Bioinformatics Platform Three-tier Architecture Object-based Relational Database implemented using Oracle Middleware implemented using Entity-Class Operations, Servlets in Java Static Pages (SHTML) for Web Site Dynamic pages (JSPs) for database driven Entry, Dissemination and Queries - Entity Relationship data model Ontology Diagram Implementation using Oracle BIO FU NC TIO N _CATE G O R Y B iofunction_key:IN TE G E R B iofunction_nam e:V A RC HA R 2(20 B IO LO G ICA L_S O UR CE biosource_key:INTEG E R Biosource_ID :V AR C HA R 2(20 kingdom :V A RC H A R2(20) Phylum :VA R C HA R2(20) Class:V A RC H A R2(20) G enus:VA R C HA R 2(20) Species:V A R CH A R 2(20) CARBOHYDRATE C arb_key:INTE G E R biosource_key:IN TEG E R C arb_ID:VA R CH AR 2(20) C arb_S cinam e:VA RC HA R 2(20) C arb_com m onN am e:V AR C HA R2(20) C arb_Fam ily:VA RC H A R2(20) C arb_S ubfam ily:VA R C HA R 2(20) C arb_Type:VA RC HA R 2(10) Carb_M W :NUM BER B iofunction_key:NU M BE R C arb_B iofunctionD esc:V AR C H AR 2(100 C arb_listdate:D ATE C arb_structure:VA RC HA R 2(500) C arb_structureIm gtype:VA RC H AR 2(10 C arb_structureIm g:B LO B A ccess_code:VA R C HA R 2(20) DNASEQ D NA SE Q _key:INTE G ER G ene_key:IN TE G E R D NA SE Q _ID :V A RC H A R2(20) D NA SE Q _ID type:VA RC H AR 2(20) D NA SE Q _sequence:V A R CH AR 2(20 GENE G ene_key:IN TE G E R G enom e:V A RC H AR 2(20) G ene_nam e:V A RC HA R 2(20 biosource_key:IN TE G E R PAPER P aper_key:NU M BE R P aper_ID :V AR CH A R2(20) ID_type:V A RC HA R 2(20) P aper_title:VA RC H AR 2(200) P aper_year:IN TEG ER Journal_nam e:VA R CH A R 2(200) P age_range:V A RC H AR 2(20) PAPER_REFERENCE Paper_key:N U M B E R Carb_key:IN TEG E R PROTEIN Protein_key:IN TE G ER Protein_ID :V AR C HA R 2(20) ProteinID _type:V A RC HAR 2(20) Protein_nam e:VA RCH AR 2(20) Protein_Com m onNam e:V A R CH A R2(20 Protein_fam ily:V A R CH A R2(20) Protein_subFam ily:V A RC HAR 2(20) Protein_superU nitK ey:IN TE G E R Protein_type:VA R C HA R 2(20) Biosource_key:IN TE G E R Biofunction_key:IN TE G ER G ene_key:V A R CH A R2(20) DN A S EQ _key:INTE G ER Protein_sequenceKey:INTE G ER Protein_biofunctionD esc:V AR CHA R2(2 Access_code:V A RC HA R 2(20) Protein_listdate:DA TE PRO TE IN S E Q UE NC E P rotein_sequenceK ey:INTE G E R P rotein_sequence:V AR CH AR 2(20 P rotein_key:INTE G ER REAGENT R eagent_key:INTEG ER R eagent_ID :V A RC HA R 2(20) R eagent_ID type:V AR C H AR 2(20) R eagnet_nam e:V A R CH AR2(20) R eagent_form ula:VA R CH A R 2(20 R eagent_M W :IN TE G E R CPBIN DING C pb_key:N U M B E R C pb_ID :VA R CH A R 2(20) C pb_ID type:V AR CH A R2(20) C arb_key:N U M B ER P rotein_key:NU M BE R C pb_flag:C HA R(1) B iofunction_key:NU M BE R C pb_B iofunctionDesc:V A R CH AR 2(100) C pb_K eq:NU M BE R C pb_D G :N U M B E R Cpb_D H:NUM BER Cpb_D S:NUM BER C pb_listdate:D A TE PROTOCOL Protocol_key:IN TE GER P rotocol_ID :V A R CHA R2(20) P rotocol_Category:V A R CH A R2(20) P rotocol_keyw ord:VA RC H A R2(20) P rotocol_Title:V AR C HA R 2(20) P rotocol_overview :V AR C HA R 2(20) P rotocol_procedure:C HA R (18) P rotocol_trobleshooting:V A R CH A R2(20) D buser_key:IN TEG E R CPATHREAGENT P rotocol_key:INTEG ER R eagent_key:INTEG ER R eactant_W eightg:IN TEG E R R eactant_m m ol:VA RCH AR 2(20 CPATHINSTRUM ENT Protocol_key:IN TE G E R Instrum ent_key:IN TE G E IN S TRU M E NT Instrum ent_key:INTEG ER Instrum ent_category:V ARC HA R 2(20 Instrum ent_nam e:V AR CHA R2(20) Instrum ent_m odel:V A RC H AR 2(20) Instrum ent_V ender:VA RCH AR 2(20) C AR B P RO FILE C arbprofile_key:N UM B ER C arbprofile_ID :V A RC HA R 2(20) C arbprofile_title:V AR CH A R2(30) C arbprofile_carbC om p:VA RC HA R 2(200) C arbprofile_avgM W :N UM BE R M ouseind_key:N U M B ER C arbprofile_source:V AR C HA R 2(100) B iofunction_key:NU M BE R C arbprofile_biofunctionDesc:V AR C HA R2(200) P arentprofile_ID :V AR C HA R2(20) CP RO FILE ID C arbprofile_key:N U M B ER C arb_key:INTEG ER C oncentration:VA R C HA R2(20) C PR O FILEE XP Cpexp_key:INTEG ER cpexp_ID :V ARC HA R 2(20) cpexp_title:VAR CH A R 2(20) Protocol_key:IN TEG ER Carbprofile_key:N U M BE R Cpexp_keyword:V AR CH AR 2(20) Cpexp_instrum ent:V AR CHA R2(20) Cpexp_date:D ATE Cpexp_com m ent:V AR CH A R2(20) Dbuser_key:INTE G ER M ICROARRAY M array_key:INTE G ER M array_ID:V A RC HA R2(20) M array_type:V A RC H AR 2(20) M array_desc:V AR C H A R2(20) M array_im gtype:V A R C HA R 2(20 M array_im g:BLOB M O U S ES TRA IN M ouse_key:INTEG ER M ouse_ID:VA RC H A R2(20) C ell_key:N UM BER M ouse_type:V A RC H AR 2(20) P rotocol_key:INTEG ER M ouse_keyword:V A RC H AR 2(2 M ouse_desc:V AR C HA R2(20) KOGENE K O gene_key:IN TEG E R K O gene_ID :VAR C H A R 2(20) M ouse_key:IN TE G E R G ene_key:IN TE G E R G ene_ID :V A R CH A R2(20) K O gene_synonym :V AR C H AR 2(20) K O gene_M type:V A R CH AR2(20) K O gene_U nigenD es:VA RCH AR 2(20) K O gene_H um anG ene:V ARC HA R 2(20) CELLSO URCE C ell_key:NU M B E R C ell_ID:V AR C H AR 2(20) biosource_key:N UM BE R C ell_line:V ARC HA R2(30) C ell_linetype:VA RC H AR 2(20 C ell_tissue:V AR C H AR 2(20) C ell_O rgan:V AR C H AR 2(20) M A E XP M aexp_key:IN TE G ER M aexp_ID :VA R C HA R2(20) M aexp_title:V A R CH AR 2(20) Protocol_key:IN TE G E R M array_key:INTE G E R M aexp_Sam pleID :V AR CH AR 2(20) M aexp_Sam pleDesc:V AR CH A R 2(20) M aexp_keyword:VA RC H AR 2(20) M aexp_readtype:V AR CH A R2(20) M aexp_raw :VA RC H AR 2(20) M aexp_date:DA TE M aexp_im gfiletype:V AR CH A R2(20) M aexp_im graw:BLO B Dbuser_key:IN TEG E R TARG ETG ENE M aexp_key:IN TEG ER G ene_key:IN TE G E R Targetgene_desc:V A RC H AR 2(20 P R O TIE N R EF Paper_key:NU M B E R Protein_key:IN TE G E R CARBPATHREF Paper_key:N UM B ER Cpath_key:INTE G ER PROTOCOLREF P aper_key:N UM B E R Protocol_key:IN TEG E CPBREF P aper_key:NU M B E R C pb_key:N U M B E R DBUSER D buser_key:IN TEG E R D buser_usernam e:VA RC H AR 2(20 D buser_passw ord:V ARC HA R 2(20 D buser_lastnam e:VA R CH AR 2(20) D buser_firstnam e:CH A R(18) D buser_em ail:V AR C H AR 2(20) D buser_em ployer:VA R CH AR 2(20) D buser_title:V AR C HA R2(20) D buser_C ore:VA R C HA R2(20) D buser_listdate:D A TE M OUSEHEM A M H_key:IN TE G E R M H_ID :V A R CH A R2(20) M ouseind_key:IN TE G ER M H_date:D A TE M H_age:IN TE G E R M H_w eight:IN TEG E R M H_W BC:INTEG ER M H_N eutrophils:INTE G ER M H_Lym phocytes:V A RC HA R 2(20) M H_H G B :IN TE G ER M H_H C T:IN TE G E R M H_P LT:INTE G E R M H_M P V :IN TE G E R D buser_key:INTE G ER M O U S EH ISTO LO G Y M H S_key:IN TE G E R M H S_ID :V A R CH A R2(20) M ouseind_key:INTE G E R M H S_date:D A TE M H S_age:IN TE G E R M H S_weight:INTEG E R P rotocol_key:INTE G ER M H S_purpose:V AR CH AR 2(20) M H S_result:VA RC HA R 2(20) M H S_com m ent:V A RC H A R2(20) D buser_key:IN TE G E R M OUSEIM M U M I_key:IN TEG E R M I_ID :V ARCHAR2(20) M ouseind_key:IN TE G E R M I_date:D ATE M I_age:IN TEG E R M I_weight:INTEG E R M I_sam pletype:VA R C HA R 2(20) M I_CD 4:IN TEG ER M I_CD 8:IN TEG ER B220:IN TE G E R IAB:INTEG ER IgM :INTEG ER IgD:IN TEG E R Dbuser_key:IN TEG E R M O USEIND M ouseind_key:IN TEG ER M IN D_ID :V A R CH AR 2(20) M ouse_key:IN TE G E R M ind_sex:V AR C H AR 2(20) MOUSEBEHAV M B_key:IN TEG E R M B_ID:VA R C H AR 2(20) M ouseind_key:IN TEG ER M B_date:D ATE M B_age:IN TEG E R M B_weight:INTE G E R M B_G rossNero:V A RC HAR 2(20) M B_SensorM otorR eflex:V AR C H AR 2(20 M B_PosturalReflex:VA RC HA R2(20) M B_m otoractivity:VA R C HA R 2(20) M B_Nocieption:VA R C HA R2(20) M B_AcousticS tartle:V ARC HA R 2(20) M B_SocialDom ine:VA RCH AR 2(20) M B_conditionedFear:VA R CH A R 2(20) M B_waterM aze:VA R CH A R 2(20) M B_radialArm M aze:V AR C H AR 2(20) Dbuser_key:INTEG ER M O USE M ETA BO LISM M M _key:INTE G E R M M _ID:VA RC H A R2(20) M ouseind_key:C HA R (18) M M _date:DA TE M M _age:INTE G E R M M _weight:INTEG ER M M _C ardiac:V AR C H AR2(20) M M _B loodDiastol:INTE G E R M M _bloodSystol:INTEG ER M M _plum onary:VA R CH AR 2(20) M M _FoodC onsum ption:IN TE G E R M M _waterConsum ption:INTEG ER M M _activityLevel:INTEGE R M M _O xygenConsum ption:IN TE G E R M M _CO 2O utput:INTE G ER M M _HeatO utput:INTEG ER D buser_key:INTE G E R M A REF M array_key:INTE G E R Paper_key:N UM B ER E NZYM E E nzym e_key:INTEG ER E nzym e_ID:V A RC H AR 2(20) E nzym e_type:V AR CH A R2(20) E nzym e_nam e:V AR CHA R2(20) E nzym e_C om m onN am e:VA R C HA R 2(20 E nzym e_fam ily:VA RC H AR 2(20) E nzym e_subFam ily:V AR CH AR2(20) biosource_key:IN TE G E R B iofunction_key:INTE G ER E nzym e_biofunctionD esc:VA R C HA R 2(2 G ene_key:V ARC HA R 2(20) D N AS E Q _key:IN TEG E R E nzym e_sequenceK ey:INTEG E R P roteindb_ID :V AR CH AR 2(20) S w issPort_ID :V A RC HAR 2(20) A ccess_Code:V A R CH A R2(20) P rotein_listdate:D A TE CARBPATHW AY C path_key:IN TEG E R C path_nam e:V AR C HA R2(20) C arb_key:IN TEG ER E nzym e_key:IN TE G E R C path__Reaction:VA R CH AR 2(20 C path_condition:VA R C H AR 2(20) C path_stepFrom C arb:INTE G ER C path_yield:IN TE G E R ENZYMESEQUENCE E nzym e_sequenceK ey:IN TE G E R E nzym e_sequence:V AR CH AR2(2 E nzym e_key:INTE G E R CARBEXP C arbexp_key:IN TE G E R carbexp_ID :VAR C H AR 2(20) carbexp_title:VA R C HA R2(30) P rotocol_key:NU M BE R C arb_key:N UM B ER C arbexp_keyw ord:VA RC H A R2(100) C arbexp_Instrum ent:V A RCH AR 2(100) C arbexp_com m ent:VA R C HA R 2(200) C arbexp_date:DA TE C abexp_batchno:VA R C HA R2(20) U ser_key:N UM B ER C A R BEXP IM G carbExpIm g_key:IN TE G E R Carbexp_key:N UM B ER CarbE xpIm g_exptype:V A RC HA R 2(2 CarbE xpIm g_filetype:VA RC H AR 2(20 CarbE xpIm g_im ageR aw:BLO B CPBEXP Cpbexp_key:NU M B E R cpbexp_ID :VA RC H AR 2(20) cpbexp_title:V AR C HA R 2(20) Protocol_key:INTEG ER Cpb_key:NUM BER Cpbexp__keyw ord:VA R C HA R2(20) Cpbexp_Instrum ent:VA RC HA R 2(20) Cpbexp_date:D ATE Cpbexp_com m ent:V ARC HA R 2(20) Dbuser_key:INTE G E R CPBEXPIM G cpbExpIm g_key:IN TE G E R C pbexp_key:N U M B ER C pbexpIm g_exptype:V A R CH AR2(20) C pbexpIm g_im ageRaw :BLO B C pbexpim g_desc:V AR C H AR 2(20) C pbexpIm g_filetype:V AR CHA R2(20) CPR OFILEE XPIM G cpexpIm g_key:IN TE G E R C pexp_key:IN TE G E R C pexpIm g_exptype:V A R C HA R 2(2 C pexpIm g_filetype:VA RC H AR 2(20 C pexpIm g_im ageR aw:B LO B C pexpIm g_desc:V AR C H A R2(20) M A EXPA N A LY SIS M aexpanaly_key:IN TE G E R M aexp_key:INTEG ER M aexpanaly_title:V A RC HA R 2(100 M aexpanaly_desc:VA R CH A R 2(50 CBPEXP C bpexp_key:IN TEG E R C bpexp_ID :V AR CH AR 2(20) C bpexp_title:VA RC HA R 2(20) P rotocol_key:INTEG ER P rotein_key:INTE G ER C bpexp_keyw ord:V AR C HA R2(20) C bpexp_Instrum ent:VA RC H AR 2(20) C bpexp_com m ent:V AR C HA R2(20) C bpexp_date:D ATE D buser_key:INTE G ER E NZEXP IM G EnzexpIm g_key:INTE G E R Enzexp_key:IN TEG E R EnzexpIm g_exptype:VA RC H A R2(2 EnzexpIm g_filetype:VA R C HA R 2(2 EnzexpIm g_im ageR aw :BLO B E N ZE E XP Enzexp_key:IN TE G E R Enzexp_ID :V A R CH AR2(20) Enzexp_title:V A RC HAR 2(20) Protocol_key:INTE G E R Enzym e_key:INTE G E R Enzexp_keyw ord:V ARC HA R 2(20) Enzexp_Instrum ent:VA R C HA R 2(20) Enzexp_com m ent:V A RC H A R2(20) Enzexp_date:D ATE User_key:IN TE G E R CBPEXP IM G C bpexpIm g_key:IN TE G E R C bpexp_key:INTE G E R C bpexpIm g_exptype:V AR C H AR2(2 C bpexpIm g_filetype:V AR CHA R2(20 C bpexpIm g_im ageRaw:BLO B GLYCOARRAY G array_key:INTEG ER G array_ID:V AR C HA R2(20) G array_type:VA RC H AR 2(20) G array_desc:V AR C HA R 2(20) G array_im gtype:V A RC H A R2(20 G array_im g:BLOB G A E XP G aexp_key:IN TEG E R G aexp_ID :V AR C H AR 2(20) G aexp_title:VA R C HA R 2(20) Protocol_key:INTEG E R G array_key:INTE GER G aexp_Sam pleID :V A RC H AR 2(20) G aexp_Sam pleD esc:VA R CH AR 2(20) G aexp_keyw ord:V AR C HA R 2(20) G aexp_readtype:VA R C HA R 2(20) G aexp_raw :V A RC H A R2(20) G aexp_date:D ATE G aexp_im gfiletype:VA RC H AR 2(20) G aexp_im graw:B LO B Dbuser_key:INTE G ER TA RG ETPR O TEIN G aexp_key:IN TE G E R P rotein_key:IN TEG E R Targetcbp_desc:VA RC HA R 2(20 CPATHEXP Cpathexp_key:IN TE G E R Cpathexp_ID :V A R CH A R2(20) Cpathexp_title:V A RC H AR 2(20) Cpath_key:INTEG ER Protocol_key:IN TE G E R Cpathexp_keyw ord:V A RC HA R 2(20) Cpathexp_Instrum ent:VA R CH A R 2(20) Cpathexp_com m ent:V A RC HA R 2(20) Cpathexp_date:D A TE User_key:INTE G ER CP A THE XP IM G C pathexpIm g_key:IN TE G E R C pathexp_key:INTE G ER C pathexpIm g_exptype:V AR C H AR 2(2 C pathexpIm g_filetype:V AR CH A R2(2 C pathexpIm g_im ageRaw :B LO B C A R BINV E NTO R Y C arbinv_key:NU M B E R C arbinv_ID:V AR C HA R2(20) C arb_key:N U M B ER C arbexp_key:V A R CH AR 2(20) Carbinv_Purity:N UM B ER C arbinv_color:V AR CHA R2(10) C arbinv_S tate:VA RC H AR 2(10) Quantity:N UM BER C arbexp_batchno:V A RC H A R2(20) CARBORDER C order_key:N UM BE R C order_ID :VA RC H AR 2(20) C order_date:D ATE C arbinv_key:N UM B ER O rder_receiver:V AR C HA R2(50) O rder_address:VA RC H AR 2(200) O rder_quantity:NU M BE R shipping_flag:CH A R(1) Part of CFG database overall ontology map - Communicates with database and user - Keeps the complexity of the database Invisible from user interface - Enables seamless acquisition and dissemination of data - Top-most layer of user interface - Static pages for web site management - Dynamic pages for database driven cont
Bioinformatics Platform Three-tier Architecture Object-based Relational Database implemented using Oracle Middleware implemented using Entity-Class Operations,
Mar 27, 2015
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Bioinformatics Platform
Three-tier Architecture
Bioinformatics Platform
Three-tier Architecture
Object-based Relational Database implemented using Oracle
Middleware implemented using Entity-Class
Operations, Servlets in Java
Static Pages (SHTML) for
Web Site
Dynamic pages (JSPs) for database driven Entry,
Dissemination and Queries
- Entity Relationship data model- Ontology Diagram- Implementation using Oracle
BIOFUNCTION_CATEGORY
Biofunction_key: INTEGER
Biofunction_name: VARCHAR2(20)
BIOLOGICAL_SOURCE
biosource_key: INTEGER
Biosource_ID: VARCHAR2(20)kingdom: VARCHAR2(20)Phylum: VARCHAR2(20)Class: VARCHAR2(20)Genus: VARCHAR2(20)Species: VARCHAR2(20)
CARBOHYDRATE
Carb_key: INTEGER
biosource_key: INTEGERCarb_ID: VARCHAR2(20)Carb_Sciname: VARCHAR2(20)Carb_commonName: VARCHAR2(20)Carb_Family: VARCHAR2(20)Carb_Subfamily: VARCHAR2(20)Carb_Type: VARCHAR2(10)Carb_MW: NUMBERBiofunction_key: NUMBERCarb_BiofunctionDesc: VARCHAR2(100)Carb_listdate: DATECarb_structure: VARCHAR2(500)Carb_structureImgtype: VARCHAR2(10)Carb_structureImg: BLOBAccess_code: VARCHAR2(20)
DNASEQ
DNASEQ_key: INTEGER
Gene_key: INTEGERDNASEQ_ID: VARCHAR2(20)DNASEQ_IDtype: VARCHAR2(20)DNASEQ_sequence: VARCHAR2(20)
GENE
Gene_key: INTEGER
Genome: VARCHAR2(20)Gene_name: VARCHAR2(20)biosource_key: INTEGER
PAPER
Paper_key: NUMBER
Paper_ID: VARCHAR2(20)ID_type: VARCHAR2(20)Paper_title: VARCHAR2(200)Paper_year: INTEGERJournal_name: VARCHAR2(200)Page_range: VARCHAR2(20)
PAPER_REFERENCE
Paper_key: NUMBERCarb_key: INTEGER
PROTEIN
Protein_key: INTEGER
Protein_ID: VARCHAR2(20)ProteinID_type: VARCHAR2(20)Protein_name: VARCHAR2(20)Protein_CommonName: VARCHAR2(20)Protein_family: VARCHAR2(20)Protein_subFamily: VARCHAR2(20)Protein_superUnitKey: INTEGERProtein_type: VARCHAR2(20)Biosource_key: INTEGERBiofunction_key: INTEGERGene_key: VARCHAR2(20)DNASEQ_key: INTEGERProtein_sequenceKey: INTEGERProtein_biofunctionDesc: VARCHAR2(20)Access_code: VARCHAR2(20)Protein_listdate: DATE
PROTEINSEQUENCE
Protein_sequenceKey: INTEGER
Protein_sequence: VARCHAR2(20)Protein_key: INTEGER
REAGENT
Reagent_key: INTEGER
Reagent_ID: VARCHAR2(20)Reagent_IDtype: VARCHAR2(20)Reagnet_name: VARCHAR2(20)Reagent_formula: VARCHAR2(20)Reagent_MW: INTEGER
CPBINDING
Cpb_key: NUMBER
Cpb_ID: VARCHAR2(20)Cpb_IDtype: VARCHAR2(20)Carb_key: NUMBERProtein_key: NUMBERCpb_flag: CHAR(1)Biofunction_key: NUMBERCpb_BiofunctionDesc: VARCHAR2(100)Cpb_Keq: NUMBERCpb_DG: NUMBERCpb_DH: NUMBERCpb_DS: NUMBERCpb_listdate: DATE
PROTOCOL
Protocol_key: INTEGER
Protocol_ID: VARCHAR2(20)Protocol_Category: VARCHAR2(20)Protocol_keyword: VARCHAR2(20)Protocol_Title: VARCHAR2(20)Protocol_overview: VARCHAR2(20)Protocol_procedure: CHAR(18)Protocol_trobleshooting: VARCHAR2(20)Dbuser_key: INTEGER
CPATHREAGENT
Protocol_key: INTEGERReagent_key: INTEGER
Reactant_Weightg: INTEGERReactant_mmol: VARCHAR2(20)
CPATHINSTRUMENT
Protocol_key: INTEGERInstrument_key: INTEGER
INSTRUMENT
Instrument_key: INTEGER
Instrument_category: VARCHAR2(20)Instrument_name: VARCHAR2(20)Instrument_model: VARCHAR2(20)Instrument_Vender: VARCHAR2(20)
CARBPROFILE
Carbprofile_key: NUMBER
Carbprofile_ID: VARCHAR2(20)Carbprofile_title: VARCHAR2(30)Carbprofile_carbComp: VARCHAR2(200)Carbprofile_avgMW: NUMBERMouseind_key: NUMBERCarbprofile_source: VARCHAR2(100)Biofunction_key: NUMBERCarbprofile_biofunctionDesc: VARCHAR2(200)Parentprofile_ID: VARCHAR2(20) CPROFILEID
Carbprofile_key: NUMBERCarb_key: INTEGER
Concentration: VARCHAR2(20)CPROFILEEXP
Cpexp_key: INTEGER
cpexp_ID: VARCHAR2(20)cpexp_title: VARCHAR2(20)Protocol_key: INTEGERCarbprofile_key: NUMBERCpexp_keyword: VARCHAR2(20)Cpexp_instrument: VARCHAR2(20)Cpexp_date: DATECpexp_comment: VARCHAR2(20)Dbuser_key: INTEGER
MICROARRAY
Marray_key: INTEGER
Marray_ID: VARCHAR2(20)Marray_type: VARCHAR2(20)Marray_desc: VARCHAR2(20)Marray_imgtype: VARCHAR2(20)Marray_img: BLOB
MOUSESTRAIN
Mouse_key: INTEGER
Mouse_ID: VARCHAR2(20)Cell_key: NUMBERMouse_type: VARCHAR2(20)Protocol_key: INTEGERMouse_keyword: VARCHAR2(20)Mouse_desc: VARCHAR2(20)
KOGENE
KOgene_key: INTEGER
KOgene_ID: VARCHAR2(20)Mouse_key: INTEGERGene_key: INTEGERGene_ID: VARCHAR2(20)KOgene_synonym: VARCHAR2(20)KOgene_Mtype: VARCHAR2(20)KOgene_UnigenDes: VARCHAR2(20)KOgene_HumanGene: VARCHAR2(20)
CELLSOURCE
Cell_key: NUMBER
Cell_ID: VARCHAR2(20)biosource_key: NUMBERCell_line: VARCHAR2(30)Cell_linetype: VARCHAR2(20)Cell_tissue: VARCHAR2(20)Cell_Organ: VARCHAR2(20)
MAEXP
Maexp_key: INTEGER
Maexp_ID: VARCHAR2(20)Maexp_title: VARCHAR2(20)Protocol_key: INTEGERMarray_key: INTEGERMaexp_SampleID: VARCHAR2(20)Maexp_SampleDesc: VARCHAR2(20)Maexp_keyword: VARCHAR2(20)Maexp_readtype: VARCHAR2(20)Maexp_raw: VARCHAR2(20)Maexp_date: DATEMaexp_imgfiletype: VARCHAR2(20)Maexp_imgraw: BLOBDbuser_key: INTEGER
TARGETGENE
Maexp_key: INTEGERGene_key: INTEGER
Targetgene_desc: VARCHAR2(20)
PROTIENREF
Paper_key: NUMBERProtein_key: INTEGER
CARBPATHREF
Paper_key: NUMBERCpath_key: INTEGER
PROTOCOLREF
Paper_key: NUMBERProtocol_key: INTEGER
CPBREF
Paper_key: NUMBERCpb_key: NUMBER
DBUSER
Dbuser_key: INTEGER
Dbuser_username: VARCHAR2(20)Dbuser_password: VARCHAR2(20)Dbuser_lastname: VARCHAR2(20)Dbuser_firstname: CHAR(18)Dbuser_email: VARCHAR2(20)Dbuser_employer: VARCHAR2(20)Dbuser_title: VARCHAR2(20)Dbuser_Core: VARCHAR2(20)Dbuser_listdate: DATE
MOUSEHEMA
MH_key: INTEGER
MH_ID: VARCHAR2(20)Mouseind_key: INTEGERMH_date: DATEMH_age: INTEGERMH_weight: INTEGERMH_WBC: INTEGERMH_Neutrophils: INTEGERMH_Lymphocytes: VARCHAR2(20)MH_HGB: INTEGERMH_HCT: INTEGERMH_PLT: INTEGERMH_MPV: INTEGERDbuser_key: INTEGER
MOUSEHISTOLOGY
MHS_key: INTEGER
MHS_ID: VARCHAR2(20)Mouseind_key: INTEGERMHS_date: DATEMHS_age: INTEGERMHS_weight: INTEGERProtocol_key: INTEGERMHS_purpose: VARCHAR2(20)MHS_result: VARCHAR2(20)MHS_comment: VARCHAR2(20)Dbuser_key: INTEGER
MOUSEIMMU
MI_key: INTEGER
MI_ID: VARCHAR2(20)Mouseind_key: INTEGERMI_date: DATEMI_age: INTEGERMI_weight: INTEGERMI_sampletype: VARCHAR2(20)MI_CD4: INTEGERMI_CD8: INTEGERB220: INTEGERIAB: INTEGERIgM: INTEGERIgD: INTEGERDbuser_key: INTEGER
MOUSEIND
Mouseind_key: INTEGER
MIND_ID: VARCHAR2(20)Mouse_key: INTEGERMind_sex: VARCHAR2(20)
MOUSEBEHAV
MB_key: INTEGER
MB_ID: VARCHAR2(20)Mouseind_key: INTEGERMB_date: DATEMB_age: INTEGERMB_weight: INTEGERMB_GrossNero: VARCHAR2(20)MB_SensorMotorReflex: VARCHAR2(20)MB_PosturalReflex: VARCHAR2(20)MB_motoractivity: VARCHAR2(20)MB_Nocieption: VARCHAR2(20)MB_AcousticStartle: VARCHAR2(20)MB_SocialDomine: VARCHAR2(20)MB_conditionedFear: VARCHAR2(20)MB_waterMaze: VARCHAR2(20)MB_radialArmMaze: VARCHAR2(20)Dbuser_key: INTEGER
MOUSEMETABOLISM
MM_key: INTEGER
MM_ID: VARCHAR2(20)Mouseind_key: CHAR(18)MM_date: DATEMM_age: INTEGERMM_weight: INTEGERMM_Cardiac: VARCHAR2(20)MM_BloodDiastol: INTEGERMM_bloodSystol: INTEGERMM_plumonary: VARCHAR2(20)MM_FoodConsumption: INTEGERMM_waterConsumption: INTEGERMM_activityLevel: INTEGERMM_OxygenConsumption: INTEGERMM_CO2Output: INTEGERMM_HeatOutput: INTEGERDbuser_key: INTEGER
MAREF
Marray_key: INTEGERPaper_key: NUMBER
ENZYME
Enzyme_key: INTEGER
Enzyme_ID: VARCHAR2(20)Enzyme_type: VARCHAR2(20)Enzyme_name: VARCHAR2(20)Enzyme_CommonName: VARCHAR2(20)Enzyme_family: VARCHAR2(20)Enzyme_subFamily: VARCHAR2(20)biosource_key: INTEGERBiofunction_key: INTEGEREnzyme_biofunctionDesc: VARCHAR2(20)Gene_key: VARCHAR2(20)DNASEQ_key: INTEGEREnzyme_sequenceKey: INTEGERProteindb_ID: VARCHAR2(20)SwissPort_ID: VARCHAR2(20)Access_Code: VARCHAR2(20)Protein_listdate: DATE
CARBPATHWAY
Cpath_key: INTEGER
Cpath_name: VARCHAR2(20)Carb_key: INTEGEREnzyme_key: INTEGERCpath__Reaction: VARCHAR2(20)Cpath_condition: VARCHAR2(20)Cpath_stepFromCarb: INTEGERCpath_yield: INTEGER
ENZYMESEQUENCE
Enzyme_sequenceKey: INTEGER
Enzyme_sequence: VARCHAR2(20)Enzyme_key: INTEGER
CARBEXP
Carbexp_key: INTEGER
carbexp_ID: VARCHAR2(20)carbexp_title: VARCHAR2(30)Protocol_key: NUMBERCarb_key: NUMBERCarbexp_keyword: VARCHAR2(100)Carbexp_Instrument: VARCHAR2(100)Carbexp_comment: VARCHAR2(200)Carbexp_date: DATECabexp_batchno: VARCHAR2(20)User_key: NUMBER
CARBEXPIMG
carbExpImg_key: INTEGER
Carbexp_key: NUMBERCarbExpImg_exptype: VARCHAR2(20)CarbExpImg_filetype: VARCHAR2(20)CarbExpImg_imageRaw: BLOB
CPBEXP
Cpbexp_key: NUMBER
cpbexp_ID: VARCHAR2(20)cpbexp_title: VARCHAR2(20)Protocol_key: INTEGERCpb_key: NUMBERCpbexp__keyword: VARCHAR2(20)Cpbexp_Instrument: VARCHAR2(20)Cpbexp_date: DATECpbexp_comment: VARCHAR2(20)Dbuser_key: INTEGER
CPBEXPIMG
cpbExpImg_key: INTEGER
Cpbexp_key: NUMBERCpbexpImg_exptype: VARCHAR2(20)CpbexpImg_imageRaw: BLOBCpbexpimg_desc: VARCHAR2(20)CpbexpImg_filetype: VARCHAR2(20)
CPROFILEEXPIMG
cpexpImg_key: INTEGER
Cpexp_key: INTEGERCpexpImg_exptype: VARCHAR2(20)CpexpImg_filetype: VARCHAR2(20)CpexpImg_imageRaw: BLOBCpexpImg_desc: VARCHAR2(20)
MAEXPANALYSIS
Maexpanaly_key: INTEGER
Maexp_key: INTEGERMaexpanaly_title: VARCHAR2(100)Maexpanaly_desc: VARCHAR2(500)
CBPEXP
Cbpexp_key: INTEGER
Cbpexp_ID: VARCHAR2(20)Cbpexp_title: VARCHAR2(20)Protocol_key: INTEGERProtein_key: INTEGERCbpexp_keyword: VARCHAR2(20)Cbpexp_Instrument: VARCHAR2(20)Cbpexp_comment: VARCHAR2(20)Cbpexp_date: DATEDbuser_key: INTEGER
ENZEXPIMG
EnzexpImg_key: INTEGER
Enzexp_key: INTEGEREnzexpImg_exptype: VARCHAR2(20)EnzexpImg_filetype: VARCHAR2(20)EnzexpImg_imageRaw: BLOB
ENZEEXP
Enzexp_key: INTEGER
Enzexp_ID: VARCHAR2(20)Enzexp_title: VARCHAR2(20)Protocol_key: INTEGEREnzyme_key: INTEGEREnzexp_keyword: VARCHAR2(20)Enzexp_Instrument: VARCHAR2(20)Enzexp_comment: VARCHAR2(20)Enzexp_date: DATEUser_key: INTEGER
CBPEXPIMG
CbpexpImg_key: INTEGER
Cbpexp_key: INTEGERCbpexpImg_exptype: VARCHAR2(20)CbpexpImg_filetype: VARCHAR2(20)CbpexpImg_imageRaw: BLOB
GLYCOARRAY
Garray_key: INTEGER
Garray_ID: VARCHAR2(20)Garray_type: VARCHAR2(20)Garray_desc: VARCHAR2(20)Garray_imgtype: VARCHAR2(20)Garray_img: BLOB
GAEXP
Gaexp_key: INTEGER
Gaexp_ID: VARCHAR2(20)Gaexp_title: VARCHAR2(20)Protocol_key: INTEGERGarray_key: INTEGERGaexp_SampleID: VARCHAR2(20)Gaexp_SampleDesc: VARCHAR2(20)Gaexp_keyword: VARCHAR2(20)Gaexp_readtype: VARCHAR2(20)Gaexp_raw: VARCHAR2(20)Gaexp_date: DATEGaexp_imgfiletype: VARCHAR2(20)Gaexp_imgraw: BLOBDbuser_key: INTEGER
TARGETPROTEIN
Gaexp_key: INTEGERProtein_key: INTEGER
Targetcbp_desc: VARCHAR2(20)
CPATHEXP
Cpathexp_key: INTEGER
Cpathexp_ID: VARCHAR2(20)Cpathexp_title: VARCHAR2(20)Cpath_key: INTEGERProtocol_key: INTEGERCpathexp_keyword: VARCHAR2(20)Cpathexp_Instrument: VARCHAR2(20)Cpathexp_comment: VARCHAR2(20)Cpathexp_date: DATEUser_key: INTEGER
CPATHEXPIMG
CpathexpImg_key: INTEGER
Cpathexp_key: INTEGERCpathexpImg_exptype: VARCHAR2(20)CpathexpImg_filetype: VARCHAR2(20)CpathexpImg_imageRaw: BLOB
CARBINVENTORY
Carbinv_key: NUMBER
Carbinv_ID: VARCHAR2(20)Carb_key: NUMBERCarbexp_key: VARCHAR2(20)Carbinv_Purity: NUMBERCarbinv_color: VARCHAR2(10)Carbinv_State: VARCHAR2(10)Quantity: NUMBERCarbexp_batchno: VARCHAR2(20)
CARBORDER
Corder_key: NUMBER
Corder_ID: VARCHAR2(20)Corder_date: DATECarbinv_key: NUMBEROrder_receiver: VARCHAR2(50)Order_address: VARCHAR2(200)Order_quantity: NUMBERshipping_flag: CHAR(1)
Part of CFG database overall ontology map
- Communicates with database and user- Keeps the complexity of the database Invisible from user interface - Enables seamless acquisition and dissemination of data
- Top-most layer of user interface- Static pages for web site management- Dynamic pages for database driven content
Data IntegrationOverall Schema for CFG Data Objects
Data IntegrationOverall Schema for CFG Data Objects
Data IntegrationApproach to Functional Glycomics
Data IntegrationApproach to Functional Glycomics
Glycan profile of spleen of FucT-VII KO mice with differences in histology staining
Data IntegrationApproach to Functional Glycomics
Data IntegrationApproach to Functional Glycomics
Expression of glycan related genes in wildtype mouse spleen
Molecule Page InterfaceMolecule Page Interface
Automated AcquisitionData from Public databases,
links to Public resources
Data from CoresInterface to CFG
resources and data
Expert Contribution
Filling out fields as experts on the molecule
MoleculeInformation
Portal
Comprises of three main components
GBP Molecule PageGBP Molecule Page
Galectin family chosen
Galectin-3 Molecule PageGalectin-3 Molecule Page
Galectin-3selected
Molecule Page of Galectin-3: General Tab
Galectin-3 Molecule PageGalectin-3 Molecule PageReference Tab: Links to Public Databases
Galectin-3 Molecule PageGalectin-3 Molecule Page
Link to CFG Transgenic mice
Genome Tab
Galectin-3 Molecule PageGalectin-3 Molecule Page
Proteome TabDomain Organization
Galectin-3 Molecule PageGalectin-3 Molecule Page
Glycome TabLink to CFG Glycan Array Data
Select High Signal Spot
Link from high affinity glycan to GBP molecule page
Link to glycan structure corresponding to high affinity ligand of GBP
Galectin-3 Molecule PageGalectin-3 Molecule Page
Biology Tab
Links to CFG Phenotyping dataon Galectin-3 KO mice
Histological Staining Data
Immunology Data
Metabolism Data
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