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