Great thanks, I'll give it a spin. On 1/4/18, 2:42 PM, "Miller, Timothy" <[email protected]> wrote:
>The UIMA Analysis Engine descriptor for the dictionary component has a >parameter for what ctakes calls a "lookup descriptor". By default the >lookup descriptor describes a lookup in a hsql engine. The xml files in >that sample directory are lookup descriptors for a lookup using the bsv >files they point to. If you want your bsv lookup to complement the >default lookup it's possible to just have two dictionaries running with >different lookup descriptors. I think it's also possible to have a lookup >descriptor have multiple lookup types (i.e. multiple <dictionary> >sections inside <dictionaries>) but I can't guarantee that works! >Tim > >________________________________________ >From: Abramowitsch, Peter <[email protected]> >Sent: Thursday, January 4, 2018 7:51 AM >To: [email protected] >Subject: Re: How to use external CSV or BSV in addition to FastUMLS >attention Sean [EXTERNAL] > >Thanks Tim, > >I did see that folder and its contents and it seemed the right place to >begin. What I couldn't find was how/where to refer to one of those >CustomCuiTui.Xml files in an engine description. > >Peter > >On 1/4/18, 1:41 PM, "Miller, Timothy" ><[email protected]> wrote: > >>Peter, I know Sean is busy this week and he may not see this for a while. >>But I tried this method over the summer and got it to work so I'm fairly >>confident that's the right approach still. Some of the details may have >>changed from two years ago, so I would also check out this directory as a >>starting point: >>https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc >>_ >>ctakes_trunk_ctakes-2Ddictionary-2Dlookup-2Dfast-2Dres_src_main_resources >>_ >>org_apache_ctakes_dictionary_lookup_fast_example_bsv_&d=DwIFAw&c=B73tqXN8 >>E >>c0ocRmZHMCntw&r=5LM1YwNyMUq7CWiSepCCsjTjwuVF4uswNF8BK5Orm10&m=j2h_timB4sk >>c >>lRz6ICf0XlmaUgJekZOOgGo_WF-iuDw&s=qbZInrnxDgeP2prW-pOoOFkVLFweja-ct48H8NW >>y >>dIM&e= >> >>Tim >> >>________________________________________ >>From: Abramowitsch, Peter <[email protected]> >>Sent: Thursday, January 4, 2018 7:28 AM >>To: [email protected] >>Subject: Re: How to use external CSV or BSV in addition to FastUMLS >>attention Sean [EXTERNAL] >> >>Further to my previous message, Sean, I was wondering if you could tell >>me whether this answer you gave in 2015, is still the right way to do >>things in ctakes4.x >> >>permalink: >>https://urldefense.proofpoint.com/v2/url?u=http-3A__markmail.org_message_ >>s >>3ztinppusvsciss&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r= >>H >>eup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Xq7U7BT >>l >>hofW8xpZfuBKuudNTqry4yt5RzaoBoPLRIg&s=BSEa_ZZMusVnqd2JbfeyoBxsDD1ZdfsHVXO >>5 >>6wR8erA&e= >> >>Subject: RE: How to update cTAKES so that new top level categories >>come out based on local >>dictionary?<https://urldefense.proofpoint.com/v2/url?u=http-3A__markmail. >>o >>rg_message_s3ztinppusvsciss&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi >>o >>CoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx667 >>4 >>h&m=Xq7U7BTlhofW8xpZfuBKuudNTqry4yt5RzaoBoPLRIg&s=BSEa_ZZMusVnqd2JbfeyoBx >>s >>DD1ZdfsHVXO56wR8erA&e=> [permalink] >><https://urldefense.proofpoint.com/v2/url?u=http-3A__markmail.org_message >>_ >>s3ztinppusvsciss&d=DwIFAg&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r >>= >>Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=Xq7U7B >>T >>lhofW8xpZfuBKuudNTqry4yt5RzaoBoPLRIg&s=BSEa_ZZMusVnqd2JbfeyoBxsDD1ZdfsHVX >>O >>56wR8erA&e=> >>From: Finan, Sean ([email protected]) >>Date: Oct 6, 2015 2:04:56 pm >>List: org.apache.incubator.ctakes-dev >> >> >>Regards >>Peter >> >>From: <Abramowitsch>, Peter Abramowitsch >><[email protected]<mailto:[email protected]>> >>Date: Thursday, January 4, 2018 at 12:50 PM >>To: "[email protected]<mailto:[email protected]>" >><[email protected]<mailto:[email protected]>> >>Subject: How to use external CSV or BSV in addition to FastUMLS >> >>Can someone point me to any up-to-date how-tos on how to include external >>CSV/BSV type resources to add synonyms, and other terms for dictionary >>lookup to augment the FAST UMLS resources that comes out of the box. >>Perhaps I have missed something, but looking at the >>CTakesDictionaryCreator UI, it looks like it is designed only to choose >>subsets of the UMLS data set rather than allowing one to bring in >>completely new information sources. I scoured the Marklogic ctakes user >>archive, but so many of the entries are old and I'm not sure they >>describe the current way of doing things. >> >>The only approach I could see would be to take use the AggregateEngine >>description and have it point to the CSV annotator, creating a completely >>new AE but this would build other types of annotation, whereas what I'm >>thinking about is a case for creating identified mentions such as a >>DiseaseDisorderMention based on finding an acronym that the UMLS resource >>doesn't know about, even though the concept in its full textual form is >>there. >> >>I'm sure this is not a unique request and apologize in advance if it has >>already been answered somewhere >> >>- Peter >
