{"id":25359652,"url":"https://github.com/monarch-initiative/mapping-walker","last_synced_at":"2025-10-29T23:31:31.057Z","repository":{"id":39848326,"uuid":"471554921","full_name":"monarch-initiative/mapping-walker","owner":"monarch-initiative","description":"walks mapping graphs running boomer","archived":false,"fork":false,"pushed_at":"2022-05-24T23:55:23.000Z","size":1786,"stargazers_count":5,"open_issues_count":3,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-06-11T16:35:58.655Z","etag":null,"topics":["bioportal","boomer","entity-normalization","knowledge-graphs","mapping-commons","mapping-tools","mappings","obofoundry","ontologies","ontology-lookup-service","sssom"],"latest_commit_sha":null,"homepage":"","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/monarch-initiative.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}},"created_at":"2022-03-19T00:38:23.000Z","updated_at":"2023-09-08T18:32:48.000Z","dependencies_parsed_at":"2022-08-27T19:12:26.084Z","dependency_job_id":null,"html_url":"https://github.com/monarch-initiative/mapping-walker","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fmapping-walker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fmapping-walker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fmapping-walker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/monarch-initiative%2Fmapping-walker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/monarch-initiative","download_url":"https://codeload.github.com/monarch-initiative/mapping-walker/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238909492,"owners_count":19550845,"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","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":["bioportal","boomer","entity-normalization","knowledge-graphs","mapping-commons","mapping-tools","mappings","obofoundry","ontologies","ontology-lookup-service","sssom"],"created_at":"2025-02-14T21:07:12.306Z","updated_at":"2025-10-29T23:31:30.565Z","avatar_url":"https://github.com/monarch-initiative.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Mapping Walker\n\nThis application will:\n\n - crawl a mapping endpoint weaving a set of SSSOM mappings\n - input these into boomer\n - visualize the results with obographviz\n\n__THIS IS ALPHA SOFTWARE__\n\n## Requirements\n\nYou need the following on your path:\n\n - [graphviz](https://graphviz.org/)\n - [boomer](https://incatools.github.io/boomer/)\n - [og2dot](https://github.com/cmungall/obographviz)\n\nOn MacOS you may need to install openblas via homebrew and set the `OPENBLAS` environment variable before installing dependencies:\n\n```\nbrew install openblas\nexport OPENBLAS=\"$(brew --prefix openblas)\"\npoetry install\n```\n\n## Running\n\n```bash\nmapcrawl OMIM:603467\n```\n\nyou can enter as many CURIEs as you like\n\nThe output looks like:\n\n![img](./docs/images/omim-example.png)\n\nNote the visualization doesn't show the mappings that were rejected - see the full boomer report file. It shows things like:\n\n- [Fanconi anemia](http://purl.obolibrary.org/obo/Orphanet_84) SiblingOf [OMIM_614087](http://purl.obolibrary.org/obo/OMIM_614087)         0.09999999999999998\n- [Fanconi anemia](http://purl.obolibrary.org/obo/Orphanet_84) ProperSuperClassOf [OMIM_614087](http://purl.obolibrary.org/obo/OMIM_603467)        (most probable) 0.8\n- [aplastic anemia](http://purl.obolibrary.org/obo/MONDO_0015909) EquivalentTo [Anemia, Aplastic](http://purl.obolibrary.org/obo/MeSH_D000741)  (most probable) 0.8\n- [Fanconi anemia](http://purl.obolibrary.org/obo/DOID_13636) EquivalentTo [Fanconi Anemia](http://purl.obolibrary.org/obo/MeSH_D005199)        (most probable) 0.8\n\n\n\n## Gallery\n\n\n### Anatomy\n\n* FMA:24879\n\n![FMA:24879](./docs/images/fma-example.png)\n\nthese are the full results:\n\n- [Lower Extremity](http://purl.obolibrary.org/obo/UMLS_C0023216) EquivalentTo [Lower Extremity](http://purl.obolibrary.org/obo/MeSH_D035002)   (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [Hindlimb](http://purl.obolibrary.org/obo/UMLS_C1522391)       (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/XAO_0003031) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/BTO_0002345) (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) SiblingOf [](http://purl.obolibrary.org/obo/NCIT_C77625)            0.09999999999999998\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [Hindlimb](http://purl.obolibrary.org/obo/MeSH_D006614)        (most probable) 0.8\n- [Lower Extremity](http://purl.obolibrary.org/obo/UMLS_C0023216) SiblingOf [](http://purl.obolibrary.org/obo/NCIT_C12742)              0.09999999999999998\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [](http://purl.obolibrary.org/obo/NCIT_C12742) (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) SiblingOf [Lower Extremity](http://purl.obolibrary.org/obo/UMLS_C0023216)           0.09999999999999998\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/XAO_0003031) (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [obsolete_hindlimb](http://purl.obolibrary.org/obo/EFO_0000883)        (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/EMAPA_17458) (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [Free lower limb](http://purl.obolibrary.org/obo/FMA_24879)    (most probable) 0.8\n- [Hindlimb](http://purl.obolibrary.org/obo/UMLS_C1522391) EquivalentTo [Hindlimb](http://purl.obolibrary.org/obo/MeSH_D006614) (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [lower limb](http://purl.obolibrary.org/obo/EHDAA2_0001033)    (most probable) 0.8\n- [leg](http://purl.obolibrary.org/obo/UBERON_0000978) EquivalentTo [Lower Extremity](http://purl.obolibrary.org/obo/MeSH_D035002)      (most probable) 0.8\n- [Lower Extremity](http://purl.obolibrary.org/obo/UMLS_C0023216) EquivalentTo [](http://purl.obolibrary.org/obo/NCIT_C77625)   (most probable) 0.8\n- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) EquivalentTo [hindlimb](http://purl.obolibrary.org/obo/MA_0000026)  (most probable) 0.8\n\nnote boomer effectively rejected some links (SiblingOf) that came from some mappings\n\n### Disease\n\nMONDO:0019249 ! mucopolysaccharidosis\n\n\n![mucopolysaccharidosis](./docs/images/muco-example.png)\n\n## How it works\n\nIt currently queries OxO - it will do a breadth first search until either saturated or either max depth or max queries is reached\n\nAll configuration is specified in LinkML yaml - docs will be up soon\n\nCurrently it applies the standard SSSOM-py mappings for all predicates obtained from OxO (most mappings in OxO are RELATED but there are some narrow/broad)\n\nDefault confidence is 0.8 (currently no mappings in OxO have confidence)\n\nWe don't yet allow plugin in of rules - e.g. boost confidence if mapping comes from a more trusted source, or is HumanCurated\n\n## TODO\n\n- fix CURIEs\n- add bioportal endpoint (currently uses oxo)\n- add ubergraph endpoint\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fmapping-walker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmonarch-initiative%2Fmapping-walker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmonarch-initiative%2Fmapping-walker/lists"}