The uni prot knowledgebase
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This document provides information about UniProt, a hub for protein knowledge that includes several databases. It summarizes the main UniProt databases: UniProtKB contains manually annotated Swiss-Prot and automatically annotated TrEMBL sections; UniParc is an archive of all protein sequences and UniRef clusters similar sequences. The document outlines the process of automatic annotation in TrEMBL and manual annotation in Swiss-Prot. It also describes search, alignment and retrieval tools on the UniProt website and options for downloading protein data.
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The uni prot knowledgebase
- 1. Marie-Claude.Blatter@isb-sib.ch Swiss-Prot group, Geneva SIB Swiss Institute of Bioinformatics The UniProt knowledgebase www.uniprot.org a hub of integrated protein data http://education.expasy.org/cours/Prague2011/
- 2. Science cover, february 2011
- 3. protein sequence functional information data knowledge
- 4. UniProt consortium EBI : European Bioinformatics Institute (UK) SIB : Swiss Institute of Bioinformatics (CH) PIR : Protein information resource (US)
- 7. UniProtKB: protein sequence knowledgebase, 2 sections UniProtKB/Swiss-Prot and UniProtKB/TrEMBL (query, Blast, download) (~15 mo entries) UniParc: protein sequence archive (ENA equivalent at the protein level). Each entry contains a protein sequence with cross- links to other databases where you find the sequence (active or not). Not annotated (query, Blast, download) (~25 mo entries) UniRef: 3 clusters of protein sequences with 100, 90 and 50 % identity; useful to speed up sequence similarity search (BLAST) (query, Blast, download) (UniRef100 10 mo entries; UniRef90 7 mo entries; UniRef50 3.3 mo entries) UniMES: protein sequences derived from metagenomic projects (mostly Global Ocean Sampling (GOS)) (download) (8 mo entries, included in UniParc)
- 8. UniProt databases The central piece
- 9. UniProtKB an encyclopedia on proteins composed of 2 sections UniProtKB/TrEMBL and UniProtKB/Swiss-Prot unreviewed and reviewed automatically annotated and manually annotated released every 4 weeks
- 10. UniProtKB Origin of protein sequences UniProtKB protein sequences are mainly derived from - INSDC (translated submitted coding sequences - CDS) - Ensembl (gene prediction ) and RefSeq sequences - Sequences of PDB structures - Direct submission or sequences scanned from literature Notes: - UniProt is not doing any gene prediction - Most non-germline immunoglobulins, T-cell receptors , most patent sequences, highly over-represented data (e.g. viral antigens), pseudogenes sequences are excluded from UniProtKB, - but stored in UniParc - Data from the PIR database have been integrated in UniProtKB since 2003. 15 % 85 %
- 11. Swiss-Prot TrEMBL EMBL Automated extraction of protein sequence (translated CDS), gene name and references. Automated annotation Manual annotation of the sequence and associated biological information
- 13. One protein sequence One species Automated annotation Keywords and Gene Ontology Automated annotation Function, Subcellular location, Catalytic activity, Sequence similarities… Automated annotation transmembrane domains, signal peptide… Cross-references to over 125 databases References Protein and gene names Taxonomic information UniProtKB/TrEMBL www.uniprot.org
- 14. UniProtKB/TrEMBL Automatic annotation Protein sequence - The quality of the protein sequences is dependent on the information provided by the submitter of the original nucleotide entry (CDS) or of the gene prediction pipeline (i.e. Ensembl). - 100% identical sequences (same length, same organism are merged automatically). Biological information Sources of annotation - Provided by the submitter (EMBL, PDB, TAIR…) - From automated annotation (automated generated annotation rules (i.e. SAAS) and/or manually generated annotation rules (i.e. UniRule))
- 17. Example of fully automatic annotation: SAAS • Rules are derived from the UniProtKB/Swiss-Prot manual annotation. • Fully automated rule generation based on C4.5 decision tree algorithm. • One annotation, one rule. • High stringency – require 99% or greater estimated precision to generate annotation (test on UniProtKB/Swiss-Prot) • Rules are produced, updated and validated at each release. UniProtKB/TrEMBL
- 19. MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAAR AFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVK NMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFL NKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRG TVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGR AGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKD EGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG One protein sequence One gene One species Manual annotation Keywords and Gene Ontology Manual annotation Function, Subcellular location, Catalytic activity, Disease, Tissue specificty, Pathway… Manual annotation Post-translational modifications, variants, transmembrane domains, signal peptide… Cross-references to over 125 databases References Protein and gene names Taxonomic information Alternative products: protein sequences produced by alternative splicing, alternative promoter usage, alternative initiation… UniProtKB/Swiss-Prot www.uniprot.org
- 20. UniProtKB/Swiss-Prot Manual annotation 1. Protein sequence (merge available CDS, annotate sequence discrepancies, report sequencing mistakes…) 2. Biological information (sequence analysis, extract literature information, ortholog data propagation, …)
- 21. UniProtKB/Swiss-Prot 1- Protein sequence curation
- 22. The displayed protein sequence: …canonical, representative, consensus… + alternative sequences (described within the entry) 1 entry <-> 1 gene (1 species) UniProtKB/Swiss-Prot a gene-centric view of the protein space
- 23. What is the current status? • At least 20% of Swiss-Prot entries required a minimal amount of curation effort so as to obtain the “correct” sequence. • Typical problems – unsolved conflicts – uncorrected initiation sites – frameshifts – wrong gene prediction – other ‘problems’
- 24. UCSC genome browser examples of CDS annotation submitted to INSDC…
- 25. UniProtKB/Swiss-Prot 2- Biological data curation
- 26. UniProtKB/Swiss-Prot gathers data form multiple sources: - publications (literature/Pubmed) - prediction programs (Prosite, TMHMM, …) - contacts with experts - other databases - nomenclature committees An evidence attribution system allows to easily trace the source of each annotation Extract literature information and protein sequence analysis maximum usage of controlled vocabulary
- 27. Protein and gene names
- 28. …enable researchers to obtain a summary of what is known about a protein… General annotation (Comments) www.uniprot.org
- 29. Human protein manual annotation: some statistics (June 2011)
- 30. Sequence annotation (Features) …enable researchers to obtain a summary of what is known about a protein… www.uniprot.org
- 31. Non-experimental qualifiers UniProtKB/Swiss-Prot considers both experimental and predicted data and makes a clear distinction between both Type of evidence Qualifier Strong experimental evidence None or Ref.X Light experimental evidence Probable Inferred by similarity with homologous protein By similarity Inferred by prediction Potential
- 32. Find all the proteins localized in the cytoplasm (experimentally proven) which are phosphorylated on a serine (experimentally proven)
- 33. • The ‘Protein existence’ tag indicates what is the evidence for the existence of a given protein; • Different qualifiers: – 1. Evidence at protein level (~18%) – (MS, western blot (tissue specificity), immuno (subcellular location),…) – 2. Evidence at transcript level (~19%) – 3. Inferred from homology (~58 %) – 4. Predicted (~5%) – 5. Uncertain (mainly in TrEMBL) ‘Protein existence’ tag http://www.uniprot.org/docs/pe_criteria
- 35. UniProtKB Additional information can be found in the cross-references (to more than 140 databases)
- 36. 2D gel 2DBase-Ecoli ANU-2DPAGE Aarhus/Ghent-2DPAGE (no server) COMPLUYEAST-2DPAGE Cornea-2DPAGE DOSAC-COBS-2DPAGE ECO2DBASE (no server) OGP PHCI-2DPAGE PMMA-2DPAGE Rat-heart-2DPAGE REPRODUCTION-2DPAGE Siena-2DPAGE SWISS-2DPAGE UCD-2DPAGE World-2DPAGE Family and domain Gene3D HAMAP InterPro PANTHER Pfam PIRSF PRINTS ProDom PROSITE SMART SUPFAM TIGRFAMs Organism-specific AGD ArachnoServer CGD ConoServer CTD CYGD dictyBase EchoBASE EcoGene euHCVdb EuPathDB FlyBase GeneCards GeneDB_Spombe GeneFarm GenoList Gramene H-InvDB HGNC HPA LegioList Leproma MaizeGDB MGI MIM neXtProt Orphanet PharmGKB PseudoCAP RGD SGD TAIR TubercuList WormBase Xenbase ZFIN Protein family/group Allergome CAZy MEROPS PeroxiBase PptaseDB REBASE TCDB Genome annotation Ensembl EnsemblBacteria EnsemblFungi EnsemblMetazoa EnsemblPlants EnsemblProtists GeneID GenomeReviews KEGG NMPDR TIGR UCSC VectorBase Enzyme and pathway BioCyc BRENDA Pathway_Interaction_DB Reactome Other BindingDB DrugBank NextBio PMAP-CutDB Sequence EMBL IPI PIR RefSeq UniGene 3D structure DisProt HSSP PDB PDBsum ProteinModelPortal SMR PTM GlycoSuiteDB PhosphoSite PhosSite UniProtKB/Swiss-Prot: 129 explicit links and 14 implicit links! Proteomic PeptideAtlas PRIDE ProMEX PPI DIP IntAct MINT STRING Phylogenomic dbs eggNOG GeneTree HOGENOM HOVERGEN InParanoid OMA OrthoDB PhylomeDB ProtClustDB Polymorphism dbSNP Gene expression ArrayExpress Bgee CleanEx Genevestigator GermOnline Ontologies GO
- 37. The UniProt web site www.uniprot.org • Powerful search engine, google-like and easy-to-use, but also supports very directed field searches • Scoring mechanism presenting relevant matches first • Entry views, search result views and downloads are customizable • The URL of a result page reflects the query; all pages and queries are bookmarkable, supporting programmatic access • Search, Blast, Align, Retrieve, ID mapping
- 38. Search A very powerful text search tool with autocompletion and refinement options allowing to look for UniProt entries and documentation by biological information
- 39. Find all human proteins located in the nucleus
- 40. The search interface guides users with helpful suggestions and hints
- 42. Advanced Search A very powerful search tool To be used when you know in which entry section the information is stored
- 43. Find all the protein localized in the cytoplasm (experimentally proven) which are phosphorylated on a serine (experimentally proven)
- 44. Result pages: highly customizable
- 47. The URL can be bookmarked and manually modified.
- 48. Blast A tool associated with the standard options to search sequences in different UniProt databases and data sets
- 49. Blast: customize the result display
- 50. Blast: local alignment sequence annotation highlighting option
- 51. Align A ClustalW multiple alignment tool with sequence annotation highlighting option
- 52. Align sequence annotation highlighting option
- 53. Retrieve A UniProt specific tool allowing to retrieve a list of entries in several standard identifiers formats. You can then query your ‘personal database’ with the UniProt search tool.
- 54. Query your own dataset
- 55. ID Mapping Gives the possibility to get a mapping between different databases for a given protein
- 56. These identifiers are all pointing to a TP53 (p53) protein sequence ! ● P04637, NP_000537, NP_001119584.1, NP_001119585.1, ● NP_001119584.1, NP_001119584.1, NP_001119584.1, ● NP_001119584.1, ENSG00000141510, CCDS11118, ● UPI000002ED67, IPI00025087, etc.
- 58. Download
- 60. Canonical and isoform sequences (fasta format)
- 61. A few words on the UniProt ‘complete proteome’ sequence sets…
- 62. 2’747 complete proteomes Genome completely sequenced Proteins mapped to the genome Entries tagged with the KW ‘Complete proteome’ UniProtKB/Swiss-Prot isoform sequences are available in FASTA format only Fully manually reviewed (e.g. S. cerevisiae) Partially manually reviewed (e.g. Homo sapiens) Unreviewed (e.g. Acinetobacter baumannii (strain 1656-2)) UniProtKB - complete proteomes
- 63. Can be downloaded: From our complete proteome page www.uniprot.org/taxonomy/complete-proteomes From the ‘ftp download ‘ page By querying UniProtKB + download Query: organism:93062 AND keyword:"complete proteome" UniProtKB - complete proteomes Additional information: www.uniprot.org/faq/15
- 64. Query UniProtKB + download
- 66. Human proteome ~ 20’200 genes Query for ‘homo sapiens’ (August 2011) • UniProtKB: 110,056 entries + alt sequences (~ 15’435) = 125’491 • UniProtKB/Swiss-Prot: 20’244 entries + alt sequences (~ 15’435) = 35’679 • UniProtKB/TrEMBL: 89,834 entries • RefSeq: 32’898 sequences • Ensembl: 90’720 sequences Query for ‘homo sapiens’ + Complete proteome (KW-181) • UniProtKB: 56’392 + alt sequences (15’435) = 71’827 • UniProtKB/Swiss-Prot: 20’238 + alt sequences (15’435) = 35’673 • UniProtKB/TrEMBL: 36’154 92% of human entries are linked with at least one RefSeq entry…
- 67. Summary
- 69. Do not hesitate to contact us ! help@uniprot.org
- 70. The UniProt Consortium SIB Ioannis Xenarios, Lydie Bougueleret, Andrea Auchincloss, Kristian Axelsen, Delphine Baratin, Marie- Claude Blatter, Brigitte Boeckmann, Jerven Bolleman, Laurent Bollondi, Emmanuel Boutet, Lionel Breuza, Alan Bridge, Edouard de Castro, Lorenzo Cerutti, Elisabeth Coudert, Béatrice Cuche, Mikael Doche, Dolnide Dornevil, Severine Duvaud, Anne Estreicher, Livia Famiglietti, Marc Feuermann, Sebastien Gehant, Elisabeth Gasteiger, Alain Gateau, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz- Gumowski, Ursula Hinz, Chantal Hulo, Nicolas Hulo, Janet James, Florence Jungo, Guillaume Keller, Vicente Lara, Philippe Lemercier, Damien Lieberherr, Xavier Martin, Patrick Masson, Anne Morgat, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Sylvain Poux, Monica Pozzato, Manuela Pruess, Nicole Redaschi, Catherine Rivoire, Bernd Roechert, Michel Schneider, Christian Sigrist, Karin Sonesson, Sylvie Staehli, Eleanor Stanley, André Stutz, Shyamala Sundaram, Michael Tognolli, Laure Verbregue, Anne-Lise Veuthey EBI Rolf Apweiler, Maria Jesus Martin, Claire O'Donovan, Michele Magrane, Yasmin Alam-Faruque, Ricardo Antunes, Benoit Bely, Mark Bingley, David Binns, Lawrence Bower, Wei Mun Chan, Emily Dimmer, Francesco Fazzini, Alexander Fedotov, John Garavelli, Leyla Garcia Castro, Rachael Huntley, Julius Jacobsen, Michael Kleen, Duncan Legge, Wudong Liu, Jie Luo, Sandra Orchard, Samuel Patient, Klemens Pichler, Diego Poggioli, Nikolas Pontikos, Steven Rosanoff, Tony Sawford, Harminder Sehra, Edward Turner, Matt Corbett, Mike Donnelly and Pieter van Rensburg PIR Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Winona C. Barker, Chuming Chen, Yongxing Chen, Pratibha Dubey, Hongzhan Huang, Kati Laiho, Raja Mazumder, Peter McGarvey, Darren A. Natale, Thanemozhi G. Natarajan, Jules Nchoutmboube, Natalia V. Roberts, Baris E. Suzek, Uzoamaka Ugochukwu, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh and Jian Zhang www.uniprot.org
- 71. UniProt is mainly supported by the National Institutes of Health (NIH) grant 1 U41 HG006104- 01. Additional support for the EBI's involvement in UniProt comes from the NIH grant 2P41 HG02273-07. Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science and the European Commission contracts SLING (226073), Gen2Phen (200754) and MICROME (222886). PIR activities are also supported by the NIH grants 5R01GM080646-04, 3R01GM080646-04S2, 1G08LM010720-01, and 3P20RR016472-09S2, and NSF grant DBI-0850319.
- 72. www.isb-sib.ch
- 73. Thank you for your attention http://education.expasy.org/cours/Prague2011/
Editor's Notes
- This Science cover clearly shows the well known discepancy between the amount of data and the amount of knowledge which are available.This is a first challenge …but there is a second one: how is to link the 2 together ?
- The mission of UniProt is….to link the protein squences (data) together with the biological knowledge (functional information)
- The UniProt databases and web site are maintained by the UniProt consortium, which is composed of:
- Screen shot of the web page
- UniProt provides 4 databases, the central one beiing the UniProtKB.
- UniProt provides 4 databases, the central one beiing the UniProtKB.
- Computer prediction: if no other evidence from this protein or a similar protein, the keyword is not put.
- &lt;number&gt; dbSNP is NOT in DR lines!!! =&gt; not included in the release notes statistics. Note : Replaces BuruList, ListiList, MypuList, PhotoList, SagaList and SubtiList
- &lt;number&gt; 3 groups working together Encyclopedia of proteins function in biology and life science Considered by the life science community as the GOLD standard in annotation practices Over 600’000 users per month originating from 149 countries. Is it uniprot or swiss-prot? Used by life science scientists (biologists, MDs), but also by chemists, engineers in nanotechnologies; Bioinformaticians; Used by pharma and biotechnology industry;
- &lt;number&gt; 3 groups working together Encyclopedia of proteins function in biology and life science Considered by the life science community as the GOLD standard in annotation practices Over 600’000 users per month originating from 149 countries. Is it uniprot or swiss-prot? Used by life science scientists (biologists, MDs), but also by chemists, engineers in nanotechnologies; Bioinformaticians; Used by pharma and biotechnology industry;
- &lt;number&gt; Take home message
- a bit of this, a bit of that…