© © cfdewey 2004 a unique opportunity in biological information standards c. forbes dewey, jr....
TRANSCRIPT
© 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
*
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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
-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-Detector_setting-Detector_unit_type_ref-Measurement
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_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
DerivedSample
-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-Process_method_ref-Description-Filename-Filetype-Length-File
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
FACS IOD (Expanded Portion)
© cfdewey 2004
-Detector-Detector_setting-Detector_unit_type_ref-Measurement
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
FACS IOD (Expanded Portion)
© cfdewey 2004
Administration Package - Object Model
Person
personIDtitlefirst_namemiddle_namelast_namesuffixposition
Address
streetcitystatezipcountry
Phone
string
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)
-Date_created-Created_by-Date_modified-Modified_by
WesternBlot 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
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_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
-Name-Software-Description-Links-Code-Filename-File
DA_method
© cfdewey 2004
MicroArray IOD--Based on Stanford Microarray Database
-Date_created-Created_by-Date_modified-Modified_by
Microarray 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
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_UID
HighLevelAnalysis
-Data_ID-Expt_refs-Data_refs-FileName-FileType-FileLength-File-Procedure_ref
PostProcessedData
-Name-Description-URL-File
Procedure
-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
-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_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
-Date_created-Created_by-Date_modified-Modified_by
OME IOD
-StudyPlan_UID
StudyPlan
-Name-Description-URL-File-Experimenter_ref-Group_ref
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-Experiment_UID
Experiment
Protocol
-Name-Description-Expt_date-Experimenter_ref-Group_ref-Type
Expt.Desciption
Instrument
-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-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_Abbrev.-SI_Unit_name
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
-Detector-Detector_setting-Detector_unit_type_ref-Measurement
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
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>
<Manufacturer>Omega Optical</Manufacturer><Model_Name>XF3084</Model_Name>
</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>
<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>
<Manufacturer>Omega Optical</Manufacturer><Model_Name>XF3084</Model_Name>
</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
PhysicalSample DerivedSample MeasuredSample
-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_ref-platesample_ref-plate_ref-spotlistID-spot-sector-sectorRow-sectorColumn
Spotlist
-Seqtype-Description
SeqType
-SUID-SeqName-SeqType_ref-Organism_ref-Source-SGDID-Description
StanfordSeq
-Date_created-Created_by-Date_modified-Modified_by
Microarray 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
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_UID
HighLevelAnalysis
-Data_ID-Expt_refs-Data_refs-FileName-FileType-FileLength-File-Procedure_ref
PostProcessedData
-Name-Description-URL-File
Procedure
-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
-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_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
MicroArray IOD (Expanded Portion)-Sample_UID
Sample
PhysicalSample DerivedSample MeasuredSample
-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_ref-platesample_ref-plate_ref-spotlistID-spot-sector-sectorRow-sectorColumn
Spotlist
-Seqtype-Description
SeqType
-SUID-SeqName-SeqType_ref-Organism_ref-Source-SGDID-Description
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
Typical user page:Pacific Northwest National Laboratory
ExperiBase
© cfdewey 2004
Web Pageshttp://schiele.mit.edu:8080/ExperiBase/