{"id":19714809,"url":"https://github.com/baranzinilab/psev","last_synced_at":"2025-06-15T05:34:33.194Z","repository":{"id":55488825,"uuid":"168082494","full_name":"BaranziniLab/PSEV","owner":"BaranziniLab","description":null,"archived":false,"fork":false,"pushed_at":"2019-03-19T21:33:35.000Z","size":124311,"stargazers_count":3,"open_issues_count":2,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-10T15:14:44.386Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/BaranziniLab.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":"2019-01-29T03:28:12.000Z","updated_at":"2022-11-16T18:18:58.000Z","dependencies_parsed_at":"2022-08-15T01:31:01.478Z","dependency_job_id":null,"html_url":"https://github.com/BaranziniLab/PSEV","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/BaranziniLab%2FPSEV","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BaranziniLab%2FPSEV/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BaranziniLab%2FPSEV/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BaranziniLab%2FPSEV/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BaranziniLab","download_url":"https://codeload.github.com/BaranziniLab/PSEV/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241035906,"owners_count":19898087,"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":[],"created_at":"2024-11-11T22:36:02.600Z","updated_at":"2025-02-27T16:42:13.765Z","avatar_url":"https://github.com/BaranziniLab.png","language":"Python","readme":"# PSEV\n\nThe data provided here is not the same as that used in the paper. \nPatient IDs have been scrambled.\nThis is only a fraction of the patient data used.\n\n###### Clone repository\ngit clone https://github.com/baranzini-lab/PSEV.git\n###### Go to constants directory\ncd PSEV/constants/\n###### Unzip lab path file\ntar -xvzf cui_to_loinc_path.tsv.tar.gz\n###### Go to build directory\ncd ../build/\n###### Unzip EHR files\ntar -xvzf EHR_DIAGNOSIS.tsv.tar.gz \n\ntar -xvzf EHR_LABS.tsv.tar.gz\n\ntar -xvzf EHR_MEDICATION.tsv.tar.gz \n###### Go to SPOKE directory\ncd ../spoke_v_1/\n###### Unzip SPOKE edge file\ntar -xvzf neo4j_edges.tsv.tar.gz \n###### Go to main PSEV directory\ncd ..\n###### Create matrix that contains patient connections to SPOKE nodes\npython connect_all_patients.py \n###### stdout (using default settings):\n\u003e\\# of LOINC mapped to SPOKE: 557\n\u003e\n\u003eMapped SPOKE breakdown from LABS: Counter({'SideEffect': 226, 'Compound': 136, 'Gene': 49, 'Symptom': 12})\n\u003e\n\u003eSEP STATS: (3183,) Counter({'SideEffect': 1851, 'Compound': 922, 'Symptom': 257, 'Disease': 137, 'Gene': 16})\n###### Create PSEV matrix for specific SEPs (by node type: -t Gene) \npython make_psevs_by_node_type.py \n\u003e**NOTE**\n\u003e\n\u003e**Default creates PSEVs for Gene SEPs.**\n\u003e_To change default settings (including number of cores to use) please see python make_psevs_by_node_type.py --help_\n\u003e\n\u003e**Beware this program will use a lot of memory and take a lot of time. Run on cluster if possible.**\n###### stdout (using default settings):\n\u003emake_psevs_by_node_type.py:83: RuntimeWarning: invalid value encountered in divide\n\u003e  add_val = np.nan_to_num(direct_hit.astype(float)/np.sum(direct_hit))\n\u003e\n\u003emake_psevs_by_node_type.py:111: RuntimeWarning: invalid value encountered in divide\n\u003e  connectivity_matrix = np.transpose(np.nan_to_num(connectivity_matrix/np.sum(connectivity_matrix, axis=0)))\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbaranzinilab%2Fpsev","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbaranzinilab%2Fpsev","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbaranzinilab%2Fpsev/lists"}