{"id":21982102,"url":"https://github.com/lhncbc/metamaplite","last_synced_at":"2025-04-30T05:20:56.990Z","repository":{"id":46318376,"uuid":"120805941","full_name":"LHNCBC/metamaplite","owner":"LHNCBC","description":"A near real-time named-entity recognizer ","archived":false,"fork":false,"pushed_at":"2024-05-28T14:58:22.000Z","size":1036,"stargazers_count":59,"open_issues_count":16,"forks_count":14,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-03-30T13:01:44.329Z","etag":null,"topics":["metamap","named-entity-recognition","umls"],"latest_commit_sha":null,"homepage":"https://metamap.nlm.nih.gov/MetaMapLite.shtml","language":"Java","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.bioc","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"2018-02-08T19:17:44.000Z","updated_at":"2024-10-19T21:55:13.000Z","dependencies_parsed_at":"2023-01-21T04:47:54.311Z","dependency_job_id":"0cdd359d-4bb6-473d-8480-a167adf55af8","html_url":"https://github.com/LHNCBC/metamaplite","commit_stats":null,"previous_names":["nlm-lhc/metamaplite","lhncbc/metamaplite"],"tags_count":32,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LHNCBC%2Fmetamaplite","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LHNCBC%2Fmetamaplite/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LHNCBC%2Fmetamaplite/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LHNCBC%2Fmetamaplite/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LHNCBC","download_url":"https://codeload.github.com/LHNCBC/metamaplite/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251645824,"owners_count":21620819,"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":["metamap","named-entity-recognition","umls"],"created_at":"2024-11-29T17:21:59.820Z","updated_at":"2025-04-30T05:20:56.900Z","avatar_url":"https://github.com/LHNCBC.png","language":"Java","funding_links":[],"categories":["人工智能"],"sub_categories":[],"readme":"## A BioC XML to A BioC XML implementation of MetaMapLite\n\nThe class gov.nih.nlm.nls.metamap.lite.BioCProcess allows MetaMapLite\nto process BioC XML input and write the results in BioC XML.\n\n### Using from Java\n\nBelow is an example using BioC Processing with MetaMapLite\n\n    // Initialize MetaMapLite\n    Properties defaultConfiguration = getDefaultConfiguration();\n\tString configPropertiesFilename =\n\t\tSystem.getProperty(\"metamaplite.propertyfile\",\n\t\t                   \"config/metamaplite.properties\");\n    Properties configProperties = new Properties();\n    // set any in-line properties here.\n    FileReader fr = new FileReader(configPropertiesFilename);\n    configProperties.load(fr);\n    fr.close();\n\n    configProperties.setProperty(\"metamaplite.semanticgroup\",\n    \"acab,anab,bact,cgab,dsyn,emod,inpo,mobd,neop,patf,sosy\");\n    Properties properties =\n        Configuration.mergeConfiguration(configProperties,\n\t\t\t\t\t   defaultConfiguration);\n    BioCProcess process = new BioCProcess(properties);\n\n    // read BioC XML collection\n    Reader inputReader = new FileReader(inputFile);\n    BioCFactory bioCFactory = BioCFactory.newFactory(\"STANDARD\");\n    BioCCollectionReader collectionReader =\n    bioCFactory.createBioCCollectionReader(inputReader);\n    BioCCollection collection = collectionReader.readCollection();\n\n    // Run named entity recognition on collection\n    BioCCollection newCollection = process.processCollection(collection);\n\n    // write out the annotated collection\n    File outputFile = new File(outputFilename);\n    Writer outputWriter = new PrintWriter(outputFile, \"UTF-8\");\n    BioCCollectionWriter collectionWriter = bioCFactory.createBioCCollectionWriter(outputWriter);\n    collectionWriter.writeCollection(newCollection);\n    outputWriter.close();\n\nThis process attempts to preserve any annotation present in the\noriginal BioC XML input.    Some annotations applied to BioC\nstructures before entity lookup, including `tokenization and\npart-of-speech-tagging, are discarded before the writing out the final\nannotated collection.   This occurs in the entity lookup class\nBioCEntityLookup (java package: gov.nih.nlm.nls.metamap.lite).\n\n### Omissions in BioC version\n\nThe current version of the BioCProcess class does not call the\nabbreviation detector or the negation detector.   This should be\nrelatively simple to add (particularly the abbreviation detector) and\nwill probably be added in the next release.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flhncbc%2Fmetamaplite","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flhncbc%2Fmetamaplite","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flhncbc%2Fmetamaplite/lists"}