{"id":22302699,"url":"https://github.com/dataoneorg/annotator","last_synced_at":"2025-03-26T00:28:32.706Z","repository":{"id":24706303,"uuid":"28117864","full_name":"DataONEorg/annotator","owner":"DataONEorg","description":"DataONE Annotation service provides functions for linking OWL concepts to DataONE data.","archived":false,"fork":false,"pushed_at":"2017-03-30T21:50:12.000Z","size":214,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":30,"default_branch":"master","last_synced_at":"2025-01-30T21:17:24.326Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Java","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/DataONEorg.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}},"created_at":"2014-12-17T02:43:09.000Z","updated_at":"2017-03-29T15:06:24.000Z","dependencies_parsed_at":"2022-08-06T02:15:59.398Z","dependency_job_id":null,"html_url":"https://github.com/DataONEorg/annotator","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataONEorg%2Fannotator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataONEorg%2Fannotator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataONEorg%2Fannotator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DataONEorg%2Fannotator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DataONEorg","download_url":"https://codeload.github.com/DataONEorg/annotator/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245565213,"owners_count":20636257,"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":[],"created_at":"2024-12-03T18:40:50.800Z","updated_at":"2025-03-26T00:28:32.670Z","avatar_url":"https://github.com/DataONEorg.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"annotator\n=========\n\nAnnotation services and utilities for the DataONE project.\n\nDesign documentation is in the [sem-prov-design](https://github.com/DataONEorg/sem-prov-design) repository.\n\nAnnotatorJS REST\n----------------\nThis project includes an implementation of the AnnotatorJS REST API for saving, searching, and retrieving annotations that are ultimately stored \nin a DataONE Member Node. The project should be included in a separate Maven webapp project that initializes and defines the paths \nto the AnnotatorRestServlet. The `annotator.nodeid` field in the annotator.properties file defines which MN will serve as the storage repository\nfor annotations. Note that the MN needs to be registered in the same environment as defined by `D1Client.CN_URL` property.\n\nA sample web.xml entry for enabling the servlet:\n\n\t\u003c!--  AnnotatorStore proxy to MN storage --\u003e\n\t\u003cservlet\u003e\n\t\t\u003cservlet-name\u003eannotatorStoreRestServlet\u003c/servlet-name\u003e\n\t\t\u003cservlet-class\u003eorg.dataone.annotator.store.AnnotatorRestServlet\u003c/servlet-class\u003e\n\t\u003c/servlet\u003e\n\t\u003cservlet-mapping\u003e\n\t\t\u003cservlet-name\u003eannotatorStoreRestServlet\u003c/servlet-name\u003e\n\t\t\u003curl-pattern\u003e/annotator/*\u003c/url-pattern\u003e\n\t\u003c/servlet-mapping\u003e\n\nFor details on the AnnotatorJS API, see [their documentation page](http://docs.annotatorjs.org/en/v1.2.x/storage.html)\n\n\nAnnotation Generation\n---------------------\nThis project also includes a command-line utility for generating annotations based on recommendations from various \"matcher\" services.\nThese include: Bioportal, ESOR, and the newer ESOR Cosine service. There is also a \"matcher\" that relies only on manually provided annotations \nfrom a spreadsheet (no external service is called to fid concepts since they are provided along with the PID/entity/attribute being annotated).\n\nOnly one `annotator.matcher.className` should be configured at any given time. Similarly, only one `annotator.store.className` should be defined. \nFor testing, a MockAnnotatorStore can be used and will only print the annotations to stdout for inspection.\n\nAfter configuring the annotator.properties as desired, the utility can be called:\n\n\tmvn exec:java -Dexec.mainClass=\"org.dataone.annotator.Annotator\" -Dexec.args=\"-create -pidfile \u003cURL to list of pids\u003e\"\n\nThere are other flag options as well, described below.\n\nFor automated annotations:\n* `create` (as above)\n* `createAll` (does not use pidfile and simply generates annotations for EVERY metadata object in the configured repo)\n* `remove` (removes annotations for pids in the file)\n* `removeAll` (removes all annotations in the repo)\n\nFor other actions:\n* `manual` (generates annotations from manual spreadsheet identified by file argument)\n* `types` (generates ontology concepts provided in the file argument)\n\nDevelopment logs\n----------------\nFor developers interested in getting an email for each push to the sem-prov repositories, you can subscribe to our mailing list:\n\n* sem-prov-dev: [List Info](http://lists.dataone.org/mailman/listinfo/sem-prov-dev/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdataoneorg%2Fannotator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdataoneorg%2Fannotator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdataoneorg%2Fannotator/lists"}