Clinical Genomics Joint with Clinical Genomics Joint with RCRIMRCRIMAmnon ShaboAmnon Shabo

Joyce HernandezJoyce HernandezMukesh SharmaMukesh Sharma

AGENDAAGENDA

• Gene Expression CMET Overview• Genetic Reports CDA Ballot Overview• Gene Expression DAM Update • Generic Assay Overview• Specimen Model

Gene Expression CMET OverviewGene Expression CMET Overview

Gene Expression DAM UpdateGene Expression DAM Update• Currently reviewing results of the last ballot• Next steps:

– Finish NCI Generic Assay (IRWG)– Changes to GE DAM

• Add “generic” classes from Generic Assay• Bring over additional BRIDGE Classes• Apply suggested changes from the ballot (use case, BRIDG

compatibility)

Clinical Genomics DAM Clinical Genomics DAM (50,000 foot level view) (50,000 foot level view)

c lass Complete Dia gra m

A-P henotype

AminoAc id

+ nam e: St ring

ArrayData Type

+ nam e: Stri ng+ versi on: St rin g

HL 7 CG E lement s

Joyce Add itio ns

NCI M ode l Elem ent s

BRIDG 2.1

Mo dified f or CG

MI AM E-M AGE

MAGE-TAB

Legend

Expression

- classCode: Strin g- id: I ntege r- cod e: Stri ng- nega tionIn d: Boole an- text : Strin g- effecti veTim e: S trin g- uncert aintyco de: String- valu e: Str ing- interpretat ion Code: Str ing- meth odCo de: St ring

This is the Do ma in Inf ormat ion Mo del for the HL 7 Clinica l Genom ics Work Gro up.

It consi sts of th e follo win g top ics:

1. Gen e Expre ssi on 2. Gen eti c Variation3. Gen otype4. Seq uen ce5. Pro teom ics6. Links to Cl inical P hen otypes

Ent ry poin t for the Gen e Expression CM ET POCG_RM 00 0031UV

As soc iate dPrope rty

- classCo de: St ring- id: Inte ger- cod e: String- text : St ring- effe ctiveTi me: St ring- valu e: String- met hod Cod e: String

Gene

+ symbol: Strin g+ fu llNa me : Strin gCo lum n+ g enbankAcce ssi on: Str ing+ g enbankAcce ssi onV ersion: Str ing+ e nsem bl gene ID: S tring+ u nigene clust erI D: Strin g+ e ntrezgen eID: String

Chromosome

+ cho rm osom eNumbe r: In teg er

DNA

- na me

Ne ed d efin ition s

Use this class for in heren t d ata abo ut th e locus, e.g . chro moson e n o.

RNA

- nam e

Nuc leoti des

+ nucleo tide Na me: Str ingIntr on

+ len gth: Integ er+ intronClass: S trin g

Exon

+ len gth: Integ er+ intronClass: Strin g

Nucle obase s

+ sho rtNam e: Strin g

Phos pha te

+ na me: String

Es ter

+ nam e: String

Suga r

+ na me : Str ing

Codon

+ cod on Id: Inte ger

Ush a: Relat ionsh ip shou ld be f rom Ge ne to DNA. Po rti ons of DNA co rresp ond to a Gen e. Chro moso nes woul d have a bun ch of gen es.

GeneticLocus

- id: Intege r- text: Strin g- me thodCo de: St ring- chrom oso me Posi tion : I nteg er- cel lType: St ring

Thi s class is a pla ceh old er f or specifyin g a loc us on t he g en ome, i.e., a p osition of a pa rticular given se qu ence in the subje ct’s ge nom e. Note that the sema ntics of the locus (e.g ., ge ne ) is defi ned by dat a a ssig ned in th e code & value attri bute s of th is class, a nd a lso by plac ing add ition al data relati ng to t his locus in to t he classes (an d CM ETs) associated wi th th is class.

Genome

- cla ssCode : Strin g- id : In teger- co de: Strin g- te xt: S tring- ef fecti veT im e: Strin g- co nfid ent iali tyCod e: St ring- va lue: Stri ng- in terp retati onCod e: St ring- m etho dCode : Stri ng

Geneti cLoci

- classCo de: S trin g- id: Inte ge r- cod e: Stri ng- negatio nIn d: Boole an- titile: S tri ng- text : Strin g- sta tusCode : String- effectiveTime : S tring- con fide ntialit yCo de: String- reason Code: Str ing- valu e: Str ing- interpre tat ion Code: Str ing- method Co de: St ring

Large Duplica iton

- classCode : Stri ng- id : In tege r- code: Str ing- ne gat ionI nd: Bo ole an- te xt: S trin g- ef fecti ve Tim e: Strin g- un cert ain tycode : S tring- confid ent iali tycode: St ring- value: St ring- in terp reta tionCod e: St ring- m etho dCode : S tring

Ge neticDocume nt

- cl assCode : Strin g- id: Inte ge r- co de: Stri ng- title : Stri ng- text: S trin g- sta tusCode : Strin g- effe cti veT ime : Strin g- co nfid ent ialit yCod e: St ring- lan gua geCod e: String- set Id: Int eger- ve rsion Nu mbe r: Inte ger

Large Dele tion

- classCode : Str ing- id: Inte ge r- code: Stri ng- text: S trin g- effe cti veTime : String- confid enti alitycode: Stri ng- uncert aint ycod e: Str ing- value: Str ing- inte rpre tat ionCod e: String- me thod Code: Str ing

Se que nce

- cla ssCode : Strin g- id: Int ege r- co de: Stri ng- ne gati onIn d: Bo ole an- titi le: Stri ng- text: S trin g- sta tusCode : Strin g- eff ecti veT ime : Strin g- rea sonCo de: Str ing- va lue: Str ing- int erpretat ionCod e: Str ing- me tho dCo de: St ring

Ne ed d efin itio ns.

Need def initi ons.

Ne ed defi nitio ns.

Use the va lue attr ibut e to enc apsula te raw dat a re lati ng to th e ent ire set o f loci. For examp le, SNP gen otypin g of a larg e n um ber of gen es/ markers.

Cytogenetics

- classCode : Str ing- id: Inte ge r- code: Stri ng- neg atio nIn d: Bo olea n- text: S trin g- effe cti veTime : String- confid enti alitycode: Stri ng- uncert aint ycod e: Str ing- value: Str ing- inte rpre tat ionCod e: String- me thod Code: Str ing

???Othe rNonLocusData

- classCode : Strin g- id: Inte ge r- code: Stri ng- neg atio nIn d: Bo olea n- text: S trin g- effe cti ve Time : String- confid enti alityco de: Stri ng- uncert aint ycode : Str ing- value: Str ing- inte rpre tat ionCod e: Str ing- me thod Code: Str ing

Need defin itio ns.

Ne ed defin itions. Ne ed def inition s.

Need defi nitio ns.

GenotypeFinding

- no rma lize dXInte nsi ty: f loa t- no rma lize dYInte nsi ty: f loa t- ra wXIn ten sity: floa t- ra wYIn ten sity: floa t- ca ll: S tring

Indiv idualA llele

- classCode: S tring- id: In tege r- cod e: Stri ng- negat ionIn d: Boolea n- titile: Strin g- text : Strin g- sta tusCode : S tring- effecti veTime : S tring- reason Code: Stri ng- valu e: Str ing- interp retat ion Code: Str ing- metho dCo de: Str ing

Se que nce Var iati on

- classCo de: String- id: Inte ger- cod e: Strin g- neg atio nIn d: Boo lea n- titile : Strin g- text : St ring- stat usCo de : Strin g- effe ctiveTi me: St ring- reasonCod e: Strin g- valu e: Stri ng- inte rpre tati onCod e: Strin g- met hod Cod e: Stri ng

DeterminantPepe tide

- cla ssCode : S tring- id: Int ege r- tex t: Strin g- eff ectiveTime : S tring- val ue: Str ing- me tho dCo de: St ring

As soc iatedO bserv a tion

- id: Inte ger- nam e: Str ing- cop yNumb er: Integ er- zygo si ty: S trin g- dom ina ncy: S tring- gen eFa mily: Stri ng

Polypeptide

- cla ssCode : S tring- id: Int ege r- tex t: Strin g- eff ectiveTime : S tring- val ue: Str ing- me tho dCo de: St ring

Ne ed defi nitio ns. Nee d d efini tions.

Shoul d we lea ve this ou t and just ad d classe s as nee ded ?

Entry pa th t o the broa dest pa th of t he gen etic var iat ion mod el.

Vir alGene tics

- cla ssCode : Strin g- id : In tege r- co de: Stri ng- ne gat ionIn d: Bo ole an- te xt: S trin g- ef fecti veT im e: Strin g- co nfid ent iali tyco de: Strin g- un cert ain tycode : S tring- va lue: Str ing- in terp retat ionCod e: St ring- m etho dCode : Str ing

Adde d as a placeh olde r. > Futu re Exp ansion <

Need defin tio ns

SNP Assay

- de sig nAll eles: S trin g- de sig nSco re: Flo at- de sig nSe que nce : Strin g- de sig nStrand : String- id: Lo ng- status: String- ven do rAssayId : Strin g- version : Strin g

SNPP ane l

- assayCou nt: Int ege r- de scriptio n: Strin g- id : Long- na me: S trin g- te chno log y: Str ing- ve ndo r: Strin g- ve ndo rPa nel Id: String- ve rsion: S tri ng

SNP De sig n classe s

Materi al

+ id: Inte ge r+ de scrip tion : Strin g+ na me: Str ing+ formcode: St ring

Ex tractedNon-Gene ticSample

- extrac tedSsa mpleId: In teg er- extrac tedAmo unt : In teger- extrac tedAmo unt UO M: Str ing- extrac tionMe thod : S tring::Ma terial+ id: Int ege r+ de scrip tion : Strin g+ na me: String+ formcode : S tring

Ex tractedGeneti cSa mpl e

+ gen eticSa mp leId: In teg er+ genet icSamp leType: Str ing+ extract edAmo unt: In teger+ extract ionMet hod : S tring+ Genet icSa mp leType : int+ hybrid ization: in t+ aut hori zat ionL ink: ur l::Ma ter ial+ id: Inte ge r+ descrip tion : Strin g+ nam e: String+ form co de: St ring

Or iginalB ioSpec ime n

+ am oun t: i nt+ uni tofM ea sure : S tring+ sta tusCode : Strin g+ sta tusDate Ran ge : Str ing::Mat erial+ id: Inte ge r+ descrip tion : Strin g+ nam e: String+ form co de: Str ing::Node+ experi men tId: Int ege r::Di mensionElement+ nod e: String::Iden tifiab le+ id: URI+ nam e: String+ pro pert ies: St ring+ descrip tion : Strin g

Ha ndlingDoc ument

- Id: int- text: Strin g

Specime nCharacte ristic s

+ Id: in t+ colo r: Stri ng+ clar ity: Strin g+ con dit ion: S tring

Collection

- coll ect ionM et hod : in t- id: int::Handl ingDocument- Id: int- text : S tring

Storage

+ id : Int ege r+ fla shFroze nMe thod: St ring+ te mp: Inte ger+ sto rage Metho d: Strin g::Hand lingDocument- Id : int- te xt: S trin g

Transporta tion

- id: Inte ger::Handl ingDocument- Id: int- text : S tring

Assum e th is is a g en eric list of a ll ma teri al. S pecific m ateria l use d an d tra cke d withi n th e cond uct of a stud y an d/o r cli nical care would be uni que ly i den tifie d via o ther cla sse s (i. e. e xtra cted or resecti ione d sam ple s). The ide ntif ier i s used onl y fo r the ori gina l bi olo gica l specim en.

Arr ayGroup

- arraySpacing X: floa t- arraySpacing Y: floa t- ba rco de: Str ing- le ngth : fl oat- nu mA rrays: Integ er- or ient atio nM ark: en um (top ,bottom ,le ft,rig ht)- wid th : float

Arr ay

+ arra yId ent ifier: String+ arra yXOrig in: Inte ger+ arra yYOrig in: Inte ger+ orig inRelativeTo : Stri ng

Ar rayDes ign

+ id: Inte ge r+ version: Stri ng+ comm ent: St ring+ sub st rateT ype : Strin g+ surfaceT yp e: Str ing+ seq uecn ePo lymerType: Str ing+ conta ctId: In tege r::Id ent ifiab le+ id: URI+ nam e: Strin g+ pro perti es: St ring+ descript ion : Strin g

ArrayManufac ture

- man ufacuru ngDate: St ring- tole rance: Integ er

Gen e expre ssion De sign classe s

Do we ne ed separa te classe s fo r Array De sign (GE versus Genetic vari ation)?Th e a ttribu tes I h ave ad ded are fro m the new MA GE -TA B mod el.Do we still ne ed nu mbe r of feat ures (this cam e fro m th e o ld versio n of the mo del )?

Label edE xtract

- flo uresce ntLa be ling Sub sta nce: Strin g- flo uresce ntLa be ling Sub sta nceA moun t: f loat- flo uresce ntLa be ling Sub sta nceUnits: f loa t

Hybr idi zation

- n ame : Stri ng- a mou ntOfM aterial: float

ArrayM anufa ctureDev iation

Thi s area o f th e M AGE mod el seem s t o be placeh olde rs. Th ere are relati onsh ips to b oth Fea ture Defect a nd Zo ne Defect both o f wh ich do n ot have a ttrib utes.

Fea ture Defect: Stores t he de fect in form ati on for a feat ure.Thi s cla ss point s to Posi tion De lta which ha s coordin ate info rm ation (delt a X ,Y). P osit ionDeltapoin ts to Distan tUnit wh ich cont ains ad diti ona l mea sure ment da ta.Fea ture Defect p oints to a n Onto logyEntry whi ch contain s co ntro lle d vo ca bul ary. The l ink constrains the voca bulary entrie s to repre se nt onl y "defe ctType" .

Zon eDe fect: Stores the defect informat ion for a zo ne .Thi s cla ss point s to th e Zo ne cla ss whi ch does have lower-Righ t X,Y a nd u ppe r-Lef t X,Y co ordinda tes,plus a ro w iden tifi er.

Channel

- cha nn el_n o: Inte ge r

BioAs sayTrea tment

+ bio AssayProcess: St rin g::Node+ exp eri men tId: In teg er::Dimensio nElement+ nod e: Str ing::Ide nt ifiab le+ id: URI+ nam e: St ring+ pro perties: String+ description : String

Ima geAcquis tion

+ image Acq uist ionMeth od

Image

+ na me: St ring+ url : String::DataFile+ id: String+ na me: St ring+ da taFi leTyp e: S trin g+ da taFo rmat: Stri ng::Data+ uri : String+ da tatype: String

Sh ou ld we embe d th e im age as blo b, ra ther tha n poin t to it? Or pro vid e bo th opt ions?ANS: To o hu ge t o sto re in th e d atab ase . I tis rare to go b ack to the m. Bu t some folks wa nt to ke ep the im ages. T hey co uld be kep t i n secon dary.

De riv e dBioAssa yData

Need Arra y M anu fact urin g co nt rol da ta. No t ch ip b ut chip by overal l.

NOTE: Im ag e is scann ed a t d ifferen t wa ve leng ths.

FactorV alue

- valu e: String::Measuremen t+ valu e: String+ min val ue: Str ing+ maxval ue: Str ing+ unit : String::Ide nt ifiab le+ id: UR I+ nam e: Stri ng+ prop erti es: Str ing+ descript ion: S trin g

Lab_Ex per iment

+ id: Inte ge r+ title : S tring+ descript ion : Strin g+ date : d ate+ assayType: St ring+ experimen talDesi gns: String+ form atV ersion: Strin g+ pub licIden tifie r: Stri ng+ sdrf File : String::Ide ntifiab le+ id: URI+ nam e: String+ prop erti es: Str ing+ descript ion : Strin g

Fa ctor

+ typ e: String::Id entifia ble+ id : URI+ n ame : String+ p rope rties: S tring+ d escri ption: Strin g

Experi mentalDes igns

+ typ e: String+ de scri ption: Strin g

Quality Control

+ typ e: Strin g+ qua lityCon trolDe scri ption : Strin g

Re pli cate types

+ rep lica teT ype : Strin g+ rep lica teDescri ption: S tring

Normalizati onTypes

+ normal ization Typ e+ normal ization De script ion: Strin g

These cla sse s ne eds to be harmonize d to Study Design portion ofthe BRIDG mo del.

GenomicP rotocol

+ id : In tege r+ na me : Strin g+ type: Stri ng+ de scri ptio n: Strin g+ ha rdware: S tring+ sof tware: Str ing+ conta ct: Stri ng+ ur l: S tring+ pu blicPro tocolUrl: S trin g

Assum e th ere can be multi ple "experime nts" for co mp lex stu die s. ? ??

Also the n ew version calls t his an Investig at ion. When tal king ab out gen om ics testing a lo t of SM Es use th e term "Expe riment ". In ve stigatio n can also b e co nn ecte d m ore ea sily to the term study wh ich alre ad y ha s a broade r sco pe since i t rep resents th e "cl inical trail " use d in the resea rch con text.

An oth er facto r is tha t th e M GED on tolo gy ma kes refe ren ces to "Expe riment alPro tocol" in a nu mbe r of pl aces, so it mig ht be be tter to kee p a known t erm .

Wh ich terms does th e te am pre fer? Is th ere a te rm that could fit b oth research and he alth care u se?

This class wil l ne ed spe cific ha rmo nizatio n to the St udy cla ss i n BRIDG.ha rdware /soft wa re re qui reme nts fo r th e arrays ne ed to a dde d. These shoul d proba bly be norm alized into separate classes.

Fo r CG DAM model reviewers:we ne ed more exam ple s: I s th ere ot her soft ware required oth er th an th e Repo rter?

ProtocolAppli cations

+ edg eId : In teg er+ ord er: Inte ge r+ not es: Str ing::Ide ntifiab le+ id: URI+ nam e: String+ pro pert ies: St ring+ descrip tion : Strin g

Is t his th e pro per way toidentif y an in dividu al cha nne l?

Germli ne/So mati c needs to b e valid ated by a la b test. Shoul d it just be rep rese nte d a s part of a te st a nd taken out of t he bio -spe cim en?

Image File

+ nam e: Str ing+ sta tus: Str ing+ type : Strin g

RawArrayData

DataFile

+ id: S tring+ name : S tring+ dataFileT ype : Strin g+ dataForm at: String::Da ta+ uri: S trin g+ datat ype: St ring

Ne ed defi nitio n on wh at t ype of data is carried here and whi ch fun ctio n in the process pop ulates it.

Valid ate that "o rde red" means se que nce d a nd doe s no t repre sent "o rde red" from la b.

Fe ature

+ fea ture Id: Integ er+ blo ckCo l: Inte ge r+ blo ckRo w: Int ege r+ col: In teg er+ row : Int eger+ rep orte rid: Inte ger::Desi gnE lement+ id: Inte ge r+ compo sitid : Int eger+ arra yDe signId : In teg er+ fea ture ID: Int ege r::Dimensio nElement+ nod e: String::Id ent ifiable+ id: URI+ nam e: String+ pro pert ies: St ring+ descrip tion : Strin g

Re porter

+ id: Inte ge r+ con tro lTyp e: Stri ng+ seq uence: St ring+ data baseE ntry: S tring: :Desig nE lement+ id: Inte ge r+ com po sitid : Integ er+ arra yDe sig nId : In teg er+ feat ureI D: Int ege r: :Dimensio nElement+ nod e: Stri ng: :Id entifi able+ id: URI+ nam e: Str ing+ prop erti es: St ring+ descript ion : Strin g

Re por terGroup

+ rep orterGroup Id: In tege r+ nam e: Str ing:: DesignEl emen t+ id: Inte ger+ com po sitid: Integ er+ arra yDe sig nId : In teg er+ fea tureI D: Int ege r:: Dimensio nElement+ nod e: Stri ng:: Id entifia ble+ id: URI+ nam e: Str ing+ pro perti es: St ring+ descript ion: Strin g

Ne ed t o diffe rent iate bet wee n froze n and fix.For bre ast can cer.Co ntai ners ne ed t o b e add ed.Exa mp le:No n-fro zen an d froze n tissue sam ple s ne ed to be include d.Un fixed tissue sectio ns (sli de t ype an d sl ide mo unt. In hea lthcare )

Ad d cla ss to h and le thechang e of sta te of th e ma teria l.

Typ ically call ed pro tocol o f tre atm en t.

In M AGE th is is th e a ctu al Im age and everyth in g tha t was d one to get it.

Can do ano th er tre atmen t a nd get ano ther im age . A ctu al st ep s are not kep t for al l ima ges. Usu ally only re cord ed for t he last ima ge.

JH: MAGE-TAB m odel co nflicts with the se stat eme nts. It ha s an Assa y Class as part of the sd rf package a nd a n Im ag e class as part of the dat a pa cka ge. I will rena me th is Bio-A ssa y cla ss t o just Assa y.

NOTE: Mollie: Wants to constrain model for clinical environment at a later point.

Ha rdw are

+ de scri ptio n: Strin g+ versio n: Str ing::Ide nti fiab le+ id : URI+ na me : Strin g+ prope rties: Strin g+ de scri ptio n: Strin g

Software

+ descript ion : Strin g+ version: Strin g::Id ent ifiable+ id: URI+ nam e: String+ prop erti es: Str ing+ descript ion : Strin g

Edge

+ id: Int ege r+ experime ntId enti fier: Strin g+ inp ut: String+ ou tput : Strin g::Ide nt ifiab le+ id: URI+ na me: String+ pro perties: S tring+ de scrip tion : Strin g

Need exa mp les f or EDGE da ta, prim aril y fo r input and ou tpu t. Could n't find an y at them agetab and ta bemag e sit es.

Node

+ exp erim en tId: Integ er::Di mensi onE lement+ nod e: Strin g::Id ent ifia ble+ id: URI+ nam e: Stri ng+ prop erti es: Str ing+ descript ion: Strin g

Dimens ionEle me nt

+ no de: Str ing::Ide nt ifiab le+ id: UR I+ na me: St ring+ pro pertie s: Strin g+ de scriptio n: Strin g

Performer

+ id : In tege r+ p erson ID: In teg er+ p rotocolID : In teger

Pe rson

+ firstnam e: St ring+ lastnam e: St ring+ midin itials: String+ affilia tion: St ring::Contact+ Ad dress: S trin g+ phone : St ring+ email : Str ing+ fax: String+ tollFre ePh one : Strin g::Ide nti fiab le+ id: UR I+ name : Str ing+ prope rties: String+ descri ption : S tring

PersonRole

+ role : S tring::Pe rson+ firstnam e: Str ing+ lastnam e: Str ing+ mid init ials: S tring+ affi liati on: St ring::Conta ct+ Ad dress: Strin g+ pho ne: String+ em ail: String+ fax: St ring+ toll Free Phone : S trin g::Ide nti fiabl e+ id: URI+ nam e: String+ pro pert ies: St ring+ descrip tion : Strin g

Publication

+ id: Inte ger+ pub Med ID: Str ing+ title : Strin g+ pub licatio nDOI : Strin g+ aut horli st: Strin g+ status: String

Contact

+ Address: String+ phone: St ring+ email: String+ fax: String+ tollFreePhone: String::Identifiable+ id: URI+ name: String+ properties: String+ descript ion: String

Ass ay

+ a rrayId en tifie r: Stri ng+ a rrayDataFile s: Strin g+ d erive dArrayDa taFi les: St ring+ a rrayDataMa tricFiles: Strin g+ d erive dArrayDa taM atrixFil es: Stri ng

Tec hnologyType

+ tec hnolog yType: St ring

CompositElement

+ id: Inte ge r+ rep orte rID: Integ er+ dat aba seEntry: S trin g::DesignE lement+ id: Inte ge r+ com positid : I ntege r+ arra yDe sign Id: In teg er+ fea ture ID: I ntege r::Dimensio nElement+ nod e: Strin g::Id ent ifiab le+ id: URI+ nam e: Strin g+ pro pert ies: St ring+ descrip tion : Strin g

Des ignEle ment

+ id: Inte ge r+ com positid : I ntege r+ arra yDe sign Id: In teg er+ fea ture ID: Intege r::D imensio nElement+ nod e: Strin g::Id entifia ble+ id: URI+ nam e: Stri ng+ pro pert ies: St ring+ descrip tion : Strin g

Quest ion on EBI examp le: ht tp:// www.ebi .ac.uk/miam exp ress/he lp/a rra y_de sign s.h tml #ADF

Sh ould the Co mpo sit eSeq uenceCom me nt b e re prese nted a s a da tab aseentry (Ontol ogy Te rm / Va lue pair) o r as variab le?

Data

+ uri : St ring+ da tatype: Stri ng

Da taEle ment

+ id : Inte ge r+ d atama trixId: Inte ge r+ col: Inte ger+ ro w: In tege r+ rowQu ant itat ionT ype : String+ in dex_: Intege r+ seconda yKey: Str ing

Da taMa tri x

Ne ed more in form at ion on h ow thi s is imp lem ente d. De scri ption se em s to ind ica te calcu lation .Se e M GED sectio n b elow:

class Quan tit ationTypede finit ion:Th e Quan tita tionTyp e p rovides a m ethod fo r cal cu latin g a sin gle datum of t he BioAssa yDa ta ma trix.sup erclasses: Qu anti tatio nType Packag epro perties: uniq ue _ide ntif ier MO_ 67 cla ss_role abst ract cla ss_source m ag econstra ints: rest rictio n: has_scale has-class Scale rest rictio n: has_typ e h as-cla ss Da taTyp e

Name: Complete DiagramAuthor: hernajoyVersion: 1.0Created: 2006-01-11 12:00:00 AMUpdated: 2010-06-17 7:10:15 PM

DATA MATRI X EX AMPLE from: http://tab2 ma ge.s ource forge.net/doc s/magetab_docs .html#datama trix

Bio-Specimen-Charac teristi cs

+ term: S tring::Ide nt ifiable+ id: URI+ na me: String+ pro pert ies: S tring+ de scrip tion : Strin g

This is e quivale nt to M ateria l class in the M AGE-TAB m od el.

M ateria l in th is m odel ap plies to BRIDG an d HL7 e xp ande d scop e which g oes b eyo nd bi ologic m ateri al.

Assum e th is cla ss need s to re pre sen t the ma ny to m any associatio ns b etween the follo wing M GE D co ncepts. T hese a ssociat ions atte mpt to g roup ma thema tical fu nctio ns into n ode s.

1 . Node s2 . Node Va lues3 . Node Va lue Types4 . BioAssays5 . BioAssayData Cluste r

Nor malization

+ de rviedArrayDataFile: St rin g::Node+ exp erime ntId: Int ege r::Dimensi onElement+ no de: S trin g::Id entif iable+ id : URI+ na me: Stri ng+ properti es: Str ing+ de script ion : Strin g

Scan

+ a rrayData File s: Strin g+ d erivedArrayDat aFiles: String+ a rrayData Ma tricFiles: S trin g+ d erivedArrayDat aMatrix Files: String::Node+ e xperim entId : In teg er::Dimensio nE lement+ n ode: St ring::Ide nt ifia ble+ i d: URI+ n ame : S tring+ p rope rties: Strin g+ d escri ptio n: Str ing

M easurement

+ va lue: St ring+ mi nva lue: Strin g+ ma xvalue : Strin g+ un it: Stri ng::Identi fiab le+ id: URI+ na me: S tring+ pro perties: Strin g+ de scriptio n: Strin g

Ne ed sa mple da ta fo r t his cl ass.

Protoc olP ara me ter

::Id ent ifia ble+ id : URI+ na me : Stri ng+ prope rties: Strin g+ de scri ptio n: Strin g

Pa ramete rVa lue

+ pro tocolPa ram ete rId: In tege r+ pro tocolAp plicatio n: Inte ger::Measurement+ valu e: Str ing+ min value: Str ing+ ma xval ue: Str ing+ uni t: S tring::Id ent ifia ble+ id: URI+ nam e: Stri ng+ pro perti es: Str ing+ descript ion : Strin g

Sourc e

+ conta ct id: In tege r::Original BioSpeci men+ amo unt : i nt+ unit ofM ea sure: S trin g+ sta tusCo de : Strin g+ sta tusDa te Ra nge : S tring::Ma terial+ id: Inte ge r+ descript ion : Strin g+ nam e: String+ form code: St ring::Node+ experimen tId: Int eg er::D imensionElemen t+ nod e: S tring::Ide ntifia ble+ id: URI+ nam e: String+ prop erti es: Str ing+ descript ion : Strin g

Tre ate dSa mple

::ExtractedGeneti cSample+ gen eticSa mpleI d: In teg er+ gen eticSa mpleT ype: St ring+ extracted Amo unt: Integ er+ extractio nMet hod : Strin g+ Genet icSa mp leType: i nt+ hybrid iza tion: in t+ aut hori zat ionL ink: ur l::Mater ial+ id: Inte ge r+ descrip tion : Strin g+ nam e: String+ form co de: Strin g

Na me ValueType

+ id: In tege r+ name : St ring+ typ e: Strin g

Definition of Experiment

SPECIMEN HANDLING

ARRAY DESIGN

RELATIONSHIPS BETWEEN: (Samples, Arrays and Data)

GENE EXPRESSION DATA

Ush a: May no t ne ed sugar a nd p ho sphate data .

Spec ime n Handling

+ typ e: S trin g+ nam e: St ring+ amo unt : I nteger: :Hand lingDocument- Id: int- text: St rin g

Shipper

- da teS hipped : S tring- sen de rType: Str ing- sen de rNa me : String::Transpo rtati on- id : In tege r::Hand lingDocument- Id : in t- te xt: S trin g

Rec eiv er

- dat eRecie ved: S trin g- receiverType : String- receiverrNa me: Stri ng::Tra nsport atio n- id: Intege r::Handlin gDocument- Id: int- text: Strin g

SpecimenContainer

+ con tai nerTyp e: Strin g+ risk: S tring+ ha ndli ng: Str ing+ cap acityQuan tity: In teger+ he ight Qu anti ty: Inte ger+ dia me terQua ntity: I nteger+ cap Type: String+ sepa ratorT ype : Str ing+ ba rrierQu anti ty: Inte ger+ bo ttom De ltaQua ntity: I nteg er::Id ent ifia ble+ id: URI+ na me: St ring+ pro perties: S tring+ de scrip tion: Strin g

Ce llSourc e

+ Type: St ring::Origi nal BioSpecimen+ am ou nt: in t+ un itof Measure: Str ing+ statu sCode: Strin g+ statu sDateRa nge : Strin g::Resul tIn terpretat ion+ id : In teger::Mate rial+ id : In teger+ de scri ption: Strin g+ na me : String+ fo rmco de : Strin g::Node+ exp eri me ntId : Inte ger::D imensio nEl ement+ no de: St ring::Id ent ifia ble+ id : URI+ na me : String+ prope rties: S tring+ de scri ption: Strin g

Re sultInterpreta tion

+ id: In tege r

1

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cont ains * /code d by 1

ma de u pof * / ispart of 1

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pro duces /pro duced by

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GeneticVariation

Bio-Specimen

Gene Expression

Color Coding SchemeColor Coding Scheme

class Gene Expression

HL7 CG Elements

Joyce Additions

NCI Model Elements

BRIDG 2.1

Modified for CG

MIAME-MAGE

MAGE-TAB

Legend

CG DAM ViewsCG DAM Views

• Process Models– Specimen Handling and Collection (based on NCI public protocol)– Genomcis Testing Process (high level)– Future – interaction diagrams for message flows per Use Case

• Gene Expression – Whole Model– Bio-specimen– Experiment Definition (Gene express specific protocol, not entire study)– Array Design– Common Classes– Data– Relationships

Study Experiment Data

ProtocolEquipment

Software

ExperimentalItem

* *

*

**

*

*

-Study may include other Studies-Study may be composed of many Experiments-Experiment may include other Experiments-Experiment may involve multiple ExperimentalItems-Experiment may be based on multiple Protocols-Experiment may be performed using multiple Equipment-Experiment may be performed using multiple Software-Experiment may produce multiple Data (Output)

Generic Assay Overview

Experiment:-Affymetrix U133P2 Gene Expression-Affymetrix U133P2 Analysis-Specimen definition information entry (might be a component of Affymetrix U133P2 Gene Expression)-Total RNA extraction and QC (might be a component of Affymetrix U133P2 Gene Expression)-cDNA synthesis and cleanup-U133P2 array scan (GCOS: create *.dat and create (.dat to) *.cel)-GCOS U133P2 Gene Expression Analysis (might be a component of Affymetrix U133P2 Analysis)

Study Experiment Data

ProtocolEquipment

Software

ExperimentalItem

* *

*

**

*

*

Study:- Gene expression analysis of tumor/non-tumor sample pair

Examples of Data (ie., Output):-A_U133P2_cDNA-A_U133P2_cDNA_gel_tif-A_U133P2_cDNA_gel_doc -A_U133P2_SpecimenHybChipWashed (ready for stain and wash)-A_U133P2_Specimen_dat-A_U133P2_Specimen_cel-A_U133P2_Specimen_chp (data file with genotypes)

ExperimentalItem:-Project-specific specimen set

Equipment:-Thermacycler-gel apparatus-camera/image system-Affymetrix Fluidics WashStation 450-Affymetrix GS3000 scanner

Protocol:-Affymetrix Cytogenetics Assay Protocol-Affymetrix Protocol for One-Cycle cDNA Synthesis

Software:-image acquisition application-Agilent 2100 Operating Software -GCOS application

Generic Assay Overview

10

Study Experiment

Data

Protocol

Equipment

Software

ExperimentalItem

*

*

*

*

*

*-Study may include other Studies-Study may be composed of many Experiments-Study may be performed according to multiple Protocols-Experiment may include other Experiments-Experiment may involve multiple ExperimentalItems-Experiment may be performed according to multiple Protocols-Experiment may be performed using multiple Equipment-Experiment may be performed using multiple Software-Experiment may produce multiple Data (Output) -Experiment may be performed on Data (data an input for analytical experiment)-Protocol may include other Protocols-Protocol may specify Equipment-Protocol may specify Software-Equipment may specify Software

Study: A detailed examination or analysis designed to discover facts about a system under investigation. Systems may include intact organisms, biologic specimens, and natural or synthetic materials.

Experiment: A coordinated set of actions and observations designed to generate data, with the ultimate goal of discovery or hypothesis testing.

Protocol: A rule which guides how an activity should be performed.

Equipment: An object intended for use whether alone or in combination for diagnostic, prevention, monitoring, therapeutic, scientific, and/or experimental purposes. For example, ….mass spectrometer, PCR machine, microscope, pH meter

ExperimentalItem: Items used in the execution of an experiment: specimens - samples either taken from nature or created for the purpose of study and which are to be the subject of an experiment, and reagents and supplies which will be used in the execution of an experiment. It is not instruments, analysis tools, and general-purpose resources (common reagents, lab equipment, personnel).

Data: A collection or single item of factual information, derived from measurement or research, from which conclusions may be drawn. For example, an image, a .DAT, or .CEL file.

ProcessedData: Data derived from other data. For example, image annotations derived from an image, or the outcome of running a .CEL file through an analytical tool.

The notion of what is data (vs. processed data) is defined by community consensus and may be mutable. Some may consider the .DAT file to be data, and that the .CEL file is processed, while others may consider the .CEL file itself to be data (unprocessed).

= Proposed last week

Generic Assay Overview

Notes:1.ProcessedData has association to Finding; not included on the diagram to keep things focused

1. Isn’t the result of an analytical experiment what we’ve called ProcessedData?2. Do we need to have distinction between Data and ProcessedData? Can we have self association

on Data to handle both in the DAM2.Software needs to be defined3.What about association from ExperimentalItem to ExperimentalStudy?

Generic Assay Overview

Specimen Model OverviewSpecimen Model Overview(Mukesh Sharma)(Mukesh Sharma)