Merge pull request #205 from ropensci/cran

JOSS Support

Author: MohammedFCIS

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dbparser
 Title: Drugs Databases Parser
-Version: 2.2.1
+Version: 2.2.1.9000
 Authors@R:
     c(
     person("Mohammed", "Ali", email = "moh_fcis@yahoo.com", role = c("aut", "cre")),

NEWS.md

@@ -1,3 +1,5 @@
+# dbparser (development version)
+
 # dbparser
 
 # dbparser 2.2.1

README.Rmd

@@ -24,6 +24,10 @@ library(ggplot2)
 [![Rdoc Documentation](https://img.shields.io/badge/Doc-Rdoc-blue.svg)](https://www.rdocumentation.org/packages/dbparser)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/3311/badge)](https://bestpractices.coreinfrastructure.org/projects/3311)
 [![rOpenSci Peer-Reviewed](https://badges.ropensci.org/347_status.svg)](https://github.com/ropensci/software-review/issues/347)
+[![JOSS Paper](https://joss.theoj.org/papers/3212f2fb07013b8fb1cec499bb9e8381/status.svg)](https://joss.theoj.org/papers/3212f2fb07013b8fb1cec499bb9e8381)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18608628.svg)](https://doi.org/10.5281/zenodo.18608628)
+
+
 
 ## Overview
 Drugs databases vary too much in their formats and structures which making related 
@@ -42,7 +46,17 @@ That should help in:
 - ease of transferring data between researchers after performing required data
 analysis or `dvobject` and storing results in the same object in a very easy manner.
 
-### dvobject Structure
+## dbparser in Advanced Research
+
+dbparser serves as data infrastructure for cutting-edge research:
+
+- **Explainable AI for Drug Repurposing**: Featured in IEEE ICEBE 2025 presentation 
+  on knowledge graph-based drug discovery (University of Technology Sydney collaboration)
+- **Systems Pharmacology**: Integrated into Multipath package for pathway modeling
+- **Pandemic Response**: Enabled rapid COVID-19 therapeutic candidate identification
+- **Cancer Research**: Supporting SURFACER workflow for pan-cancer biomarker detection
+
+## dvobject Structure
 `dvobject` introduces a unified and compressed format of drugs data.
 It is an R list object. 
 

README.md

@@ -18,6 +18,9 @@ Documentation](https://img.shields.io/badge/Doc-Rdoc-blue.svg)](https://www.rdoc
 Practices](https://bestpractices.coreinfrastructure.org/projects/3311/badge)](https://bestpractices.coreinfrastructure.org/projects/3311)
 [![rOpenSci
 Peer-Reviewed](https://badges.ropensci.org/347_status.svg)](https://github.com/ropensci/software-review/issues/347)
+[![JOSS
+Paper](https://joss.theoj.org/papers/3212f2fb07013b8fb1cec499bb9e8381/status.svg)](https://joss.theoj.org/papers/3212f2fb07013b8fb1cec499bb9e8381)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18608628.svg)](https://doi.org/10.5281/zenodo.18608628)
 
 ## Overview
 
@@ -45,7 +48,21 @@ That should help in:
   required data analysis or `dvobject` and storing results in the same
   object in a very easy manner.
 
-### dvobject Structure
+## dbparser in Advanced Research
+
+dbparser serves as data infrastructure for cutting-edge research:
+
+- **Explainable AI for Drug Repurposing**: Featured in IEEE ICEBE 2025
+  presentation on knowledge graph-based drug discovery (University of
+  Technology Sydney collaboration)
+- **Systems Pharmacology**: Integrated into Multipath package for
+  pathway modeling
+- **Pandemic Response**: Enabled rapid COVID-19 therapeutic candidate
+  identification
+- **Cancer Research**: Supporting SURFACER workflow for pan-cancer
+  biomarker detection
+
+## dvobject Structure
 
 `dvobject` introduces a unified and compressed format of drugs data. It
 is an R list object.
@@ -196,15 +213,15 @@ citation("dbparser")
 #> To cite dbparser in publications use:
 #> 
 #>   Mohammed Ali, Ali Ezzat ().  dbparser: DrugBank Database XML Parser.
-#>   R package version 2.2.0.
+#>   R package version 2.2.1.9000.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
 #>     title = {DrugBank Database XML Parser},
 #>     author = {Mohammed Ali and Ali Ezzat},
 #>     organization = {Interstellar for Consultinc inc.},
-#>     note = {R package version 2.2.0},
+#>     note = {R package version 2.2.1.9000},
 #>     url = {https://CRAN.R-project.org/package=dbparser},
 #>   }
 ```