{"id":50277877,"url":"https://github.com/imsweb/pub.tools","last_synced_at":"2026-05-27T22:02:16.094Z","repository":{"id":145106683,"uuid":"132953542","full_name":"imsweb/pub.tools","owner":"imsweb","description":null,"archived":false,"fork":false,"pushed_at":"2025-07-11T15:06:39.000Z","size":5983,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-14T14:03:00.968Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/imsweb.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":null,"funding":null,"license":null,"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,"zenodo":null}},"created_at":"2018-05-10T20:57:05.000Z","updated_at":"2025-07-11T15:06:19.000Z","dependencies_parsed_at":null,"dependency_job_id":"a6bbc878-8710-4dd2-8ae0-a8742d53f05b","html_url":"https://github.com/imsweb/pub.tools","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/imsweb/pub.tools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/imsweb%2Fpub.tools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/imsweb%2Fpub.tools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/imsweb%2Fpub.tools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/imsweb%2Fpub.tools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/imsweb","download_url":"https://codeload.github.com/imsweb/pub.tools/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/imsweb%2Fpub.tools/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33585203,"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":"2026-05-27T02:00:06.184Z","response_time":53,"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":"2026-05-27T22:02:14.515Z","updated_at":"2026-05-27T22:02:16.082Z","avatar_url":"https://github.com/imsweb.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Installation\n\n    pip install pub.tools\n\nTo use this tool you are advised to create an Entrez account and use the associated email and API key.\n\n    from Bio import Entrez\n    Entrez.email = \"myemailhere@imsweb.com\"\n    Entrez.tool = \"pub.tools\"\n    Entrez.api_key = \"mykeyhere\"\n\nTools available:\n\n* entrez - a wrapper API for BioPython\n* citations - creates citations for 6 different types using IMS standards\n* date - formats dates into our desired format\n\n## Citations\n\nCitations are based on a standard defined by PubMed https://www.ncbi.nlm.nih.gov/books/NBK7256/.\nFor some publication types, passing the italicize parameter with a True value will return\nHTML with italic tagged journals or conference names.\n\nYou can easily create a citation from a retrieved PubMed record:\n\n    \u003e\u003e\u003e from pub.tools import entrez\n    \u003e\u003e\u003e from pub.tools import citations\n    \u003e\u003e\u003e if pub := entrez.get_publication(pmid=12345678):\n    \u003e\u003e\u003e     citations.publication_citation(publication=pub)\n\nAlternatively, you can pass one of the following to the citation function:\n\n1. An instance of one of the dataclasses in schema.py\n2. Keyword arguments directly\n\n## Journals\n\nThe journals module uses the PMC source file https://www.ncbi.nlm.nih.gov/pmc/journals/?format=csv\nto construct a library of journals keyed by abbreviation or full title.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimsweb%2Fpub.tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fimsweb%2Fpub.tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fimsweb%2Fpub.tools/lists"}