{"id":25360688,"url":"https://github.com/callahantiff/pheknowvec","last_synced_at":"2025-04-09T03:33:08.318Z","repository":{"id":37627759,"uuid":"174068649","full_name":"callahantiff/PheKnowVec","owner":"callahantiff","description":"Translational Computational Phenotyping","archived":false,"fork":false,"pushed_at":"2023-05-22T22:19:00.000Z","size":18602,"stargazers_count":2,"open_issues_count":25,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-14T21:55:31.747Z","etag":null,"topics":["abra-collaboratory","computational-phenotyping","omop","open-biomedical-ontologies","phenotyping"],"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/callahantiff.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-03-06T04:03:13.000Z","updated_at":"2021-07-19T19:13:08.000Z","dependencies_parsed_at":"2022-09-06T09:11:02.394Z","dependency_job_id":null,"html_url":"https://github.com/callahantiff/PheKnowVec","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/callahantiff%2FPheKnowVec","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/callahantiff%2FPheKnowVec/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/callahantiff%2FPheKnowVec/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/callahantiff%2FPheKnowVec/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/callahantiff","download_url":"https://codeload.github.com/callahantiff/PheKnowVec/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247973922,"owners_count":21026736,"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":["abra-collaboratory","computational-phenotyping","omop","open-biomedical-ontologies","phenotyping"],"created_at":"2025-02-14T21:55:34.365Z","updated_at":"2025-04-09T03:33:08.299Z","avatar_url":"https://github.com/callahantiff.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## PheKnowVec\nPheKnowVec is a novel method for deriving, implementing, and validating computational phenotypes. PheKnowVec leverages standardized clinical terminologies and open biomedical ontologies to derive, implement, and validate computational phenotype definitions in a scalable embedded structure.\n\nPlease see the [Project Wiki](https://github.com/callahantiff/PheKnowVec/wiki) for more information!\n\n\n\u003cbr\u003e\n\n#### This is a Reproducible Research Repository\nThis repository contains more than just code, it provides a detailed and transparent narrative of our research process. For detailed information on how we use GitHub as a reproducible research platform, click [here](https://github.com/callahantiff/PheKnowVec/wiki/Using-GitHub-as-a-Reproducible-Research-Platform).\n\n\u003cimg src=\"https://img.shields.io/badge/ReproducibleResearch-AbraCollaboratory-magenta.svg?style=flat-square\" alt=\"git-AbraCollaboratory\"\u003e\n\n\u003cbr\u003e\n\n**Preliminary results were presented at the 2020 Joint Meeting of the American Medical Informatics Association:**  \nCallahan TJ, Wyrwa J, Trinkley KE, Hunter LE, Kahn MG, Bennett TD. (2020, March). Towards Automating Computational Phenotyping: Exploring the Trade-offs of Different Vocabulary Mapping Strategies. Talk; Informatics Summits of the American Medical Informatics Association, Houston, TX; [Podium Abstract](https://www.dropbox.com/s/mccv9b10m4arvt3/2020%20AMIA%20Informatics%20Summit%20-%20Revision.pdf?dl=1)\n\n______\n### Getting Started\n\n**Dependencies**\nThis repository is built using Python 3.6.2. To install the libraries used in this repository, run the line of code shown below from the within the project directory.\n```\npip install -r requirements.txt\n```\n\n**Data**  \nThis code assumes that input data is stored in a GoogleSheet, thus this repository contains code which relies on \nGoogle's [DriveAPI](https://developers.google.com/drive/) and \n[SheetsAPI](https://developers.google.com/sheets/api/). In order to use this functionality you will need to:\n- Complete the steps described [here](https://github.com/burnash/gspread)\n- Save the json file containing your credentials to `./resources/programming/Google_API/` \n- Rename the credential file to \"secret_client_gs.json\"\n\nThis code assumes that your input Google Sheet will follow a specific format:\n\nPhenotype | Cohort | Criteria | Phenotype_Criteria | Input_Type | Source_Domain | Source_Vocabulary | Source_Code | Source_Label\n-- | -- | -- | -- | -- | -- | -- | -- | --\nADHD | Case | Include | Presence of at least 1 relevant code in \u003e1 in-person visits, on separate calendar days | Code | Condition | ICD9CM | '314.0' | Attention deficit disorder of childhood\nADHD | Case | Include | Presence of  \u003e1 prescriptions of ADHD-related medications | String | Drug | None | '%adderall%' | adderall\n\n\n\n\n**SQL Queries**\n- This project assumes that you will want to use the SQL queries that we have prepared and store as GitHub Gist. \nThere are two types of queries run:\n  1. Queries to map code sets\n  2. Queries to create patient cohorts\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcallahantiff%2Fpheknowvec","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcallahantiff%2Fpheknowvec","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcallahantiff%2Fpheknowvec/lists"}