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Application Domain DB Characteristics of typical application
Scientist(s) performing the experiment On objects and preexisting information & data On which processes operate
That use apparatus with specific properties Resulting in new data and information
A domain-specific flow of processes
Expressive MACS EFC Examples:Expressive, MACS, EFC, ...
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VL Experimentation Environment Data Model
DNA micro-arrayexperiment
Micro-beamexperiment
LIB RARYname: STRI NGid: STRINGpurchase_date: DATEnum_plates : SHORTnum_clones : SHORTmat erial: STRI NGcatalogue_no: STRINGpr ice: FLOATdata_sheet: STRINGpcr_primers: STRINGvolume: SHORTdescription: STRI NG
ORGANISMname: STR INGid: STRING
GENEname: STRI NGid: ST RINGchrom _ l oc: STRINGchrom _start: STRINGchrom _end: STRING
CLONEname: STRI NGid: STRINGvendor_id: STR INGinsert_size: INTEGERdescription: ST RING
WELLgr id: INTEGE Rrow: INTEGE Rcol : INTEGERfl ag: SHORT
LIB_ PLATESUB_ LIBRARYvol ume: SHORTlocation: STRING
CLONE _LIB_ ALIQUOTING SUB_ LIB _ PLATE
P IPETTING_ ROBOThas_program: PIPETTING_ROBOT_PRG
CLONE_ SELECTION CLONE_ SEL_ LISTCLONE_ ASSORTING CLO NE_ PICK ING CULTURE_ INO CULATIO NCLONE_ SEL_ PLATE PLAS MID_ DNA_ ISOLATION
CULT URE_ INCUBATIONvolume: SHORT
temp: FLOATtime: STRI NGrpm: SHORT
CULTURE_ PLATE
CULTURE_ CENTRIFUGATIONt emp: FLOATt ime: STRINGr pm: SHORT
PLAS MID_ DNA_ EXTRACTION
DNA_ COL_ PLATE
DNA_ EXT_ M EMB_ PLATE
CULTURE_ ME DIUM
SHAKING_INCUBATOR
CE NTRIFUGE
PIPETTING_ ROBOThas_pr ogram: PIPETTING_ROBOT_PRG
PCR_ SRC_ DNA_ DILUTION PCR_ SRC_ DNA_ DILUTION _ PLATE
PIP ETTING_ ROBOThas_program: PIPETTING_ROBOT_PRG
PCR_ AM PL IFICATION
PCR_ M IX_ MAKINGhas_ taq _suppl ier: ORGANIZATION
taq_lot_no: STRINGhas_ nucl_suppl ier: ORGANIZATION
nucl _lot_no: STRING
PCR_ PRODUCT _P LATE
PCR_ MIX_ PLATE
PCR_ RXN_ M IX_ DISTRIBUTION
PCR_ TC_ PLATE
PCR_ TC_ RXN
PCR_ PRODUCT_ POOLING
PCR_ RXN_ SETUP
PCR_ M ASTER_ M IX
PCR_ PRIMERname: STRI NGid: STRING
PCR_ PRIMERname: STRI NGid: STRING
PCR_ MIXTURE
PIPETTING_ ROBOThas_pr ogram: PIPET TING_ROBOT_PRG
PIPETTING_ ROBOThas_pr ogram: PIPETTING_ROBOT_PRG
THERM OCYCLERhas_progr am: THERMOCYCLER_PRG
PCR_ VALIDATION
GEL_ MAKING
GELtype: STRING
GE L_ SETUP
GE L_ ELECTROPHORESISloading_buffer: STRING
curr ent: FLOATtime: STRING
GE L_ IMAGING GEL_ IMG_ ANALYSIShas_pr ogram: IMG_ANALYSIS_PRG
GEL_ IMAGE
GEL_ INTERPRE TATION
GEL_ DNA_ MARKER
GEL_ DNA_ SAMPLEname: STRINGid: STRI NG
PIPETTING_ ROBOThas_progr am: PI PETTING_ROBOT_PR G EL ECTROPHORESIS_ APP
CAMERA
PCR_ CLEANUP
DNA_ BIND_ MEMB_ PLATEPIPETTING _RO BO Thas_program: PIPETTING_ROBOT_PRG
PCR_ CLEAN_ PLATE PCR_ EQUILIBRATION
OD_ CALIBRATION DNA_ CONC_ EQUILIBRATIONvolume: SHOR T
OD_ MEASUREMENT
OD_ SAMPLE_ PREPARATIONvolume: SHORT
OD_ SAMPLE _ PLATE
DNA_ DESICCATION
DNA_ EQUILIBRATED_PL ATE
OD_ DATA OD_ CONC_ CALCULATION
DNA_ CONCENTRATION
PIPETTING_ ROBOThas_program: PIPET TING_ROBOT_PRG
DENSITOMETERhas_program: OD_PRG
SPEED_ VAChas_program: VAC_PRG
DNA_ REPLATING P3 8 4 _ SPO TTER_ PLATE
PIPETTING _ ROBO Thas_pr ogram: PIPET TING_ROBOT_PRG
ARRAY_SPOTTING
MICRO_ ARRAYplatform_type: STRINGarray_dimensions : STRINGspot_dimensions : STRINGpitch: STRINGnum _grids: INTEGERnum _rows : INT EGERnum _cols : INT EGERsubstrate: STRINGbinding_protocol : STRINGlocation: STRING
SPOTgrid: I NTEGERrow: I NTEGERcol: INTEGERflag: SHORT
ARRAY_ SPOTTERhas_program: ARRAY_SPOTTER_PRG
O RG ANISMname: STRINGid: STRING
CELL_ SAMPLEorgan: STRINGtissue: STRINGcell_type: STRINGcell_line: STRINGcell_culture: STRINGdevelopment_stage: STRINGsex: STRINGstrain: STRING
CE LL _SAM PL E_ TREATMENTm RNA_ EXTRACTION
cel l_rupture: ST RI NGrna _isolated: ST RING
volume: SHORT
m RNA TREATED_ CELL_ SAMPLEcDNA _L ABELING
label: STRI NGeffi ciency: FLOAT
cDNA _ PROBE
ARRAY_ HYBRIDIZATIONmanual : BOOLEANhyb _t emp: FLOAThyb _t ime: STRING
wash_t emp: FLOATwash_t ime: STR INGdry_t ime: STRINGsol ut ion: STRING
HYBRIDIZED_ ARRAYlocation: STRING
ARRAY_ SCANNINGphotomul tiplier : STRING
ARRAY_ IMAGE
SLIDE_ PROCESSORhas_program: SLIDE_PROCESSOR_PRG
SCANNER
BLOCKING_ AGENT
ARRAY_ IMG_ ANALYSIShas_program: IMG_ANALYSIS_PRG
ARRAY_ MEASUREM ENTraw_result s: STRING
SP OT_ M EASUREME NTgri d: I NTEGE Rrow: I NTEGE Rcol umn: INTEGERflag: SHORTder ived_val ue: DOUBLEder ivat ion_method: STRI NG
CHANNEL_ MEASUREMENTint ensi ty: DOUBLEbkg _intens it y: DOUBL E
Process Flow Template
Expressive MACS EFC
Application databases
DATA_ELEMENT
has_parameter 0 ..*
PARAMETERhas_parameter 0..*
has_comment0..*
has_sub_elm
0..*
has_super_elm0 ..1
PROPERTYname : STRINGnum_val : DOUBLEtext_val : STRINGunit : STRING
has_property0..*
has_prev_elm 0..*
has_next_elm 0..*
has_hardware1..1
HW_TOOL 0 ..*
has_software
1..1
SW_TOOL 0..*
has_p rotocol 0..1
PROTOCOLname : STRINGid : STRINGdescription : STRING
has_comment0..*
COMMENTdate : DATEcomment : STRINGcreator : PERSON
has_related_exp
0..*
has_next_exp
0..1
has_prev_exp
0 ..1
has_exp0..*
experiment_in
1..*
has_element 0..*
EXP_ELEMENTname : STRINGid : STRINGexp_id : STRINGdescription : STRING
0..*
0..*
0 ..1
0..*
0..*
0..*
element_of1..*
has_address0..*
has_project
1..*
PROJECTname : STRINGid : STRINGdescription : STRINGstart_date : DATEend_date : DATEurl : STRING
project_of
has_vendor 0..*
HARDWAREname : STRINGid : STRINGdescription : STRING
1..1
has_vendor 0..*
SOFTWAREname : STRINGid : STRINGdescription : STRING
1..1
has_address0..*
ADDRESSstreet : STRINGpostal_code : STRINGcity : STRINGstate : STRINGcountry : STRING
has_performed
0..*
performed_by1 ..*
PROCESSdate : DATE
0..1
defined_by1..1
TEMPLATEname : STRINGid : STRING
has_defined0..*
has_submitter
1..1
has_submitted0. .*
has_contributor
0..*
EXPERIMENTname : STRINGid : STRINGproject_id : STRINGtype : STRINGsubject : STRINGdate : DATEdescription : STRINGpublished_in : STRINGliterature : STRINGurl : STRING
0..*
0..*
0..1
0 ..1
0..* 1..*
0..* 1..*
has_contributed0..*
employee_of
0..*
PERSONname : STRINGid : STRINGtitle : STRINGphone : STRINGfax : STRINGemail : STRINGurl : STRING
0..*0..*
1 ..*
1..1
0..*
1..1
0. .*
0..*
0..*
has_employee
0 ..*
ORGANIZATIONname : STRINGactivity_ type : STRINGphone : STRINGfax : STRINGemail : STRINGurl : STRING
0..*
1..*
0..*0..*
0..*0 ..*
Experimentation Environment Data Model
Common aspects of an experiment
Process and data flow in an experiment
Annotations on an experiment