{"id":32619167,"url":"https://github.com/fnl/chemcheck","last_synced_at":"2026-06-29T01:31:56.767Z","repository":{"id":9773218,"uuid":"11744249","full_name":"fnl/chemcheck","owner":"fnl","description":"a syntax checker for BioCreative IV CHEMDNER task annotations","archived":false,"fork":false,"pushed_at":"2015-03-30T11:06:37.000Z","size":208,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-10-30T18:03:01.985Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fnl.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-07-29T16:31:33.000Z","updated_at":"2024-05-29T14:46:03.000Z","dependencies_parsed_at":"2022-07-12T15:03:49.298Z","dependency_job_id":null,"html_url":"https://github.com/fnl/chemcheck","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/fnl/chemcheck","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fchemcheck","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fchemcheck/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fchemcheck/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fchemcheck/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fnl","download_url":"https://codeload.github.com/fnl/chemcheck/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fchemcheck/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34910177,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-28T02:00:05.809Z","response_time":54,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2025-10-30T18:00:27.220Z","updated_at":"2026-06-29T01:31:56.760Z","avatar_url":"https://github.com/fnl.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"chemcheck\n=========\n\na syntax checker for BioCreative IV CHEMDNER_ task annotations\n\nSynopsis\n--------\n\nA tool to ensure a CHEMDNER_ annotation file is syntactically correct::\n\n  chemcheck sorted_text.tsv sorted_annotations.tsv \u003e pruned_annotations.tsv\n\nRequirements\n------------\n\nTo compile this library, glib (``apt-get install libglib2.0-dev``) and libcsv_\nneed to be installed and visible via pkg-config::\n\n\n  export PKG_CONFIG_PATH=.\n  export LD_LIBRARY_PATH=/usr/local/lib\n  make chemcheck\n\nNote that if libcsv_ is not installed in the standard location at\n``/usr/local`` you need to adapt the ``libcsv-3.0.pc`` file.\n\nUsage\n-----\n\nBefore using chemcheck, ensure that your data is sorted::\n\n  sort input \u003e sorted_input\n\nchemcheck reads the text file one article per row (containing an ID, title\nand abstract column), while at the same time checking the annotations for the\ngiven ID in the annotation file. (This is why the input has to be sorted;\nActually, only the articles and corresponding annotations have to appear in\nthe same order.) The annotation file is expected to contain the following\ncolumns: ID, section ('A' or 'T'), start offset, end offset, annotated string,\nclass. Note that the offsets are character offsets, not byte offsets, while\nall strings should be encoded with UTF-8::\n\n  chemcheck sorted_text.tsv sorted_annotations.tsv \u003e checked_annotations.tsv\n\nchemcheck strips leading and trailing whitespaces on both the annotated string\nas well as the offsets. Then, it checks if the annotated string and the\noffsets have matching lenghts. Third, it ensures that the annotated string and\nthe string found at the given character (not byte!) offset in the text file\nmatch. Last, a check is made to ensure the annotation does not (partially or\nfully) overlap with any other annotation.\n\nIf all these checks pass, the (possibly whitespace-corrected) annotation is\nprinted to STDOUT; If not, a warning (or simple message in case of duplicates)\nis printed to STDERR and the annotation is not printed.\n\n.. _CHEMDNER: http://www.biocreative.org/tasks/biocreative-iv/chemdner/\n.. _libcsv: http://libcsv.sourceforge.net/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffnl%2Fchemcheck","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffnl%2Fchemcheck","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffnl%2Fchemcheck/lists"}