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
