Value-adding, Access, and Use: Biological Databases as a Case Study.

transcript

Value-adding, Access, and Use: Biological Databases as a Case Study

Genes…..

…….make proteins

Proteins form complex 3D structures

Molecules interact

the right molecules need to bepresent at the right time

EMBL-BankDNA sequences

SWISS-PROT+ TrEMBL

InterPro

SWISS-PROT+ TrEMBL

InterPro

EnsEMBLMetazoan GenomeGene Annotation

SWISS-PROT+ TrEMBL

InterPro

Array-ExpressMicroarray

Expression Data

SWISS-PROT+ TrEMBL

InterPro

Expression Data

SWISS-PROT+ TrEMBL

InterPro

Expression Data

EMSDMacromolecularStructure Data

SWISS-PROT+ TrEMBL

InterPro

Expression Data

EnsEMBL

Expression Data IntActProtein ProteinInteraction Data

SWISS-PROT+ TrEMBL

InterPro

Integr8

EnsEMBL

Expression Data IntActProtein ProteinInteraction Data

SWISS-PROT+ TrEMBL

InterPro

IntActProtein ProteinInteraction Data

SWISS-PROT+ TrEMBL

InterPro

Running a database project

Service DB

Add value(computation)

Add value (review etc.)Q/C etc

Databasedesign

Releases&Updates

GenomesGenesPatentsUpdates

Service DB

Databasedesign

Releases&Updates

Production DB

Service DB

Databasedesign

Releases&Updates

Production DB

Service DBProduction DB

Databasedesign

Releases&Updates

Databasedesign

Releases&Updates

Databasedesign

Releases&Updates

Data Distrib.

Databasedesign

Releases&Updates

Data Distrib.

Add value (review etc.)

Data exchange

Other archives

Q/C etc

Databasedesign

Releases&Updates

Data Distrib.

DevelopmentDB

Data exchange

Other archives

Q/C etc

Databasedesign

Releases&Updates

Data Distrib.

DevelopmentDB

Data exchange

Other archives

Q/C etc

Databasedesign

Releases&Updates

EMBL nucleotide sequence database

Dataflow

EMBLFlat File

ID SLD746 standard; DNA; PRO; 477 BP.XXAC D83746;XXNI g1772347XXDT 18-JAN-1997 (Rel. 50, Created)DT 17-FEB-1997 (Rel. 50, Last updated, Version 2)XXDE Streptomyces lividans DNA for ribosomal protein S12, complete cds.XXKW ribosomal protein S12.XXOS Streptomyces lividansOC Eubacteria; Firmicutes; Actinomycetes; Streptomycetes;OC Streptomycetaceae; Streptomyces.XXRN [1]RP 1-477RA Shima J.;RT ;RL Submitted (06-MAR-1996) to the EMBL/GenBank/DDBJ databases.RL Jun Shima, National Food Research Institute; Kannondai 2-1-2, Tsukuba,RL Ibaraki 305, Japan (E-mail:shimaj@ss.nfri.affrc.go.jp, Tel:0298-38-8124,RL Fax:0298-38-7996)XXDR SPTREMBL; P97222; P97222.XXFH Key Location/QualifiersFHFT source 1. .477FT /organism="Streptomyces lividans"FT /strain="TK21"FT CDS 28. .399FT /db_xref="PID:g1772348"FT /db_xref="SPTREMBL:P97222"FT /product="ribosomal protein S12"FT /translation="MPTIQQLVRKGRQDKVEKNKTPALEGSPQRRGVCTRVFTTTPKKPFT NSALRKVARVRLTSGIEVTAYIPGEGHNLQEHSIVLVRGGRVKDLPGVRYKIIRGSLDTFT QGVKNRKQARSRYGAKKEK"FT mutation 289FT /replace="g"FT /phenotype="streptomycin resistant mutant TK24"XXSQ Sequence 477 BP; 99 A; 153 C; 152 G; 73 T; 0 other; ATTCGGCACA CAGAAACCGG AGAAGTAGTG CCTACGATCC AGCAGCTGGT CCGGAAGGGC 60 CGGCAGGACA AGGTCGAGAA GAACAAGACG CCCGCACTCG AGGGTTCGCC CCAGCGCCGT 120 GGCGTCTGCA CGCGTGTGTT CACGACCACC CCGAAGAAGC CGAACTCGGC CCTGCGTAAG 180 GTCGCGCGTG TGCGTCTGAC CAGTGGGATC GAGGTCACCG CTTACATTCC GGGTGAGGGG 240 CACAACCTGC AGGAGCACTC CATCGTGCTC GTGCGCGGCG GCCGTGTGAA GGACCTGCCG 300 GGTGTTCGCT ACAAGATCAT CCGCGGTTCG CTTGACACCC AGGGTGTGAA GAACCGCAAG 360 CAGGCCCGCA GCCGCTACGG CGCCAAGAAG GAGAAGTAAG AATGCCTCGT AAGGGCCCCG 420 CCCCGAAGCG CCCGGTCATC ATCGACCCGG TCTACGGTTC TCCTCTGGTG ACCTCCC 477//

EMBL Relational Schema

VARI ATIONFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# o FREQ UENCY o REPLACE * USERSTAM P * TI M ESTAM P

UNCLASSI FI EDFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# o USERSTAM P o TI M ESTAM P

TRANSLATIONEXCEPTI ON @ PRDB1 (#)

* AM I NO ACI D * FEATI D * TRANSXEND# * TRANSXI D * TRANSXSTART o BI O SEQ I D * USERSTAM P * TI M ESTAM P

TRANSCRI PTFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# o ENUM BER o FI VE_CO NS o PSEUDO o READI NG FRAM E o THREE_CO NS * USERSTAM P * TI M ESTAM P

THESIS @ PRDB1 (#)

* I NSTI TUTE## * PUBI D o ADVI SO R o DEG REE * USERSTAM P * TI M ESTAM P

SUBMI SSIONREF @ PRDB1 (#)

# * PUBI D o DS# o M EDI UM * USERSTAM P * TI M ESTAM P

SOURCEFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# o O RG ANI SM o CHRO M O SO M E o FREQ UENCY o HAPLO TYPE o NUCSO URCE o O RG ANELLE o SEQ UENCED o SEX o VI RI O N * USERSTAM P * TI M ESTAM P

SI GNALFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# o DI RECTI O N o PSEUDO * USERSTAM P * TI M ESTAM P

SEQFEATURE_NOTE @ PRDB1

* FEATI D * LI NE# * NO TE# * TEXT o USERSTAM P o TI M ESTAM P

SEQFEATURE @ PRDB1 (#)

* BI O SEQ I D# * FEATI D * FTYPE# * LO CATI O N * O RDER_I N o EVI DENCE o FEAT_LABEL o I NCO M PLETE o SUBM I TTO R * USERSTAM P * TI M ESTAM P

RPTUNI T @ PRDB1

* FEATI D o RPTI D o LABEL o RPTEND o RPTSTART * USERSTAM P * TI M ESTAM P

RNAFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# o ANTI CO DO NAA o ANTI CO DO NEND o ANTI CO DO NSTART o PSEUDO * USERSTAM P * TI M ESTAM P

PUB_XREF @ PRDB1

* PUBI D * DBCO DE * PRI M ARYI D

PUBLICATION @ PRDB1 (#)

# * PUBI D * PUBLANG * PUBSTATUS * PUBTYPE o PUBDATE o TI TLE * USERSTAM P * TI M ESTAM P

PUBAUTHOR @ PRDB1

* O RDERI N * PERSO N * PUBI D o EDI TO RFLAG * USERSTAM P * TI M ESTAM P

PROTEINSEQ @ PRDB1 (#)

# * SEQ I D o DERI VED o M O LW EI G HT * USERSTAM P * TI M ESTAM P

PROTEINCODINGFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# * PRO TEI NSEQ I D o ENUM BER o PSEUDO o READI NG FRAM E o TRANSL_TABLE_I D * USERSTAM P * TI M ESTAM P

PHYSICALSEQ @ PRDB1 (#)

# * PHYSEQ I D * SEQ TEXT * USERSTAM P * TI M ESTAM P

PERSONALCOMM @ PRDB1

* ADDRESS * PUBI D * RECI PI ENT o PHO NEI D * USERSTAM P * TI M ESTAM P

PERSON @ PRDB1 (#)

# * PERSO NI D * SURNAM E o FI RSTNAM E o M I DI NI TI ALS * USERSTAM P * TI M ESTAM P

PATENT_BIOSEQ @ PRDB1 (#)

* O RDERI N# * PUBI D# * SEQ I D * USERSTAM P * TI M ESTAM P

PATENTPRIORITY @ PRDB1

* PRI O RI TY_DATE * PRI O RI TY_NO * PRI O RI TY_O FFI CE * PRI O RI TY_O RDER * PUBI D * USERSTAM P * TI M ESTAM P

PATENTCLASS @ PRDB1

* CLASS * CLASS_O RDER * PUBI D * USERSTAM P * TI M ESTAM P

PATENTAPPLICANT @ PRDB1

* APPNAM E * O RDERI N * PUBI D * USERSTAM P * TI M ESTAM P

PATENTABSTRACT @ PRDB1 (#)

* ABSTRACT# * PUBI D * USERSTAM P * TI M ESTAM P

PATENT @ PRDB1 (#)

* DO CNUM * DO CO FFI CE * DO CTYPE# * PUBI D o APPDATE o APPNUM o APPO FFI CE * USERSTAM P * TI M ESTAM P

NUCSTRUCTUREFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# o ENUM BER o FREQ UENCY o M O DBASE o O RG ANI SM o RPTFAM I LY * USERSTAM P * TI M ESTAM P

NUCSEQ @ PRDB1 (#)

* A_CO UNT * C_CO UNT * G _CO UNT * O THER_CO UNT# * SEQ I D * T_CO UNT o STRAND o TO PO LO G Y * USERSTAM P * TI M ESTAM P

NTX_TAX_NODE @ PRDB1 (#)

# * TAX_I D o PARENT_I D o RANK o EM BL_CO DE o DI V_I D * I NHERI T_DI V_I D o G C_I D o I NHERI T_G C_I D o M G C_I D o I NHERI T_M G C_I D * HI DDEN o NO _SEQ UENCE o REM ARK

NTX_SYNONYM @ PRDB1

* TAX_I D * NAM E_TXT o UNI Q UE_NAM E o NAM E_CLASS * UPPER_NAM E_TXT

NTX_RANK @ PRDB1 (#)

o RANK_I D# * RANK_TXT

NTX_CLASS @ PRDB1 (#)

o CLASS_CO DE# * CLASS_TEXT o PRI O RI TY

LOCATION_TREE @ PRDB1 (#)

# * LO CNO DEI D * O RDER_I N o CO M PLEM ENT o END_FSI ZE o END_FTYPE o G AP_FSI ZE o G AP_FTYPE o LI TERAL o O PERATO R o PARENTI D o REPLACE o REPL_STRI NG o SEG _END o SEG _G AP o SEG _START * SEQ I D o START_FSI ZE o START_FTYPE * USERSTAM P * TI M ESTAM P

KEYWORD_SYNONYM @ PRDB1 (#)

# * KEYW O RDI D1# * KEYW O RDI D2

KEYWORD @ PRDB1 (#)

* CO M PRESSED_KW * KEYW O RD# * KEYW O RDI D o DBCO DE o DESCRI PTI O N * USERSTAM P * TI M ESTAM P

JOURNALARTI CLE @ PRDB1 (#)

* FI RSTPAG E * I SSN# * PUBI D * VO LUM E o ARTI CLETYPE o I SSUE o LASTPAG E o O RDER_O N_PAG E o SUPPLEM ENT * USERSTAM P * TI M ESTAM P

INSTITUTE @ PRDB1 (#)

# * I NSTI TUTE# * I NSTI TUTE_NAM E * USERSTAM P * TI M ESTAM P

IMMUNOFEATURE @ PRDB1 (#)

# * FEATI D * FKEY# o CHI M ERI C o PSEUDO o READI NG FRAM E o TRANSL_TABLE_I D * USERSTAM P * TI M ESTAM P

GENE @ PRDB1 (#)

# * G ENEI D * G ENENAM E o DBCO DE o EXTDBI D o O RG ANI SM o PATHO LO G Y o PRO DUCT * USERSTAM P * TI M ESTAM P

FEATURE_RELATIONSHIP @ PRDB1 (#)

# * FEATI D1# * FEATI D2# * RELATI O N * USERSTAM P * TI M ESTAM P

FEATURE_QUALIFIERS @ PRDB1 (#)

# * FEATI D# * O RDER_O N * Q UAL# o TEXT o USERSTAM P o TI M ESTAM P

ERROR_QUALIFI ERS @ PRDB1 (#)

# * FEATI D# * O RDER_O N

DBENTRY_KEYWORD @ PRDB1

* KEYW O RDI D * DBENTRYI D o USERSTAM P o TI M ESTAM P

DBENTRY_DESCR @ PRDB1 (#)

# * DBENTRYI D# * LI NE# * TEXT o USERSTAM P o TI M ESTAM P

DBENTRY_COMMENT @ PRDB1 (#)

# * CO M M ENTI D# * DBENTRYI D * USERSTAM P * TI M ESTAM P

DBENTRY @ PRDB1 (#)

* BI O SEQ I D# * DBENTRYI D * ENTRY_NAM E * ENTRY_STATUS * PRI M ARYACC# * VERSI O N# o ANN_DATE o CLEAN_LI STI NG o CO NFI DENTI AL o DBCO DE o EXT_DATE o EXT_VER o FI RST_CREATED o FI RST_PUBLI C o HO LD_DATE o M I SSI NG _PAPER o PRO JECT# o SUBM I T_TO O L o W AI T_FO R_PAPER * USERSTAM P * TI M ESTAM P o FFDATE

DATABASE_XREF @ PRDB1

* EBI _DB * ACC# o NI D_TEXT o PI D_TEXT * EXT_DB * PRI M ARYI D o SECO NDARYI D

COMMENT_TEXT @ PRDB1 (#)

# * CO M M ENTI D# * LI NE# * TO PI CTYPE o PRI VATE o TEXT. . .

CODONEXCEPTION @ PRDB1 (#)

* AM I NO ACI D * CO DO NSEQ# * CO DO NXI D * FEATI D o USERSTAM P o TI M ESTAM P

CI TATI ONSEQFEATURE @ PRDB1 (#)

# * FEATI D# * PUBI D# * SEQ I D * USERSTAM P * TI M ESTAM P

CI TATI ONBIOSEQ @ PRDB1 (#)

* O RDERI N# * PUBI D# * SEQ I D o CI TCO M M ENT o FULLSEQ o LO CNO DEI D o LO CTYPE * USERSTAM P * TI M ESTAM P

BOOK @ PRDB1 (#)

* BO O KTI TLE * FI RSTPAG E * LASTPAG E# * PUBI D * PUBLI SHER o EDI TI O N o I SBN o PUBPLACE o SERI ES o VO LUM E * USERSTAM P * TI M ESTAM P

BI OSEQ @ PRDB1 (#)

* BI O SEQ TYPE * CHKSUM * M O LECULETYPE# * SEQ I D * SEQ LEN o DDBJSI D o EBI SI D o LO G SEQ o NCBI G I o PHYSEQ * USERSTAM P * TI M ESTAM P

ACCPAI R @ PRDB1 (#)

# * PRI M ARY# * SECO NDARY * USERSTAM P * TI M ESTAM P

ACCEPTED @ PRDB1 (#)

* I SSN# * PUBI D o ARTI CLETYPE o FI RSTPAG E o I SSUE o LASTPAG E o O RDER_O N_PAG E o SUPPLEM ENT o VO LUM E * USERSTAM P * TI M ESTAM P

FK_ACCFK_ACCPAIR_127

FK_BIOSEQ_4

FK_BIOSEQ_5

FK_BOOK_59

FK_CITATIONBIOSEQ_60

FK_CITATIONBIOSEQ_61

FK_CITATIONSEQFEATURE_10

FK_CITATIONSEQFEATURE_92

FK_CODONEXCEPTI ON_50

FK_DBENTRY_25

FK_DBENTRY_COMMENT_100

FK_DBENTRY_DESCR_117

FK_DBENTRY_KEYWORD_39

FK_DBENTRY_KEYWORD_40

FK_ERROR_QUALIFIERS_122

FK_FEATURE_QUALI FI ERS_121

FK_FEATURE_RELATI ONSHI P_28

FK_FEATURE_RELATI ONSHI P_29

FK_GENE_64

FK_I MMUNOFEATURE_7

FK_JOURNALARTI CLE_66

FK_LOCATI ON_TREE_68

FK_LOCATI ON_TREE_72

FK_NAME_CLASS

FK_NTX_SYNONYM_46

FK_NUCSEQ_76

FK_NUCSTRUCTUREFEATURE_55

FK_NUCSTRUCTUREFEATURE_57

FK_PATENTABSTRACT_1

FK_PATENTAPPLICANT_2FK_PATENTCLASS_98

FK_PATENTPRI ORITY_97

FK_PATENT_77

FK_PATENT_BI OSEQ_107

FK_PATENT_BI OSEQ_108

FK_PERSONALCOMM_3

FK_PROTEI NCODINGFEATURE_12

FK_PROTEI NCODINGFEATURE_13

FK_PROTEI NSEQ_80

FK_PROTEI NSEQ_81

FK_PUBAUTHOR_82

FK_PUBAUTHOR_83FK_PUB_XREF_1

FK_RANK

FK_RNAFEATURE_15

FK_RPTUNIT_109

FK_SEQFEATURE_35

FK_SEQFEATURE_36

FK_SEQFEATURE_NOTE_78

FK_SIGNALFEATURE_18

FK_SOURCEFEATURE_20

FK_SOURCEFEATURE_21

FK_SUBMISSI ONREF_119

FK_THESI S_106

FK_THESI S_84

FK_THESI S_85

FK_TRANSCRIPTFEATURE_52

FK_TRANSLATI ONEXCEPTION_110

FK_TRANSLATI ONEXCEPTION_51

FK_UNCLASSIFIEDFEATURE_118

FK_UNPUBLI SHED_114

FK_VARIATI ONFEATURE_48

Location Info

Feature Info

Taxonomy Info

Reference InfoSequence Info

Data Access and Use Network services Sequence Retrieval System (SRS)

integrating and linking the main nucleotide and protein databases plus many specialized databases

Database releases are produced quarterly- via FTP (inc. mirror sites) and CD-ROM

Daily and cumulative updates via FTP Sequence search servers

April 2003: TrEMBL 23.4 + SWISS-PROT 41.2 829,111 TrEMBL entries 123,721 SWISS-PROT entries weekly production of a non-redundant and

comprehensive protein sequence database consisting of SWISS-PROT, TrEMBL, and TrEMBLnew: ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/

Goals High level of annotation Minimal redundancy High level of integration with other

databases Complete and up-to-date Availability

Growth of TrEMBL and SWISS-PROT

Nov-96 May-97 Nov-97 May-98 Nov-98 May-99 Nov-99 May-00 Nov-00 May-01 Nov-01 May-02

Publication Date

SWISS-PROT TrEMBL

Automatic annotation of TrEMBL

Data-mining to extract conditions from InterPro

Extract SWISS-PROT reference entries fulfilling the conditions

Extract common annotation Store conditions and common

annotation in RuleBase Group TrEMBL by conditions Add common annotation to

TrEMBL

TrEMBLTrEMBL

InterProInterPro

RuleBasRuleBasee

SWISS-PROT

Cross-referencesDomains, functionalsites, protein familiesInterProPROSITEPfamPRINTSProDomSMART

Nucleotide sequence dbEMBL, GenBank, DDBJ

3D/Structural dbsHSSPPDB

Organism-spec.dbsDictyDbEcoGeneFlyBaseHIVLepromaMaizeDBMGDMypuListSGDStyGeneSubtiListTIGRTubercuListWormPepYEPDZfin

Protein-specificdbsGCRDbMEROPSREBASETRANSFAC

SWISS-PROT/

TrEMBL2D-gel protein dbsSWISS-2DPAGEANU-2DPAGECOMPLUYEAST-2DPAGEECO2DBASEHSC-2DPAGEAarhus and GhentMAIZE-2DPAGEPHCI-2DPAGEPMMA-2DPAGESiena-2DPAGE

Human diseasesMIM

PTMCarbBankGlycoSuiteDB

TrEMBL

UniProt Archive

EnsEMBL PDB PatentData

DDBJ/EMBL/

GenBank PIR

UniProt Knowledgebase:TrEMBL + SWISS-PROT

UniProt NREF100

UniProt NREF90

UniProtNREF50

SWISS-PROT

OtherData…

Classification

Automated Annotation Literature Based Annotation

RefSeq

Funding

EMBL European Commission NIH Industrial licenses MRC IUPHAR

SWISS-PROT, TrEMBL, InterPro, etc, at EBI and SIB •Group leaders: Rolf Apweiler, Amos Bairoch

•Co-ordinators:Wolfgang Fleischmann, Henning Hermjakob, Michele Magrane, Maria-Jesus Martin, Nicola Mulder, Claire O’Donovan, Manuela Pruess

•Annotators/curators: Philippe Aldebert, Andrea Auchincloss, Kirsty Bates, Marie-Claude Blatter Garin, Brigitte Boeckmann, Silvia Braconi Quintaj, Paul Browne, Evelyn Camon, Danielle Coral, Elisabeth Coudert, Tania de Oliveria Lima, Kirill Degtyarenko, Sylvie Dethiollaz, Ann Estreicher, Livia Famiglietti, Nathalie Farriol-Mathis, Stephanie Federico, Serenella Ferro, Gill Fraser, Raffaella Gatto, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Florence Jungo, Vivien Junker, Youla Karavidopoulou, Maria Krestyaninova, Kati Laiho, Minna Lehvaslaiho, Karine Michoud, Virginie Mittard, Madelaine Moinat, Sandra Orchard, Sandrine Pilbout, Sylvain Poux, Sorogini Reynaud, Catherine Rivoire, Bernd Röchert, Michel Schneider, Christian Sigrist, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Sandra van den Broek, Bob Vaughan, Eleanor Whitfield

•Programmers: Daniel Barrell, David Binns, Michael Darsow, Ujjwal Das, Eduardo de Castro, Alexander Fedotov, Astrid Fleischmann, Elisabeth Gasteiger, Alain Gateau, Andre Hackmann, Ivan Ivanyi, Eric Jain, Alexander Kanapin, Paul Kersey, Ernst Kretschmann, Corinne Lachaize, Chris Lewington, Xavier Martin, John Maslen, Peter McLaren, Rupinder Singh Mazara, Lorna Morris, John O’Rourke, Isabelle Phan, Astrid Rakow, Kai Runte, Florence Servant, Allyson Williams, Dan Wu

•Research staff: Kristian Axelsen, Pierre-Alain Binz, Nicolas Hulo, Anne-Lise Veuthey

•Clerical/secretarial assistance: Veronique Mangold, Claudia Sapsezian, Margaret Shore-Nye, Veronique Verbegue

•Students: Pavel Dobrokhotov, Alexandre Gattiker, various MCF, etc

Value-adding, Access, and Use: Biological Databases as a Case Study.

Documents