© © cfdewey 2004 A Unique Opportunity in Biological Information Standards C. Forbes Dewey, Jr....

© cfdewey 2004

A Unique Opportunity in Biological Information Standards

C. Forbes Dewey, Jr.Massachusetts Institute of Technology

A Unique Opportunity in Biological Information Standards

C. Forbes Dewey, Jr.Massachusetts Institute of Technology

ExperiBase

© cfdewey 2004

*

*

KA-D

KD-A

KPAT+

KPAT-

KPAD+

KPAD

KBAD+

KBAD-

KBAT+

KBAT-

Kp-

Kp+

Kb+

Kb-

KmD-AKmA-D

ModelsDatabases

Experiments

Interpretation

????Query

0.5

0 0.2 0.4 0.6 0.8 1polymer fraction

cell

spe

ed

(m

icro

ns/

min

.)

bovine endothelium

mouse fibroblast0

0.1

0.2

0.3

0.4

0.6

x* human melanoma

x

x G-

G+

F+

F-

Our view of experimental biology

© cfdewey 2004

Driving issues in experimental biological computing Large data sets

Terabytes in every lab Petabytes at national labs

Large calculations Petaflop level computing for days

Time is critical Biologists want infrastructure yesterday

Interchange is crucial Unshared data is unused data

We need standards

© cfdewey 2004

Keys to biological computing standards

SemanticsInvestigators can agree on meaningOntologies for standardizing meaningCuration of ontologies – the LSID

Schema Share schema and concepts

Scaleability The ability to scale to larger problems in the future

Standard tools Ontologies and schema for storage and query

Possibility to write reusable software!!!

© cfdewey 2004

ExperiBase

Based on ontology standards

Conceptual consistency between different experimental methods

Reuse of concepts between different experimental methods

Portable platform independent of OS

“DICOM for Biology”

© cfdewey 2004

ExperiBase top-level design

Sample

Study Plan

Experiment High Level Analysis

Administration

Most “silo” applications

© cfdewey 2004

•Gel Electrophoresis Western Blot1D Gel2D Gel

•Flow Cytometry / FACS•Microarray Experiments•Mass Spectrometry•Microscope Images

Supported Object Models for Experimental Biology

Complete In progress Preliminary

………….…………..HUPo

…………..…..HUPoBASE, MAGE-OM

..……………..OME

..…CytometryML

© cfdewey 2004

FACS Experiments

Data Storage

AnalysisDisplay

Computer

LaserLens (typ)

Flow cell

Cell suspension

Forward scatter

Side Scatter

Dichroic mirror

Fluorescence detectorTreated Cell

Sample (Cell)Sample TreatmentBinding SpeciesReactive Func.

Hardware (Parts Info)Parameter Detector Beam-Splitter Emission-Filter Amplifier Light-Source Excitation-FilterSettings

Data File (FCS)

MethodMeta Data Histogram Dot Plot Density Plot Contour Plot

Experiment Description Protocol

© cfdewey 2004

CytometryML --Robert C. Leif, Suzanne B. Leif, et al., XML_Med, a Division of Newport Instruments

© cfdewey 2004

FACS IOD-Date_created-Created_by-Date_modified-Modified_by

FACS IOD

-StudyPlan_UID

StudyPlan

-Name-Description-URL-File

StudyPlanDescription

-Name-Decription-Acronym-Source

Ontology

-Name-Decription-URL-File

Hypothesis

-Name-Description-URL-File-RefType

Reference


ProjectReport

-Sample_UID

Sample

-Name-Desciption-Tissue_Ref-Cell_Ref-Rest_62_Refs

PhysicalSample

-Name-Desciption-PhysicalSample_Refs-Method-source_ref-date_collected-location_ref-label-owner

MeasuredSample

-Experiment_UID

Experiment

Protocol

-Name-Description-Expt_date-Expt_Person

Expt.Desciption

-Target_ID-TargetName-TargetType-TargetDescription

Target

-SampleID_ref-Treatment_name-chemical_ref-dose-dose_unit-duration-duration_unit-temperature-temperature_unit-date

SampleTreatment

-Detector-Detector_setting-Detector_unit_type_ref-Measurement

Detector_Desc

-Name-Procedure-Comments

ProtocolDescription

-RawData_ID

RawData

-PreprocessedDataID

PreprocessedData

-HighLevelAnalysis_UID

HighLevelAnalysis

-Data_ID-Expt_refs-Data_refs-FileName-FileType-FileLength-File-Procedure_ref

PostProcessedData


ProcessMethod

-Name-Abstract-URL-File-Expt._refs-Data_refs

Publication

-Administration_UID

Administration

-Title-Firstname-Middlename-Lastname-Suffix-PositionTitle-Username-Userstatus

Person

-Name-Organization-Acronym-Address-Description-ContactPerson

Lab

-Unit_Abbrev.-SI_Unit_name

Unit

-Unit_prefix

Unit_prefix

-Unit_exponant

Unit_exponant

Unit_type

-Beam_Splitter-Low_Cut_Off_1-High_Cut_Off_1-Low_Cut_Off_2-High_Cut_Off_2-Low_Cut_Off_3-High_Cut_Off_3-Unit_type_ref-Description-Item_General_info_ref

Beam_Splitter

-Manufacturer-Model_Name-Serial_Number-Lot_Number

Item_General_Info

-Emission_Filter-Band_Width_Location-Peak_1-Band_Width_1-Peak_2-Band_Width_2-Peak_3-Band_Width_3-Unit_type_ref-Description-Item_General_Info_Ref

Emission_Filter

-Mode-Gain

Amplifier_info Excitation_Info

-Emitter-Polarization-Power-Power_unit_type_refs-Wavelength-Description-Item_General_Info

Light_Source

-Excitation_Filter-Band_Width_Location-Peak_1-Band_Width_1-Peak_2-Band_Width_2-Peak_3-Band_Width_3-Unit_type_ref-Description-Item_General_Info_Ref

Excitation_Filter

Detector_Info

-SampleID_ref-RawDataDesc-Num_Parameters-Num_Events-Acquisition_Date

FCS_Desc

-Waveform_Channel_Number

FC_Parameter

-Short_name

Parameter_DescAnalyte_Info

-Binding_Species-Binding_Species_Name-Analyte_Formula_Wt-Comment-Item_General_Info_Ref

Analyte_Desc

-Tag_name-Tag_Abbreviation

Tag

-Tag_refs-Reactive_Functionality_Name-Reactive_Functionality_Num

Reactive_Functionality

-SampleID_ref-Filename-FileType-Length-File

FCS_File

-Trigger_Source-Trigger_Source_Long_Name

Triggers

-name-software-description-links-code-binaryfile

FC_DA_Method

-Imagefile_ref-Rawdata_ref-Sample_ref-Description-Total_events-Quad_Loc_x-Quad_Loc_y-UL_Events-UL_Precent_Event-UL_X_Mean-UL_Y_Mean-UL_X_Median-UL_Y_Median-...

FC_Dotplot

-PreprocessedDataID-Process_method_ref-Description-Filename-Filetype-Length-File

FC_Pre_Proc

-Imagefile_ref-Rawdata_ref-Sample_ref

FC_Histogram

-Description-Gates-Parameters-Total_events-Gated_Events-System-Means

FC_Histo_Desc

-Param_name-M-Low-High-Total_Events-Total_Percent_Event-Gated_Percent_Event-GMean-CV-Peak-Value

FC_Histo_Data

Ref: Leif, Leif, and Leif, Ref: Leif, Leif, and Leif, Cytometry Cytometry 54A54A 56-65 (2003) 56-65 (2003)

© cfdewey 2004


Detector_Desc


Beam_Splitter


Emission_Filter

Detector_Info

-Date_created-Created_by-Date_modified-Modified_by

FACS IOD

-StudyPlan_UID

StudyPlan




Ontology


Hypothesis


Reference


ProjectReport

-Sample_UID

Sample


PhysicalSample

-Name-Desciption-PhysicalSample_Refs-Method-source_ref-date_collected-location_ref-label-owner

DerivedSample

-Experiment_UID

Experiment

Protocol

-Name-Description-Expt_date-Expt_Person

Expt.Desciption


Target

-SampleID_ref-Treatment_name-chemical_ref-dose-dose_unit-duration-duration_unit-temperature-temperature_unit-date

SampleTreatment


Detector_Desc


ProtocolDescription

-RawData_ID

RawData


PreprocessedData


HighLevelAnalysis


PostProcessedData


ProcessMethod


Publication

-Administration_UID

Administration


Person


Lab


Unit

-Unit_prefix

Unit_prefix

-Unit_exponant

Unit_exponant

Unit_type


Beam_Splitter

-Manufacturer-Model_Name-Serial_Number-Lot_Number

Item_General_Info


Emission_Filter

-Mode-Gain

Amplifier_info Excitation_Info

-Emitter-Polarization-Power-Power_unit_type_refs-Wavelength-Description-Item_General_Info

Light_Source

-Excitation_Filter-Band_Width_Location-Peak_1-Band_Width_1-Peak_2-Band_Width_2-Peak_3-Band_Width_3-Unit_type_ref-Description-Item_General_Info_Ref

Excitation_Filter

Detector_Info

-SampleID_ref-RawDataDesc-Num_Parameters-Num_Events-Acquisition_Date

FCS_Desc

-Waveform_Channel_Number

FC_Parameter

-Short_name

Parameter_DescAnalyte_Info

-Binding_Species-Binding_Species_Name-Analyte_Formula_Wt-Comment-Item_General_Info_Ref

Analyte_Desc

-Tag_name-Tag_Abbreviation

Tag

-Tag_refs-Reactive_Functionality_Name-Reactive_Functionality_Num

Reactive_Functionality

-SampleID_ref-Filename-FileType-Length-File

FCS_File

-Trigger_Source-Trigger_Source_Long_Name

Triggers

-name-software-description-links-code-binaryfile

FC_DA_Method

FACS IOD (Expanded Portion)

© cfdewey 2004


Detector_Desc


Beam_Splitter


Emission_Filter

Detector_Info

FACS IOD (Expanded Portion)

© cfdewey 2004

Administration Package - Object Model

Person

personIDtitlefirst_namemiddle_namelast_namesuffixposition

Address

streetcitystatezipcountry

Phone

string

Email

string

Institution

institutionIDname

Account

usernamepasswordactivelast_login

!

!

!

*

*

+

?

?

!

Group

groupIDnamedescription

+

!

!

!

?

! !

*

*

Administrator

privileges

Curator

privileges

DefaultUser

privileges

Fax

string

URL

string

*

*

!

!

© cfdewey 2004

Study Plan Package - Object Model

File

fileIDtypeurllengthbinary

Ontology

termdefinitionsourceacronym

StudyPlan

study_planIDname

Hypothesis

statement

ProjectReport

titleabstractdate

Reference

authorsourcedate

Description

summary

* + ++

© cfdewey 2004

Database

Separation of data from analysis

Gel electrophoresis exampleImage analyzedAnalysis saved with object

© cfdewey 2004

Gel Electrophoresis Information Object Definitions (IOD)


WesternBlot IOD

-StudyPlan_UID

StudyPlan




Ontology


Hypothesis


Reference


ProjectReport

-Sample_UID

Sample


PhysicalSample

-Name-Desciption-PhysicalSample_Refs-Method

DerivedSample

-Name-label-Description-PhysicalSample_Refs-DerivedSample_Refs-sample_source-Date_collected-Location-owner

MeasuredSample

-Experiment_UID

Experiment

Protocol

-Name-Description-Expt_date-Contact_Person-StudyPlan_Ref

Expt.Desciption


Target

-Label-Sample-Treatment_name-Material-Dose-Dose_unit_prefix-Dose_unit-Duration-Duration_unit_prefix-Duration_unit-Temperature-Temperature_unit_prefix-Temperature_unit-Date-Description

SampleTreatment

-CellExtractionBuffer-ProteinLoadingBuffer-WashCondition-IncubationTime-RunningBuffer-WesternTransferBuffer-BlockingBuffer-Stain-WashBuffer-1st_Antibody-2nd_Antibody-DevelopmentBuffers-kDa

ParameterSet


ProtocolDescr

-RawData_ID-RawDataDesc-Filename-FileType-Length-File

RawData


PreprocessedData


HighLevelAnalysis


PostProcessedData


ProcessMethod


Publication

-Administration_UID

Administration


Person


Lab

-Name-Software-Description-Links-Code-Filename-File

DA_method

© cfdewey 2004

MicroArray IOD--Based on Stanford Microarray Database


Microarray IOD

-StudyPlan_UID

StudyPlan




Ontology


Hypothesis


Reference


ProjectReport

-Sample_UID

Sample

PhysicalSample DerivedSample MeasuredSample

-Experiment_UID

Experiment

-ID

ProtocolPkg

-ID

DesciptionPkg


Target

-ID

ExptSample

-RawData_ID-slidename-gridfile-ch1file-ch2file-ch1desc-ch2desc-scanparam-image

RawData

-PreprocessedDataID-spotlist_ref-stanfordSeq_ref-print_ref-CH1I_mean-CH1D_median-CH1I_median-CH1_per_sat-CH1I_SD-CH1B_mean-CH1B_median-CH1B_SD-CH1D_mean-CH2...-...

PreprocessedData

-ID

SpecialDesignElementPkg


HighLevelAnalysis


PostProcessedData


Procedure


Publication

-Administration_UID

Administration


Person


Lab

-Abbrev-CommonName-Genusspecies

Organism

-Patient_ID-Age-Sex-Ethnicity-Family_history-Status-Time_OD-Lost_PT_Followup-FollowUp_Date-Patient-Notes

Patient

-StudyPlan_ref-Organism_ref-PlateLocation_ref-DBUSER_ref-OrigPlate_ref-PlateID-PlateNo-PlatePrefix-PlateSource

Plate

-Stanfordseq_ref-Plate_ref-sampleID-platerow-platecolumn-failed-is_verified-is_contaminiated-LUID-source-PCR_length-description

platesample

-Patient_ref-clinical_no-clinical_sample_id-sample_database-sample_source-granularity-sample_size-sample_size_units-time_pm-organ-sample_provider-...

Clinical_Sample

-Clinical_Sample_ref-Clinical_tag-Clinical_value

Clinical_eav

-DBUSER_ref-Printer_ref-TIPConfig_ref-Organism_ref-printID-printname-numOfSlides-colsPerSector-rowsPerSector-columnSpacing-rowSpacing-description

Print

-Print_ref-platesample_ref-plate_ref-spotlistID-spot-sector-sectorRow-sectorColumn

Spotlist

-Seqtype-Description

SeqType

-SUID-SeqName-SeqType_ref-Organism_ref-Source-SGDID-Description

StanfordSeq

-clinical_sample_t

Expt_Clinical

-patient_t

SMD Expt Patient

-Print_t-Organism_t

Expt Print

-tipconfig-...

TIPConfig

-printer-...

Printer

-normalization_t

Exptnorm

-normtype-...

Normalization

-Tag_t

Expt_Tag_Eav

-Tag_no-TagSet_t-...

Tag

-Organism_t-Tag_t

Tag_Organism

-TagSet_no-...

TagSet

-...

SMD Protocol

-DBUSER_t

SMD ExptAttr

-access_group_t

SMD Expt_Access

-...

ExptType

-Expttype_t-Tagset_t

ExptType_TagSet

-...

SubCategory

-...

Category

-Description

SMD ExptDescr

-probe_t

SMD Expt Probe

-probe_no-...

Probe

-Condition_value_t-probe_t

Probe_value

-Seed_source_t-probe_t

Probe_seed

-Condition_no-...

Condition

-condition_value_no-condition_t

Condition_value

-condset_t-condition_t

Conset_cond

-seed_source_no-...

Seed_source

-Condset_no-...

Condset

-Exptset_no-ExptsetType_t-...

ExptSet

-exptTypeset_no-...

Exptset_type

-exptset_t

SMD Exptset_Expt

PublicationPkg

-publication_t

Abstract

-publication_t-exptSet_t

Pub_ExptSet

-publication_t-URL_t

Pub_URL URL

-URL_t-Meta_t

Meta_URL Meta

DataPkg

© cfdewey 2004

Microscope Image IOD

Converted from OME


OME IOD

-StudyPlan_UID

StudyPlan

-Name-Description-URL-File-Experimenter_ref-Group_ref



Ontology


Hypothesis


Reference


ProjectReport

-Sample_UID

Sample-Experiment_UID

Experiment

Protocol

-Name-Description-Expt_date-Experimenter_ref-Group_ref-Type

Expt.Desciption

Instrument


HighLevelAnalysis


PostProcessedData


ProcessMethod


Publication

-Administration_UID

Administration

-Title-Firstname-Middlename-Lastname-Suffix-PositionTitle-Institution-OMEName-GroupRef

Experimenter

-Name-Organization-Acronym-Address-Description-ContactPerson-Leader

Group

-Name-software-description-links-code-filename-file

DA_method

-Treatment_name-chemical_ref-dose-dose_unit-duration-duration_unit-temperature-temperature_unit-date

SampleTreatment

-SampleID_ref-well-sample

SampleTr

-RawData_ID

RawData

DisplayOptions

-Plate_ref-Filename-FileType-Length-File

Raw_image

-OTFRef-FilterRef-Name-SamplesPerPixel-IlluminationType-PinholeSize-PhotometricInterpretation-Mode-ContrastMethod-ExWave-EmWave-Fluor-NDfilter

ChannelInfoDescr

-ChannelInfoID_ref

ChannelInfo

-ColorDomain-Index

ChannelInfoComponent

-description-CreationDate-GroupRef-Type-Name-SizeX-SizeY-SizeZ-NumChannels-NumTimes-PixelSizeX-PixelSizeY-PixelSizeZ-TimeIncrement-WaveStart-WaveIncrement-CustomeAttributes

ImageDescr

-ExternalLink-ImageFile_ref-PixelsID-DimensionOrder-PixelType-BigEndian-DerivedFromMethod

Pixels

-PreprocessedDataID

PreprocessedData


Pre_Proc_File


Unit

-Unit_prefix

Unit_prefix

-Unit_exponant

Unit_exponant

Unit_type

PhysicalSample MeasuredSample

-species_name-organismabbrev-commonname-genuspecies-label-content

Organism Cell_type

-abbrev-commonname-genusspecies-type-source-label-content

Cell Tissue_type Tissue

DerivedSample

-PlateID-Name-ScreenRef-ExternRef-Description-PhysicalSample_ref-Method-source_ref-date_collected-location_ref-label-owner

Plate

-ScreenID-Name-ExternRef-Description

Screen

-Type-Manufacturer-Model-Serial_number

Microscope

-LightSource_ID-Manufacturer-Model-Serial_number

LightSource

-type-power

Arc

-type-Medium-Wavelength-FrequencyDoubled-Tunable-Pulse-Power

LaserDescr

-LightSource_ref

Pump

Laser

-type-power

Filament

-Manufacturer-Model-Serial_number-Gain-Voltage-Offset-DetectorID-Type

Detector

-ObjectiveID-manufacturer-model-serial_number-LensNA-magnification

Objective

-FilterID

Filter

-manufacturer-model-lot_number-type

ExFilter

-manufacturer-model-lot_number

Dichroic

-manufacturer-model-lot_number-type

EmFilter

-description-manufacturer-model-lot_number

FilterSet

-OTFID

OTF

-ObjectiveRef-FilterRef-BinData-External_link

OTFData

-PixelType-OpticalAxisAvrg-SizeX-SizeY

OTFDescr

-ChannelNumber-BlackLevel-WhiteLevel-Gamma

RedChannel


GreenChannel


BlueChannel

-ChannelNumber-BlackLevel-WhiteLevel-Gamma-ColorMap

GreyChannel

-X0-Y0-Z0-T0-X1-Y1-Z1-T1

ROI

-Zstart-Zstop-Tstart-Tstop-Zoom

DisplayOptionsDescr

-href-MIMEType-filename-filelength-file

Thumbnail

-Name-X-Y-Z

StageLabel

-Temperature-AirPressure-Humidity-CO2Percent

ImagingEnvironment

-CustomAttributes-Tag-Name-FeatureID

Feature

-Name-DatasetID-Locked-Description-Experimenter_ref-Group_ref-customAttributes

DataSet

-LightSource_ref-AuxTechnique-Attenuation-Wavelength

AuxLightsourceRef

-Detector_ref-Offset-Gain

DetectorRef

-Instrument_ref-Objective_ref

InstrumentRef

-PlateID_ref-Well-Sample

Plate_ref

-LightSource_ref-Attenuation-WaveLength

LightSourceRef

-Declaration-ExecutionInstuctions

AnalysisModule

© cfdewey 2004


Detector_Desc


Beam_Splitter


Emission_Filter

Detector_Info

ExperiBase XMLCREATE TYPE detector_desc_t UNDER detector_info_t AS(detector varchar(64),detector_setting real,detector_unit_pref REF(unit_prefix_t),detector_unit REF(unit_t),measurement varchar(64))MODE DB2SQL;

CREATE TYPE beam_splitter_t UNDER detector_info_t AS(beam_splitter varchar(64),low_cut_off_1 real,high_cut_off_1 real,low_cut_off_2 real,high_cut_off_2 real,low_cut_off_3 real,high_cut_off_3 real,unit_prefix REF(unit_prefix_t),unit REF(unit_t),description varchar(64),item_info REF(item_info_t))MODE DB2SQL;

<?xml version="1.0" encoding="UTF-8"?><params:Parameter xmlns:params="parameters.xsd" xsi:schemaLocation="parameters.xsd">

<Dectector_Info><Detector>PMT</Detector><Detector_Setting>600</Detector_Setting><Detector_Units Prefix="none" Si_Unit_Name="volt"/><Measurement>Flourescence</Measurement><Beam_Splitter_Info Prefix="nano" Unit="meter">

<Beam_Splitter>Dichroic_Reflect_Low</Beam_Splitter><Low_Cut_Off_1>505</Low_Cut_Off_1><Description>505DRLP</Description><Item_General_Info>

<Manufacturer>Omega Optical</Manufacturer><Model_Name>XF2010</Model_Name>

</Item_General_Info></Beam_Splitter_Info><Emission_Filter_Info Prefix="nano" Unit="meter">

<Emission_Filter>Band_Block</Emission_Filter><Band_Width_Location>unknown</Band_Width_Location><Peak_1>535</Peak_1><Band_Width_1>45</Band_Width_1><Description>535AF45</Description><Item_General_Info>


</Item_General_Info></Emission_Filter_Info>

</Dectector_Info></params:Parameter>

Object-Relational Database Schema

XML Schema

<?xml version="1.0" encoding="UTF-8"?><params:Parameter xmlns:params="parameters.xsd" xsi:schemaLocation="parameters.xsd">

<Dectector_Info><Detector>PMT</Detector><Detector_Setting>600</Detector_Setting><Detector_Units Prefix="none" Si_Unit_Name="volt"/><Measurement>Flourescence</Measurement><Beam_Splitter_Info Prefix="nano" Unit="meter">

<Beam_Splitter>Dichroic_Reflect_Low</Beam_Splitter><Low_Cut_Off_1>505</Low_Cut_Off_1><Description>505DRLP</Description><Item_General_Info>


</Item_General_Info></Beam_Splitter_Info><Emission_Filter_Info Prefix="nano" Unit="meter">

<Emission_Filter>Band_Block</Emission_Filter><Band_Width_Location>unknown</Band_Width_Location><Peak_1>535</Peak_1><Band_Width_1>45</Band_Width_1><Description>535AF45</Description><Item_General_Info>


</Item_General_Info></Emission_Filter_Info>

</Dectector_Info></params:Parameter>

XML Document

© cfdewey 2004

Recommendations and implementationConsensus on ontological standards

LSID OWL

Backing of major players Industry Government International

Semantic Web Use RDF to represent data in ExperiBase and make

the data available through web services

Use OWL for a collaborative semantic network

© cfdewey 2004

Additional sponsorship by the NIH and DARPA

Ubiquitous Networked Biological Computing

Sponsored by a continuing grant from DOE (PNNL)

Put your company logo here

© cfdewey 2004

The informaticscollaborators

Howard Chou

JeannetteStephenson

CatherineHowell

Ngon Dao

Shixin ZhangBen Fu

Aidan Downes

Pat McCormack

Shiva Ayyadurai

© cfdewey 2004

Data integration today

Database federation and distributed intelligence Correlation of data in disparate databases Archiving and analysis of derived data

Integration of higher-level analyses Imaging and image analysis Multiple-protein interactions

© cfdewey 2004

Open Microscopy Environment (OME) http://openmicroscopy.org/index.html

The Open Microscopy Project (OME) is an open source software project to develop a database-driven system for the quantitative analysis of biological images.

Founders: Ilya Goldberg (MIT/NIH), Jason Swedlow (Welcome Trust Biocentre- Dundee), and Peter Sorger (MIT)

© cfdewey 2004

Group OME objects into ExperiBase

ExperiBase OME

Study PlanProject Package Project

Reference DocumentGroup

Sample

Physical Sample

Derived Sample

Measured Sample Plate, Screen

Experiment

Protocol Instrument, Microscope, LightSource, Detector, Objective, Filter, OTF

Sample Treatment PlateRef

Target

Description Experiment

Raw Data Image, ChannelInfo, DisplayOptions, Feature, StageLabel

Pre-Processed Data Pixels, Thumbnail

HighLevelAnalysis High Level Analysis Dataset, AnalysisModelue, Program

AdministrationPersonnel Experimenter, Group

Audit and Security

© cfdewey 2004

MicroArray IOD (Expanded Portion)

-Sample_UID

Sample



Organism


Patient


Plate


platesample


Clinical_Sample


Clinical_eav


Print


Spotlist


SeqType


StanfordSeq


Microarray IOD

-StudyPlan_UID

StudyPlan




Ontology


Hypothesis


Reference


ProjectReport

-Sample_UID

Sample


-Experiment_UID

Experiment

-ID

ProtocolPkg

-ID

DesciptionPkg


Target

-ID

ExptSample

-RawData_ID-slidename-gridfile-ch1file-ch2file-ch1desc-ch2desc-scanparam-image

RawData

-PreprocessedDataID-spotlist_ref-stanfordSeq_ref-print_ref-CH1I_mean-CH1D_median-CH1I_median-CH1_per_sat-CH1I_SD-CH1B_mean-CH1B_median-CH1B_SD-CH1D_mean-CH2...-...

PreprocessedData

-ID

SpecialDesignElementPkg


HighLevelAnalysis


PostProcessedData


Procedure


Publication

-Administration_UID

Administration


Person


Lab


Organism


Patient


Plate


platesample


Clinical_Sample


Clinical_eav


Print


Spotlist


SeqType


StanfordSeq

-clinical_sample_t

Expt_Clinical

-patient_t

SMD Expt Patient

-Print_t-Organism_t

Expt Print

-tipconfig-...

TIPConfig

-printer-...

Printer

-normalization_t

Exptnorm

-normtype-...

Normalization

-Tag_t

Expt_Tag_Eav

-Tag_no-TagSet_t-...

Tag

-Organism_t-Tag_t

Tag_Organism

-TagSet_no-...

TagSet

-...

SMD Protocol

-DBUSER_t

SMD ExptAttr

-access_group_t

SMD Expt_Access

-...

ExptType

-Expttype_t-Tagset_t

ExptType_TagSet

-...

SubCategory

-...

Category

-Description

SMD ExptDescr

-probe_t

SMD Expt Probe

-probe_no-...

Probe

-Condition_value_t-probe_t

Probe_value

-Seed_source_t-probe_t

Probe_seed

-Condition_no-...

Condition

-condition_value_no-condition_t

Condition_value

-condset_t-condition_t

Conset_cond

-seed_source_no-...

Seed_source

-Condset_no-...

Condset

-Exptset_no-ExptsetType_t-...

ExptSet

-exptTypeset_no-...

Exptset_type

-exptset_t

SMD Exptset_Expt

PublicationPkg

-publication_t

Abstract

-publication_t-exptSet_t

Pub_ExptSet

-publication_t-URL_t

Pub_URL URL

-URL_t-Meta_t

Meta_URL Meta

DataPkg

© cfdewey 2004

MicroArray IOD (Expanded Portion)-Sample_UID

Sample



Organism


Patient


Plate


platesample


Clinical_Sample


Clinical_eav


Print


Spotlist


SeqType


StanfordSeq

© cfdewey 2004

ExperiBaseData Transformer

Experiment Data File

Experiment Data File

Data DescriptionFile

Data DescriptionFile

General transformation process

© cfdewey 2004

ExperiBase

Storage Database

RequestDispatcher

ExperiBaseSpecific Component

MiamExpress Translator

MIAMExpress transformation

© cfdewey 2004

Feeding ArrayExpress

ExperiBase

TranslatorTranslator

MAGE-MLMAGE-ML MAGE-MLMAGE-ML

ArrayExpress

Storage Database

© © cfdewey 2004 A Unique Opportunity in Biological Information Standards C. Forbes Dewey, Jr....

Documents

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