Introduction | Overview of Semantic MEDLINE | Graph representation of SemMedDB | Full data availability | Note about processed data | Installation | Example workflow | Loading packages and data | Finding nodes | Growing understanding by connecting nodes | Aim 1: Connecting different node sets | Information from find_paths() | Displaying paths | Refining paths with weights | Weighting option: make_edge_weights() | Summarizing information in paths | Aim 2: Expanding a single node set | Summary | Session Info | References
Package: rsemmed 1.23.0
Leslie Myint
rsemmed: An interface to the Semantic MEDLINE database
A programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.
Authors:
rsemmed_1.23.0.tar.gz
rsemmed_1.23.0.zip(r-4.7)rsemmed_1.23.0.zip(r-4.6)rsemmed_1.23.0.zip(r-4.5)
rsemmed_1.23.0.tgz(r-4.6-any)rsemmed_1.23.0.tgz(r-4.5-any)
rsemmed_1.23.0.tar.gz(r-4.7-any)rsemmed_1.23.0.tar.gz(r-4.6-any)
rsemmed_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rsemmed/json (API)
| # Install 'rsemmed' in R: |
| install.packages('rsemmed', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lmyint/rsemmed/issues
Datasets:
On BioConductor:rsemmed-1.23.0(bioc 3.24)rsemmed-1.22.0(bioc 3.23)
softwareannotationpathwayssystemsbiology
Last updated from:4377ba5b2a. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 140 | ||
| linux-devel-x86_64 | OK | 192 | ||
| source / vignettes | OK | 175 | ||
| linux-release-x86_64 | OK | 194 | ||
| macos-release-arm64 | OK | 85 | ||
| macos-oldrel-arm64 | OK | 82 | ||
| windows-devel | OK | 374 | ||
| windows-release | OK | 90 | ||
| windows-oldrel | OK | 404 | ||
| wasm-release | OK | 121 |
Exports:find_nodesfind_pathsget_edge_featuresget_middle_nodesgrow_nodesmake_edge_weightsplot_pathsummarize_predicatessummarize_semtypestext_path
Dependencies:clicpp11dplyrgenericsglueigraphlatticelifecyclemagrittrMatrixpillarpkgconfigR6rlangstringistringrtibbletidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Search for nodes by name or semantic type | find_nodes |
| Shortest paths between node sets | find_paths |
| Example data for the rsemmed package | g_mini |
| Example data for the rsemmed package | g_small |
| Get information about edges | get_edge_features |
| Obtain the middle nodes of a path | get_middle_nodes |
| Obtain immediate neighbors | grow_nodes |
| Create edge weights | make_edge_weights |
| Display path (plot form) | plot_path |
| Summarize predicates | summarize_predicates |
| Summarize semantic types | summarize_semtypes |
| Display path (text form) | text_path |
