{"id":32619426,"url":"https://github.com/fnl/bceval","last_synced_at":"2026-07-04T15:32:02.007Z","repository":{"id":139222855,"uuid":"2083690","full_name":"fnl/bceval","owner":"fnl","description":"BioCreative Evaluation Scripts and Library","archived":false,"fork":false,"pushed_at":"2014-05-19T10:43:39.000Z","size":308,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-10-30T18:03:02.694Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"www.biocreative.org","language":"Python","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":"2011-07-21T13:59:27.000Z","updated_at":"2018-05-22T19:17:05.000Z","dependencies_parsed_at":"2023-03-12T13:21:28.027Z","dependency_job_id":null,"html_url":"https://github.com/fnl/bceval","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/fnl/bceval","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fbceval","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fbceval/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fbceval/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fbceval/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fnl","download_url":"https://codeload.github.com/fnl/bceval/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fnl%2Fbceval/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35127443,"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":"2026-07-04T02:00:05.987Z","response_time":113,"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":"2025-10-30T18:01:12.532Z","updated_at":"2026-07-04T15:32:01.997Z","avatar_url":"https://github.com/fnl.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Official BioCreative Evaluation Script\n**************************************\n\nThis package contains the official evaluation script for BioCreative challenges.\n\nIt is compatible with Python 2.5-2.7.\nIt is not compatible with earlier versions of Python.\nIt has not been tested with Python 3+ and will most likely not work.\n\nAuthor: Florian Leitner \u003cfleitner@cnio.es\u003e\nThe BioCreative homepage: http://www.biocreative.org/\n\nGeneral information on the evaluation script: http://www.biocreative.org/resources/biocreative-ii5/evaluation-library/\n\n.. image:: https://zenodo.org/badge/doi/10.5281/zenodo.9970.png\n   :target: https://zenodo.org/record/9970\n   :alt: DOI:10.5281/zenodo.9970\n\nVersion 3.2\nDOI:10.5281/zenodo.9970\n\n============\nINSTALLATION\n============\n\nExtract the library from the tar.gz::\n\n  tar zxvf bc_evaluation-X.X.tar.gz\n\nAnd move into the created directory::\n\n  cd bc_evaluation-X.X.X\n\nGlobal, system wide installation (you need to have admin/sudo permissions)::\n\n  sudo python setup.py install\n\nLocal, user-only installation (in your home directory, in \"~/.local\")::\n\n  python setup.py install --user\n\nIn case you do a local (user) install, you will have to make sure that the bin directory in \"~/.local\" is on you PATH, otherwise the bc-evaluate executable will not be found::\n\n  export PATH=$PATH:~/.local/bin\n\nTo only test if the installation command will work as you think it should, add the option '--dry-run' to the above commands - you will see what will happen, but the setup script will not copy or do anything.\n\nDocumentation on installing python packages (using setup.py)::\n\n  python setup.py --help\n  python setup.py --help-commands\n  python setup.py \u003ccommand\u003e --help\n  python setup.py install --help\n\n==================\nUSAGE INSTRUCTIONS\n==================\n\nUNIX, LINUX, OSX\n----------------\n\nThe installation process should take care that the executable is installed in a way that it can be run from the command-line without further issues. If not, check the last lines when running the script:\n\ncopying build/scripts-2.X/bc-evaluate -\u003e /path/to/some/bin\n\nAnd make sure that path is in your shell's $PATH environment variable. By default, these locations should be:\n\n- Global install: `/usr/local/bin`\n- Local user-install: `~/.local/bin`\n\nAfter installing, you can read instructions on how to use this tool by running its help and documentation commands::\n\n  bc-evaluate --documentation\n  bc-evaluate --help\n\nGENERAL NOTES\n-------------\n\nThe general way of using this tool is::\n\n  bc-evaluate [options] your_result_files... gold_standard_file\n\nThe default (w/o options) works for INT/normalizations and results files that have both confidence and rank values, returning a verbose evaluation report. For all other input/output options, please read the --documentation and the --help output carefully.\n\n============\nDEPENDENCIES\n============\n\nIf you want to use the plotting functionality of the script, you need to install matplotlib, a Python plotting library:\n\nhttp://matplotlib.sourceforge.net/\n\nMatplotlib requires the following external packages:\n\n- python 2.4 (or later, but not python3)\n- numpy 1.1 (or later)\n- libpng 1.1 (or later)\n- freetype 1.4 (or later) [not required to use the plotting functionality of bc-evaluate]\n\nFor more information about installing matplotlib, see:\nhttp://matplotlib.sourceforge.net/users/installing.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffnl%2Fbceval","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffnl%2Fbceval","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffnl%2Fbceval/lists"}