tag:blogger.com,1999:blog-7583720.post2764209934984752902..comments2024-03-05T03:17:02.289-08:00Comments on Salmon Run: SoDA - A Dictionary Based Entity Recognition ToolSujit Palhttp://www.blogger.com/profile/06835223352394332155noreply@blogger.comBlogger21125tag:blogger.com,1999:blog-7583720.post-48598955694659583912020-04-29T12:42:13.972-07:002020-04-29T12:42:13.972-07:00I apologize for the delay in reply, my comment not...I apologize for the delay in reply, my comment notifications have been turned off for a while, and I didn't realize it until someone pointed it out to me. In your case, I am guessing you might have figured out the answer already, but ADD supports POST only since you have to package data into it. Here is the <a href="https://github.com/elsevierlabs-os/soda/blob/master/docs/api.md#Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-10241826578969025272019-03-02T21:58:29.154-08:002019-03-02T21:58:29.154-08:00Hi All,
I have deployed soda war into jetty serve...Hi All,<br /><br />I have deployed soda war into jetty server, when i am trying to access add.json getting below error. please help me on this.<br /><br />I have followed the below steps for configuration<br /><br />https://github.com/elsevierlabs-os/soda/blob/master/docs/installation.md<br /><br />http://ec2-34-238-254-45.compute-1.amazonaws.com:8080/soda/add.json<br /><br />Error message:<br />Anonymoushttps://www.blogger.com/profile/13868272269023277340noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-75027032184810056492017-06-11T09:23:30.475-07:002017-06-11T09:23:30.475-07:00Hi Zaki, I have added a project/plugins.sbt to the...Hi Zaki, I have added a project/plugins.sbt to the SoDA project that has these addSbtPlugin calls, if you git pull it you should get it. According to everything I have read it should work. Also it seems to work on my local installation. One suggestion -- if the JettyPlugin is causing problems, try commenting it out. Your package will still build but you will not be able to start and stop Jetty Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-37288293275477918802017-06-09T12:59:08.324-07:002017-06-09T12:59:08.324-07:00Hi Sujit,
Great work, and like Brian, i would lik...Hi Sujit, <br />Great work, and like Brian, i would like to use the SODA project for annotation - however i am facing the same issue as Brian <br /><br />i.e. when I try to package the SODA project with SBT it fails with "build.sbt:11: error: not found: value JettyPlugin enablePlugins(JettyPlugin)<br /><br />I followed your suggestion above, but it doesnt seem to make a difference. <br /><brZakinoreply@blogger.comtag:blogger.com,1999:blog-7583720.post-3785180277952256762017-01-30T09:45:03.064-08:002017-01-30T09:45:03.064-08:00Hi Brian, sorry about the delay in responding. I a...Hi Brian, sorry about the delay in responding. I also have a installation wide plugins.sbt in my $HOME/.sbt/0.13/plugins/plugins.sbt file that contain the following lines (each line should end with \n\n). In retrospect, a better approach should have been to include this in the project, I will figure out how to do this and update the repository when I have some time.<br /><br />"""<Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-74795942988257830852017-01-19T20:43:55.803-08:002017-01-19T20:43:55.803-08:00Hi Sujit, This is a great find - love the idea of ...Hi Sujit, This is a great find - love the idea of this project. I am picking up Scala. I can run through all of your installation instructions on Github - yet when I try and package the SODA project with SBT it fails with "build.sbt:11: error: not found: value JettyPlugin enablePlugins(JettyPlugin)". It seems like some dependency is missing, but I have re-installed a few times to Brian Burdicknoreply@blogger.comtag:blogger.com,1999:blog-7583720.post-1799657629678355552016-01-08T12:02:25.466-08:002016-01-08T12:02:25.466-08:00@nk_2015: apologies for the delay in replying, jus...@nk_2015: apologies for the delay in replying, just saw your comment in my queue, must have missed it when you posted it. Regarding the "fuzzy" comment above, LDA is generally used to group terms into a single topic, and these terms tend to be "related" rather than "similar".Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-14865813079722575352015-12-21T06:18:52.976-08:002015-12-21T06:18:52.976-08:00Hi JG, thanks for the kind words, and your underst...Hi JG, thanks for the kind words, and your understanding is correct. You load (one or more) dictionaries into the index, then throw documents at it, and it comes back with a structured list of entities found in the text - each entity is a flat structure of the IDs (TUIs in your case), matched string, start and end character offset and the confidence of the match. You can deploy this on a local Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-8141580042775881162015-12-20T19:56:50.486-08:002015-12-20T19:56:50.486-08:00Also, how hard would it be to deploy this thing on...Also, how hard would it be to deploy this thing on a local box as it stands now, not as outlined in the configuration page?JohnThttps://www.blogger.com/profile/07792777974717291048noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-5510535374366958552015-12-20T19:54:08.868-08:002015-12-20T19:54:08.868-08:00Sujit, wonderful post. As a physician and avid rea...Sujit, wonderful post. As a physician and avid read of your blog it left me very excited. I wish I was involved in such a wonderful project! <br /><br />Anyways, I haven't looked at the code as I fire off this message: but as I understand it, I can deploy this as a RESTful server and throw a dictionary at it, say a subset of the UMLS, like relevant TUIs etc, and it should achieve pretty good JohnThttps://www.blogger.com/profile/07792777974717291048noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-14001034908580985582015-12-16T07:16:25.606-08:002015-12-16T07:16:25.606-08:00Thanks Xiangtao, I will check it out. Because it l...Thanks Xiangtao, I will check it out. Because it looks like I will have to do individual diffs and then try to adapt to SBT, it might take me a while before I get back.Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-62998754345333533922015-12-14T19:37:39.348-08:002015-12-14T19:37:39.348-08:00Hi, Attach the code in the ISSUE at the github si...Hi, Attach the code in the ISSUE at the github site. <br /><br />https://github.com/elsevierlabs-os/soda/issues/1<br /> <br />Because integration with my company java project. I use maven instead of SBT. <br /><br />Please let me know if have any issue. <br /><br />ThanksXiangtao Wanghttps://www.blogger.com/profile/03208823068107334073noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-44562878711346137562015-12-13T21:27:57.837-08:002015-12-13T21:27:57.837-08:00Hi Sujit, thanks for the reply. Could you please b...Hi Sujit, thanks for the reply. Could you please be more elaborate about "fuzzy" type of similarity or if you could suggest a blog from where i would be able to understand it. I just need to ensure whether the technique i am applying with my data-set is worth it or not.nk_2015https://www.blogger.com/profile/12080442002858887646noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-2792986258099740932015-12-12T11:44:20.518-08:002015-12-12T11:44:20.518-08:00@nk_2015: thanks for sharing the link to lucene-ld...@nk_2015: thanks for sharing the link to lucene-lda, seems like an interesting approach. Could be useful for situations where the similarity needs to be more "fuzzy", for example related search terms. Regarding confusing dependencies, all of these are packaged with the project - I just did a git clone and was able to do the "ant jar" successfully. If you are using Maven or Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-67443801499601796772015-12-12T11:34:52.423-08:002015-12-12T11:34:52.423-08:00@Xiangtao: Very cool idea, and you are welcome, gl...@Xiangtao: Very cool idea, and you are welcome, glad I could help! For the change, if you can do a patch or a pull request and post it into the Issues at the github site, I can check it out and apply.Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-18016724164431140282015-12-09T23:03:49.953-08:002015-12-09T23:03:49.953-08:00Hi Sujit, i saw your blog and it has been really h...Hi Sujit, i saw your blog and it has been really helping me with work on Apache lucene which i am currently doing. Till now,i have implemented TF-IDF Cosine similarity on set of IT service desk tickets to compute similarity between tickets. Also, before experimenting this i had performed Topic modeling using LDA approach with Mallet on the same set of tickets but could not come up with concrete nk_2015https://www.blogger.com/profile/12080442002858887646noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-43426884009542227262015-12-09T22:09:17.232-08:002015-12-09T22:09:17.232-08:00Btw, I have changed the code a little bit by usin...Btw, I have changed the code a little bit by using Spring Boot( jetty and tomcat embed), It is convenient for debugging and deployment without manually copy the war file to jetty server. I would like to contribute the code but do not how... <br />you may take a look the spring boot http://projects.spring.io/spring-boot/<br />ThanksXiangtao Wanghttps://www.blogger.com/profile/03208823068107334073noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-17598793200557849622015-12-09T21:37:32.826-08:002015-12-09T21:37:32.826-08:00Currently i try to use it to add the whole wikiped...Currently i try to use it to add the whole wikipedia article into solr and annotate text. then use the result for entity type inference based on the categories of wiki articles and the hierarchical categories linkage (use neo4j). Your effort help me a lot. <br />Very appreciate ! ThanksXiangtao Wanghttps://www.blogger.com/profile/03208823068107334073noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-30723987968373697262015-12-02T11:58:44.431-08:002015-12-02T11:58:44.431-08:00@Xiangtao: I have updated the documentation and up...@Xiangtao: I have updated the documentation and upgraded to use xsbt-web-plugin 2.1.0 (latest as of today). I did not need to specify in compile for the containerConfigFile. Thanks again for the feedback.Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-45545376879940341312015-12-01T09:09:20.134-08:002015-12-01T09:09:20.134-08:00Thanks for the jetty plugins fix for latest versio...Thanks for the jetty plugins fix for latest version of xsbt-web, I will upgrade in the project and incorporate your fix.<br /><br />For the error you are seeing, this is because of a NPE in line 24 of SodaUtils. It is looking for a file called soda.properties. You will need to copy soda.properties.template into soda.properties and update the values in there. Thanks for pointing this out, I need Sujit Palhttps://www.blogger.com/profile/06835223352394332155noreply@blogger.comtag:blogger.com,1999:blog-7583720.post-26531193786445254782015-11-30T23:34:39.463-08:002015-11-30T23:34:39.463-08:00Thanks for open source this amazing project. It i...Thanks for open source this amazing project. It is a quite useful tool for NER. <br /><br />I would like to play with the project, but got some issue after deploy it on jetty. <br /><br />There is the log file from jetty :<br />https://docs.google.com/document/d/1nLUGbxA8AHkz9SkP0x_K-rvvrunYEyWOIiLV_rVI63U/edit?usp=sharing<br /><br />Could you help me to take a look and tell the problem if Xiangtao Wanghttps://www.blogger.com/profile/03208823068107334073noreply@blogger.com