Value-adding, Access, and Use: Biological Databases as a Case Study.
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Transcript of Value-adding, Access, and Use: Biological Databases as a Case Study.
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
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
InterPro
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
InterPro
EnsEMBLMetazoan GenomeGene Annotation
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
InterPro
EnsEMBLMetazoan GenomeGene Annotation
Array-ExpressMicroarray
Expression Data
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
InterPro
EnsEMBLMetazoan GenomeGene Annotation
Array-ExpressMicroarray
Expression Data
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
InterPro
EnsEMBLMetazoan GenomeGene Annotation
Array-ExpressMicroarray
Expression Data
EMSDMacromolecularStructure Data
EMBL-BankDNA sequences
SWISS-PROT+ TrEMBL
InterPro
EnsEMBLMetazoan GenomeGene Annotation
Array-ExpressMicroarray
Expression Data
EMSDMacromolecularStructure Data
EnsEMBL
EMBL-BankDNA sequences
Array-ExpressMicroarray
Expression Data IntActProtein ProteinInteraction Data
SWISS-PROT+ TrEMBL
InterPro
EMSDMacromolecularStructure Data
Integr8
EnsEMBL
EMBL-BankDNA sequences
Array-ExpressMicroarray
Expression Data IntActProtein ProteinInteraction Data
SWISS-PROT+ TrEMBL
InterPro
EMSDMacromolecularStructure Data
EMBL-BankDNA sequences
IntActProtein ProteinInteraction Data
SWISS-PROT+ TrEMBL
InterPro
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DB
Sub
mit
ters
Add value(computation)
Add value (review etc.)Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DB
Sub
mit
ters
Add value(computation)
Add value (review etc.)Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Production DB
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DB
Sub
mit
ters
Sub
mis
sion
tool
s
Add value(computation)
Add value (review etc.)Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Production DB
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DBProduction DB
Sub
mit
ters
Sub
mis
sion
tool
s
Add value(computation)
Add value (review etc.)Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DBProduction DB
Sub
mit
ters
Sub
mis
sion
tool
s
Add value(computation)
Add value (review etc.)Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DBProduction DB
Sub
mit
ters
Sub
mis
sion
tool
s
Add value(computation)
Add value (review etc.)Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Data Distrib.
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DBProduction DB
Sub
mit
ters
Sub
mis
sion
tool
s
Add value(computation)
Add value (review etc.)Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Data Distrib.
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DBProduction DB
Sub
mit
ters
Sub
mis
sion
tool
s
Add value (review etc.)
Data exchange
Other archives
Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Data Distrib.
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DBProduction DB
DevelopmentDB
Sub
mit
ters
Sub
mis
sion
tool
s
Add value (review etc.)
Data exchange
Other archives
Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
Data Distrib.
Running a database project
Ser
vice
Too
ls
End
Use
rs
Service DBProduction DB
DevelopmentDB
Sub
mit
ters
Sub
mis
sion
tool
s
Add value(computation)
Add value (review etc.)
Data exchange
Other archives
Q/C etc
Databasedesign
Releases&Updates
GenomesGenesPatentsUpdates
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:[email protected], 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
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Publication Date
En
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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