{"id":9716,"library":"edam-ontology","title":"EDAM Ontology Python Package","description":"The edam-ontology library provides versioned, Python-packaged data for the EDAM ontology (http://edamontology.org/). It offers convenient access to the ontology as an `owlready2` World object, enabling programmatic querying and navigation. The current version is 1.25.3, with releases typically tied to new EDAM ontology versions and Python compatibility updates.","status":"active","version":"1.25.3","language":"python","source_language":"en","source_url":"https://github.com/edamontology/edam-ontology.py","tags":["ontology","bioinformatics","data-science","semantics","owlready2"],"install":[{"cmd":"pip install edam-ontology","lang":"bash","label":"Install latest version"}],"dependencies":[{"reason":"Required to load and query the ontology data.","package":"owlready2","optional":false}],"imports":[{"wrong":"from edam_ontology import EDAM","symbol":"EDAM","correct":"from edam_ontology import EDAM"}],"quickstart":{"code":"from edam_ontology import EDAM, EDAM_ONTOLOGY_VERSION\n\nprint(f\"EDAM Ontology version: {EDAM_ONTOLOGY_VERSION}\")\n\n# EDAM is an OWLReady2 World object that can be queried.\n# For example, count all individuals (entities) in the ontology:\nnum_entities = len(EDAM.individuals())\nprint(f\"Number of EDAM entities: {num_entities}\")\n\n# Accessing a specific class (e.g., 'data'):\ndata_class = EDAM.data\nif data_class:\n    print(f\"Found EDAM class: {data_class.label.first()}\")\nelse:\n    print(\"EDAM.data class not found.\")","lang":"python","description":"This quickstart demonstrates how to import the EDAM ontology and its version, and then perform a basic query to count entities and access a specific class using the `owlready2` API."},"warnings":[{"fix":"Upgrade your Python environment to version 3.9 or higher.","message":"Version 1.25.3 dropped support for Python 3.5-3.8. The library now requires Python 3.9 or newer.","severity":"breaking","affected_versions":"1.25.3 and later"},{"fix":"Refer to the `owlready2` documentation (e.g., `owlready2.readthedocs.io`) to understand how to interact with OWL `World` objects, classes, properties, and individuals.","message":"The `EDAM` object is an `owlready2.World` instance. Effective use of the ontology requires familiarity with `owlready2`'s API for querying, navigating, and manipulating OWL ontologies.","severity":"gotcha","affected_versions":"All versions"},{"fix":"Ensure sufficient memory is available. For very large-scale or resource-limited applications, consider designing your workflow to only load necessary parts or explore alternative methods like SPARQL queries against an external EDAM endpoint if applicable.","message":"Loading the full EDAM ontology into memory (via `edam_ontology.EDAM`) can consume significant RAM (several hundred MBs), especially in resource-constrained environments.","severity":"gotcha","affected_versions":"All versions"}],"env_vars":null,"search_vec":"'/).':22 '1.25.3':44 'access':26 'bioinformat':59 'compat':56 'conveni':25 'current':41 'data':15,61 'data-sci':60 'edam':1,7,18,51 'edam-ontolog':6 'edamontology.org':21 'edamontology.org/).':20 'enabl':35 'librari':9 'navig':39 'new':50 'object':34 'offer':24 'ontolog':2,8,19,29,52,58 'owlready2':32,64 'packag':4,14 'programmat':36 'provid':10 'python':3,13,55 'python-packag':12 'queri':37 'releas':46 'scienc':62 'semant':63 'tie':48 'typic':47 'updat':57 'version':11,42,53 'world':33","created_at":"2026-04-17T01:20:20.727679+00:00","updated_at":"2026-04-17T01:20:20.727679+00:00","problems":{"verify_error":"Traceback (most recent call last):\n  File \"<string>\", line 1, in <module>\nImportError: cannot import name 'EDAM' from 'edam_ontology' (/tmp/tmp4o2djvf3/venv/lib/python3.12/site-packages/edam_ontology/__init__.py)"},"ecosystem":"pypi","meta_description":null,"install_score":null,"quickstart_score":null,"quickstart_tag":null,"pypi_latest":"1.25.3","cli_name":"","cli_version":null,"type":"library","homepage":"http://edamontology.org","github":"https://github.com/edamontology/edam-ontology.py","docs":null,"changelog":null,"pypi":"https://pypi.org/project/edam-ontology/","npm":null,"openapi_spec":null,"status_page":null,"smithery":null,"categories":["data","serialization"],"base_url":null,"auth_type":null,"provenance":{"verified_status":"import_fail","verified_at":"2026-07-03","last_verified":"2026-07-03","next_check":"2026-07-10","install_tag":null}}