Society for Bioinformatics
194:that provides online access to the
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1534:Pacific Symposium on Biocomputing
1438:Australia Bioinformatics Resource
1405:Swiss Institute of Bioinformatics
1388:Netherlands Bioinformatics Centre
1348:European Bioinformatics Institute
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209:Data Curation and Quality Control
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1336:Database Center for Life Science
1324:Computational Biology Department
1212:Arabidopsis Information Resource
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408:Posts to the research community
275:Subunit composition of complexes
260:genes (manually curated dataset)
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1182:Specialised genomic databases:
225:Types of data curated include:
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1220:Zebrafish Information Network
1188:Saccharomyces Genome Database
781:10.1093/bioinformatics/btu103
637:10.1093/bioinformatics/btt266
463:
1633:List of biological databases
1152:Protein Information Resource
863:Eukaryotic Genomic Databases
402:News updates on the PomBase
363:unsolved problems in biology
349:Gene Characterization Status
44:The scientific resource for
7:
1126:European Nucleotide Archive
1036:10.1534/genetics.115.181503
975:(Database issue): D656–61.
871:10.1007/978-1-4939-7737-6_4
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1365:J. Craig Venter Institute
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1394:Philippine Genome Center
830:10.1093/database/baaa028
492:10.1093/genetics/iyae007
371:priority unstudied genes
316:PomBase JBrowse instance
252:Human and budding yeast
115:Rutherford, et al (2024)
1638:Molecular phylogenetics
1134:China National GeneBank
414:NAR () database updates
192:model organism database
86:University of Cambridge
1342:DNA Data Bank of Japan
1130:DNA Data Bank of Japan
523:Nucleic Acids Research
440:Pombase provides both
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1623:Computational biology
1138:Secondary databases:
397:Knowledgebase Updates
391:annotation stats page
389:PomBase maintains an
377:Community co-Curation
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1120:Sequence databases:
671:Nature Biotechnology
1416:Whitehead Institute
1204:Rat Genome Database
981:10.1093/nar/gku1040
730:10.1098/rsob.180241
683:10.1038/nbt0808-864
585:10.1098/rsob.200149
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1706:Genetics databases
1653:Sequence alignment
1360:Flatiron Institute
969:Nucleic Acids Res.
931:10.1093/nar/gkr853
919:Nucleic Acids Res.
535:10.1093/nar/gky961
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1648:Sequence database
1162:Protein Data Bank
1156:Other databases:
880:978-1-4939-7736-9
529:(D1): D821–D827.
339:Sequence Ontology
304:Chica et al. 2016
280:Data Organization
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232:Protein and
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176:Bookmarkable
143:Download URL
120:Release date
105:Steve Oliver
18:
1557:CRAM format
1478:(CSIR-IGIB)
296:cytokinesis
137:pombase.org
101:Jürg Bähler
41:Description
1700:Categories
1643:Sequencing
1607:GTF format
1602:GFF format
1597:VCF format
1587:SAM format
1350:(EMBL-EBI)
1276:SOAP suite
1196:VectorBase
1158:BioNumbers
1144:Swiss-Prot
464:References
330:biological
52:Data types
1470:(ISCB-SC)
1440:(EMBL-AR)
1373:(MPI-CBG)
1114:Databases
699:205270043
302:26776736
254:orthologs
245:genotypes
147:Downloads
64:Organisms
1672:Category
1542:(RECOMB)
1492:Meetings
1446:(EMBnet)
1296:Server:
1271:SAMtools
1266:PANGOLIN
1229:Software
1208:PHI-base
1200:WormBase
1170:InterPro
1054:26447128
1023:Genetics
999:25361970
949:22039153
899:29761456
848:32353878
799:24574118
748:30938578
691:18688235
655:23658422
604:32875947
553:30321395
501:38376816
483:Genetics
454:S. pombe
419:@PomBase
417:Tweets (
404:homepage
312:datasets
258:S. pombe
178:entities
54:captured
1684:Commons
1519:(InCoB)
1464:(ISCB)
1452:(INSDC)
1434:(ASBCB)
1338:(DBCLS)
1332:(COSBI)
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1166:Ensembl
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1122:GenBank
1071:PomBase
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890:6440643
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646:3694669
595:7536087
544:6324063
444:and an
241:alleles
188:PomBase
159:License
133:Website
96:Authors
75:Contact
36:Content
22:PomBase
1525:(CIBB)
1513:(ISMB)
1507:(ECCB)
1484:(JSBi)
1390:(NBIC)
1379:(NCBI)
1367:(JCVI)
1356:(EMBL)
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202:genome
128:Access
1536:(PSB)
1458:(ISB)
1407:(SIB)
1396:(PGC)
1326:(CBD)
1290:Other
1256:HMMER
1236:BLAST
695:S2CID
456:as a
384:Canto
234:ncRNA
190:is a
1218:and
1184:BOLD
1174:KEGG
1150:and
1132:and
1050:PMID
995:PMID
945:PMID
895:PMID
875:ISBN
844:PMID
822:2020
795:PMID
744:PMID
687:PMID
651:PMID
600:PMID
549:PMID
497:PMID
353:The
290:pat1
243:and
123:2011
88:and
1040:PMC
1032:doi
1028:201
985:PMC
977:doi
935:PMC
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539:PMC
531:doi
487:doi
446:FAQ
256:of
181:Yes
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