Very nice! Thank you, Tim and Sean. Dima
> On Feb 15, 2017, at 13:25, Miller, Timothy > <[email protected]> wrote: > > Lol was just about to send this: > https://github.com/tmills/umls-graph-api > > It points at your umls META directory, reads in the ctakes list of TUIs, and > builds a neo4j graph database with all the ISA links, and has a simple API > for getting parent/child CUIs. > I used it for coreference. > Tim > > ________________________________________ > From: Finan, Sean <[email protected]> > Sent: Wednesday, February 15, 2017 2:23 PM > To: [email protected] > Subject: RE: Phenotype-specific entities [SUSPICIOUS] [SUSPICIOUS] > > The dictionary gui doesn't walk the ontology. There are umls tables that > list relations, wherein things like "isa" (is a) relations may satisfy a > hypernym requirement. If you have the umls rrf files look at mrrel.rrf. The > structure is basically concept1|..| concept2|..|relationtype|.. See section > 3.3.9: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_books_NBK9685_&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=agwhlSpSUQ0H6VeJpnACDGcka2fVYSy3HaITKaJN9S8&s=aODQU20_0mAv1i_izwB3RZGOBB0U0ZucFkByxovUJJc&e= > > If anybody has made anything that parses/uses umls relations and can be used > by ctakes, please contribute! Something like a simple traversable umls > graphdb would be a great addition ... Even if it is incomplete or rough, it > could be a valuable seed for a new effort. > > Sean > > -----Original Message----- > From: Savova, Guergana [mailto:[email protected]] > Sent: Wednesday, February 15, 2017 1:54 PM > To: [email protected] > Subject: RE: Phenotype-specific entities [SUSPICIOUS] > > I don't believe there is a tool for walking the UMLS ontology, Dima. But Sean > should confirm that his dictionary building tool does not have that > functionality. > > I think you can use the UMLS tables to get that information. It has been > quite a while I have used these tables, but I remember I was able to get that > information from them... > > Sean, > Does your dictionary building tool implement ontology walking? > > --Guergana > > -----Original Message----- > From: Dligach, Dmitriy [mailto:[email protected]] > Sent: Wednesday, February 15, 2017 1:50 PM > To: [email protected] > Subject: Re: Phenotype-specific entities > > Guergana, thank you. > > Is there anything in cTAKES now for walking the UMLS ontology (e.g. for > finding hypernyms, synonyms, etc.)? > > Dima > > > >> On Feb 15, 2017, at 12:45, Savova, Guergana >> <[email protected]> wrote: >> >> Hi Erin, >> Yes, creating your customized dictionary is the way to go. You can prune by >> semantic types of interest and then remove branches that are not relevant to >> your specific phenotype. I am not aware of cTAKES implementing such a tool >> for a very customized dictionary. >> >> You can also start with a few terms that you know are relevant to your >> phenotype and then find their synonyms in the UMLS. Then, you can further >> walk a specific ontology and take siblings, parents if you think they are >> relevant. >> >> Then, there is the whole field of using word embeddings to find >> synonyms/related terms from unlabeled data if you want to become really >> fancy :-) At this point, cTAKES does not implement any deep learning >> algorithms, in the future we are planning to release a bridge to KERAS. >> >> I hope this makes sense. >> >> -- >> Guergana Savova, PhD, FACMI >> Associate Professor >> PI Natural Language Processing Lab >> Boston Children's Hospital and Harvard Medical School >> 300 Longwood Avenue >> Mailstop: BCH3092 >> Enders 144.1 >> Boston, MA 02115 >> Tel: (617) 919-2972 >> Fax: (617) 730-0817 >> [email protected] >> Harvard Scholar: >> https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.harvard.edu_guergana-5Fk-5Fsavova_biocv&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=EMsbVKH4fuTPUXGVRWfjw4vqV3ifyKdh-3K3OLUIogI&s=oAz3p_diNUmQdKL6UIfE9Vsnj1T4H5xq6CIof1jXisU&e= >> ctakes.apache.org >> thyme.healthnlp.org >> cancer.healthnlp.org >> share.healthnlp.org >> >> >> -----Original Message----- >> From: Erin Nicole Gustafson [mailto:[email protected]] >> Sent: Wednesday, February 15, 2017 1:38 PM >> To: [email protected] >> Subject: Phenotype-specific entities >> >> Hi all, >> >> I would like to be able to only identify entities that are relevant for some >> specific phenotype. One step towards achieving this would be to build a >> custom dictionary with a limited set of semantic types. However, this is not >> quite specific enough to only identify mentions related to one disease while >> ignoring those related to some other disease, for example. >> >> Does cTAKES currently have a way to do this sort of filtering? Or, has >> anyone developed their own tools that they'd be willing to share? >> >> Thanks, >> Erin >
