{"id":28465336,"url":"https://github.com/frankkramer-lab/multipath","last_synced_at":"2025-09-07T22:37:12.178Z","repository":{"id":37089422,"uuid":"260184833","full_name":"frankkramer-lab/Multipath","owner":"frankkramer-lab","description":"Integrating pathways and related knowledge in a multilayer framework","archived":false,"fork":false,"pushed_at":"2025-03-15T09:11:25.000Z","size":2452,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-06-07T05:12:29.718Z","etag":null,"topics":["biological-pathways","biopax-encoded-pathways","data-integration","data-visualization","drugbank-database","graph-theory","knowledge-representation","multilayer-networks","reproducibility","uniprot"],"latest_commit_sha":null,"homepage":"","language":"R","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/frankkramer-lab.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":"2020-04-30T10:45:42.000Z","updated_at":"2025-03-15T09:11:29.000Z","dependencies_parsed_at":"2025-03-06T12:35:12.883Z","dependency_job_id":null,"html_url":"https://github.com/frankkramer-lab/Multipath","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/frankkramer-lab/Multipath","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/frankkramer-lab%2FMultipath","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/frankkramer-lab%2FMultipath/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/frankkramer-lab%2FMultipath/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/frankkramer-lab%2FMultipath/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/frankkramer-lab","download_url":"https://codeload.github.com/frankkramer-lab/Multipath/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/frankkramer-lab%2FMultipath/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262838200,"owners_count":23372484,"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":["biological-pathways","biopax-encoded-pathways","data-integration","data-visualization","drugbank-database","graph-theory","knowledge-representation","multilayer-networks","reproducibility","uniprot"],"created_at":"2025-06-07T05:11:13.728Z","updated_at":"2025-06-30T19:32:02.389Z","avatar_url":"https://github.com/frankkramer-lab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Multipath\nCreating integrated reproducible pathway multilayer models\n\n![alt\ntext](https://github.com/frankkramer-lab/Multipath/blob/master/img/multipath.png \"multipath\")\n\\## Introduction Biological pathway data integration has become a topic\nof interest in the past years. This interest originates essentially from\nthe continuously increasing size of existing prior knowledge as well as\nfrom the many challenges scientists face when studying biological\npathways. Multipath is a framework that aims at helping re-trace the use\nof specific pathway knowledge in specific publications, and easing the\ndata integration of multiple pathway types and further influencing\nknowledge sources. Using Multipath, BioPax-encoded pathways can be\nparsed and embedded into multilayered graphs. Modifications can be\napplied to these graphs to generate different views. The package is\nimplemented as a part of [the Multipath\nProject](https://www.sys-med.de/en/junior-research-groups/multipath/)\ndirected by [Dr. Frank\nKramer](https://www.uni-augsburg.de/de/fakultaet/fai/informatik/prof/misit/mitarbeiter/)\n. \\## Publication More information and references can be found in the\nMultipath paper:\n\n\u003chttps://www.mdpi.com/2079-7737/9/12/483\u003e\n\n## Installation\n\n### Preinstallation\n\nMultipath depends on multiple packages. The packages are the following:\n[queryup](https://cran.r-project.org/web/packages/queryup/index.html),\n[dbparser](https://cran.r-project.org/web/packages/dbparser/index.html),\n[rBiopaxParser](https://github.com/frankkramer-lab/rBiopaxParser),\n[mully](https://github.com/frankkramer-lab/mully),\n[KEGGREST](https://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html),\n[KEGGgraph](https://www.bioconductor.org/packages/release/bioc/html/KEGGgraph.html),\n[romim](https://github.com/davetang/romim),\n[stringr](https://cran.r-project.org/web/packages/stringr/),\n[svMisc](https://cran.r-project.org/web/packages/svMisc/),\n[uuid](https://cran.r-project.org/web/packages/uuid/),\n[dplyr](https://cran.r-project.org/web/packages/dplyr/),\n[crayon](https://cran.r-project.org/web/packages/crayon/) Please make\nsure to install the packages\n[UniProt.ws](https://www.bioconductor.org/packages/release/bioc/html/UniProt.ws.html),\n[rBiopaxParser](https://github.com/frankkramer-lab/rBiopaxParser) and\n[mully](https://github.com/frankkramer-lab/mully) before using the\npackage.\n\nTo install the [mully](https://github.com/frankkramer-lab/mully)\npackage:\n\n``` r\nrequire(devtools)\ninstall_github(\"frankkramer-lab/mully\")\nlibrary(mully)\n```\n\nTo install the\n[rBiopaxParser](https://github.com/frankkramer-lab/rBiopaxParser)\npackage:\n\n``` r\nrequire(devtools)\ninstall_github(\"frankkramer-lab/rBiopaxParser\")\nlibrary(rBiopaxParser)\n```\n\n### Dependencies\n\nTo simplify the pre-installation, all dependencies can be downloaded\nusing the following script.\n\n``` r\n#Install CRAN Dependencies\ninstall.packages(c(\"queryup\",\"remotes\",\"mully\", \"svMisc\", \"uuid\", \"dplyr\", \"crayon\", \"igraph\", \"RCurl\", \"XML\", \"xml2\", \"XML2R\", \"devtools\"))\n\n#Install BioConductor and remotes Dependencies\nif (!require(\"BiocManager\", quietly = TRUE))\n  install.packages(\"BiocManager\")\n\nBiocManager::install(\"KEGGREST\",force = TRUE)\nBiocManager::install(\"KEGGgraph\")\nBiocManager::install(\"graph\")\n\nremotes::install_github('davetang/romim')\n```\n\n### Installation via Github\n\n``` r\nrequire(devtools)\ninstall_github(\"frankkramer-lab/Multipath\")\nlibrary(Multipath)\n```\n\n## Test the package\n\nIn this section, we provide a demo to test the package by calling some\nof the function. To run the script, you need to download the [Signaling\nby Wnt from the Reactiome\ndatabase](https://reactome.org/content/detail/R-HSA-195721) in the\nBioPax format. \\### Create a mully graph from a BioPax-encoded pathway\n\n``` r\nwntBiopax=readBiopax(\"wntpathway_reactome.owl\")\npathwayID=listPathways(wntBiopax)$id[1]\nwntmully=pathway2Mully(wntBiopax,pathwayID)\nplot3d(wntmully,layers=T,vertex.label=NA,edge.width=5,edge.arrow.size=5)\n```\n\n![alt\ntext](https://github.com/frankkramer-lab/Multipath/blob/master/img/wntpathway.png \"Wnt pathway mully model\")\n\n### Generate Views\n\n``` r\nview1=pathwayView(wntmully,\"View1\")\nview1=addStep(view1,action = \"remove\",element=\"layer\",name=\"Rna\",trans = T)\nsuppressWarnings(plot3d(view1$modified))\n```\n\n![alt\ntext](https://github.com/frankkramer-lab/Multipath/blob/master/img/view1rna.png \"view1\")\n\n``` r\nview2=pathwayView(wntmully,\"View2\")\nview2=addStep(view2,action = \"remove\",element=\"layer\",name=\"PhysicalEntity\",trans=T)\nsuppressWarnings(plot3d(view2$modified))\n```\n\n![alt\ntext](https://github.com/frankkramer-lab/Multipath/blob/master/img/view2physentity.png \"view2\")\n\n``` r\nview3=pathwayView(wntmully,\"View3\")\nview3=addStep(view3,action = \"remove\",element=\"layer\",name=\"Complex\",trans=T)\nsuppressWarnings(plot3d(view3$modified))\n```\n\n![alt\ntext](https://github.com/frankkramer-lab/Multipath/blob/master/img/view3complex.png \"view3\")\n\n## Available Functions\n\nMultipath functions are divided into different files depending on their\nfunctionnality range:\n[Reactome](https://github.com/frankkramer-lab/Multipath/blob/master/R/Reactome.R)\n, [Views'\nFunctions](https://github.com/frankkramer-lab/Multipath/blob/master/R/Views.R)\n, [DrugBank\nFunctions](https://github.com/frankkramer-lab/Multipath/blob/master/R/DrugBank.R)\n, [UniProt\nFunctions](https://github.com/frankkramer-lab/Multipath/blob/master/R/UniProtKB.R)\n, [Intraedges between nodes\nFunctions](https://github.com/frankkramer-lab/Multipath/blob/master/R/DrugBank.R)\n, [Demo\nFunctions](https://github.com/frankkramer-lab/Multipath/blob/master/R/wnt_pathway.R)\n, [Integrated Model\nFunction](https://github.com/frankkramer-lab/Multipath/blob/master/R/Multipath.R)\n\n| Function | Description |\n|-----------------------------------------|-------------------------------|\n| `downloadPathway(pathwayID,biopaxLevel,destDirectory,overwrite)` | Download a BioPax encoded Reactome pathway function |\n| `pathway2Mully(biopax,pathwayID)` | Build a mully graph from a BioPax encoded pathway function |\n| `pathwayView(g,name)` | Constructor Function, Create an empty view |\n| `print(v)` | Print function |\n| `addStep(v,action,element,name,layerName,V1,V2,attributesnames,attributes,multi,trans)` | Document the modification of a graph function |\n| `undo(v,stps)` | Undo stps number of steps from the view v |\n| `loadDBXML(file)` | Parse DrugBank XML file function |\n| `getDBDrug(data,drug)` | Get a DrugBank entry from DrugBank function |\n| `getDBDrugInteractions(data,drug)` | Get Drugs interactions from DrugBank function |\n| `getDBDrugEnzymes(data,drugList)` | Get Drug-Enzymes relations from DrugBank function |\n| `getDBDrugTransporters(data,drugList)` | Get Drug-Transporters relations from DrugBank function |\n| `getDBDrugCarriers(data,drugList)` | Get Drug-Carriers relations from DrugBank function |\n| `getDBDrugTargets(data,drugList)` | Get Drug-Targets relations from DrugBank function |\n| `addDBLayer(g,data,drugList)` | Add a DrugBank Layer to a graph function |\n| `getDBtoUPKB(data,drugLiy,proteinList)` | Get Drug-Proteins relations from DrugBank function |\n| `getAllUPKB(up)` | Get all UniProt protein entries function |\n| `getUPKBInfo(proteins,col)` | Get UniProt protein entry infos function |\n| `getUPKBInteractions(proteins)` | Get Proteins interactions from UniProt function |\n| `getUPKBtoDB(proteinList,drugList)` | Get Proteins-Drug relations from UniProt function |\n| `addUPKBLayer(g,proteinList)` | Add a UniProt Layer to a graph function |\n| `getUPKBDBRelations(data,proteinList,drugList)` | Get Proteins-Drug relations from UniProt and DrugBank function |\n| `multipath(name,proteinList,data,drugList)` | Build integrated model function |\n| `wntpathway(file)` | Track and undo demo function |\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffrankkramer-lab%2Fmultipath","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffrankkramer-lab%2Fmultipath","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffrankkramer-lab%2Fmultipath/lists"}