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12 changes: 11 additions & 1 deletion README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,17 @@ 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.

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20 changes: 17 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,21 @@ 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.
Expand Down Expand Up @@ -196,15 +210,15 @@ 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},
#> }
```
2 changes: 1 addition & 1 deletion docs/404.html

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2 changes: 1 addition & 1 deletion docs/CODE_OF_CONDUCT.html

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2 changes: 1 addition & 1 deletion docs/CONTRIBUTING.html

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2 changes: 1 addition & 1 deletion docs/LICENSE-text.html

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4 changes: 2 additions & 2 deletions docs/articles/dbparser.html

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2 changes: 1 addition & 1 deletion docs/articles/drugbank_nside.html

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2 changes: 1 addition & 1 deletion docs/articles/index.html

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6 changes: 3 additions & 3 deletions docs/authors.html

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4 changes: 2 additions & 2 deletions docs/authors.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,12 +16,12 @@ Source:
[`inst/CITATION`](https://github.com/ropensci/dbparser/blob/HEAD/inst/CITATION)

Mohammed Ali, Ali Ezzat (). dbparser: DrugBank Database XML Parser. R
package version 2.2.1.
package version 2.2.1.9000.

@Manual{,
title = {DrugBank Database XML Parser},
author = {Mohammed Ali and Ali Ezzat},
organization = {Interstellar for Consultinc inc.},
note = {R package version 2.2.1},
note = {R package version 2.2.1.9000},
url = {https://CRAN.R-project.org/package=dbparser},
}
29 changes: 22 additions & 7 deletions docs/index.html

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20 changes: 17 additions & 3 deletions docs/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,21 @@ 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.
Expand Down Expand Up @@ -195,15 +209,15 @@ 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},
#> }
```
20 changes: 17 additions & 3 deletions docs/llms.txt
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,21 @@ 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.
Expand Down Expand Up @@ -195,15 +209,15 @@ 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},
#> }
```
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7 changes: 5 additions & 2 deletions docs/news/index.html

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4 changes: 4 additions & 0 deletions docs/news/index.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,11 @@
# Changelog

## dbparser (development version)

## dbparser 2.2.1

CRAN release: 2026-01-08

This is a major feature release focused on expanding `dbparser`’s
capabilities into real-world pharmacovigilance and drug-drug interaction
analysis. The integration engine has been formalized around a “Hub and
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