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[bioontology-support] Annotator running very slowly

Joey Geiger jfgeiger at mcw.edu
Tue Apr 27 08:59:30 PDT 2010


On Apr 27, 2010, at 10:51 AM, Trish Whetzel wrote:

> Hi Joey,
> 
> Thanks for the note. Can you send along the parameters you are using? For example, are you sending a large block of text and using many ontologies for the annotation and including expansion or is the web service very slow with smaller chunks of text (200-300 words) and only using 1 ontology?
> 

stopwords: a,about,above,across,after,again,against,all,almost,alone,along,already,also,although,always,among,an,and,another,any,anybody,anyone,anything,anywhere,are,area,areas,around,as,ask,asked,asking,asks,at,away,b,back,backed,backing,backs,be,became,because,become,becomes,been,before,began,behind,being,beings,best,better,between,big,both,but,by,c,came,can,cannot,case,cases,certain,certainly,clear,clearly,come,could,d,did,differ,different,differently,do,does,done,down,down,downed,downing,downs,during,e,each,early,either,end,ended,ending,ends,enough,even,evenly,ever,every,everybody,everyone,everything,everywhere,f,face,faces,fact,facts,far,felt,few,find,finds,first,for,four,from,full,fully,further,furthered,furthering,furthers,g,gave,general,generally,get,gets,give,given,gives,go,going,good,goods,got,great,greater,greatest,group,grouped,grouping,groups,h,had,has,have,having,he,her,here,herself,high,high,high,higher,highest,him,himself,his,how,however,i,if,important,in,interest,interested,interesting,interests,into,is,it,its,itself,j,just,k,keep,keeps,kind,knew,know,known,knows,l,large,largely,last,later,latest,least,less,let,lets,like,likely,long,longer,longest,m,made,make,making,man,many,may,me,member,members,men,might,more,most,mostly,mr,mrs,much,must,my,myself,n,necessary,need,needed,needing,needs,never,new,new,newer,newest,next,no,nobody,non,noone,not,nothing,now,nowhere,number,numbers,o,of,off,often,old,older,oldest,on,once,one,only,open,opened,opening,opens,or,order,ordered,ordering,orders,other,others,our,out,over,p,part,parted,parting,parts,per,perhaps,place,places,point,pointed,pointing,points,possible,present,presented,presenting,presents,problem,problems,put,puts,q,quite,r,rather,really,right,right,room,rooms,s,said,same,saw,say,says,second,seconds,see,seem,seemed,seeming,seems,sees,several,shall,she,should,show,showed,showing,shows,side,sides,since,small,smaller,smallest,so,some,somebody,someone,something,somewhere,state,states,still,still,such,sure,t,take,taken,than,that,the,their,them,then,there,therefore,these,they,thing,things,think,thinks,this,those,though,thought,thoughts,three,through,thus,to,today,together,too,took,toward,turn,turned,turning,turns,two,u,under,until,up,upon,us,use,used,uses,v,very,w,want,wanted,wanting,wants,was,way,ways,we,well,wells,went,were,what,when,where,whether,which,while,who,whole,whose,why,will,with,within,without,work,worked,working,works,would,x,y,year,years,yet,you,young,younger,youngest,your,yours,z,et,al


text:
Replicate 1 for control rat adult extraocular muscle; raw data from RGU34A array using antibody scan. Keywords = skeletal muscle, extraocular muscle, microarray

      parameters = {
        "email" => jfgeiger at mcw.edu,
        "longestOnly" => "false",
        "wholeWordOnly" => "true",
        "stopWords" => stopwords,
        "minTermSize" => "2",
        "withSynonyms" => "true",
        "scored" => "true",
        "ontologiesToKeepInResult" => "1000",
        "isVirtualOntologyId" => "true",
        "levelMax" => "0",
        "textToAnnotate"  => text,
        "format" => "xml"


Really I'm sending 14,000 jobs over. The text is a sample of what I'm sending with some being shorter and some being longer. I've included my email address in all the requests so you should be able to track them. It was working well for the last few days until this morning.






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