batch

This command creates prompts from all phenopackets in the input directory.

Getting the input data

Go to the Releases section of phenopacket-store, and download the latest release (currently 0.1.5 on April 29, 2024, but evolving rapidly). Currently, this resource contains over 4300 phenopackets.

Download one of the archives (e.g., all_phenopackets.zip) and unpack in a location of your choice.

Then run the following command.

batch

java -jar phenopacket2prompt.jar batch  -d <all_phenopackets>

where <all_phenopackets> is the complete relative or absolute path to the unpacked directory.

phenopacket2prompt will create a new subdirectory called promptsin the current directory. It will contain one folder for each language (currently, English-en and Spanish-es), as well as a file called correct_results.tsv with the following structure

Disease name	OMIM identifier	Prompt file name
Birt-Hogg-Dube syndrome 2	OMIM:620459	PMID_36440963_IIIPMID_36440963_III-33-prompt.txt
Immunodeficiency 115 with autoinflammation	OMIM:620632	PMID_26008899_patient-prompt.txt
Jacobsen syndrome	OMIM:147791	PMID_15266616_148-prompt.txt

Note that the prompt file name is the same for every language.