This tool has been created for the situation when you have created a set of text documents and have used Phenotero to annotate HPO or MONDO entries within the texts. Now, you might want to perform sophisticated analyses using your data or exchange the ontology references with a third party.
Our software Text2Onto extracts ontology terms from all your documents and creates a tab-separated file of the form:
/patient_132.docx HP:0000232,MONDO:0010561,HP:0000767,HP:0010864 /patient_4322.odt HP:0000077,HP:0000767 /rare/patient_66322.docx HP:0000232,HP:0000767,HP:0010864,HP:0000445 /rare/lastyear/patient_3.docx HP:0000232,MONDO:0010561,HP:0000767,HP:0000445 /lastyear/patient_3322.docx MONDO:0009162,HP:0000773,HP:0000774
This can then be used for any downstream analysis like patient clustering etc.
Our software is freely available at our GitHub repository.