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(C0000786) >> >> 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.spontaneous(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 -- Jennifer L. Wilson Bioengineering, Stanford University jen.wilson...@gmail.com / 703.969.3318
