experibase

© cfdewey 2004

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

spee

d (m

icro

ns/m

in.)

bovine endothelium

mouse fibroblast00.10.20.30.4

0.6

x* human melanoma

xx 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 Semantics

Investigators 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

StorageAnalysisDisplay

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-Name-Description-URL-File

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-Name-Description-URL-File

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-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-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

Detector_Info

-Date_created-Created_by-Date_modified-Modified_by

FACS IOD

-StudyPlan_UIDStudyPlan


StudyPlanDe scription-Name-Decription-Acronym-Source



Refere nce-Name-Description-URL-File

ProjectReport

-Sample_UIDSample


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

DerivedSample

-Experiment_UIDExperiment

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


Detec tor_ Desc

-Name-Procedure-Comments

ProtocolDescription

-RawData_IDRa wData

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

Preprocess edData

-HighLevelAnalysis_UIDHighLevelAnalysis

-Data_ID-Expt_refs-Data_r efs-FileName-FileType-FileLength-File-Pro cedure_ref

PostProcessedData-Name-Descript ion-URL-File

ProcessMethod-Name-Abst ract-URL-File-Expt ._refs-Data_refs

Publication

-Admin istration_UIDAdministration

-Tit le-Fir stname-Middlen ame-Lastname-Suffix-Posit ionTitle-Username-Userstatus

Person-Name-Organization-Acron ym-Address-Descr iption-ContactPerson

Lab


Unit-Unit_prefix

Unit_prefix-Unit_expo nant

Unit_exponant

Unit_type

-Beam_Splitter-Low_Cut_Of f_1-High_Cut_Off_1-Low_Cut_Of f_2-High_Cut_Off_2-Low_Cut_Of f_3-High_Cut_Off_3-Unit_type_ref-Description-Item_General_info_ref

Beam_Splitter

-Ma nu facturer-Mo de l_Name-Serial_Number-Lot_Numbe r

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

-Emit ter-Polarization-Power-Power_un it_type_refs-Wavelength-Description-Item_General_ Info

Light_Source-Excitation_Filter-Ban d_Width_Locat ion-Pea k_1-Ban d_Width_1-Pea k_2-Ban d_Width_2-Pea k_3-Ban d_Width_3-Unit_typ e_ref-Descript ion-Item_General_Info_Ref

Excita tion_Fil ter

Detec tor_Info

-SampleID_ref-RawDataDesc-Num_Parameters-Num_Events-Acquisitio n_Date

FCS_Desc-Waveform_Chann el_Numb er

FC_Parameter

-Short_name

Parameter_De scAnalyte_Info

-Binding_Species-Binding_Species_Na me-Analyte_Formula_Wt-Comment-Item_General_Info_Ref

Analyte _Desc-Tag_name-Tag_Abbreviation

Tag-Tag_refs-Reactive_Functionality_Name-Reactive_Functionality_Num

Reac tive_Functionality

-SampleID_ref-Filename-FileType-Length-File

FCS_File-Tr igg er_Source-Tr igg er_Source_Long_Na me

Triggers-na me-sof tware-de scription-links-code-bin aryfile

FC_DA_Method

FACS IOD (Expanded Portion)

© cfdewey 2004




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






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_ID-TargetName-TargetType-TargetDescription

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-Name-Procedure-Comments

ProtocolDescr

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

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

PreprocessedData


HighLevelAnalysis




Publication

-Administration_UID

Administration



Lab

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

DA_method

© cfdewey 2004

MicroArray IOD--Based on Stanford Microarray Database


Microarray IOD

-StudyPlan_UID

StudyPlan






ProjectReport

-Sample_UID

Sample

PhysicalSample DerivedSample MeasuredSample

-Experiment_UID

Experiment

-ID

ProtocolPkg-ID

DesciptionPkg-Target_ID-TargetName-TargetType-TargetDescription

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

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

Publication

-Administration_UID

Administration



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





ProjectReport

-Sample_UID

Sample-Experiment_UID

Experiment

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

Expt.Desciption

Instrument


HighLevelAnalysis




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

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

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-ChannelNumber-BlackLevel-WhiteLevel-Gamma

GreenChannel-ChannelNumber-BlackLevel-WhiteLevel-Gamma

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




Emission_Filter

Detector_InfoExperiBase 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)

http://openmicroscopy.org/index.html

© cfdewey 2004

Group OME objects into ExperiBase

ExperiBase OME

Study PlanProject Package Project

Reference DocumentGroup

SamplePhysical 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












StanfordSeq

-Da te_ creat ed-Cre at ed_b y-Da te_ modi fied-Mo dif ied_by

Microa rr ay IOD

-StudyPla n_ UI DStudy Plan

-Name-Descript ion-URL-File

StudyPlanDescription-Nam e-Dec rip tion-Acronym-Sou rce

Ontology-Na me-De cript ion-URL-File

Hy pothe si s-Name-Descript ion-URL-File-RefType

Re fer ence-Nam e-Des cript ion-URL-File

Projec tReport

-Sa mple _UIDSa mple

PhysicalSampl e Deri ve dSample Mea suredSampl e

-E xpe rime nt_UI DExperiment

-IDProtocolPk g

-IDDe sc iptionPkg

-Target _ID-Target Na me-Target Typ e-Target De scrip tion

Targe t- IDExptSa mple

-Ra wData_ ID-sli de na me-gridfile-ch1file-ch2file-ch1desc-ch2desc-scan param-image

RawData-Pre processedData ID-spo tlist_ ref-stanf ordSeq_ ref-pr int_ ref-CH1I _mea n-CH1D_me dian-CH1I _med ian-CH1_ pe r_sat-CH1I _SD-CH1B _me an-CH1B _me dia n-CH1B _SD-CH1D_me an-CH2. ..- ...

Prepr oces se dData-IDSpecia lDesi gnEle mentP kg

-High Le velAnalysis_UIDHi ghLe ve lAnal ys is

-Da ta_ID-Expt_refs-Da ta_refs-FileName-FileType-FileLength-File-Proced ure _ref

PostProce ss edDa ta

-Na me-De scrip tio n-URL-File

Procedure

-Nam e-Abstra ct-URL-File-Expt._re fs-Dat a_refs

Public ati on

-Ad min ist rat ion_UIDAdminist ration

-Title-First na me-Middlename-La stname-Suff ix-Posi tion Title-Use rna me-Use rstatus

Per son-Na me-Organiza tion-Acron ym-Add ress-De script ion-Co ntactPerson

Lab

-Abb rev-Com mon Na me-Ge nu sspecies

Organism-Patient_ ID-Age-Sex-Et hn icit y-Family_ his to ry-St atus-Time _OD-Lo st _PT_Fo llowup-FollowUp_Date-Patient-Notes

Pati ent-St ud yPlan_ref-Orga nism_ref-Pl ateLo ca tion_ref-DB USER_re f-Orig Pla te_re f-Pl ateID-Pl ateNo-Pl atePrefi x-Pl ateSo urce

Plate-Sta nfo rdse q_ ref-Pla te_re f-samp leID-pla terow-pla tecolum n-faile d- is_v erified- is_c on ta min ia ted-LUI D-sou rce-PCR_lengt h-descripti on

plates ampl e-Patient_ref-clinical_no-clinical_sampl e_ id-sam pl e_d a tabas e-sam pl e_s ource-granularity-sam pl e_s ize-sam pl e_s ize_units-t ime _p m-organ-sam pl e_p rovider-. ..

Clinic al_Sample-Clin ica l_S amp le_ ref-Clin ica l_t ag-Clin ica l_v alue

Clinic al_eav-DB USER_re f-Print er_ ref-TI PCon fig _ref-Orga nism_ref-pr intI D-pr intn ame-nu mOfSlid es-colsPerSector-ro wsPe rSect or-columnSp aci ng-ro wSpa cin g-de scriptio n

Print-Prin t_ ref-pla tesampl e_ ref-pla te_ ref-spo tlistID-spo t-secto r-secto rRo w-secto rCo lumn

Spotlist-Se qtype-De scriptio n

SeqTy pe-SU ID-Seq Name-Seq Type _ref-Organis m_ref-Sou rce-SGDI D-De script ion

StanfordS eq-cli nic al_ sample _t

Expt_Clinica l-pa tie nt_tSMD Expt Patie nt

-Prin t_t-Organism _t

Expt Print-tipco nfig-...

TI PConfig-printer-.. .

Pri nter-normal iza tion_t

Exptnorm-no rmtype-...

Normali za tion-Tag_tExpt_ Tag_Ea v

-Tag_no-TagSet_t-...

Tag-Or gan ism_ t-Ta g_ t

Tag_Organis m-TagSet _n o-...

TagSe t-...SMD Pr otocol

-DBUSER_tSMD Ex ptAttr

-acc ess_ gro up _tSMD Expt_Access

-.. .Ex ptTy pe

-Expt type_t-Tagset _t

ExptType _TagSe t-...SubCat egory

-...Category

-DescriptionSMD ExptDesc r

-probe_tSMD Ex pt Probe

-pr obe _n o-...

Probe-Condit ion_va lu e_ t-probe_ t

Probe _val ue-Seed_ so urce_ t-probe_t

Probe_ seed-Condit ion_no-...

Condition-cond ition_va lue_no-cond ition_t

Condition_value-condset_t-condi tion_t

Conse t_cond-seed_source_no-...

Seed_source-Co nd set _n o-...

Condset-Exptset_ no-ExptsetTyp e_ t-...

ExptSet-exp tTypese t_no-...

Ex ptset_type-exp tset_tSMD Exptset_E xpt

PublicationPk g

-publica tion_tAbstract

-pu blicat ion_t-exptSet _t

Pub_ExptS et-publicati on_ t-URL_t

Pub_URL URL-URL_t-Met a_t

Met a_URL Meta

DataPk g

© cfdewey 2004

ExperiBase

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ExperiBaseSpecific Component

MiamExpress Translator

MIAMExpress transformation

experibase

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