hpo-downloader 1.0.0

Python package to download HPO annotations

Python package to download HPO annotations

How do I install this package?

As usual, just download it using pip:

pip install hpo_downloader

Tests Coverage

Since some software handling coverages sometime get slightly different results, here’s three of them:

Usage examples

The library offers mainly two methods:

Map HPO ids to Uniprot ids

To map the available HPO ids to Uniprot Ids (when possible, not all geneIds used in HPO map to Uniprot Ids) use the following method:

from hpo_downloader import map_phenotype_to_uniprot
phenotype_to_uniprot = map_phenotype_to_uniprot()

The resulting dataframe will look like this:

Uniprot_ID	HPO-Term-ID
A2MG_HUMAN	HP:0410054
A2MG_HUMAN	HP:0001425
A2MG_HUMAN	HP:0001300
A2MG_HUMAN	HP:0000006
A2MG_HUMAN	HP:0000726
A2MG_HUMAN	HP:0002423
A2MG_HUMAN	HP:0002185

The last version of the mapping is available here in tab format.

Download HPO Phenotype annotations

To download the phenotype annotations you can use the following method:

from hpo_downloader import get_phenotype_annotations

annotations = get_phenotype_annotations()

The resulting dataframe will look like this:

DB	DB_Object_ID	DB_Name	Qualifier	HPO_ID	DB_Reference	Evidence_Code	Onset modifier	Frequency	Sex	Modifier	Aspect	Date_Created	Assigned_By
DECIPHER	1	Wolf-Hirschhorn Syndrome		HP:0001249	DECIPHER:1	IEA				P	WOLF-HIRSCHHORN SYNDROME	HPO:skoehler[2013-05-29]
DECIPHER	1	Wolf-Hirschhorn Syndrome		HP:0001250	DECIPHER:1	IEA				P	WOLF-HIRSCHHORN SYNDROME	HPO:skoehler[2013-05-29]
DECIPHER	1	Wolf-Hirschhorn Syndrome		HP:0001252	DECIPHER:1	IEA				P	WOLF-HIRSCHHORN SYNDROME	HPO:skoehler[2013-05-29]
DECIPHER	1	Wolf-Hirschhorn Syndrome		HP:0001518	DECIPHER:1	IEA				P	WOLF-HIRSCHHORN SYNDROME	HPO:skoehler[2013-05-29]
DECIPHER	14	Prader-Willi syndrome (Type 1)		HP:0000135	DECIPHER:14	IEA				P	PRADER-WILLI SYNDROME (TYPE 1)	HPO:skoehler[2013-05-29]
DECIPHER	14	Prader-Willi syndrome (Type 1)		HP:0001249	DECIPHER:14	IEA				P	PRADER-WILLI SYNDROME (TYPE 1)	HPO:skoehler[2013-05-29]