Hi Ted, I'm reviving this old email thread since this work is becoming relevant to my project again. I realized I never asked - do you have any flat files of disease distances that are pre-calcuated?
I'm looking to cluster down my list of MeSH termed-diseases (all pulled from DisGeNet) into groups of related diseases. For instance, I might want to clump 'Diabetes Mellitus' and 'Diabetes Mellitus, Non-Insulin Dependent' and have a separate group for things such as 'Depressive Symptoms' and 'Depressive Episodes'. Do you have an easy way to create these clusters? Thank you again for your help! On Mon, Jun 5, 2017 at 5:50 PM, Ted Pedersen duluth...@gmail.com [umls-similarity] <umls-similarity@yahoogroups.com> wrote: > > > When I am just trying to get a sense of a measure or test out something > we've added, I often tend to use FMA / Foundational Model of Anatomy as my > source. This is because it includes some fairly intuitive terms and is > structured in a hierarchical fashion, so similarity measures like path and > wup work fairly nicely. I tend to prefer wup over path since wup includes a > kind of correction for the depth of the concepts involved, but at this > point that might be a finer point. But, below are some examples of > intuitive results which I think make some sense at least, and might be a > good starting point for exploring. > > tpederse@maraca:~$ query-umls-similarity-webinterface.pl --sab FMA > --measure wup femur skull > Default Settings: > --default http://atlas.ahc.umn.edu/ > --rel PAR/CHD > User Settings: > --measure wup > > 0.8<>femur(C0015811)<>skull(C0037303) > > > tpederse@maraca:~$ query-umls-similarity-webinterface.pl --sab FMA > --measure wup femur bone > Default Settings: > --default http://atlas.ahc.umn.edu/ > --rel PAR/CHD > User Settings: > --measure wup > > 0.8333<>femur(C0015811)<>bone(C0262950) > > > tpederse@maraca:~$ query-umls-similarity-webinterface.pl --sab FMA > --measure wup skull bone > Default Settings: > --default http://atlas.ahc.umn.edu/ > --rel PAR/CHD > User Settings: > --measure wup > > 0.8696<>skull(C0037303)<>bone(C0262950) > > > tpederse@maraca:~$ query-umls-similarity-webinterface.pl --sab FMA > --measure wup finger hand > Default Settings: > --default http://atlas.ahc.umn.edu/ > --rel PAR/CHD > User Settings: > --measure wup > > 0.6923<>finger(C0016129)<>hand(C0018563) > > > tpederse@maraca:~$ query-umls-similarity-webinterface.pl --sab FMA > --measure wup toe foot > Default Settings: > --default http://atlas.ahc.umn.edu/ > --rel PAR/CHD > User Settings: > --measure wup > > 0.6923<>toe(C0040357)<>foot(C0016504) > > > On Mon, Jun 5, 2017 at 7:30 PM, Ted Pedersen <duluth...@gmail.com> wrote: > >> Hi Jen, >> >> I looked at those particular CUIs and don't think they are in MSH or >> SNOMEDCT - that's why you are getting the -1 even though one would imagine >> there is some similarity between them. To find some other examples using >> Alzheimer's I used UTS Metathesaurus to look up CUIs in MSH that included >> the term Alzheimer's (and 9 were found in MSH). >> >> I took 2 of those and ran them with path and got -1, indicating no path >> found. However, when I used lesk or vector I found non-zero values. Lesk >> and vector are both based on comparing the definitions of two CUIs and do >> not rely on finding paths. >> >> tpederse@maraca:~$ perl query-umls-similarity-webinterface.pl C0002395 >> C0299337 --measure vector --sab MSH >> Default Settings: >> --default http://atlas.ahc.umn.edu/ >> --rel CUI/PAR/CHD/RB/RN >> User Settings: >> --measure vector >> >> 0.3131<>Disease, Alzheimer's(C0002395)<>familial Alzheimer's disease >> protein 1(C0299337) >> >> >> tpederse@maraca:~$ perl query-umls-similarity-webinterface.pl C0002395 >> C0299337 --measure lesk --sab MSH >> Default Settings: >> --default http://atlas.ahc.umn.edu/ >> --rel CUI/PAR/CHD/RB/RN >> User Settings: >> --measure lesk >> >> 19<>Disease, Alzheimer's(C0002395)<>familial Alzheimer's disease protein >> 1(C0299337) >> >> So, the tricky part is sometimes the coverage in different sources - two >> CUIs might be intuitively similar but simply not found in the source being >> used (or not path between them may exist) so will show a -1 value. >> >> I'm not sure this exactly answers your question, but I will think a >> little more and add what I can... >> >> More soon, >> Ted >> >> On Mon, Jun 5, 2017 at 5:41 PM, Jennifer Wilson jen.wilson...@gmail.com >> [umls-similarity] <umls-similarity@yahoogroups.com> wrote: >> >>> >>> >>> Hey Ted, >>> >>> So I haven't quite figured out the MetaMap, but I have a set of diseases >>> that I mapped to CUIs another way. I'm still getting negative results with >>> diseases that I think should be "similar". For example: >>> >>> ./query-umls-similarity-webinterface.pl --sab MSH --rel PAR/CHD >>> "C1864828" "C3810041" >>> >>> Default Settings: >>> >>> --default http://atlas.ahc.umn.edu/ >>> >>> --measure path >>> >>> >>> User Settings: >>> >>> --rel PAR/CHD >>> >>> >>> ["b'-1", 'ALZHEIMER DISEASE 10(C1864828)', "ALZHEIMER DISEASE >>> 18(C3810041)\\n'"] >>> >>> You can see my results on the last row. Could you advise- Would you >>> expect that these two CUIs would not be similar? I wanted to measure path >>> as a simple starting point, but could you recommend that another distance >>> might be more informative? Thanks again for your help! >>> >>> On Mon, Jun 5, 2017 at 1:43 PM, Jennifer Wilson <jen.wilson...@gmail.com >>> > wrote: >>> >>>> Hey Ted, >>>> >>>> Thanks for all of the help. I found the interactive interface really >>>> helpful and had been able to create inputs similar to what you shared. I >>>> have an open help ticket now on trying to get the file to download. He gave >>>> me some commands to try that I had already tried, so there must be >>>> something else to unzipping the code... >>>> >>>> Thanks again. Hopefully I'm close to a solution! >>>> >>>> On Mon, Jun 5, 2017 at 11:21 AM, Ted Pedersen duluth...@gmail.com >>>> [umls-similarity] <umls-similarity@yahoogroups.com> wrote: >>>> >>>>> >>>>> >>>>> Hi Jen, >>>>> >>>>> Nothing to be embarrassed about at all!. If you haven't already used >>>>> MetaMap interactively you might want to try that before you attempt a >>>>> local >>>>> install : >>>>> >>>>> https://ii.nlm.nih.gov/Interactive/UTS_Required/metamap.shtml >>>>> >>>>> (You would need to be logged into UTS for the link to work I think...) >>>>> >>>>> Anyway, once at that site on the right side there are some links for >>>>> using MetaMap interactively. Below is an example of what that looks like >>>>> (where the first line is my input and the rest is the output). I turned on >>>>> the option to show CUIs, since I think that is your desire output... >>>>> >>>>> About the bz2 file, I think you'd need to uncompress that with >>>>> bunzip2, although I have not done a local install for a while so I am not >>>>> 100 percent sure if that is the issue or not. But, I've cc'd the MetaMap >>>>> help line on this note, they are usually very good about following up on >>>>> issues like this. >>>>> >>>>> I hope this helps! >>>>> Ted >>>>> >>>>> Processing 00000000.tx.1: I have a really bad headache, and my joints >>>>> ache. >>>>> >>>>> Phrase: I >>>>> >>>>> Phrase >>>>> i >>>>> <<<<< Phrase >>>>> >>>>> Mappings >>>>> Meta Mapping (1000): >>>>> 1000 C0021966:I- (Iodides) [Inorganic Chemical] >>>>> Meta Mapping (1000): >>>>> 1000 C0221138:I NOS (Blood group antibody I) [Amino Acid, Peptide, or >>>>> Protein,Immunologic Factor] >>>>> <<<<< Mappings >>>>> >>>>> Phrase: have >>>>> >>>>> Phrase >>>>> <<<<< Phrase >>>>> >>>>> Phrase: a really bad headache, >>>>> >>>>> Phrase >>>>> really bad headache >>>>> <<<<< Phrase >>>>> >>>>> Mappings >>>>> Meta Mapping (790): >>>>> 660 C0205169:Bad [Qualitative Concept] >>>>> 827 C0018681:HEADACHE (Headache) [Sign or Symptom] >>>>> <<<<< Mappings >>>>> >>>>> Phrase: and >>>>> >>>>> Phrase >>>>> <<<<< Phrase >>>>> >>>>> Phrase: my joints >>>>> >>>>> Phrase >>>>> joints >>>>> <<<<< Phrase >>>>> >>>>> Mappings >>>>> Meta Mapping (1000): >>>>> 1000 C0022417:Joints [Body Space or Junction] >>>>> Meta Mapping (1000): >>>>> 1000 C0392905:Joints (Articular system) [Body System] >>>>> <<<<< Mappings >>>>> >>>>> Phrase: ache. >>>>> >>>>> Phrase >>>>> ache >>>>> <<<<< Phrase >>>>> >>>>> Mappings >>>>> Meta Mapping (1000): >>>>> 1000 C0234238:ACHE (Ache) [Sign or Symptom] >>>>> <<<<< Mappings >>>>> >>>>> >>>>> >>>>> On Mon, Jun 5, 2017 at 12:25 PM, Jennifer Wilson >>>>> jen.wilson...@gmail.com [umls-similarity] < >>>>> umls-similarity@yahoogroups.com> wrote: >>>>> >>>>>> >>>>>> >>>>>> Hey Ted, >>>>>> >>>>>> I'm (embarrassingly) having some trouble navigating the NLM site. I >>>>>> think I have an account and am trying to download some of the MetaMap >>>>>> software (I think that the "Lite" version is sufficient). But when I >>>>>> download the bz2 file, it won't open because I think I need to >>>>>> authenticate >>>>>> it. Do you know how I'm supposed to access this software? Sorry if this >>>>>> is >>>>>> out of your realm, I can try someone else at NLM. This has just been a >>>>>> lot >>>>>> more difficult and confusing than I thought it should be! Thanks, >>>>>> >>>>>> On Fri, Jun 2, 2017 at 7:07 PM, Ted Pedersen duluth...@gmail.com >>>>>> [umls-similarity] <umls-similarity@yahoogroups.com> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> Hi Jennifer, >>>>>>> >>>>>>> Mapping terms to CUIs is it's own problem, and there are a few nice >>>>>>> tools already available that might be of some use. We've used MetaMap to >>>>>>> good effect for this problem, so you might want to consider looking >>>>>>> there. >>>>>>> >>>>>>> https://metamap.nlm.nih.gov/ >>>>>>> >>>>>>> I'd be curious if other users have recommendations as well.. >>>>>>> >>>>>>> Good luck, >>>>>>> Ted >>>>>>> >>>>>>> On Fri, Jun 2, 2017 at 7:56 PM, Jennifer Wilson >>>>>>> jen.wilson...@gmail.com [umls-similarity] < >>>>>>> umls-similarity@yahoogroups.com> wrote: >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Hi Ted, >>>>>>>> >>>>>>>> Thank you again for all of this. I'm sorry I had to put down this >>>>>>>> project for a few days and am only now getting back to it. >>>>>>>> >>>>>>>> I see that ontologies change and reproducing that result might not >>>>>>>> be the best sanity check on the scripts that I wrote. >>>>>>>> >>>>>>>> I'm going to try and figure out how to map to CUI terms and I'll be >>>>>>>> in touch if I get stuck again. Thanks, >>>>>>>> >>>>>>>> On Sun, May 28, 2017 at 10:59 AM, Ted Pedersen duluth...@gmail.com >>>>>>>> [umls-similarity] <umls-similarity@yahoogroups.com> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> This is perhaps a bit more than you were looking for, but there >>>>>>>>> are quite a few command line tools available with UMLS::Similarity >>>>>>>>> when you >>>>>>>>> install locally that can be helpful for digging into situations like >>>>>>>>> this. >>>>>>>>> When I look for the path from each of these CUIs to the ROOT (of MSH) >>>>>>>>> I >>>>>>>>> find that one of them does not have a path to the root, while the >>>>>>>>> other >>>>>>>>> does (see command output below) >>>>>>>>> >>>>>>>>> The lack of a path to the root is going to cause a lot of >>>>>>>>> measures to report a -1 value (since path, for example, relies on >>>>>>>>> finding >>>>>>>>> this path as a part of its computation). In fact, not having a path >>>>>>>>> to the >>>>>>>>> root makes me question if C0156543 is in MSH at all, so it might even >>>>>>>>> be >>>>>>>>> that the CUI is no longer a part of MSH (and not just lacking a path >>>>>>>>> to the >>>>>>>>> root). But, regardless, clearly something has changed since 2009 that >>>>>>>>> is >>>>>>>>> causing this measure to return a different value. This happens in some >>>>>>>>> cases since UMLS continues to evolve and CUIs are added, removed, >>>>>>>>> etc. It's >>>>>>>>> important to know what version of the UMLS a previous study has used >>>>>>>>> if you >>>>>>>>> are interested in getting a very exact comparison. In the case of our >>>>>>>>> AMIA >>>>>>>>> 2009 paper we used 2008AB, so things have no doubt changed a bit >>>>>>>>> since then. >>>>>>>>> >>>>>>>>> tpederse@maraca:~$ findPathToRoot.pl C0156543 >>>>>>>>> >>>>>>>>> UMLS-Interface Configuration Information: >>>>>>>>> (Default Information - no config file) >>>>>>>>> >>>>>>>>> Sources (SAB): >>>>>>>>> MSH >>>>>>>>> Relations (REL): >>>>>>>>> PAR >>>>>>>>> CHD >>>>>>>>> >>>>>>>>> Sources (SABDEF): >>>>>>>>> UMLS_ALL >>>>>>>>> Relations (RELDEF): >>>>>>>>> UMLS_ALL >>>>>>>>> >>>>>>>>> >>>>>>>>> There are no paths from the given C0156543 to the root. >>>>>>>>> tpederse@maraca:~$ findPathToRoot.pl C0000786 >>>>>>>>> >>>>>>>>> >>>>>>>>> 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 paths between abortions, spontaneous (C0000786) and the root: >>>>>>>>> => C0000000 (**UMLS ROOT**) C1135584 (mesh headings) C1256739 >>>>>>>>> (mesh descriptors) C1256741 (topical descriptor) C0012674 (diseases >>>>>>>>> (mesh >>>>>>>>> category)) C1720765 (female urogenital dis pregnancy compl) C0032962 >>>>>>>>> (compl >>>>>>>>> pregn) C0000786 (abortions, spontaneous) >>>>>>>>> >>>>>>>>> >>>>>>>>> On Sun, May 28, 2017 at 12:43 PM, Ted Pedersen < >>>>>>>>> duluth...@gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi Jennifer, >>>>>>>>>> >>>>>>>>>> Thanks for sharing this question. I think in general if you have >>>>>>>>>> a choice between using CUIs or terms with UMLS::Similarity, your best >>>>>>>>>> option is to use the CUIs. Terms can map to multiple CUIs, and >>>>>>>>>> UMLS::Similarity might pick a CUI associated with a sense of the >>>>>>>>>> term you >>>>>>>>>> aren't intending. Also, if you misspell a term or don't specify it >>>>>>>>>> exactly >>>>>>>>>> correctly, then it shows up as not found. One useful resource for >>>>>>>>>> replicating similarity measure studies (like the one you cite) is the >>>>>>>>>> following page which includes term mappings for several of the >>>>>>>>>> datasets >>>>>>>>>> we've worked with over the years. >>>>>>>>>> >>>>>>>>>> http://www-users.cs.umn.edu/~bthomson/corpus/corpus.html >>>>>>>>>> >>>>>>>>>> I will admit to being a little puzzled about the case of abortion >>>>>>>>>> - miscarriage. The paper you cite clearly reports a value based on >>>>>>>>>> MSH, but >>>>>>>>>> as I try to run that query now I get a value of -1 (even when using >>>>>>>>>> the >>>>>>>>>> CUIs). However, it appears that each of the CUIs is found in MSH, >>>>>>>>>> but that >>>>>>>>>> somehow we are not able to compute some of the measures (a path >>>>>>>>>> length, for >>>>>>>>>> example). This suggests that there is not a path between the two >>>>>>>>>> CUIs, >>>>>>>>>> which has something to do with the structure of UMLS/MSH. >>>>>>>>>> >>>>>>>>>> One quick and dirty way to see if a CUI is in MSH is to find the >>>>>>>>>> path length between a CUI and itself. If it is present in MSH, that >>>>>>>>>> value >>>>>>>>>> will be 1. We see that for each of the CUIs used for abortion and >>>>>>>>>> miscarriage. >>>>>>>>>> >>>>>>>>>> tpederse@maraca:~$ perl query-umls-similarity-webinterface.pl >>>>>>>>>> --measure path --sab MSH C0156543 C0156543 >>>>>>>>>> Default Settings: >>>>>>>>>> --default http://atlas.ahc.umn.edu/ >>>>>>>>>> --rel PAR/CHD >>>>>>>>>> User Settings: >>>>>>>>>> --measure path >>>>>>>>>> >>>>>>>>>> 1<>Unspecified abortion NOS(C0156543)<>Unspecified abortion >>>>>>>>>> NOS(C0156543) >>>>>>>>>> >>>>>>>>>> tpederse@maraca:~$ perl query-umls-similarity-webinterface.pl >>>>>>>>>> --measure path --sab MSH C0000786 C0000786 >>>>>>>>>> Default Settings: >>>>>>>>>> --default http://atlas.ahc.umn.edu/ >>>>>>>>>> --rel PAR/CHD >>>>>>>>>> User Settings: >>>>>>>>>> --measure path >>>>>>>>>> >>>>>>>>>> 1<>Abortions.spontaneous(C0000786)<>Abortions.spontaneous(C0 >>>>>>>>>> 000786) >>>>>>>>>> >>>>>>>>>> However, when I try to find the path length between the two CUIs, >>>>>>>>>> I get -1. This suggests that the CUIs are not jointed by PAR/CHD >>>>>>>>>> relations...note that below you can see that the terms for the CUIs >>>>>>>>>> have >>>>>>>>>> been looked up, which shows us that MSH knows about them... >>>>>>>>>> >>>>>>>>>> tpederse@maraca:~$ perl query-umls-similarity-webinterface.pl >>>>>>>>>> --measure path --sab MSH C0156543 C0000786 >>>>>>>>>> Default Settings: >>>>>>>>>> --default http://atlas.ahc.umn.edu/ >>>>>>>>>> --rel PAR/CHD >>>>>>>>>> User Settings: >>>>>>>>>> --measure path >>>>>>>>>> >>>>>>>>>> -1<>Unspecified abortion NOS(C0156543)<>Abortions.spont >>>>>>>>>> aneous(C0000786) >>>>>>>>>> >>>>>>>>>> So, in any case, it would appear that something has changed in >>>>>>>>>> the structure of MSH since we reported our results in the 2009 AMIA >>>>>>>>>> paper >>>>>>>>>> you mention. I'm not sure what that is. But, I think the general >>>>>>>>>> message is >>>>>>>>>> that if you can use CUIs it will normally be more reliable to do >>>>>>>>>> that. >>>>>>>>>> Mapping terms to CUIs is of course it's own problem, but >>>>>>>>>> UMLS::Similarity >>>>>>>>>> doesn't do anything terribly fancy with that, and so probably >>>>>>>>>> whatever you >>>>>>>>>> do will be more extensive and reliable than what UMLS::Similarity >>>>>>>>>> would >>>>>>>>>> do... >>>>>>>>>> >>>>>>>>>> I hope this helps somehow, and please do feel free to follow up. >>>>>>>>>> Thoughts from other users on this issue would also be most welcome! >>>>>>>>>> >>>>>>>>>> Cordially, >>>>>>>>>> Ted >>>>>>>>>> >>>>>>>>>> On Sat, May 27, 2017 at 12:18 PM, Jennifer Wilson >>>>>>>>>> jen.wilson...@gmail.com [umls-similarity] < >>>>>>>>>> umls-similarity@yahoogroups.com> wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hi all, >>>>>>>>>>> >>>>>>>>>>> I'm resending this now that I'm subscribed. Any advice would be >>>>>>>>>>> much appreciated! Thank you, >>>>>>>>>>> >>>>>>>>>>> ---------- Forwarded message ---------- >>>>>>>>>>> From: Jennifer Wilson <jen.wilson...@gmail.com> >>>>>>>>>>> Date: Tue, May 23, 2017 at 6:13 PM >>>>>>>>>>> Subject: Help with the best approach for using the query-UMLS >>>>>>>>>>> interface >>>>>>>>>>> To: umls-similarity@yahoogroups.com >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Hello UMLS similarity team, >>>>>>>>>>> >>>>>>>>>>> I am trying to compute the similarity between ~30K >>>>>>>>>>> disease/phenotype terms. Ideally, I would have a matrix of >>>>>>>>>>> similarity for >>>>>>>>>>> these terms. >>>>>>>>>>> >>>>>>>>>>> My first attempt was to write a python script to call the >>>>>>>>>>> query-umls-similarity-webinterface.pl script. Though, before >>>>>>>>>>> releasing the script on my dataset, I was trying to recreate the >>>>>>>>>>> scores >>>>>>>>>>> from this paper (https://www.ncbi.nlm.nih.gov/ >>>>>>>>>>> pmc/articles/PMC2815481/) in table 1. >>>>>>>>>>> >>>>>>>>>>> Here's the command I am using: >>>>>>>>>>> >>>>>>>>>>> ./query-umls-similarity-webinterface.pl --sab MSH --rel PAR/CHD >>>>>>>>>>> "Abortion" "Miscarriage" >>>>>>>>>>> >>>>>>>>>>> Default Settings: >>>>>>>>>>> >>>>>>>>>>> --default http://atlas.ahc.umn.edu/ >>>>>>>>>>> >>>>>>>>>>> --measure path >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> User Settings: >>>>>>>>>>> >>>>>>>>>>> --rel PAR/CHD >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> (-1.0, 'Abortion', 'Miscarriage') >>>>>>>>>>> >>>>>>>>>>> I also have not processed the text in my dataset much. I have >>>>>>>>>>> basically pulled diseases and phenotypes from DisGeNet, OMIN, >>>>>>>>>>> PheWas, and >>>>>>>>>>> the GWAS catalogue. If I'm using data from all of these sources - >>>>>>>>>>> do you >>>>>>>>>>> recommend sending them directly to the query interface? Should I >>>>>>>>>>> try and >>>>>>>>>>> map to CUI terms? (examples below) >>>>>>>>>>> >>>>>>>>>>> Before I download the database and attempt to query the database >>>>>>>>>>> (it's not a language that I use in my current work), I just wanted >>>>>>>>>>> an >>>>>>>>>>> outside perspective to see if there are best practices for using >>>>>>>>>>> this data. >>>>>>>>>>> Thank you in advance for your time! >>>>>>>>>>> >>>>>>>>>>> (examples) >>>>>>>>>>> Here are two more examples showing the disease descriptions in >>>>>>>>>>> my dataset. Is the UMLS interface robust to these various formats >>>>>>>>>>> or do >>>>>>>>>>> they need to be an exact match? >>>>>>>>>>> >>>>>>>>>>> ./query-umls-similarity-webinterface.pl --sab MSH --rel PAR/CHD >>>>>>>>>>> "Testicular Neoplasms" "Amelogenesis imperfecta local hypoplastic >>>>>>>>>>> form" >>>>>>>>>>> >>>>>>>>>>> Default Settings: >>>>>>>>>>> >>>>>>>>>>> --default http://atlas.ahc.umn.edu/ >>>>>>>>>>> >>>>>>>>>>> --measure path >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> User Settings: >>>>>>>>>>> >>>>>>>>>>> --rel PAR/CHD >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> (-1.0, 'Testicular Neoplasms', 'Amelogenesis imperfecta local >>>>>>>>>>> hypoplastic form') >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ./query-umls-similarity-webinterface.pl --sab MSH --rel PAR/CHD >>>>>>>>>>> "Hypotrichosis 2, 146520 (3)" "PERIODONTITIS, LOCALIZED AGGRESSIVE" >>>>>>>>>>> >>>>>>>>>>> Default Settings: >>>>>>>>>>> >>>>>>>>>>> --default http://atlas.ahc.umn.edu/ >>>>>>>>>>> >>>>>>>>>>> --measure path >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> User Settings: >>>>>>>>>>> >>>>>>>>>>> --rel PAR/CHD >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> (-1.0, 'Hypotrichosis 2, 146520 (3)', 'PERIODONTITIS, LOCALIZED >>>>>>>>>>> AGGRESSIVE') >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Jennifer L. Wilson >>>>>>>>>>> Bioengineering, Stanford University >>>>>>>>>>> jen.wilson...@gmail.com / 703.969.3318 <(703)%20969-3318> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Jennifer L. Wilson >>>>>>>>>>> Bioengineering, Stanford University >>>>>>>>>>> jen.wilson...@gmail.com / 703.969.3318 <(703)%20969-3318> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Jennifer L. Wilson >>>>>>>> Bioengineering, Stanford University >>>>>>>> jen.wilson...@gmail.com / 703.969.3318 <(703)%20969-3318> >>>>>>>> -- >>>>>>>> Jennifer L. Wilson >>>>>>>> Bioengineering, Stanford University >>>>>>>> jen.wilson...@gmail.com / 703.969.3318 <(703)%20969-3318> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Jennifer L. Wilson >>>>>> Bioengineering, Stanford University >>>>>> jen.wilson...@gmail.com / 703.969.3318 <(703)%20969-3318> >>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> Jennifer L. Wilson >>>> Bioengineering, Stanford University >>>> jen.wilson...@gmail.com / 703.969.3318 <(703)%20969-3318> >>>> >>> >>> >>> >>> -- >>> Jennifer L. Wilson >>> Bioengineering, Stanford University >>> jen.wilson...@gmail.com / 703.969.3318 <(703)%20969-3318> >>> >>> >> > > -- Jennifer L. Wilson Bioengineering, Stanford University jen.wilson...@gmail.com / 703.969.3318
