Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host–pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 3.0 is a resource for HPI data, and contains 45, 238 manually curated entries in the current release.

Citing HPIDB

Statistics

Database Construction and Data Source

External Database Citations

• Ammari, M.G., Gresham, C.R., McCarthy, F.M. and Nanduri, B., 2016. HPIDB 2.0: a curated database for host–pathogen interactions. Database, 2016. [DOI]
• Kumar, R. and Nanduri, B., 2010. HPIDB-a unified resource for host-pathogen interactions BMC bioinformatics, 11(6), p.S16. [DOI]

Currently HPIDB contains 55,505 unique protein interactions between 55 host and 523 pathogen species. Unique protein interactions are defined by unique values in the following columns: host protein id, pathogen protein id, pmid, interaction type and detection method.

• Download the HPIDB (excluding predicted interologs) database in PSI-MITAB(2.5) file format.
• Download the HPIDB interolog predictions database in PSI-MITAB(2.5) file format.

Distributions within HPIDB

To see pie charts for the following: distribution of HPIs from different sources, distribution of the host and pathogen species in HPIDB, distribution of abundant host and pathogen species in HPIDB, please visit our old site.

Most abundant pathogen species in HPIDB

Pathogen Species	Host Species	Interactions
Influenza	Multiple Hosts	9,957
Herpes viruses	Multiple Hosts	8,174
Saccharomyces cerevisiae	Multiple Hosts	6,862
Papillomaviruses	Multiple Hosts	6,515
Human immunodeficiency virus	Multiple Hosts	4,366
Yersinia	Multiple Hosts	4,026
Bacillus	Multiple Hosts	3,069
Hepatitis C virus	Multiple Hosts	2,617
Francisella tularensis	Multiple Hosts	1,371
Measles virus	Multiple Hosts	1,030

The database is organized as a 26 column table. The first 15 columns are the standard PSI-MI TAB Format/MITAB25 format columns available for most PPI databases. The 11 additional columns specific to HPIDB along with the standard 15 columns are described below. Each row in the database represents one protein-protein interaction pair.

Description of first 15 standard PSI-MI Tab format columns

1. protein_xref_1 (identifier for the first protein)
2. protein_xref_2 (identifier for the second protein)
3. alternative_identifiers_1 (alternative identifiers for the first protein)
4. alternative_identifiers_2 (alternative identifiers for the second protein)
5. rotein_alias_1 (alias name for the first protein)
6. protein_alias_2 (alias name for the second protein)
7. detection_method (detection method used)
8. author_name (author’s name)
9. pmid (publication id)
10. protein_taxid_1 (taxonomy id for the first protein)
11. protein_taxid_2 (taxonomy id for the second protein)
12. interaction_type (interaction type)
13. source_database_id (source database)
14. database_identifier (identifier for the source database)
15. confidence (confidence score for interaction)

Description of 10 columns unique to HPIDB

16. protein_xref_1_unique (unique id for the first protein)
17. protein_xref_2_unique(unique id for the second protein)
18. protein_taxid_1_cat (taxonomy category for the first protein)
19. protein_taxid_2_cat (taxonomy category for the second protein)
20. protein_taxid_1_name (taxonomy name for the first protein)
21. protein_taxid_2_name (taxonomy name for the second protein)
22. protein_seq1 (sequence of the first protein)
23. protein_seq2 (sequence of the second protein)
24. source_database (source database for the derived PPI)
25. protein_xref_1_display_id (display identifier for first protein)
26. protein_xref_2_display_id (display identifier for second protein)

• Aranda, B. et al. (2011) "PSICQUIC and PSISCORE: accessing and scoring molecular interactions." Nat Meth 8 2010; 528-529. doi:10.1038/nmeth.1637. [Nature] [PSICQUIC Registry]
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• The UniProt Consortium (2015) "UniProt: a hub for protein information." Nucleic Acids Res. 43: D204-D212. [DOI] UniProtKB
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