{"id":20074712,"url":"https://github.com/greenelab/annotation-refinery","last_synced_at":"2026-02-27T15:34:23.052Z","repository":{"id":79359002,"uuid":"99031828","full_name":"greenelab/annotation-refinery","owner":"greenelab","description":"A python package that consists of functions that process publicly available annotated sets of genes","archived":false,"fork":false,"pushed_at":"2017-12-18T20:45:36.000Z","size":346,"stargazers_count":5,"open_issues_count":6,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-05-23T00:26:41.610Z","etag":null,"topics":["gene-sets","ontology","package","script","tool"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/greenelab.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2017-08-01T18:34:15.000Z","updated_at":"2020-09-29T19:55:59.000Z","dependencies_parsed_at":"2023-06-13T17:16:31.135Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/annotation-refinery","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/greenelab/annotation-refinery","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fannotation-refinery","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fannotation-refinery/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fannotation-refinery/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fannotation-refinery/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/annotation-refinery/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fannotation-refinery/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29901751,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-27T14:46:13.553Z","status":"ssl_error","status_checked_at":"2026-02-27T14:46:10.522Z","response_time":57,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["gene-sets","ontology","package","script","tool"],"created_at":"2024-11-13T14:53:51.922Z","updated_at":"2026-02-27T15:34:23.008Z","avatar_url":"https://github.com/greenelab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"===================\nAnnotation Refinery\n===================\n\nThe Annotation Refinery python package consists of functions that process\npublicly available annotated sets of genes, such as Gene Ontology and Disease\nOntology terms.\n\n\nRequirements\n------------\n\nBefore you begin, make sure you have the required packages installed in your\nlocal Python environment.\n\n```shell\n# Run this command from the root directory of this repository, where the\n# \"requirements.txt\" file is.\npip install -r requirements.txt\n```\n\nConfiguration files\n-------------------\n\nThe Annotation Refinery requires at least two ``.ini`` configuration files in\nthe main directory to run:\n\n1. A ``main_config.ini`` file with the main configuration settings, and\n\n2. At least one ``\u003cspecies\u003e.ini`` file, which will contain the locations of\n   the desired annotation files for that species, among other things. Users\n   can add configuration files in the main directory for as many species as\n   they want the refinery to process.\n\n\nOptionally, there can also be a ``secrets.ini`` file, which stores values like\nusernames and passwords for access to restricted URLs.\n\n\nThe Main Configuration File\n~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe main configuration file includes settings like the location(s) of the\nspecies file(s), where the output of the refinery (the processed genesets)\nshould be uploaded to, the name of the base directory for all the downloaded\nfiles, and optionally, the location of the secrets file.\n\n.. code-block::\n\n    [main]\n    SECRETS_FILE: secrets.ini\n    PROCESS_TO: Tribe\n\n\n    # All other download folders specified in the configuration files should\n    # be subdirectories of this folder.\n    [download_folder]\n    BASE_DOWNLOAD_FOLDER: download_files\n\n\n    [Tribe parameters]\n    TRIBE_URL: https://tribe.greenelab.com\n\n\n    [species files]\n    SPECIES_FILES: human.ini\n\n\nThe Species File(s)\n~~~~~~~~~~~~~~~~~~~\n\nEach species file should contain the URLs of the desired annotation files to be\ndownloaded.\n\n.. code-block::\n\n    # File for human settings\n\n    [species_info]\n    SCIENTIFIC_NAME: Homo sapiens\n    TAXONOMY_ID: 9606\n\n    # *Note: This should be a subdirectory of the BASE_DOWNLOAD_FOLDER\n    # specified in the main_config.ini file.\n    SPECIES_DOWNLOAD_FOLDER: download_files/Human\n\n\n    # ***********************************************\n    # Below, add as sections the types of annotations\n    # that should be downloaded and processed\n    # ***********************************************\n\n    [GO]\n    DOWNLOAD: TRUE\n\n    GO_OBO_URL: ftp://ftp.geneontology.org/go/ontology/obo_format_1_2/gene_ontology.1_2.obo\n    ASSOC_FILE_URL: ftp://ftp.geneontology.org/go/gene-associations/gene_association.goa_human.gz\n\n    EVIDENCE_CODES: EXP, IDA, IPI, IMP, IGI, IEP\n\n    TAG_MAPPING_FILE: tag_mapping_files/brenda-gobp-all_mapping.dir.v2.txt\n    GO_ID_COLUMN: 2\n    GO_NAME_COLUMN: 3\n    TAG_COLUMN: 1\n    TAG_FILE_HEADER: TRUE\n\n\n    [KEGG]\n    DOWNLOAD: TRUE\n    KEGG_ROOT_URL: http://rest.kegg.jp\n    DB_INFO_URL: /info/kegg\n    SETS_TO_DOWNLOAD: /link/hsa/pathway, /link/hsa/module, /link/hsa/disease\n    SET_INFO_DIR: /get/\n\n    # This is the type of gene identifier used by KEGG for this species\n    XRDB: Entrez\n\n    [DO]\n    DOWNLOAD: TRUE\n    DO_OBO_URL: http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanDO.obo?format=raw\n    MIM2GENE_URL: http://omim.org/static/omim/data/mim2gene.txt\n    GENEMAP_URL: http://data.omim.org/downloads/\u003cSecretKey\u003e/genemap.txt\n\n    # This is the type of gene identifier used by DO\n    XRDB: Entrez\n\n    TAG_MAPPING_FILE: tag_mapping_files/tissue-disease_curated-associations.txt\n    DO_ID_COLUMN: 2\n    DO_NAME_COLUMN: 3\n    TAG_COLUMN: 1\n    TAG_FILE_HEADER: TRUE\n\n\nThe Secrets File\n~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nThe secrets file contains things like usernames and passwords for databases,\nsecret keys for APIs where annotation files will be downloaded from, etc.\n\n.. code-block::\n\n    [OMIM API secrets]\n    SECRET_KEY: ExampleSecretKey\n\n    [Tribe secrets]\n    TRIBE_ID: asdf1234\n    TRIBE_SECRET: qwerty1234\n\n    USERNAME: example_username\n    PASSWORD: password\n\n\nInstructions for getting an OMIM API secret key can be found here:\nhttp://omim.org/downloads\n\nInstructions for getting the Tribe secrets can be found here:\nhttp://tribe-greenelab.readthedocs.io/en/latest/api.html#creating-new-resources-through-tribe-s-api\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fannotation-refinery","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fannotation-refinery","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fannotation-refinery/lists"}