Bioinformatics Platform Three-tier Architecture Object-based Relational Database implemented using...
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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