The AfCS Bioinformatics Laboratory 2002. The AfCS Data Coordination and Bioinformatics Laboratory 2002 Goal 1 Acquire, Process, and Disseminate Information

The AfCS Bioinformatics Laboratory

2002

The AfCS Data Coordination and Bioinformatics Laboratory

2002

Goal 1

Acquire, Process, and Disseminate Information

The AfCS Website (www.afcs.org)

2002

WebMaster: Stephen Lyon

Web related design:

Stephen Lyon

Brad Kroeger

Dawn Cotter

Timo Hannay (NPG)

The AfCS Website (www.afcs.org)

2002

Website Users• Anonymous Public

• Registered Public

• AfCS Personnel

• Content Contributors

• Website Developers

Website Developers•Overall Development

•Molecule Pages

•Protein Lists

•Experimental Data

•Reports

•Database Search Utilities

The AfCS Website

2002

Website Content

Public Areas•About AfCS•Data•Home•Login•Membership•Molecule Pages•Protein Lists•Protocols•Reports•Signaling Maps•Sponsors

Restricted Areas•Access Control Administration•Protein List Administration•E-mail Aliases•Progress Reports

•View•Upload

•System Committees•Message Boards•Barcode•Data•DataScope

AfCS Website Content

2002

HTTP request from user

HTTP response from server

Apache mod_perl

Static HTML

Perl CGI

Java servlets

Oracle database

Access Control Layers

1. Web server layer:General access control for all users of the website

2. Application layer:More specific access control and personalization for users of each application (username can be read from cookie set by Layer 1)

3. Database layer:Database gives different access privileges to each application

Overview of Access Control Layers

2002

UserRequest

Dynamic Pages

Dynamically GeneratedStatic Pages

Static PagesWebServer

Access Check

User Database

Program Access Check

Page Types & Access Control

2002

The primary purpose of the bulletin board is to facilitate the exchange of ideas, documents and data between Alliance members and provide the public a forum for providing feed back.

AfCS Bulletin Board

2002

• Posting featuresdefine by the board administrator or moderator

• Security featuresdefined by the board administrator or moderator

• Formatting featuresuser controlled

• User profile featuresdefined by the user board administrator

• Searching features

AfCS Bulletin Board

2002

2002

Topic Views

On line documentation

Search and administration

2002

2002


2002

Goal 2

Design and Develop a Laboratory Information Management System

Lothar Krause

Madhusudan

Lonnie Sorrels (SWMED)

Ron Taussig (SWMED)

Dallas Expt. Lab.

Yuhong Ning

Ilango Vadivelu

Peter Morrison

AfCS Barcode/LIM System

2002

Facilitate Sample Tracking

Standardize Data Inputs/Outputs

Automate Data Transfer between Labs

Maintain Data Integrity

AfCS Barcode/LIM System

2002

AfCS Data Flow

2002

Inputs Cell Prep ID and yields unique treatment and sample IDs. This application also requires a protocol that is tied to the assay for which the sample is created, e.g. Western, Microarray etc. It captures the treatment details including incubation conditions, cell density, ligand and its concentration and time of exposure.

This GUI also functions as a query tool. By entering an ID into the ‘Experiment ID’ and clicking on ‘barcode’, it re-loads the data previously submitted for that ID.

Treatment GUI

2002

Treatment GUI

2002

TREATMENTEXP

PROTOCOLIDTREATMENTEXPIDCELLPREPIDDESIGNERSUBMISSIONDATELABCO2TEMPERATUREMEDIUMCULTURECOMMENTSUSERDATEDISHMATRIXPLATING_DENSITYTARGETPURPOSE

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)NUMBERDATEVARCHAR2(10)VARCHAR2(10)NUMBERVARCHAR2(100)VARCHAR2(100)VARCHAR2(1000)DATEVARCHAR2(12)VARCHAR2(24)NUMBERNUMBER(3)VARCHAR2(50)

<fk2><pk><fk3><fk1>

REAGENT

USERIDCONCENTRATIONUNITCONCENTRATIONREAGENTNAMEREAGENTIDLOTNOCOMMENTSSTDCONCENTRATIONSUBMISSIONDATECHEMICALIDPRICEPRICE_UNITSTORAGECONDITIONPROTOCOLID

NUMBERVARCHAR2(20)NUMBERVARCHAR2(100)VARCHAR2(12)VARCHAR2(30)VARCHAR2(200)VARCHAR2(10)DATEVARCHAR2(12)NUMBERVARCHAR2(10)VARCHAR2(50)VARCHAR2(12)

<fk3>

<pk>

<fk2>

<fk1>

CELLPREP

CELLPREPIDUSERIDLABTECHPREPDATEPROTOCOLIDPREPNUMBERMOUSEID1MOUSE1AGEMICE1USEDTOTALMICEUSEDSTARTTIMESTOPTIMEDURATIONDURATIONINMINUTESRBC_LYSISBUFVOLRBC_LYSISBUFREFIDPRESORT_VOLPRESORT_GRIDSCOUNTEDPRESORT_GRIDAREAFACTORPRESORT_CELLSCOUNTEDPRESORT_DILUTIONFACTOR

VARCHAR2(12)NUMBERVARCHAR2(1)VARCHAR2(80)DATEVARCHAR2(12)VARCHAR2(3)VARCHAR2(20)NUMBERNUMBERNUMBERDATEDATEVARCHAR2(15)NUMBERFLOATVARCHAR2(20)FLOATNUMBERNUMBERNUMBERFLOAT

<pk><fk>

GENERICSAMPLE

SAMPLEIDUSERIDTREATMENTIDPREINCUBATIONTIMETREATMENTEXPIDTYPESTEPNUMSTATUS

VARCHAR2(13)NUMBERNUMBERNUMBERVARCHAR2(12)NUMBERNUMBERVARCHAR2(1)

<pk><fk1>

<fk2>

TREATMENTDETAIL

DETAILIDTIMESTOPTIMESTARTINCUBATIONTIMECONCENTRATIONCONCENTRATIONUNITEXPOTIMEREAGENTIDCONDITIONOTHERTREATMENT

NUMBERNUMBERNUMBERVARCHAR2(50)NUMBERVARCHAR2(50)NUMBERVARCHAR2(20)VARCHAR2(100)VARCHAR2(30)

<pk>

TREATMENT

STEPNUMDETAILIDDETAILTYPETREATMENTID

NUMBERNUMBERVARCHAR2(30)NUMBER

<pk><fk>

<pk>

Treatment Tables

2002

Barcode GUI

2002

Reagent GUI Barcode

Ligand GUI Barcode

Solution GUI Barcode

Protocol GUI Printed protocol with barcode

Protocols: Interaction of the GUIs

2002

Protocol GUI

2002

Solution GUI

2002

REAGENT

USERIDCONCENTRATIONUNITCONCENTRATIONREAGENTNAMEREAGENTIDLOTNOCOMMENTSSTDCONCENTRATIONSUBMISSIONDATECHEMICALIDPRICEPRICE_UNITSTORAGECONDITIONPROTOCOLID

NUMBERVARCHAR2(20)NUMBERVARCHAR2(100)VARCHAR2(12)VARCHAR2(30)VARCHAR2(200)VARCHAR2(10)DATEVARCHAR2(12)NUMBERVARCHAR2(10)VARCHAR2(50)VARCHAR2(12)

<fk3>

<pk>

<fk2>

<fk1>

CHEMICAL

IDNAMEFORMULABARCODEDTYPEABBREVMWVENDORIDCATALOGNODESCRIPTIONALTNAMESDESIGNATOR

VARCHAR2(12)VARCHAR2(100)VARCHAR2(100)CHARVARCHAR2(20)VARCHAR2(50)NUMBERVARCHAR2(12)VARCHAR2(30)VARCHAR2(100)VARCHAR2(100)VARCHAR2(3)

<pk>

<fk>

LIGAND

LIGANDIDSOLVENTSOL_VOLSOL_VOL_UNITRECEPTORS

VARCHAR2(12)VARCHAR2(30)FLOATVARCHAR2(5)VARCHAR2(200)

<pk,fk>ANTIBODY

ANTIBODYIDLCHAIN_MWHCHAIN_MWMONO_POLYCONJUGATESPECIESORIGINCOMMENTSUTILITYIGCLASSIMMUNOGENAFCSNOAASEQRECOGNIZED_RANGEPRIM_SEC

VARCHAR2(12)FLOATFLOATVARCHAR2(5)VARCHAR2(20)VARCHAR2(10)VARCHAR2(20)VARCHAR2(200)VARCHAR2(100)VARCHAR2(20)VARCHAR2(75)VARCHAR2(30)VARCHAR2(500)VARCHAR2(50)VARCHAR2(5)

<pk,fk>

LIGAND_LOOKUP

LIGANDNAMEABBREVIATIONRECEPTORRECEPTOR_COMMONNAMEPRIORITYDESCRIPTIONSOURCECATALOGNOUNITPRICEIDCHEMICALIDVENDORIDLIGANDSCREEN

VARCHAR2(60)VARCHAR2(10)VARCHAR2(200)VARCHAR2(200)VARCHAR2(1)VARCHAR2(500)VARCHAR2(50)VARCHAR2(50)VARCHAR2(30)NUMBER(15)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)CHAR

SOLUTION_CONSTITUENT

SOLUTIONIDSTEPNUMCOMPONENTIDCOMPONENTTYPE

VARCHAR2(12)NUMBERVARCHAR2(12)VARCHAR2(20)

<pk,fk><pk>

VENDOR

PHONEEMAILFAXURLVENDORIDNAMEADDRESSVISIBLE

VARCHAR2(20)VARCHAR2(50)VARCHAR2(20)VARCHAR2(100)VARCHAR2(12)VARCHAR2(100)VARCHAR2(200)CHAR

<pk>

Reagent, Ligand & Solution Tables

2002


2002

Goal 3

Create Efficient Internet Sites for Deposition, Inspection, and Utilization of Primary and Processed Data

2002

AfCS Data Store

2002

Robert Sinkovits

Dennis Mock

Brad Kroeger

Chic Barna

Richard Schuermann (Visitor)

Yuhong Ning

• Data transfer from Dallas/Caltech SDSC

• Parsing of transfer log files to identify new data

• Parsing of data files / database loading• Generation of graphics, tables, etc.• Displaying results for ligand/assay• Data Curation• Update of ligand screen page• Ligand descriptions

Data handling

2002

• Set of four cron jobs (microarray,cAMP, Ca++,Western blot) run each night. Names of newly uploaded files passed as arguments to loader scripts.

• Log files created so that experiment schemas can be easily repopulated

auto-ftp log

western master

Ca master

cAMP master

micro master

western loader

Ca loader

cAMP loader

micro loader

western@afcs

Ca@afcs

cAMP@afcs

micro@afcs

Parsing log files / loading db

2002

• Scripts generate libraries of static images, html, tab-delimited files. Data pulled from experiment and barcode schemas

• Ligand screen data directories purged and reloaded with new graphics, etc.

western@afcs

Ca@afcs

cAMP@afcs

micro@afcs

barcode@afcs

western process

Ca process

cAMP process

micro process

data/western

data/Ca

data/cAMP

data/micro

Graphics generation

2002

• Argument passed to CGI script to specify graphics, etc. to be displayed

cal_ligscr.cgi

data/Ca

AIG_0.3_uM_BC

Text, graphics, links, etc. for Ca

assay 0.3 uM anit-Ig using B

cells

Display

2002

Ligand screen display (partial)

2002

Ca++ display

Automatically generated graph of Ca++ time courses for B cells treated with Antigen (Anti-Ig). Curves color coded by experiment.

2002

cAMP display

Automatically generated bar graph of cAMP assays for B cells treated with Prostaglandin E2.

2002

Western blot display

Automatically generated graph of phosphoprotein immunoblot results for B cells treated with CD40 Ligand.

2002

Western blot display

Automatically generated graph of phosphoprotein immunoblot results for B cells treated with IL-4. Large pSTAT6 response plotted on right axis.

2002

cDNA display

Clicking on cluster returns annotation for all clones belonging to cluster

2002

cDNA Analysis Interface

2002

• Array display and analysis for AfCS Members

SWMED SDSC server

graphicslog data

cal_master.pl

cal_loader.plcal schema

cal_graph.plbarcode schema

curate.cgi

cal_disp.cgi

internal.htmlpublic.html

display.html

SRB

Data flow overview: Ca++

2002


2002

Goal 4

Design and Implement the Infrastructure for Molecule Pages Database

2001

Joshua Li

Yuhong Ning

Warren Hedley

Brian Saunders

TBK Reddy (BW)

Andrea Maer (BW)

Yousheng Chen

Derren Barken (UCSD)

Timo Hannay (NPG)

Nicole Tindill (NPG)

& Dallas AfCS Team

The AfCS Molecule Pages

2002

• A comprehensive literature-derived, object-relational database of signaling molecules

• Distributed data entry by experts • Link to AfCS experimental data• A dynamic source of protein interactions with

genomic and domain data from other databases• Definition of the “Functional State” of each

signaling protein

2001

MP Features

2002

• The author is responsible for entering information about– AfCS protein’s functional states – Interactions of their protein with other

proteins, and small molecules– Mutations of the protein, and their

consequences and/or phenotypes– Relevant experimental information

Molecule Pages – Author-Entered Data

2002

• “Automated Data” for each protein is provided to both the public and the authors, and can be referenced by the author when entering their own data

• The types of automated data made available will include:– Summaries of and links to external database records

that correspond to, or are related to, the author’s protein

• (e.g., Genbank, SwissProt and PDB records)

Molecule Pages – Automated Data

2002

• The Molecule Pages website is generated by a 3-tier application

• The web and middle tiers are Enterprise Java application running on the “Oracle Components 4 Java (OC4J)” application server

• The database tier is Oracle 8.1.7

System Architecture

2002

Oracle 8i/9i database object-relational database

Java procedures/ EJB(back-end)

Oracle AS 9iEJB

Servelets/JSP(m iddle-tier)

Brow serthin client

HTM L/XML (Servlet/JSP)(front-end )

AM Pthree-tier Infrastructure

(on SUN Servers)

2001

Molecule Pages Multi-Tier Infrastructure

2002

Ontology: Ontology in the database world associates definition and knowledge about objects contained in the database. The knowledge pertains to properties of the object and its relationships to other objects coded as tables or indexes.

E.g., Ion channel:

Object properties: sequence, structure, gating, kinetic…etc.

Relationships: other channels, physiology, cell locations, diseases…etc.

Ontology

2002

FK_PEPTIDE_REFERENCE_ANTIGENFK_ANTIGEN__REFERENCE_ANTIGEN

FK_PROT_ANT_REFERENCE_ANTIGEN

FK_ANTIBODY_REFERENCE_ANTIGEN

FK_ANTIBODY_REFERENCE_ANTIBODY


FK_ANTIBODY_REFERENCE_SPECIES


FK_ANTIGEN_REFERENCE_ANTIGEN_

ANTIGEN

ANTIGEN_IDENTRY_IDANTIGEN_TYPE

VARCHAR(12)VARCHAR(12)VARCHAR(12)

<pk>

<fk>

ANTIGEN_SITE

ANTIGEN_SIITE_IDANTIGEN_IDSEQ_ENDSEQ_STARTANTIBODY_IDDOMAIN_ID

VARCHAR(12)VARCHAR(12)NUMBERNUMBERVARCHAR(12)VARCHAR(50)

<pk><fk>

PROT_ANTIGEN

PV_IDSTATEIDANTIGEN_ID

VARCHAR(12)VARCHAR(12)VARCHAR(12)

<pk><pk><pk,fk>

PEPTIDE

PEPTIDE_IDPEPTIDE_NAMEPEPTIDE_SYN_LISTPEPTIDE_SEQANTIGEN_IDNOTE

VARCHAR(12)VARCHAR(50)VARCHAR(300)VARCHAR(3000)VARCHAR(12)VARCHAR(300)

<pk>

<fk>

ANTIBODY

ANTIGEN_IDANTIBODY_SPANTIBODY_NAMEMONOCLONAL_FLAGNOTEANTIBODY_UTILITYANTIBODY_TYPEANTIBODY_IDSPECIES

VARCHAR(12)VARCHAR(12)VARCHAR(55)CHAR(1)VARCHAR(300)VARCHAR(25)VARCHAR(12)VARCHAR(12)VARCHAR(12)

<fk1><fk3>

<fk2><fk5><pk><fk4>

ANTIBODY_UTILITY

ANTIBODY_UTILITYDESCRIPTION

VARCHAR(12)VARCHAR(300)

<pk>

ANTIBODY_SPECIFICITY

ANTIBODY_SPDESCRIPTION


<pk> ANTIBODY_TYPE

ANTIBODY_TYPEDESCRIPTION


<pk>

SPECIES

SPECIESDESCRIPTION


<pk>link to the

protein and state tables

entry_id is fortien key to

l ink to the entry table

ANTIGEN_TYPE

ANTIGEN_TYPEDESCRIPTION


<pk>

Database schema for antibody

2002

PhysicalData

Model for

Molecule Pages

REF

REF_IDJ_ABBREVENTRY_IDTITLEREF_CREATORREF_TYPEAFCS_KEYWORDSUBJECTABSTRACTCONTRIBUTORSTART_PAGEEND_PAGEVOLISSUEPUBLICATION_DATEREF_FORMATLANGUAGEIDENTIFIER

VARCHAR2(12)VARCHAR2(25)VARCHAR2(12)VARCHAR2(95)VARCHAR2(95)VARCHAR2(25)VARCHAR2(55)VARCHAR2(95)VARCHAR2(3000)VARCHAR2(55)NUMBER(5)NUMBER(5)NUMBER(10)NUMBER(10)VARCHAR2(25)VARCHAR2(5)VARCHAR2(25)VARCHAR2(55)

<pk><fk1><fk2>

PROTEIN

PV_IDSPECIESMUTANT_TYPEPROT_IDAFCS_PIDPROTEIN_NAMEPROT_SYNONYMVERSIONSTATUS_FLAGSUBMIT_DATEAPPROVED_DATEAPPROVED_BYDISULFIDE_NUMBERNOTEGENBANK_ACCESSIONISOELECTRIC_POINTPROT_SEQPROT_MWIN_COMPLEX

VARCHAR2(12)VARCHAR2(25)VARCHAR2(12)VARCHAR2(12)VARCHAR2(25)VARCHAR2(75)VARCHAR2(300)VARCHAR2(10)VARCHAR2(5)DATEDATEVARCHAR2(55)NUMBER(10)VARCHAR2(300)VARCHAR2(12)NUMBER(10)CLOBNUMBER(10)VARCHAR2(5)

<pk><fk1><fk2>

MOLECULAR_FUNC

MOL_FUNC_IDUPPER_MOL_FUNC_IDMOL_FUNCMOL_FUNC_EVIDENCEMOL_FUNC_GO_ID

VARCHAR2(12)VARCHAR2(12)VARCHAR2(95)VARCHAR2(5)VARCHAR2(12)

<pk><fk>

CELL

CELL_IDCELLCELL_TYPE

VARCHAR2(12)VARCHAR2(95)VARCHAR2(55)

<pk>

TISSUE

TISSUETISSUE_TYPE

VARCHAR2(55)VARCHAR2(55)

<pk>

SPECIES

SPECIES VARCHAR2(25) <pk>

EXPRESSION

EXPRESSION_IDPV_IDMRNA_IDEXPRESSION_TYPEENTRY_IDEXPRS_OTHER NOTEEXPRS_TISSUEEXPRS_CELLEXPRS_SPECIES

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(300)VARCHAR2(300)VARCHAR2(55)VARCHAR2(55)VARCHAR2(25)

<pk><fk1><fk2><fk3><fk4>

DISTRIBUTION

DISTRIBUTION_IDCOMPONENTIDSPECIESMUTANT_EFFECTDETERMINING_SEQUENCENOTE

VARCHAR2(12)VARCHAR2(12)VARCHAR2(25)VARCHAR2(10)VARCHAR2(300)VARCHAR2(300)

<pk><fk1><fk2><fk3>

MANIPULATION

MANIPULATIONIDMANIPULATION_METHODENTRY_IDCHANGE_SCALEFUNC_CONSEQUENCENOTE


<pk><fk1><fk2>

DET_METHOD

DET_METHODIDENTRY_IDDET_METHOD


<pk><fk>

COVALENT_MODIFICATION

CVL_MODIFICATION_IDCVL_MODIFICATION_TYPEENTRY_IDCVL_MODIFICATION_NAMENOTE


<pk><fk1><fk2>

ANTIBODY

AFCS_RIDANTIBODY_IDENTRY_IDREA_NOTEANTIBODY_SOURCEANTIBODY_SPECIESMONOCLONAL_POLYCLONALANTIBODY_TYPEIMMUNOGEN_TYPESEQ_RESID_PROT_IMMUNOGENSEQ_PEPTIDE_IMMUNOGENUTILITY_TYPENOTELIGHT_CHAIN_MWHEAVY_CHAIN_MWTOTAL_MW

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(300)VARCHAR2(95)VARCHAR2(25)VARCHAR2(10)VARCHAR2(25)VARCHAR2(25)NUMBER(10)VARCHAR2(95)VARCHAR2(55)VARCHAR2(300)NUMBER(10)NUMBER(10)NUMBER(10)

<pk,fk2><pk><fk1>

REAGENT

AFCS_RIDSPECIESENTRY_IDASSAYREAGENT_TYPENOTE



CONCENTRATION

CONCENTRATION_IDCELL_IDCOMPONENTIDMUTANT_EFFECTORGANELLE_TYPECONCENTRATIONUNITNOTEMETHOD

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(10)VARCHAR2(12)NUMBER(10)VARCHAR2(10)VARCHAR2(300)VARCHAR2(95)


PROT_MUTATION

PROT_MUT_ IDPV_IDGENEIDCPD_MUTATION_IDPROT_TAGPROT_MUTATION_TYPEFUNC_CONSEQUENCENOTETYPE_CPD_OMUTATIONMUT_SPECIES

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(25)VARCHAR2(12)VARCHAR2(95)VARCHAR2(300)VARCHAR2(25)VARCHAR2(25)

<pk><fk1><fk2><fk3><fk4><fk5>

AUTHOR

AU_IDPASSWDFAMILY_NAMEGIVEN_NAMEINITIALHONORIFIC_SUFFIXHONORIFIC_PREFIXJOB_TITLERELEVANT_URIADDRESSCITYSTATECOUNTRYPOSTALCODEPHONEFAXEMAIL

VARCHAR2(10)VARCHAR2(10)VARCHAR2(40)VARCHAR2(40)VARCHAR2(5)VARCHAR2(5)VARCHAR2(5)VARCHAR2(25)VARCHAR2(95)VARCHAR2(80)VARCHAR2(20)VARCHAR2(25)VARCHAR2(25)NUMBER(10)NUMBER(10)NUMBER(10)VARCHAR2(25)

<pk>

TRANSGENIC

TRANSGENICIDPROT_MUT_ IDTRANSGENIC_NAMEHOMOZYGOUSSTRUCTURAL_TRANSGENEPROMOTEREXPRESSION_SOURCEPHENOTYPE_CONSEQUENCEPHENOTYPE_COMMENTPHENOTYPE_LINKFUNCTIONLINK_JACKSON

VARCHAR2(12)VARCHAR2(12)VARCHAR2(55)VARCHAR2(10)VARCHAR2(55)VARCHAR2(300)VARCHAR2(25)VARCHAR2(55)VARCHAR2(300)VARCHAR2(55)VARCHAR2(120)

<pk><fk>

INTERACTION_RESULT

INTERACTIONIDMUTANT_EFFECTINTERACTION_TYPEINTERACTION_PROPERTYFUNC_CONSEQUENCE


<pk><fk1><fk2>

MRNA

MRNA_IDGENEIDPV_IDMRNA_NAMEMRNA_LENGTHMRNA_SEQMRNA_MGDEMBL_IDRIKEN_IDMRNA_GI

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(25)NUMBER(10)CLOBVARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)

<pk><fk1><fk2>

PRODUCT

PRODUCTIDPRODUCT_NAMEPRODUCT_TYPE


<pk>

GENE

GENEIDSEQ_NAMECHROMOSOMEGENE_GIDNA_MGDFULL_DNA_GILOCUS_ID

VARCHAR2(12)VARCHAR2(95)VARCHAR2(300)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)

<pk>

Physical Data Model

Model: MP8c

Package:

Diagram: Mol Page DB_ MODEL_ v8a_ 2001

Author : joshuali Date : 10/4/01

Version :

REF_SUBJECT_LOOKUP

REF_SUBJECTSHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

REF_SUBJ

REF_SUBJ IDREF_IDPV_IDDET_METHODIDPROT_MUT_ IDINDUCING_MUTATIONIDEXPRESSION_IDAFCS_RIDANTIBODY_IDMANIPULATIONIDMRNA_IDREG_REGION_IDGENEIDREF_SUBJECTCVL_MODIFICATION_IDCPD_MUTATION_IDKNOCK_IDTRANSGENICIDCONCENTRATION_IDDISTRIBUTION_IDINTERACTIONIDENZ_INTERACTIONIDCHA_INTERACTIONIDREC_INTERACTIONID

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)

<pk><fk1><fk5><fk6><fk7><fk8><fk9><fk10><fk10><fk11><fk12><fk13><fk14><fk15><fk16><fk17><fk18><fk19><fk21><fk22><fk20><fk3><fk2><fk4>

CELLULAR_COMPONENT

COMPONENTIDUPPER_COMPONENTIDCELL_COMPONENTCELL_COMP_EVIDENCECELL_COMP_GO_IDCOMPONENT_SYNONYM


<pk><fk>

REGULATORY_REGION

REG_REGION_IDREG_REGION_TYPEREG_REGION_SEQREG_REGION_LOCATION

VARCHAR2(12)VARCHAR2(12)VARCHAR2(300)VARCHAR2(55)

<pk><fk>

MOTIF

MOTIF_IDWILD_MOTIFMUTANT_EFFECTPRINTSIDMOTIF_TITLEMOTIF_NOMOTIF_NAMEMOTIF_SEQMOTIF_LENGTHMOTIF_POSITIONMATCH_PCTPF_SCOREP_VALUE

VARCHAR2(12)VARCHAR2(12)VARCHAR2(10)VARCHAR2(12)VARCHAR2(95)NUMBER(10)VARCHAR2(55)VARCHAR2(300)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)

<pk><fk1><fk2>

RNA_EXON

RNA_EXONIDMRNA_IDGENE_EXONIDEXON_STARTEXON _END

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)NUMBER(10)NUMBER(10)

<pk><fk1><fk2>

INTRON

INTRON_IDGENEIDINTRON _STARTINTRON _END

VARCHAR2(12)VARCHAR2(12)NUMBER(10)NUMBER(10)

<pk><fk>

PROSTHETIC_GROUP

PROSTHETIC_IDBINDING_SITESPROSTHETIC_GROUP


<pk>

POINT

POINT_IDPROT_MUT_ IDOLD_AANAMENEW_AANAMEPOINT_POSITION

VARCHAR2(12)VARCHAR2(12)VARCHAR2(10)VARCHAR2(10)NUMBER(10)

<pk><fk>

INSERTION

INSERTION_IDPROT_MUT_ IDINSERTION_POSITIONINSERTED_SEQUENCE

VARCHAR2(12)VARCHAR2(12)NUMBER(10)VARCHAR2(990)

<pk><fk>

DELETION

DELETION_IDPROT_MUT_ IDPOSITION_STARTPOSITION_END


<pk><fk>

FUSION

FUSION_IDPROT_MUT_ IDTAG_POSITION_TYPEADDED_SEQ


<pk><fk1><fk2>

RECEPTOR_PARAM

INTERACTIONIDBIND_SITES_NOKDIC50EC50HILL_COEFFICIENTCONDITION_INFONOTE

VARCHAR2(12)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)VARCHAR2(300)VARCHAR2(300)

<pk,fk>

ENZYME_PARAM

INTERACTIONIDKINETIC_PATTERNKMAPPARENT_KMHILL_COEFFICIENTBIND_SITES_NOSUBSTRATE_CONCENTRATIONC_MAX_RATE_VMAXC_MAX_RATE_KCATENZYME_CONDITIONCONDITION_INFONOTE

VARCHAR2(12)VARCHAR2(25)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)VARCHAR2(95)VARCHAR2(300)VARCHAR2(300)

<pk,fk>

CHANNEL_PARAM

INTERACTIONIDIONIC_SELECTIVITYGAMMA_SUBCONDUCTI_V_CURVETAU_OPENTAU_CLOSEACTIVATION_GATINGINACTIVATION_GATINGLONIC_BLOCKREG_ANY_PARAMETERPARAMETER_NAMEPARAMETER_TYPEREG_PARAM_CONSEQFUNC_CONSEQUENCE

VARCHAR2(12)VARCHAR2(55)NUMBER(10)blobNUMBER(10)NUMBER(10)VARCHAR2(55)NUMBER(10)VARCHAR2(10)VARCHAR2(10)VARCHAR2(55)VARCHAR2(10)VARCHAR2(95)VARCHAR2(95)

<pk,fk>

SUBSTRATE

AFCS_RIDAFCS_SIDENTRY_IDSMALL_MOL_TYPENOTESUBSTRATECHEM_FORMULARSTRUCTURECHARGEMW

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(300)VARCHAR2(95)VARCHAR2(300)blobNUMBER(10)NUMBER(10)

<pk,fk3><pk><fk1><fk2>

PROT_CLEAVAGE

PROT_CLV_IDMUTANT_EFFECT

NUMBER(10)VARCHAR2(10)

<pk><fk>

KNOCK

KNOCK_IDPROT_MUT_ IDPV_IDPHENOTYPE_STATUSKNOCK_NAMEHOMOZYGOUSKNOCK_EVENTKOCONSTRUCTIS_CODE_SEQNONCODING_MUTATIONPHENOTYPE_FUNCTIONPHENOTYPE_LINKFUNCNOTELINK_JACKSON

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(25)VARCHAR2(55)VARCHAR2(10)VARCHAR2(10)VARCHAR2(300)VARCHAR2(10)VARCHAR2(300)VARCHAR2(25)VARCHAR2(55)VARCHAR2(300)VARCHAR2(120)

<pk><fk1><fk2><fk3>

COMPOUND_ORG_MUTATION

CPD_MUTATION_IDGENEIDCPD_MUTATION_TYPECPD_MUTATION_NAMEPHENOTYPENOTELINK_JACKSON


<pk><fk1><fk2>

INDIRECT_MUTATION

INDUCING_MUTATIONIDCPD_MUTATION_IDKNOCK_IDTRANSGENICIDORGANISM_MUTATION_TYPELINK_JACKSONNOTE



CONC_REGULATION

CONC_REG_IDCONCENTRATION_IDSTIM_PROTFOLD_CHANGE_REGEFFECT_REGMECHANISM_REG

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)NUMBER(10)VARCHAR2(95)VARCHAR2(300)

<pk><fk1><fk2>

TRANSPORTER_PARAM

INTERACTIONIDTRANSPORTER_PARAMSTOICHEMETRYKMCOMMON_DIRECTIONSYMPORT_ANTIPORTELECTROGENICATPASEPUMP_DIRECTIONKM _ ATP

VARCHAR2(12)VARCHAR2(25)NUMBER(10)NUMBER(10)VARCHAR2(10)VARCHAR2(10)NUMBER(10)VARCHAR2(10)VARCHAR2(10)NUMBER(10)

<pk,fk>

BIND

BINDIDAFCS_RIDAFCS_SIDPROT_CLV_IDCVL_MODIFICATION_IDRESIDUE_NAMEMAIN_PROT_IDCELL_IDMODIFICATION_TYPEBIND_MOL_TYPEALTERNATIVE_BINDFUNC_STATEBIND_NAMECOMPOUND_BIND_FLAGMODIFICATION_LAYERCONSTITUTIVE_FLAGSTOICHIOMETRYMODIFIED_FUNCTION

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)NUMBER(10)VARCHAR2(12)VARCHAR2(25)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(55)VARCHAR2(95)VARCHAR2(10)NUMBER(10)VARCHAR2(5)NUMBER(10)VARCHAR2(55)

<pk><fk1><fk1><fk2><fk3><fk4><fk5><fk6><fk7><fk8><fk9>

AARESIDUE_LOOKUP

RESIDUE_NAMELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>ADAPTER_PARAM

INTERACTIONIDBINDING_PARAM


<pk,fk>

PROT_TAG

PROT_TAGPROT_TAG_TYPETAG_POSITION_TYPETAG_SEQ


<pk><fk1><fk2>

STATE

STATEIDWILD_STATEMUTANT_EFFECTPROT_TYPEMWSTATE_NAMESTATE_SYNONYMCONSTITUTIVE_FLAGMUTANT_EFFECT_LAYER

VARCHAR2(12)VARCHAR2(12)VARCHAR2(10)VARCHAR2(12)NUMBER(10)VARCHAR2(25)VARCHAR2(55)VARCHAR2(5)NUMBER(10)

<pk><fk1><fk2><fk3>

UNIQUE_STATUS

PV_IDSTATEIDSTATUS_IDINTERACTIONIDBIO_PROCESS_IDCONCENTRATION_IDMOL_FUNC_ID


<pk,fk4><pk,fk5><pk><fk1><fk6><fk2><fk3>

SUBSTITUTION

SUBSTITUTIONIDPROT_MUT_ IDPOSITION_STARTDELETED_SEQUENCEADDED_SEQ

VARCHAR2(12)VARCHAR2(12)NUMBER(10)VARCHAR2(300)VARCHAR2(3000)

<pk><fk>

GENE_REGULATION

INTERACTIONIDREG_REGION_IDREG_SUBJECT_TYPE


<pk,fk3><fk1><fk2>

INTERACT_PROT

INTERACT_PROT_IDBINDIDPV_IDSTATEID


<pk><fk1><fk2>

BLAST

BLAST_TYPEBLAST_IDPV_IDBLAST_SUBJECT_IDP_MATCH_COUNTE_VALUESCOREIDENTITY_PCTPOSITIVE_PCTQUERY_COVERAGE_PCTSUBJECT_COVERAGE_PCTFRAMEHSPMATCH_LENGTHIDENTITYPOSITIVEGAPQUERY_STARTQUERY_ENDQUERY_LENGTHSUBJECT_STARTSUBJECT_LENGTH

VARCHAR2(25)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)NUMBER(10)

<pk><fk>

SNP

SNP_IDGENEIDSNPSNP_POSITIONDISEASE

VARCHAR2(12)VARCHAR2(12)VARCHAR2(5)NUMBER(10)VARCHAR2(55)

<pk><fk>

PARTIAL_DNA

PARTIAL_DNA_GIGENEID


<pk><fk>

OTHERID

OTHERIDMRNA_IDID_TYPEDB_NAMEID_VALUE


<pk><fk>

JOURNAL

J_ABBREVJOURNALPUBLISHER


<pk>

PATHWAY_STEP

STEP_IDSTATEIDPATHWAYIDUPPER_STEP_ID


<pk><fk1><fk2><fk3>

PATHWAY

PATHWAYIDPATHWAY_NAME


<pk>

SITE

SITE_IDINTERACT_PROT_IDBINDIDPROT_SITE

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)NUMBER(10)

<pk><fk1><fk2>

REG_SITE

REG_SITE_IDINTERACTIONIDSTARTEND


<pk><fk>

GENE_EXON

GENE_EXONIDGENEIDEXON_STARTEXON _END


<pk><fk>

MATCH_LOCATION

MATCH_LOC_IDMATCHIDMATCH_STARTMATCH_STATUSMATCH_ENDMATCH_EVIDENCE

VARCHAR2(12)VARCHAR2(12)NUMBER(10)VARCHAR2(10)NUMBER(10)VARCHAR2(25)

<pk><fk>

DOMAIN_CLASS

CLASS_IDINTERPRO_IDCLASS_TYPECATEGORY


<pk><fk>

DISPLAY

DISPLAY_IDMATCHIDPV_IDDISPLAY

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)blob

<pk><fk1><fk2>

DOMAIN

MATCHIDINTERPRO_IDDOMAIN_DBDB_IDDOMAIN_NAMEPROT_COUNT

VARCHAR2(12)VARCHAR2(12)VARCHAR2(25)VARCHAR2(12)VARCHAR2(95)NUMBER(10)

<pk><fk1><fk2>

INTERPRODB

INTERPRO_NAMESHORT_NAMEINTERPROT_COUNTINTERPRO_IDINTERPRO_QUERY_TYPE

VARCHAR2(55)VARCHAR2(10)NUMBER(10)VARCHAR2(12)VARCHAR2(12)

<pk>

MATCH_SEQ

MOTIF_IDSPTREMBL_IDSPTREMBL_NAMEMOTIF_SEQMOTIF_POSITION

VARCHAR2(12)VARCHAR2(12)VARCHAR2(300)VARCHAR2(300)NUMBER(10)

<pk,fk><pk>

Package1_Interaction1

Domail Motif PackageGenomic PackageBiostructure Package

Misc Package

STRUCTURE

STRUCTURE_IDPV_IDPDB_IDSTRUCTURE_IMAGSTRUCTURE_INFO

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)blobVARCHAR2(990)

<pk><fk>

DISULFIDE_XLINK

XLINK_IDPV_IDPOSTION2POSTION1


<pk><fk>

MODIFICATION_TYPE_LOOKUP

MODIFICATION_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

MUTANT_EFFECT_LOOKUP

MUTANT_EFFECTLONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

COVALENCE_FORM_LOOKUP

CVL_MODIFICATION_TYPESHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

DOMAIN_DATABASE_LOOKUP

DOMAIN_DBLONG_DESCRIPTION


<pk>

INTERACTION_TYPE_LOOKUP

INTERACTION_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

PHENOTYPE_STATUS_LOOKUP

PHENOTYPE_STATUSLONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

EXPRESSION_TYPE_LOOKUP

EXPRESSION_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

MANIPULATION_METHOD_LOOKUP

MANIPULATION_METHODLONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

COMPOUND_ORG_MUT_LOOKUP

CPD_MUTATION_TYPESHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

PROT_MUTANT_LOOKUP

MUTANT_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

PROTEIN_MUTATION_LOOKUP

P_MUTATION_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

PROT_TAG_LOOKUP

PROT_TAG_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

PROT_TERMINAL_LOOKUP

TAG_POSITION_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

CONC_ORGANELLE_LOOKUP

ORGANELLE_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

DATA_ENTRY

ENTRY_IDAU_IDENTRY_SUBJECTSUBMIT_DATESUBMIT_BYAPPROVED_DATEAPPROVED_BYVERSIONVERSION_NOTESTATUS_FLAG

VARCHAR2(12)VARCHAR2(10)VARCHAR2(12)DATEVARCHAR2(55)DATEVARCHAR2(55)VARCHAR2(10)VARCHAR2(95)VARCHAR2(5)

<pk><fk1><fk2>

DATA_ENTRY_SUBJ_LOOKUP

ENTRY_SUBJECTLONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

REGION_FORM_LOOKUP

REG_REGION_TYPESHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

REGULATION_FORM_LOOKUP

REG_SUBJECT_TYPESHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

PROTEIN_TYPE_LOOKUP

PROT_TYPESHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

BIND_MOL_LOOKUP

BIND_MOL_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

SMALL_MOLECULE_LOOKUP

SMALL_MOL_TYPESHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

REAGENT_TYPE_LOOKUP

REAGENT_TYPESHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

ASSAY_TEST_LOOKUP

ASSAYSHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

ORGANISM_MUT_LOOKUP

ORGANISM_MUTATION_TYPELONG_DESCRIPTIONSHORT_DESCRIPTION


<pk>

TISSUE_CELL

TISSUECELL_ID


<pk,fk1><pk,fk2>

SPECIES_TISSUE

SPECIESTISSUE


<pk,fk1><pk,fk2>

PROT_AUTHOR

PV_IDAU_ID


<pk,fk1><pk,fk2>

PROT_ANTIBODY

PV_IDAFCS_RIDANTIBODY_ID


<pk,fk1><pk,fk2><pk,fk2>

CELL_SUBCELL

CELL_IDCOMPONENTID


<pk,fk1><pk,fk2>

DET_METHOD_GENE

DET_METHODIDGENEID


<pk,fk1><pk,fk2>

DET_METHOD_MRNA

DET_METHODIDMRNA_ID


<pk,fk1><pk,fk2>

DET_METHOD_PROTEIN

DET_METHODIDPV_ID


<pk,fk1><pk,fk2>

GENE_REG_REGION

GENEIDREG_REGION_ID


<pk,fk1><pk,fk2>

MRNA_REG_REGION

MRNA_IDREG_REGION_ID


<pk,fk1><pk,fk2>

PROT_MOTIF

PV_IDMOTIF_ID


<pk,fk1><pk,fk2>

PROSTHTIC_PROT

PROSTHETIC_IDPV_ID


<pk,fk1><pk,fk2>

PROT_CMUTATION

PV_IDCPD_MUTATION_ID


<pk,fk1><pk,fk2>OMUTATION_PROT

INDUCING_MUTATIONIDPV_ID


<pk,fk1><pk,fk2>

COMPONENT_FUNCSTATE

COMPONENTIDBINDID


<pk,fk1><pk,fk2>

BIND_STATE

BINDIDSTATEID


<pk,fk1><pk,fk2>

STATE_PRODUCT

STATEIDPRODUCTID


<pk,fk1><pk,fk2>

PROT_CONC

PV_IDCONCENTRATION_ID


<pk,fk1><pk,fk2>

PROT_DISTRIBUTION

PV_IDSTATEIDSTATUS_IDDISTRIBUTION_ID


<pk,fk1><pk,fk1><pk,fk1><pk,fk2>

PROT_OTHERID

PV_IDOTHERID


<pk,fk1><pk,fk2>

METHOD_STATE

DET_METHODIDSTATEID


<pk,fk1><pk,fk2>

PROT_DOMAIN

PV_IDMATCHID


<pk,fk1><pk,fk2>BIO_PROCESS

BIO_PROCESS_IDUPPER_BIO_PROCESSPATHWAYIDBIOLOGICAL_PROCESSBIO_PROCESS_EVIDENCEBIO_PROCESS_GO_IDBIO_PROCESS_TYPE


<pk><fk1><fk2>

Experiment PackagePackage_8Package_2_interaction_result

PROT_MANIPULATION

PV_IDMANIPULATIONID


<pk,fk1><pk,fk2>

20012002

S ta tus

O th er IDA nn o ta tio ns

F u nction alS ta te

M u ta tionD ata

M o lecu leS eq u en ce /Nam e/AfC S ID

A uthor

2001

Molecule Pages

2002

Protein GI

Defining protein record (type 0)

+ Identical sequence records (type 1)

+ SwissProt discrepancies and their identities (type 1)

+ SwissProt / TrEMBL variants (type 2)

+ Clustered sequences and their identities (type 3)

+ Variants of clustered sequences (type 4)

sequence has no defining GI

(LocusLink + CNR)

(CNR)

(CNR)

(CNR)

(CNR)

(CNR)

CNR = Combined non-redundant protein database

Molecule Page External DB

2002

• Genbank, Swissprot, and LocusLink records referenced through protein database links

• Specific fields of interest included in annotation database schema (e.g. Genbank feature information, Swissprot external database references, LocusLink chromosomal information)

• Records obtained from in-house relational databases or flat files

External Database Records

2002

Protein Database Links +Component Databases Schema

2002

Locus Link Schema

2002

Domain, Motif, and Family Schema

2002

Blast Schema

2002

Status

Submit_Date

Revised_Date

Approval_Date

Reviewers

Editor

Privileges

D a tab a seL ia ison

A u to m a tedV a lida tionP u b lic D B

F ie ld s

R e v ie w e rs

C o n trib u to rs

A u th o r(s)

A fC S -N a tu reC h ie f E d ito r


2002

R e cep tor Io n C h an n e l T ra n sp o rte r E n zym e A d ap to r T ra n sc rip tionF a c to r

StateProcedure

M o le cu le (P ro te in )A F C S P ID

2001

Functional State

2002

Substrate Binding

CovalentModification

Protein Dissociation

ProteinInteraction

FS1-5 FS1-5 FS1-5 FS1-5

DO ALL STATES

Do i= 1, FS1; if more

Do j = 1, FS2; if more

Do k = 1, FS3; if more

Do l = 1, FS4; if more

Do m = 1, FS5;

For State i, is X an R, E, C, T, A, TF or combination

Launch state specific quantitative table

List interactions

Lookup Mutant List

Do Tables Change? If yes go to top; else add mut ID

ProteinLocalization

FS1-5

2001

Procedure for launching context-specific state tables/interactions

2002

P ro te in T ype S u b ce llu la rL o ca liza tion

In te ra ctionT yp e

M o le cu la rF u nc tion

In te ra c tio ns C o n ce n tra tion

Q u an tita tiveD a ta

F u n ctio n a lC o nse qu e nces

M u ta n tE ffe ct

F u n ctio n a lS ta te

2001

FUNCTIONAL STATE

2002

ENZYME_PARAM

kinetic_patternkmapparent_kmhill_coefficientnumber_binding_sitessubstrate_concentrationc_max_rate_vmaxc_max_rate_kcatenzyme_conditioncondition_infonote

VA25N10N10N10N10N10N10N10VA95VA300VA300

RECEPTOR_PARAM

number_binding_siteskdic50ec50hill_coefficientcondition_infonote

N10N10N10N10N10VA300VA300

CHANNEL_PARAM

ionic_selectivitygamma_subconducti_v_curvetau_opentau_closeactivation_gatinginactivation_gatinglonic_blockreg_any_parameterparameter_nameparameter_typereg_param_conseqfunc_consequence

VA55N10LBINN10N10VA55N10VA10VA10VA55VA10VA95VA95

TRANSPORTER_PARAM

transporter_paramstoichemetrykmcommon_directionsymport_antiportelectrogenicatpasepump_directionkm _ atp

VA25N10N10VA10VA10N10VA10VA10N10

20012002

DELETION

deletion_idposition_startposition_end

<pi> VA12N10N10

SUBSTITUTION

substitutionidposition_startdeleted_sequenceadded_sequence

<pi> VA12N10VA300VA3000

PROTEIN_MUTATION_LOOKUP

prot_mutation_typelong_descriptionshort_description

<pi> VA12VA150VA40

INSERTION

insertion_idinsertion_positioninserted_sequence

<pi> VA12N10VA990

PROT_MUTATION

prot_mut_idfunc_consequencenotetype_cpd_omutationmut_species

<pi> VA12VA95VA300VA25VA25

COMPOUND_ORG_MUTATION

cpd_mutation_idcpd_mutation_namephenotypenotelink_jackson

<pi> VA12VA25VA300VA300VA120

COMPOUND_ORG_MUT_LOOKUP

cpd_mutation_typeshort_descriptionlong_description

<pi> VA12VA40VA150

FUSION

fusion_idadded_sequence

<pi> VA12VA3000

POINT

point_idold_aanamenew_aanamepoint_position

<pi> VA12VA10VA10N10

20012002

REF

REF_IDJ_ABBREVENTRY_IDTITLEREF_CREATORREF_TYPEAFCS_KEYWORDSUBJECTABSTRACTCONTRIBUTORSTART_PAGEEND_PAGEVOLISSUEPUBLICATION_DATEREF_FORMATLANGUAGEIDENTIFIER

VARCHAR2(12)VARCHAR2(25)VARCHAR2(12)VARCHAR2(95)VARCHAR2(95)VARCHAR2(25)VARCHAR2(55)VARCHAR2(95)VARCHAR2(3000)VARCHAR2(55)NUMBER(5)NUMBER(5)NUMBER(10)NUMBER(10)VARCHAR2(25)VARCHAR2(5)VARCHAR2(25)VARCHAR2(55)

<pk><fk1><fk2>

REF_SUBJECT_LOOKUP

REF_SUBJECTSHORT_DESCRIPTIONLONG_DESCRIPTION


<pk>

REF_SUBJ

REF_SUBJ IDREF_IDPV_IDDET_METHODIDPROT_MUT_ IDINDUCING_MUTATIONIDEXPRESSION_IDAFCS_RIDANTIBODY_IDMANIPULATIONIDMRNA_IDREG_REGION_IDGENEIDREF_SUBJECTCVL_MODIFICATION_IDCPD_MUTATION_IDKNOCK_IDTRANSGENICIDCONCENTRATION_IDDISTRIBUTION_IDINTERACTIONID

VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)VARCHAR2(12)

<pk><fk1><fk2><fk3><fk4><fk5><fk6><fk7><fk7><fk8><fk9><fk10><fk11><fk12><fk13><fk14><fk15><fk16><fk17><fk18><fk19>

JOURNAL

J_ABBREVJOURNALPUBLISHER


<pk>

Dublin CoreOntology

20012002

Molecule Pages

2002

Molecule PageInterface and

Demo

Molecule Pages

2002

Molecule PageAuthor Interface


2002

Clicking on any hyperlinked word within an individual record view searches all Mini Molecule Pages for that keyword.

Mini Molecule Pages Record View

2002

http://www.afcs.org/molecule_pages/Seeker.cgi?S=_ALL_&D=V&T=MINI_MOLECULE_PAGES&C=Y&C_0=2&F_0=afcs_pid&Q_0=A000139&GC_0=1&EP_0=&OP_0=

Register Login

Create

Browse

Search

Person

RequestedMolecules

UserGroups

Protein List

Mini MoleculePages(Oracle)

Edit

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Approve

AuthenticationAnd Access Control

Overview of Mini Molecule PagesDatabase System

2002

• A main source for protein functions and signaling protein interactions

• A signaling pathway database

• Virtual cell - modeling and simulation

• Other species

2001

Molecule Pages

2002

Querying AfCS Databases

Roger Unwin

DataScope

2002

Web Server

Database(Oracle)

CGI Scripts

DataScope

Custom Searches Images

HTML Documents

Site Hierarchy

2002

DataScope Actions

User Actions

Select Search

What Happens During A Search

Request Start Page

Connect To DB

Select Record to ViewSubmit Search Specs.

Obtain List of Searches

Beautify List

Connect To DB

Obtain Search Meta Code

Generate SQL

Run SQL

Get Results

Run Morph-Its

Connect To DB

Obtain Search Input Form

Beautify Results

Connect To DB

Obtain Search Meta Code

Generate SQL

Run SQL

Get Results

Run Morph-Its

Beautify Results


2002

DataScope Sample Search

2002

DataScope Sample Search Results

2002

DataScope Sample Search Record

2002

Developer Start Screen

2002

Developer Search Configuration

2002

Developer Search Add Screen Item

2002

Developer Search Help Instructions Sample

2002

Developer Result Configuration

2002

Developer Record Configuration Sample

2002

Developer Record - Choose Pretty Printers

2002


2002

“The” Goals

Data Analysis in the Long Term

Modeling Cellular Response to Input

Data Analysis

2002

Unsupervised Learning

Supervised Learning

Intermediate output Constraints Knowledge-based Constraints

Hypothesis-driven Constraints

Data Analysis

2002

How do we decide whether two responses differ?

Can we distinguish functionally distinct sets of ligands, each acting on a pathway?

Can we identify functionally significant patterns of responses across many ligands?

Can we more efficiently construct epistasis maps connecting signaling proteins in pathways?