https://github.com/pharmcat/odmxmltools.jl

ODM-XML Tools
https://github.com/pharmcat/odmxmltools.jl

clinical-trials julia odm odm-database odm-xml

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ODM-XML Tools

• Host: GitHub
• URL: https://github.com/pharmcat/odmxmltools.jl
• Owner: PharmCat
• License: mit
• Created: 2022-01-23T19:10:27.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2024-05-09T18:05:48.000Z (6 months ago)
• Last Synced: 2024-10-09T23:15:54.209Z (27 days ago)
• Topics: clinical-trials, julia, odm, odm-database, odm-xml
• Language: Julia
• Homepage:
• Size: 485 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# ODMXMLTools.jl

ODMXMLTools.jl is a simple tool set for working with ODM-XML.

| Version | pkgeval | Cover | Build | Docs |

|--------|-------|-------|-------|------|

|[![version](https://juliahub.com/docs/ODMXMLTools/version.svg)](https://docs.juliahub.com/ODMXMLTools/stbAr)|[![pkgeval](https://juliahub.com/docs/ODMXMLTools/pkgeval.svg)](https://docs.juliahub.com/ODMXMLTools/stbAr)|[![codecov](https://codecov.io/gh/PharmCat/ODMXMLTools.jl/branch/main/graph/badge.svg?token=3DksoMcfzh)](https://codecov.io/gh/PharmCat/ODMXMLTools.jl)| [![Tier 1](https://github.com/PharmCat/ODMXMLTools.jl/actions/workflows/Tier1.yml/badge.svg)](https://github.com/PharmCat/ODMXMLTools.jl/actions/workflows/Tier1.yml) | [![Latest docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://pharmcat.github.io/ODMXMLTools.jl/dev/) [![Stable docs](https://img.shields.io/badge/docs-stable-blue.svg)](https://pharmcat.github.io/ODMXMLTools.jl/stable/)|

[ODM-XML](https://www.cdisc.org/standards/data-exchange/odm) is a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data, along with their associated metadata, administrative data, reference data, and audit information. ODM-XML facilitates the regulatory-compliant acquisition, archival and exchange of metadata and data. It has become the language of choice for representing case report form content in many electronic data capture (EDC) tools.

The ODM has been designed to be compliant with guidance and regulations published by the FDA for computer systems used in clinical studies.

See [CDISK](https://www.cdisc.org/) site for more information.

This program comes with absolutely no warranty. No liability is accepted for any loss and risk to public health resulting from use of this software.

# Install

```

import Pkg; Pkg.add(url="https://github.com/PharmCat/ODMXMLTools.jl.git")

```

Or from registry:

```

import Pkg; Pkg.add("ODMXMLTools")

```

# Usage

```

# Import ODM xml file

odm = ODMXMLTools.importxml("odm.xml")

# Get table of MetaDataVersion

ODMXMLTools.metadatalist(odm)

# Find study element

st1 =  ODMXMLTools.findstudy(odm, "ST1")

# Find MetaDataVersion element in study `st1`

ODMXMLTools.findelement(st1, :MetaDataVersion, "v2")

# Find MetaDataVersion element version `v2` in study `st1`

ODMXMLTools.findstudymetadata(odm, "ST1", "v2")

# Build MetaDataVersion - recursive resolve all includes

mdb = ODMXMLTools.buildmetadata(odm, "ST1", "v2")

# Study list

ODMXMLTools.studylist(odm)

# Events table

ODMXMLTools.eventlist(mdb)

# Forms table

ODMXMLTools.formlist(mdb)

# ItemGroups table

ODMXMLTools.itemgrouplist(mdb)

# Items table

ODMXMLTools.itemlist(mdb)

# Items table with optional attributes

ODMXMLTools.itemlist(mdb; optional = true)

# Items table within ItemGoup "IG_1"

ODMXMLTools.itemgroupcontent(mdb, "IG_1")

# Study subject information

ODMXMLTools.subjectdatatable(odm)

# Study information

ODMXMLTools.studyinfo(odm; io = io)

# Get ClinicalData list

ODMXMLTools.clinicaldatalist(odm)

# Get data from ClinicalData in "long" format

ODMXMLTools.clinicaldatatable(odm, "ST1", "v2")

```