Hi Shameer, >Is it possible to traverse from a CUI till the root of UMLS using any functions in UMLS::Inteface ?
Yes, there is the findPathToRoot.pl program should be able to do that for you. For example, if you would like to find all the paths to the root for the concept C0018563 (hand) using the MSH source using only the PAR/CHD relations. You would run the program as follows: findPathToRoot.pl --config configfile hand where the config file contains: SAB :: include MSH REL :: include PAR, CHD I hope this helps. Thanks! Bridget On Wed, Oct 22, 2014 at 3:49 PM, Khader, Shameer <shameer.kha...@mssm.edu> wrote: > Quick question: > > Is it possible to traverse from a CUI till the root of UMLS using any > functions in UMLS::Inteface ? > > Thanks again, > Shameer > > From: <Khader>, Shameer Khader <shameer.kha...@mssm.edu> > Date: Wednesday, October 22, 2014 at 10:20 AM > To: Bridget McInnes <btmcin...@gmail.com> > Subject: Re: UMLS::Interface - getparents > > Thanks Bridget ! > > From: Bridget McInnes <btmcin...@gmail.com> > Date: Tuesday, October 21, 2014 at 2:37 PM > To: Shameer Khader <shameer.kha...@mssm.edu> > Subject: Re: UMLS::Interface - getparents > > Hello Shameer, > > I am glad that you are finding it useful. Off hand there is not a way to > do this specifically with the tools in the package. If I was doing this, I > would probably write a Perl script to run getParents.pl over your dataset, > pick out the parent CUIs loading them into a hash table with the parent as > a key, and then print out all the parents with their associated CUIs ... I > am not certain if this is easy or helpful though. > > I apologize that I can not be of more assistance. > > Best regards, > > Bridget > > > > On Tue, Oct 21, 2014 at 11:01 AM, Khader, Shameer <shameer.kha...@mssm.edu > <https://urldefense.proofpoint.com/v2/url?u=http-3A__mailto-3Ashameer.khader-40mssm.edu&d=AAMFaQ&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=JQ3rpYn2qFuUyCjr3ZDvsexgkQMYxXkSdHHp26idAp0&m=K7XMWa0ThpRZwkWUDqyVYGIb6va10cTcOeAQfykH2oc&s=LGFU7qeidW9_GKawb0mHo7VNuNZ0_v9vdx9sRo6l5ao&e=> > > wrote: > >> Hi Bridget, >> >> Congrats on such a very useful UMLS package. >> >> I am trying to run your script getParents.pl, it is working for me >> using the examples you have given. >> I have a task to find common parent of a bunch of CUI IDs is that >> something any of your methods do at the moment ? >> For example I have the following CUI IDs and I need to find their common >> parent terms. Is there any quick way to do that with UMLS::Interface at the >> moment ? >> >> Appreciate your help. >> Sincerely, >> Shameer >> >> >> C0021080"immunosuppression" >> C0026987"myelofibrosis" >> C0037998"Splenic infarction" >> C0023467"acute myeloblastic leukemia" >> C0023470"myeloid leukemia" >> C0019214"hepatosplenomegaly" >> C2242826"myeloblastic leukemia" >> C0853697"neutrophil count decreased" >> C0023510"white blood cell disorder" >> C0024236"lymphedema" >> C0024141"disseminated lupus erythematosus" >> C0857305"thrombocytopenic purpura" >> C0343387"neutropenic enterocolitis" >> C0030491"parapsoriasis" >> C0836924"thrombocythemia" >> C0162316"iron deficiency anaemia" >> > >
