{"id":26674408,"url":"https://github.com/multiomics-analytics-group/orthohpi2.0","last_synced_at":"2025-03-26T02:19:06.875Z","repository":{"id":110564483,"uuid":"481598992","full_name":"Multiomics-Analytics-Group/OrthoHPI2.0","owner":"Multiomics-Analytics-Group","description":null,"archived":false,"fork":false,"pushed_at":"2024-06-07T09:49:26.000Z","size":21496,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-06-07T10:28:22.839Z","etag":null,"topics":[],"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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Multiomics-Analytics-Group.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2022-04-14T12:38:43.000Z","updated_at":"2024-06-07T10:28:30.042Z","dependencies_parsed_at":"2024-06-07T10:28:28.044Z","dependency_job_id":"0f648aea-0be7-44f4-ab25-65d78611f952","html_url":"https://github.com/Multiomics-Analytics-Group/OrthoHPI2.0","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/Multiomics-Analytics-Group%2FOrthoHPI2.0","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Multiomics-Analytics-Group%2FOrthoHPI2.0/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Multiomics-Analytics-Group%2FOrthoHPI2.0/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Multiomics-Analytics-Group%2FOrthoHPI2.0/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Multiomics-Analytics-Group","download_url":"https://codeload.github.com/Multiomics-Analytics-Group/OrthoHPI2.0/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245573892,"owners_count":20637674,"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":"2025-03-26T02:19:06.183Z","updated_at":"2025-03-26T02:19:06.863Z","avatar_url":"https://github.com/Multiomics-Analytics-Group.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# OrthoHPI2.0\n\nOrthoHPI 2.0 is a resource that provides homology-derived predictions of host-parasite protein-protein interactions (PPI). This work renews and extends OrthoHPI by integrating new versions of databases, predictors and proteomes of 24 eukaryotic parasites such as apicomplexa and trypanosomatids.\n\nThis resource provides tissue and cell type resolution interactions as well as annotation of Biological Processes that allows a comprehensive analysis and comparison of all the parasitic species studied.\n\n\n\u003cimg width=\"1760\" alt=\"Screenshot 2022-10-08 at 20 25 11\" src=\"https://user-images.githubusercontent.com/1425851/194722121-b6f01c52-57d7-4676-aefe-239a2be3e78a.png\"\u003e\n\n\n## Development\n\nOrthoHPI 2.0 has been developed entirely with **Python 3.8.2** and Streamlit (https://docs.streamlit.io/) for visualization and analysis of the results.\n\nThe **homology prediction** has been done using:\n\n\u003ca src=\"http://eggnog5.embl.de/\"\u003e\u003cimg width=100 alt=\"eggnog\" src=\"https://github.com/Multiomics-Analytics-Group/OrthoHPI2.0/blob/main/images/eggnog.png\"\u003e \u003c/a\u003e\n\n\n\u003ca src=\"https://string-db.org/\"\u003e\u003cimg width=100 alt=\"string\" src=\"https://github.com/Multiomics-Analytics-Group/OrthoHPI2.0/blob/main/images/string.png\"\u003e\u003c/a\u003e\n\n\nThe **tissue and cellular compartment annotation** used to filter the proteomes come from:\n\n\u003ca src=\"https://compartments.jensenlab.org/\"\u003e\u003cimg width=100 alt=\"compartments\" src=\"https://github.com/Multiomics-Analytics-Group/OrthoHPI2.0/blob/main/images/compartments.png\"\u003e\u003c/a\u003e\n\n\u003ca src=\"https://tissues.jensenlab.org/\"\u003e\u003cimg width=100 alt=\"tissues\" src=\"https://github.com/Multiomics-Analytics-Group/OrthoHPI2.0/blob/main/images/tissues.png\"\u003e\u003c/a\u003e\n\n\nThe **cell type expression** information has been downloaded from:\n\n\u003ca src=\"https://www.proteinatlas.org/humanproteome/tissue+cell+type\"\u003e\u003cimg width=200 alt=\"hpa\" src=\"https://github.com/Multiomics-Analytics-Group/OrthoHPI2.0/blob/main/images/hpa.png\"\u003e\u003c/a\u003e\n\n## Getting started\n\n### Running the website\n\nAll the necessary data (predictions and annotations) have been precalculated so you can run the web server:\n``` \n$ streamlit run orthohpi_web.py\n```\n\nThis will open your browser at http://localhost:8501 with the functionality shown in the video:\n\n\n\nhttps://user-images.githubusercontent.com/1425851/194722960-e42a191f-1cec-4c49-a96e-5a03b351677d.mp4\n\n\n### Installation\n\nIf you want to rerun the predictions, you can install and run the pipeline following these instructions.\n\n```\n$ pip install -r requirements.txt\n```\n\nTo obtain the Human-Parasite PPI predictions run:\n``` \n$ python main.py\n```\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultiomics-analytics-group%2Forthohpi2.0","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmultiomics-analytics-group%2Forthohpi2.0","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultiomics-analytics-group%2Forthohpi2.0/lists"}