hpo-downloader 1.0.1

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(
    cafa4_only=False # To not filter for uniprot_ids present only in CAFA4
)

phenotype_to_uniprot_cafa4_only = map_phenotype_to_uniprot(
    cafa4_only=True # To filter for uniprot_ids present only in CAFA4
)

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 with all the mapping is available here in tab format. Similarly, the CAFA4 only mapping is available here in tab format.

N.B.: CURRENTLY 55 gene IDs (1.28% of total) are not mapped by uniprot to curresponding uniprot IDs

N.B.: CURRENTLY 16187 CAFA4 Uniprot_Ids (79.23% of total) are not mapped by uniprot to curresponding HPO IDs

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]

Download CAFA4 Ids

To download the CAFA4 and Uniprot Ids mapping use the following method:

from hpo_downloader import load_cafa4_uniprot_ids

cafa_mapping = load_cafa4_uniprot_ids()

The resulting dataframe will look like this:

CAFA_Id	Uniprot_Id
T96060000001	1433B_HUMAN
T96060000002	1433E_HUMAN
T96060000003	1433F_HUMAN
T96060000004	1433G_HUMAN
T96060000005	1433S_HUMAN
T96060000006	1433T_HUMAN
T96060000007	1433Z_HUMAN
T96060000008	1A01_HUMAN
T96060000009	1A02_HUMAN
T96060000010	1A03_HUMAN