{"id":17099062,"url":"https://github.com/dhimmel/myelinet","last_synced_at":"2026-05-02T14:44:55.704Z","repository":{"id":82487681,"uuid":"52992875","full_name":"dhimmel/myelinet","owner":"dhimmel","description":"Hetnet prediction of candidate remyelinating compounds","archived":false,"fork":false,"pushed_at":"2016-03-31T22:47:57.000Z","size":72,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-28T23:50:07.615Z","etag":null,"topics":["baranzini-lab","hetionet","multiple-sclerosis","myelin"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/dhimmel.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":"2016-03-02T20:09:38.000Z","updated_at":"2023-03-18T13:10:40.000Z","dependencies_parsed_at":null,"dependency_job_id":"ee166790-f60a-4c64-b7c5-d74a3bbc7222","html_url":"https://github.com/dhimmel/myelinet","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fmyelinet","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fmyelinet/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fmyelinet/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhimmel%2Fmyelinet/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dhimmel","download_url":"https://codeload.github.com/dhimmel/myelinet/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245144972,"owners_count":20568056,"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":["baranzini-lab","hetionet","multiple-sclerosis","myelin"],"created_at":"2024-10-14T15:08:54.289Z","updated_at":"2026-05-02T14:44:55.669Z","avatar_url":"https://github.com/dhimmel.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Hetnet prediction of candidate remyelinating compounds\n\nMultiple sclerosis destroys the myelin coating neurons leading to disability. Here, we aim to find small molecules compounds that will promote remyelination. We base our search on our drug repurposing hetnet -- a network with multiple node and relationship types -- which provides a comprehensive framework for data integration. The hetnet is stored in a graph database called neo4j, which we use to compute network features.\n\nOur approach to identify candidate compounds is unsupervised. We look for compounds that highly connected to myelination or oligodendrocyte differentiation. We specify the types of paths we are interested in. For example we look for paths where a _Compound - targets - Gene - interacts - Gene - participates - Biological Process_ where the biological process is myelination.\n\nSee [`query.ipynb`](query.ipynb) for the queries and [`data/queries.tsv`](data/queries.tsv) for the results.\n\n## Queries for visualization\n\nThese queries should be run in the neo4j browser. They were chosen to produce\nillustrative and appropriately sized visualizations.\n\n```cypher\n// Find paths between Marimastat and myelination\nMATCH paths =\n  (s1:Compound)-[:BINDS_CbG]-(n1)-[:INTERACTS_GiG]-()\n               -[:PARTICIPATES_GpBP]-(t1:BiologicalProcess)\nWHERE s1.identifier = 'DB00786' // Marimastat\n  AND t1.identifier = 'GO:0042552' // myelination\n  // Expressed in the central nervous system\n  AND exists((:Anatomy {identifier: 'UBERON:0001017'})-[:EXPRESSES_AeG]-(n1))\nRETURN paths\nUNION ALL\nMATCH paths = (s2:Compound)-[:BINDS_CbG]-(n1)-[:INTERACTS_GiG]-()\n             -[:REGULATES_BPrG]-(t2:BiologicalProcess)\nWHERE s2.identifier = 'DB00786' // Marimastat\n  AND t2.identifier = 'GO:0048709' // oligodendrocyte differentiation\nRETURN paths\n```\n\n## Installation\n\nThis repository assumes a neo4j server containing the hetio-ind database is\nrunning on port 7474.\n\n## License\n\nAll original content in this repository is released under [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/ \"Creative Commons · Public Domain Dedication\").\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fmyelinet","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdhimmel%2Fmyelinet","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhimmel%2Fmyelinet/lists"}