Hi Jen, I'm going to answer your question in a few notes maybe over the next few days...so your first problem with finding a term is not unusual - sometimes small variations in a term can cause a lookup to fail. I usually try to work with Cuis as a result. In your example for whatever reason the (t2d) seems to be causing a problem - when I omit that things seem to work ok...
More soon! Ted tpederse@maraca:~$ getAssociatedCuis.pl 'type 2 diabetes mellitus' UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL The CUIs associated with type 2 diabetes mellitus are: 1. C0011860 tpederse@maraca:~$ getAssociatedCuis.pl 'type 2 diabetes mellitus (t2d)' UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL No CUIs are associated with type 2 diabetes mellitus (t2d). tpederse@maraca:~$ getAssociatedCuis.pl 'type 2 diabetes mellitus' UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL The CUIs associated with type 2 diabetes mellitus are: 1. C0011860 tpederse@maraca:~$ getChildren.pl 'type 2 diabetes mellitus' UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL The children of type 2 diabetes mellitus (C0011860) are: lipoatrophic diabetes (C0011859) tpederse@maraca:~$ getChildren.pl 'type 2 diabetes mellitus (t2d)' UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL Input type 2 diabetes mellitus (t2d) does not exist in this view of the UMLS. On Thu, Aug 31, 2017 at 4:03 PM, Jennifer Wilson jen.wilson...@gmail.com [umls-similarity] <umls-similarity@yahoogroups.com> wrote: > > > Hi Ted, > > You've been incredibly helpful, on this whole project. Thanks for that. > > Part of my problem was that I was avoiding installing the full UMLS > distribution because of storage, and then had a lot of trouble getting it > downloaded, installed, and set up on my computer! But having access to the > UMLS::Interface and UMLS::Similarity scripts is really helpful. > > I'm now at a more specific use of the UMLS in my project. I have a list of > drugs with their disease indications (*most *map to a CUI term) and then > for each drug I have predicted a list of disease for which the drugs could > be used. I want to know "how semantically similar" are my predictions to > the original diseases (to check how often my algorithm is "right"). > > There are few bugs in that for some reason, some diseases return an error > that a CUI doesn't exist, even though, I can find a CUI for the disease in > my umls database: > > > > > *getChildren.pl 'type 2 diabetes mellitus (t2d)'...Input type 2 diabetes > mellitus (t2d) does not exist in this view of the UMLS.* > I also don't always get a match between diseases that I think are > semantically similar, is this just a product of how the hierarchy works? I > would like to capture these as matches if possible! > > > *Hormone receptor positive malignant neoplasm of breast (C1562029) & > Breast Carcinoma (C0678222) = -1* > Also, because I am new to perl, I have been using the --infile option (for > instance with getAssociatedCuis.pl script), piping the output to a text > file and then using Python to awkwardly extract the disease -> CUI > mappings. Is there a better way to do this? Ideally, I could implement a > tiered system for checking matches where I look for an exact match, look > for a matched parent or child term, and then as a last resort look for > matched words (because the of the breast cancer example). > > Any and all advice is much appreciated. Thank you! > > On Tue, Aug 22, 2017 at 5:49 AM, duluth...@gmail.com [umls-similarity] < > umls-similarity@yahoogroups.com> wrote: > >> >> >> Hi Jen, >> >> Here are some ideas about using some of the commands in the installed >> version of UMLS::Similarity to find nearby branches of a given term of CUI. >> A lot more information about the different commands available can be found >> at : >> >> http://search.cpan.org/dist/UMLS-Interface/ >> >> I'm not certain how useful this all will be, but wanted to let you know >> what I was thinking at least. Please feel free to follow up as needed. >> >> >> tpederse@maraca:~$ getAssociatedCuis.pl "Diabetes Mellitus" >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The CUIs associated with Diabetes Mellitus are: >> 1. C0011849 >> >> tpederse@maraca:~$ getChildren.pl C0011849 >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The children of Diabetes mellitus NOS (C0011849) are: >> leprechaunism (C0265344) >> experimental diabetes mellitus (C0011853) >> compl diabetes mellitus (C0342257) >> diabetes mellitus, sudden-onset (C0011854) >> pregnancy-induced diabetes (C0085207) >> states, prediabetic (C0362046) >> noninsulin-dependent diabetes mellitus (C0011860) >> acidoses, diabetic (C0011880) >> >> tpederse@maraca:~$ getParents.pl C0011849 >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The parents of Diabetes mellitus NOS (C0011849) are: >> endocrine system diseases(C0014130) >> metabolism disorder, glucose(C1257958) >> >> tpederse@maraca:~$ getAssociatedCuis.pl >> No term was specified on the command line >> Usage: getAssociatedCuis.pl [OPTIONS] TERM >> Type getAssociatedCuis.pl --help for help. >> tpederse@maraca:~$ getAssociatedCuis.pl "Diabetes Mellitus" >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The CUIs associated with Diabetes Mellitus are: >> 1. C0011849 >> tpederse@maraca:~$ getChildren.pl C0011849 >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The children of Diabetes mellitus NOS (C0011849) are: >> leprechaunism (C0265344) >> experimental diabetes mellitus (C0011853) >> compl diabetes mellitus (C0342257) >> diabetes mellitus, sudden-onset (C0011854) >> pregnancy-induced diabetes (C0085207) >> states, prediabetic (C0362046) >> noninsulin-dependent diabetes mellitus (C0011860) >> acidoses, diabetic (C0011880) >> tpederse@maraca:~$ getParents.pl C0011849 >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The parents of Diabetes mellitus NOS (C0011849) are: >> endocrine system diseases(C0014130) >> metabolism disorder, glucose(C1257958) >> >> tpederse@maraca:~$ getRelated.pl C0011849 RB >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> No CUIs are associated with diabetes mellitus (C0011849) given the >> relation (RB). >> >> >> tpederse@maraca:~$ getRelated.pl C0011849 RN >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The related (RN) CUIs to diabetes mellitus (C0011849): >> premature aging, okamoto type (C2930860) >> lipoatrophy with diabetes, hepatic steatosis, cardiomyopathy, and >> leukomelanodermic papules (C2931057) >> feigenbaum bergeron richardson syndrome (C2931125) >> thiamine responsive megaloblastic anemia syndrome (C0342287) >> yorifuji okuno syndrome (C2931296) >> extrapyramidal disorder, progressive, with primary hypogonadism, mental >> retardation, and alopecia (C0342286) >> pancreatic beta cell agenesis with neonatal diabetes mellitus (C1838655) >> photomyoclonus, diabetes mellitus, deafness, nephropathy, and cerebral >> dysfunction (C1809475) >> furukawa takagi nakao syndrome (C2931765) >> diabetes mellitus, neonatal, with congenital hypothyroidism (C1857775) >> diabetes mellitus, transient neonatal, 2 (C1835887) >> developmental delay, epilepsy, and neonatal diabetes (C1853564) >> mitochondrial myopathy with diabetes (C1839028) >> diabetes mellitus, transient neonatal, 3 (C1864623) >> diabetes mellitus, insulin-resistant, with acanthosis nigricans >> (C0342278) >> maturity-onset diabetes of the young, type 7 (C1864839) >> mitchell-riley syndrome (C2748662) >> hyperproinsulinemia (C0342283) >> muscular atrophy, ataxia, retinitis pigmentosa, and diabetes mellitus >> (C0342281) >> 6q24-related transient neonatal diabetes mellitus (C3711391) >> diabetes mellitus, congenital autoimmune (C1857958) >> pancreatic and cerebellar agenesis (C1836780) >> stimmler syndrome (C1859965) >> atherosclerosis, premature, with deafness, nephropathy, diabetes >> mellitus, photomyoclonus, and degenerative neurologic disease (C1859596) >> diabetes insipidus and mellitus with optic atrophy and deafness, >> mitochondrial form (C1838782) >> diabetes mellitus, transient neonatal, 1 (C1832386) >> pancreatic hypoplasia, congenital, with diabetes mellitus and >> congenital heart disease (C1838780) >> lymphedema-distichiasis syndrome with renal disease and diabetes >> mellitus (C2675066) >> diabetes mellitus, permanent neonatal, with neurologic features >> (C1833102) >> diabetes mellitus, permanent, of infancy (C1833104) >> martinez frias syndrome (C1832443) >> >> >> >> >> >> >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The CUIs associated with Diabetes Mellitus are: >> 1. C0011849 >> >> tpederse@maraca:~$ getChildren.pl C0011849 >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The children of Diabetes mellitus NOS (C0011849) are: >> leprechaunism (C0265344) >> experimental diabetes mellitus (C0011853) >> compl diabetes mellitus (C0342257) >> diabetes mellitus, sudden-onset (C0011854) >> pregnancy-induced diabetes (C0085207) >> states, prediabetic (C0362046) >> noninsulin-dependent diabetes mellitus (C0011860) >> acidoses, diabetic (C0011880) >> >> tpederse@maraca:~$ getParents.pl C0011849 >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The parents of Diabetes mellitus NOS (C0011849) are: >> endocrine system diseases(C0014130) >> metabolism disorder, glucose(C1257958) >> >> tpederse@maraca:~$ getAssociatedCuis.pl >> No term was specified on the command line >> Usage: getAssociatedCuis.pl [OPTIONS] TERM >> Type getAssociatedCuis.pl --help for help. >> tpederse@maraca:~$ getAssociatedCuis.pl "Diabetes Mellitus" >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The CUIs associated with Diabetes Mellitus are: >> 1. C0011849 >> tpederse@maraca:~$ getChildren.pl C0011849 >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The children of Diabetes mellitus NOS (C0011849) are: >> leprechaunism (C0265344) >> experimental diabetes mellitus (C0011853) >> compl diabetes mellitus (C0342257) >> diabetes mellitus, sudden-onset (C0011854) >> pregnancy-induced diabetes (C0085207) >> states, prediabetic (C0362046) >> noninsulin-dependent diabetes mellitus (C0011860) >> acidoses, diabetic (C0011880) >> tpederse@maraca:~$ getParents.pl C0011849 >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The parents of Diabetes mellitus NOS (C0011849) are: >> endocrine system diseases(C0014130) >> metabolism disorder, glucose(C1257958) >> >> tpederse@maraca:~$ getRelated.pl C0011849 RB >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> No CUIs are associated with diabetes mellitus (C0011849) given the >> relation (RB). >> >> >> tpederse@maraca:~$ getRelated.pl C0011849 RN >> >> >> UMLS-Interface Configuration Information: >> (Default Information - no config file) >> >> Sources (SAB): >> MSH >> Relations (REL): >> PAR >> CHD >> >> Sources (SABDEF): >> UMLS_ALL >> Relations (RELDEF): >> UMLS_ALL >> >> >> The related (RN) CUIs to diabetes mellitus (C0011849): >> premature aging, okamoto type (C2930860) >> lipoatrophy with diabetes, hepatic steatosis, cardiomyopathy, and >> leukomelanodermic papules (C2931057) >> feigenbaum bergeron richardson syndrome (C2931125) >> thiamine responsive megaloblastic anemia syndrome (C0342287) >> yorifuji okuno syndrome (C2931296) >> extrapyramidal disorder, progressive, with primary hypogonadism, mental >> retardation, and alopecia (C0342286) >> pancreatic beta cell agenesis with neonatal diabetes mellitus (C1838655) >> photomyoclonus, diabetes mellitus, deafness, nephropathy, and cerebral >> dysfunction (C1809475) >> furukawa takagi nakao syndrome (C2931765) >> diabetes mellitus, neonatal, with congenital hypothyroidism (C1857775) >> diabetes mellitus, transient neonatal, 2 (C1835887) >> developmental delay, epilepsy, and neonatal diabetes (C1853564) >> mitochondrial myopathy with diabetes (C1839028) >> diabetes mellitus, transient neonatal, 3 (C1864623) >> diabetes mellitus, insulin-resistant, with acanthosis nigricans >> (C0342278) >> maturity-onset diabetes of the young, type 7 (C1864839) >> mitchell-riley syndrome (C2748662) >> hyperproinsulinemia (C0342283) >> muscular atrophy, ataxia, retinitis pigmentosa, and diabetes mellitus >> (C0342281) >> 6q24-related transient neonatal diabetes mellitus (C3711391) >> diabetes mellitus, congenital autoimmune (C1857958) >> pancreatic and cerebellar agenesis (C1836780) >> stimmler syndrome (C1859965) >> atherosclerosis, premature, with deafness, nephropathy, diabetes >> mellitus, photomyoclonus, and degenerative neurologic disease (C1859596) >> diabetes insipidus and mellitus with optic atrophy and deafness, >> mitochondrial form (C1838782) >> diabetes mellitus, transient neonatal, 1 (C1832386) >> pancreatic hypoplasia, congenital, with diabetes mellitus and >> congenital heart disease (C1838780) >> lymphedema-distichiasis syndrome with renal disease and diabetes >> mellitus (C2675066) >> diabetes mellitus, permanent neonatal, with neurologic features >> (C1833102) >> diabetes mellitus, permanent, of infancy (C1833104) >> martinez frias syndrome (C1832443) >> >> >> >> > > > -- > Jennifer L. Wilson > Bioengineering, Stanford University > jen.wilson...@gmail.com / 703.969.3318 <(703)%20969-3318> > > >