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Vocabulary 21-Oct-2015

Vocabulary Users
#1

To initiate our new tag for vocabulary, let me share my experience with the newest release.

I was able to download via http://www.ohdsi.org/web/athena/ (Athena) the terminologies.
(As of today - i did not experience the zip-file-size-0 bug; Thank you, Athena Team)

I checked quite a lot of terminologies.
The download was 1.015 gigabytes.

For the community benefit, if people want to explore it in R, they can use this R code

concept <-read.delim(‘inst/extdata/concept.csv’,as.is=T,quote = “”)
vocabulary <-read.delim(‘inst/extdata/vocabulary.csv’,as.is=T,quote = “”)
cRelationship <-read.delim(‘inst/extdata/concept_relationship.csv’,as.is=T,quote = “”)
relationship<-read.delim(‘inst/extdata/relationship.csv’,as.is=T,quote = “”)
#cAncestor <-read.delim(‘inst/extdata/concept_ancestor.csv’,as.is=T,quote = “”)

library(dplyr)

#what version
print(filter(vocabulary,VOCABULARY_ID==‘None’)$VOCABULARY_VERSION)

stats<- concept %>% group_by(VOCABULARY_ID) %>% summarise(count= n()) %>% arrange(-count)
write.csv(stats,file=“stats.csv”,row.names=F,quote=F,na=’’)
as.data.frame(stats)

#relationships

library(dplyr);library(tidyr)
#glimpse(cRelationship)
rel_stats<- cRelationship %>% group_by(RELATIONSHIP_ID) %>% summarise(count= n()) %>% arrange(-count) %>% left_join(relationship) %>% separate(col=RELATIONSHIP_NAME,into=c(‘rel’,‘source’),sep=’\\(’,remove=F)

rel2<-rel_stats %>% group_by(source) %>% summarize(distinct_rels = n(),row_cnt=sum(count))
write.csv(rel2,file=“statsTWO.csv”,row.names=F,quote=F,na=’’)

Empty zip file when downloading vocabularies from Athena
Release of new Vocabulary and Download Page
Athena Bug -- zip file download was 0KB, failed to open
#2

@Vojtech_Huser and friends:

Don’t use it right now. We are having a problem with the SPL to RxNorm mapping. RxNav gives us so plentiful relationships that the concept_ancestor table literally blows up, creating this gigantic zip file. Debugging this now. I’ll keep you posted.

Never a dull moment.

1 Like
Bad row in CONCEPT_ANCESTOR
#3

Update: We identified the problem. We had a similar problem with ETC, but never to the degree we got it now with the new SPL: Dailymed links SPL to NDC. RxNav adds to that the relationships to the ingredient of these NDC. The ancestor constructor picks these up but now connects all the SPLs to all other drugs which also contain at least on of those ingredients. As the result we get a gigantic porridge, blowing up the size of the CONCEPT_ANCESTOR table by a factor of 100.

Will remove those and re-release. Till then, don’t download. I’ll take the website down.

1 Like
#4

Friends:

Update. Fixed all the issues, re-releasing now. Should be back in full swing tomorrow. Sorry for all this.

2 Likes
#5

I’m looking forward to the new release, can we grab it from ATHENA yet?

:heartpulse: :dancers: :heartpulse:

#6

Go for it.

#7

I was able to download successfully. The size is 353 MB with most of the non license options checked plus cpt4.

#8

download link is broken for a while

#9

Hello. When did you try to download the archive? Did you do it straight away after receiving the email? Archives are deleted from the server after 72 hours.

#10

“This repo contains the content of the Athena download page, available at http://www.ohdsi.org/web/athena. You don’t need to use any of this code if you are interested in getting the data tables of the Standardized Vocabularies. Just visit the website, choose your vocabularies and download the material.”
Email? i dont receive any

#11

@wanghaisheng:

You did. It’s probably in the Junk folder, because it looks to the mail servers like SPAM. Take a look.

#12

i receive a mail 2015 and have downloaded file successfully ,but the link is broken now when I try to download again.

#13

@wanghaisheng:

As @Alexandr_Tkach said after 72 hours the file is deleted. You have to submit a new request.

#14

the question is i cannot find the submit link ,
weired ,
http://www.ohdsi.org/web/athena/ is ok now
thx again.

t