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[bioontology-support] Annotator running very slowly

Trish Whetzel whetzel at stanford.edu
Tue Apr 27 09:23:06 PDT 2010


Thanks.  Alex, is there a high load on the Annotator this morning?

Trish



On Apr 27, 2010, at 8:59 AM, Joey Geiger wrote:

> 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,alread 
> y,also,although,always,among,an,and,another,any,anybody,anyone,anythin 
> g,anywhere,are,area,areas,around,as,ask,asked,asking,asks,at,away,b,ba 
> ck,backed,backing,backs,be,became,because,become,becomes,been,before,b 
> egan,behind,being,beings,best,better,between,big,both,but,by,c,came,ca 
> n,cannot,case,cases,certain,certainly,clear,clearly,come,could,d,did,d 
> iffer,different,differently,do,does,done,down,down,downed,downing,down 
> s,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,f 
> urthered,furthering,furthers,g,gave,general,generally,get,gets,give,gi 
> ven,gives,go,going,good,goods,got,great,greater,greatest,group,grouped 
> ,grouping,groups,h,had,has,have,having,he,her,here,herself,high,high,h 
> igh,higher,highest,him,himself,his,how,however,i,if,important,in,inter 
> est,interested,interesting,interests,into,is,it,its,itself,j,just,k,ke 
> ep,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,ne 
> wer,newest,next,no,nobody,non,noone,not,nothing,now,nowhere,number,num 
> bers,o,of,off,often,old,older,oldest,on,once,one,only,open,opened,open 
> ing,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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