Parses an specification mapping csv to markdown ready for bioschemas.org web.
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README.md

BIOSCHEMAS.ORG GOWEB

The mapping information on the Bioschemas.org specification tables is stored (and transformed into HTML for display purposes) in a human friendly but machine readable format YAML. A simple way to generate and maintain this mapping is using Google Sheet application given its user experience and user interface which is familiar to anyone who has used Spreadsheet applications before. Thus, we have created a template that aids the specification mapping process and provides a suitable way to deliver the information to the website. More information about the template and the specification process here.

This tool helps you transform the Bioschemas Fields sheet on the template into a YAML file that can be stored and displayed on the Bioschemas.org specification page.

Getting the specifications CSV


Stored on the BIOSCHEMAS.ORG gdrive specification folder you will find the specification mappings there on the mapping sheet:

  • Go to File > Publish to the web... > Link
  • Select "Bioschemas fields" and "Comma separated values (.csv)" as the output format.
  • Click on Publish

If the Publish button is not enable, use the URL provided there. You should get an URL similar to this:

https://docs.google.com/spreadsheets/d/e/2PACX-1vTjBKpODC7xTXlfw3P_VffN0u5zdoPt-2bZ4m3_kMGx16lQlz4XH9LyT5y_m-_Tk2AlAO2ID_MFXlTW/pub?gid=292464567&single=true&output=csv

Use it directly on the tool, or download it and feed the CSV file to the tool using the -f command.

Anyone can use it!


It's just as simple as downloading the right executable file according your Operating System and Architecture.

SO Link
alt text Windows
alt text Linux
alt text MAC Darwin

Note: Log and YAML result files will be placed on the folder the program is executed.

Example getting markdown from the GDrive spreadsheet URL


MAC Darwin / Linux

./bioschema-goweb -u "https://docs.google.com/spreadsheets/d/e/2PACX-1vTjBKpODC7xTXlfw3P_VffN0u5zdoPt-2bZ4m3_kMGx16lQlz4XH9LyT5y_m-_Tk2AlAO2ID_MFXlTW/pub?gid=292464567&single=true&output=csv"

Windows

bioschema-goweb_windows_64.exe -u "https://docs.google.com/spreadsheets/d/e/2PACX-1vTjBKpODC7xTXlfw3P_VffN0u5zdoPt-2bZ4m3_kMGx16lQlz4XH9LyT5y_m-_Tk2AlAO2ID_MFXlTW/pub?gid=292464567&single=true&output=csv"

Note: Use quotation marks for the URL.

Example getting markdown from the GDrive spreadsheet CSV downloaded file

./bioschema-goweb -f "Beacon Mapping - Bioschemas fields.csv"

Help

Use the -h parameter to get info about the command tool.

./bioschema-goweb -h