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AMASS data dictionary files for ACORN project

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posted on 2023-03-15, 04:52 authored by Prapass WannapinijPrapass Wannapinij

  

Updated on 15 March 2023

AutoMated tool for Antimicrobial resistance Surveillance System (AMASS) was developed as an offline, open-access and easy-to-use application that allows a hospital to perform data analysis independently and generate isolate-based and sample-based surveillance reports stratified by infection origin from routinely collected electronic databases. AMASS performs data analysis and generates reports automatically. The application can be downloaded from https://www.amass.website

ACORN is a Wellcome funded human health clinical AMR surveillance project led by the Mahidol-Oxford Tropical Medicine Research Unit (MORU) and the Oxford University of Oxford Clinical Research Unit (OUCRU). ACORN site can run AMASS at their local site on a notebook/computer with Microsoft Window operating system (Window7 or higher). 

[a] To run AMASS from .acorn files, ACORN site requires to:  

  1. Download AMASS tool from https://www.amass.website      and extract it on a notebook/computer.
  2. Have your ACORN site's .acorn      file which contains hospital admission and microbiology data load into ACORN Dashboard and convert (i.e. save) into ACORN data file in Microsoft Excel (.xlsx) format.
  3. From the ACORN data file (.xlsx), there are multiple sheets. Please copy the whole sheet of "redcap_f01f05_dta", paste it to a new Microsoft Excel (.xlsx) file, save the new file as "hospital_admission_data.xlsx", and put it in (i.e. save as in) the AMASS folder (i.e. AMASSv2.0 after unzipped)
  4. From the ACORN data file (.xlsx), copy the whole sheet of "lab_dta", paste it to a new Microsoft Excel (.xlsx) file, save the new ffile "microbiology_data.xlsx", and put it (i.e. save as in) the AMASS folder (i.e. AMASSv2.0 after unzipped)
  5. Download "dictionary_for_hospital_admission_data.xlsx" and "dictionary_for_microbiology_data.xlsx" from this Figshare link, and put it (i.e. save as in) the AMASS folder (i.e. AMASSv2.0 after unzipped)
  6. Run AMASS tool by double click "amass.bat" file which is in the AMASS folder (i.e. AMASSv2.0 after unzipped)

Please note that AMASS follows the WHO GLASS definitions, and results shown on the PDF generated could be minimally different from the ACORN dashboard. For example, WHO GLASS stratified the origin of infection to community-origin (CO) and hospital-origin (HO), while ACORN stratified the infection into community-acquired infection (CAI), healthcare associated infection (HCAI) and hospital-acquired infection (HAI) using different set of criteria. 

If the AMASS cannot run or cannot generate report (in PDF format), please look into the VDO on the landing page of www.amass.website for details. 

[b] To run AMASS from their routine electronical data, ACORN site may learn how to perform it via the VDO on the landing page of www.amass.website or the main article of the AMASS (https://www.jmir.org/2020/10/e19762/

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