{"categories":[{"label":"Application Frameworks","url":"https://skillfed.io/packages/category/software-development-libraries-application-frameworks/4"},{"label":"XML","url":"https://skillfed.io/packages/category/text-processing-markup-xml"}],"enrichment":{"capability":"Reads and writes biomedical text annotation formats\u2014BioC XML/JSON, Brat standoff, and PubTator\u2014with a marshal/pickle-like API.","skillfed_tags":["biomedical-nlp","annotation-formats","abandoned"],"use_cases":["Load BioC XML annotation files from biomedical corpora for downstream NLP processing or analysis","Convert between Brat standoff format and BioC format for annotation tool interoperability","Parse PubTator Central output to extract biomedical entity and relation annotations from literature","Serialize processed annotation objects back to BioC or Brat format for sharing with collaborators","Build reproducible biomedical text mining pipelines that depend on standardized annotation formats"],"what_it_does":"bioc is a Python library for serializing and deserializing three biomedical text annotation formats: BioC (XML and JSON), Brat standoff, and PubTator. It exposes a familiar API modeled on Python's standard library marshal and pickle modules, making it straightforward to load annotation files into Python objects and dump them back to disk.\n\nThe package is designed for biomedical NLP workflows where text documents and their annotations need to be exchanged or processed. It depends on lxml for XML parsing, jsonlines for JSON line handling, intervaltree for interval operations, tqdm for progress bars, and docopt for command-line argument parsing. The library has been stable since its 2016 release but is no longer actively maintained.","worth_installing":"Yes, if you work with BioC, Brat, or PubTator formats in a stable biomedical NLP pipeline. The package is mature and has no known vulnerabilities, but it is abandoned and will not receive updates. Install only if you are confident the format specifications and your dependencies will remain compatible, or if you plan to maintain a fork yourself."},"id":"bioc","links":{"html":"https://skillfed.io/packages/bioc","md":"https://skillfed.io/packages/bioc.md","pypi":"https://pypi.org/project/bioc/"},"maintenance":{"status":"abandoned"},"meta":{"latest_release":"2023-08-15","license_spdx":null,"license_treatment":"permissive","name":"bioc","python_support":"supports_current","summary":"bioc - Processing BioC, Brat, and PubTator with Python."},"popularity":{"monthly_downloads":165686,"position":10520,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"2.1"}