{"id":21982130,"url":"https://github.com/lhncbc/ctb","last_synced_at":"2025-03-23T01:20:17.232Z","repository":{"id":86312666,"uuid":"163870823","full_name":"LHNCBC/ctb","owner":"LHNCBC","description":"Custom Taxonomy Builder","archived":false,"fork":false,"pushed_at":"2022-12-10T00:19:40.000Z","size":252,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-28T04:30:24.090Z","etag":null,"topics":["clojure","lvg","taxonomy-construction","umls"],"latest_commit_sha":null,"homepage":"","language":"Clojure","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LHNCBC.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-01-02T17:40:59.000Z","updated_at":"2024-03-12T12:44:01.000Z","dependencies_parsed_at":"2023-03-13T09:45:54.311Z","dependency_job_id":null,"html_url":"https://github.com/LHNCBC/ctb","commit_stats":null,"previous_names":["nlm-lhc/ctb","lhncbc/ctb"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LHNCBC%2Fctb","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LHNCBC%2Fctb/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LHNCBC%2Fctb/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LHNCBC%2Fctb/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LHNCBC","download_url":"https://codeload.github.com/LHNCBC/ctb/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245041603,"owners_count":20551434,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["clojure","lvg","taxonomy-construction","umls"],"created_at":"2024-11-29T17:22:18.514Z","updated_at":"2025-03-23T01:20:17.183Z","avatar_url":"https://github.com/LHNCBC.png","language":"Clojure","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CTB - Custom Taxonomy Builder\n\n## Description\n\nGiven a list of terms and a set of UMLS files, the CTB generates a\nsubset the of UMLS containing the supplied terms and their word-based\nvariants.\n\n## Inputs\n\nThe following files should be placed in the data/input directory:\n\n+ MRCONSO.RRF concepts file\n+ MRSTY.RRF concept -\u003e semantic types file\n\nSupplied to Web Interface\n\n+ list of supplied terms\n\n## Outputs\n\n+ Custom version of mrconso.rrf\n+ Custom version of mrsty.rrf\n\n## Usage\n\nTo use CTB you must first create indexes of your UMLS files and then\nstart the tool.\n\n### Prepare Knowledge Sources\n\nCopy MRCONSO.RRF, MRSTY.RRF to ctb/data/input/*your data set name*/.\n\nIn the ctb directory run:\n\n    bin/prepumls.sh 'your data set name'\n\nFor example:\n\n    bin/prepumls.sh 2016AA\n\nNote: When using the GITHUB release, the name and path the standalone\njar will vary based on version in the project.clj file and the version\nof Leiningen used, the CLASSPATH variable in the script\nbin/prepumls.sh must be modified to match the current location of the\nstandalone jar (or uberjar).\n\n### Update the system configuration file\n\nThere should be a file called ctb.properties in the `config`\ndirectory.  In ctb.properties change:\n\n    ctb.ivf.dataroot: ...\n\nto:\n\n    ctb.ivf.dataroot: data/ivf/\u003cyour data set name\u003e\n\n### Adding LVG to configuration file for term expansion\n\nIf you want to use the Lexical Tools Lexical Variant Generator (LVG)\nto supply term combinations not found in the UMLS then download LVG\nfrom the Lexical Systems Group website\n(https://lsg3.nlm.nih.gov/LexSysGroup/Projects/lvg/current/web/index.html)\nand install it according to its directions.  After installing the\nLexical Tools then add the following to the ctb.properties file:\n\n    ctb.lvg.directory: {LVGDIR}\n\nWhere LVGDIR is the location of your LVG installation.\n\n### Missing directories when using GITHUB release\n\nIf you are using the GITHUB release of CTB then you will need the a\ndirectory for the output.\n\n    mkdir -p resources/public/output\n\n### Start up system\n\nIn the top-level ctb directory run:\n\n    java -jar target/ctb-0.1.3-SNAPSHOT-standalone.jar [port]\n\nNote: When using the GITHUB release, the name and path the standalone\njar will vary based on version in the project.clj file and the version\nof Leiningen used.\n\nor if you have Leiningen:\n\n    lein ring server [port]\n\nThen point your web browser to localhost:3000 (or if you supplied a\nport number, that port number.)\n\n### Supply Term List\n\nPaste your term list into the \"Input Terms\" (first) page and press\n\"Submit\".\n\n### Filter synonyms\n\nSelect or de-select terms in Synonym Set View to filter the synonyms\ngenerated by the tool and press \"Submit\".\n\n### Generate Data Set\n\nThe generated dataset will be placed in the directory\nresources/public/output/user\u003cnumber\u003e/\u003cqueryhash\u003e/.\n\nThe directory should contain the following files:\n\n    filtered-synset\n    filtered-termlist.edn\n    mrconso.rrf\n    mrsty.rrf\n    params\n    synonyms.checksum\n    termlist\n\n## For Users of the Github release\n\nYou will need both [Leiningen](https://leiningen.org/) and\n[Maven](https://maven.apache.org/) to be installed.\n\nIrutils 2.1 inverted file library is necessary to use the latest\nversion of CTB.  In separate directory clone, compile and install\nirutils version 2.1 into your local maven (and leiningen) repository:\n\n    $ git clone https://github.com/willjrogers/irutils.git\n\t$ cd irutils/java\n\t$ git branch rel2.1 rel-2.1\n\t$ git checkout rel2.1\n\t$ mkdir -p src/main\n\t$ (cd src/main \u0026\u0026 ln -s ../../sources java)\n\t$ mvn install\n\nGoto The \"ctb\" directory and compile and package CTB:\n\n    $ cd ctb\n\t$ lein uberjar\n \nIf the uberjar builds successfully, the steps in the usage section\nabove should work normally.\n\n## For Developers\n\n### Running the system in Apache Tomcat\n\nIf you have tomcat you can use the file\ntarget/ctb-0.1.0-SNAPSHOT-standalone.war to deploy the system to\ntomcat.\n\nThe application now expects the config directory containing\nctb.properties and the data directory containing the indexes to be in\nsub-directory war-resources before deployment using the command:  `lein\nring uberwar`.\n\nNote: CTB has not been extensively tested in Tomcat and may require\nmodification to work properly.\n\n## License\n\nCTB is product of the U.S. Government and is not subject to copyright.\n\nFor more information see:\n  http://www.usa.gov/government-works\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flhncbc%2Fctb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flhncbc%2Fctb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flhncbc%2Fctb/lists"}