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 [email protected]
[umls-similarity] <[email protected]> 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, [email protected] [umls-similarity] <
> [email protected]> 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
> [email protected] / 703.969.3318 <(703)%20969-3318>
>
>
>
