{"id":15686384,"url":"https://github.com/cmungall/sweet-obo-alignment","last_synced_at":"2026-01-08T15:05:16.673Z","repository":{"id":66914533,"uuid":"102162648","full_name":"cmungall/sweet-obo-alignment","owner":"cmungall","description":"Alignment between ESIP SWEET and Open Bio Ontologies","archived":false,"fork":false,"pushed_at":"2019-07-22T06:20:35.000Z","size":643,"stargazers_count":9,"open_issues_count":4,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-30T11:29:47.643Z","etag":null,"topics":["environment","environment-variables","mapping","obo","obofoundry","ontology","sssom","sweet"],"latest_commit_sha":null,"homepage":"","language":"Makefile","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/cmungall.png","metadata":{"files":{"readme":"README.md","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-09-02T00:34:32.000Z","updated_at":"2022-06-15T14:34:54.000Z","dependencies_parsed_at":"2023-06-18T18:59:08.612Z","dependency_job_id":null,"html_url":"https://github.com/cmungall/sweet-obo-alignment","commit_stats":{"total_commits":14,"total_committers":2,"mean_commits":7.0,"dds":0.0714285714285714,"last_synced_commit":"bfa474a1cd421547fad3dc19c4194d119a1ccf81"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/cmungall/sweet-obo-alignment","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fsweet-obo-alignment","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fsweet-obo-alignment/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fsweet-obo-alignment/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fsweet-obo-alignment/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cmungall","download_url":"https://codeload.github.com/cmungall/sweet-obo-alignment/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cmungall%2Fsweet-obo-alignment/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28246414,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2026-01-08T02:00:06.591Z","response_time":241,"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":["environment","environment-variables","mapping","obo","obofoundry","ontology","sssom","sweet"],"created_at":"2024-10-03T17:39:08.965Z","updated_at":"2026-01-08T15:05:16.605Z","avatar_url":"https://github.com/cmungall.png","language":"Makefile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Alignment between SWEET and OBOs\n\n__ALPHA__ DO NOT TRUST THE RESULTS HERE YET\n\nThis repo contains a pipeline and results for aligning the various ESIP SWEET ontologies with OBOs.\n\nCurrently this is automated but the goal is to learn from a seed of initial curated equivalence axioms using kboom.\n\n## Running the pipeline\n\n```\nmake setup\n. env.sh\nmake\n```\n\nOn subsequent runs, you do not need `make setup`. This clones SWEET into this repo and downloads owltools.\n\nIn the same terminal session you only need to do `. env.sh` once\n\n## Results\n\nEach file is the export of a python dataframe with a mapping and a variety of scores and information. Consult ontobio docs for explanation (TODO)\n\nNote that at this stage it is expected the results include false positives, e.g:\n\n```\nhttp://sweetontology.net/realmCryo#Calf,,UBERON:0003823,hindlimb zeugopod\n```\n\nclearly an ice calf is not the same as the \"calf\" of your leg. We will add high level axioms as 'training' and iterate improving results\n\n## Methods\n\nWe use ontobio-lexmap\n\nsweet classes typically do not have rdfs:labels (some do). We take the\nURI fragment and split the camel case to generate tokenized labels for\neach class (this is done automatically by lexmap.py).\n\nNote that sweet classes do not have synonyms - instead sweet has\nequivalence axioms linking two concepts deemed identical. This is in\ncontrast to OBOs, where we would merge equivalent classes and make the\nlabel from one be a synonym of the other.\n\nWhen attempting to map, we treat each sweet class as distinct, even if\nthey are connected by equivalence axioms. We opt not to do a\npre-merging step. This means that we will have some apparent false\nnegatives, but these will be incorporated at the reasoning stage.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmungall%2Fsweet-obo-alignment","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcmungall%2Fsweet-obo-alignment","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcmungall%2Fsweet-obo-alignment/lists"}