Hi Tim, Lol rbay, I remembered your talking about this and wondered if you would bite! Cheers! Sean
-----Original Message----- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Wednesday, February 15, 2017 2:26 PM To: dev@ctakes.apache.org Subject: Re: Phenotype-specific entities [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] Lol was just about to send this: https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tmills_umls-2Dgraph-2Dapi&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=qRZhkS_DX1IuuFC4Yk5QiDUt-vqEIeGD7jH-6f_bOFg&s=WhgfFeTaNOm4ZqVuro3orZC12EMUcVlawyJy6RSpj9w&e= 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 <sean.fi...@childrens.harvard.edu> Sent: Wednesday, February 15, 2017 2:23 PM To: dev@ctakes.apache.org 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:guergana.sav...@childrens.harvard.edu] Sent: Wednesday, February 15, 2017 1:54 PM To: dev@ctakes.apache.org 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:ddlig...@luc.edu] Sent: Wednesday, February 15, 2017 1:50 PM To: dev@ctakes.apache.org 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 > <guergana.sav...@childrens.harvard.edu> 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 > guergana.sav...@childrens.harvard.edu > 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:erin.gustaf...@northwestern.edu] > Sent: Wednesday, February 15, 2017 1:38 PM > To: dev@ctakes.apache.org > 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
