The Interacting Species Database (ISDB)

A Comprehensive Resource for Ecological Interactions at the Molecular Level. The ISDB aggregates data on species interactions from 21 distinct sources, including protein-protein interaction, species scientific names, Taxon IDs, UniProt IDs, interaction types, ontology identifiers, references, and original database sources. ISDB is implemented using Python and Bash scripts and is freely available as open-source software under the MIT License.

Figure 1. (A) Flowchart illustrating key steps in ISDB creation: data retrieval, standardization, taxonomy annotation, and aggregation. (B–D) Ring diagrams depicting (B) species distribution by superkingdom, (C) classification of interactions according to superkingdom, and (D) predominant interaction types categorized by keywords. (E) Example ecological network showing interconnected species within ISDB.

Web Interface

The ISDB web interface (www.elhabashylab.org/isdb) is hosted by the German Network for Bioinformatics Infrastructure (de.NBI).The interface supports batch downloads, data search, result export, and data deposition. Manual can be found here: ISDB Manual

How to download ISDB?

Prebuilt versions of ISDB are available in the versions directory and can be accessed via the GitHub interface, the ISDB web interface, or directly via command line:

wget https://github.com/ElhabashyLab/ISDB/tree/main/versions/ISDB_2026_04_02.<tsv/csv>.gz

Building ISDB Locally

To build and run ISDB locally, follow these steps:

1. Ensure internet connectivity

   Verify that your system is connected to the internet.

2. Clone the Repository and navigate into it

   git clone https://github.com/ElhabashyLab/ISDB.git
   cd ISDB

3. Set Up the Python Environment

   ISDB requires Python 3.11.7 or later. If your system has a different version, we recommend creating a dedicated Conda environme**

   conda create --name isdb_env python=3.11.7
   conda activate isdb_env

4. Install Dependencies

   ISDB relies on the following Python packages:

   • pandas 2.0.3
   • numpy 1.24.3
   • requests
   • xmltodict 0.14.2
   • multipledispatch 0.6.0
   • xlrd
   • dotenv

   Install all dependencies via:

     pip install -r requirements.txt

5. Download Resources

   Most databases are parsed automatically. Some must be downloaded manually from their respective websites:

   • FGSCdb: Go to (https://edelponte.shinyapps.io/FGSCdb/). Click Select All in each of the following filters: Species, Genotype, Host, Country, and Reference. Click the "Get Data" button to download the full dataset.

   • EID2: Click this link to download the resource directly: (https://figshare.com/ndownloader/files/2196534)

   • DIP: Go to (https://dip.doe-mbi.ucla.edu/dip/Download.cgi). Click on Full complete DIP data set.

   • GMPD: Go to (https://parasites.nunn-lab.org/data/). Download the data for primates, carnivore, and ungulate.

   • Bat Eco-Interactions (https://www.batbase.org/explore)

   • BV-BRC (https://www.bv-brc.org)

   • PHILM2Web (https://phim2web.lailab.info/pages/index.html)

   • PHISTO (https://www.phisto.org/browse.xhtml)

6. Configure Build Parameters

   After downloading the required databases, Edit the main/config.env script to customize parameters:

   1. OUT_DIRECTORY — Directory in which ISDB is built.
   2. Decide which steps to (re)run
      1. DOWNLOAD — Whether to download files from scratch (true / false).
      2. PROCESS — Whether to process downloaded files (true / false).
      3. AGGREGATE — Whether to summon processed files (true / false).
   3. OVERWRITE — Whether to overwrite existing stages (true / false).
   4. ADDITIONAL_DATA — Path to additional data files or directories. Each file must include at least two species columns.
   5. DELETE — Whether to delete intermediate files after build (true / false).
   6. MANUAL_DATABASES — Include databases that cannot be downloaded automatically (true / false). If true, paths must be specified.
   7. SOURCE_DIR — Directory where manual downloaded files are stored

7. Build the ISDB Database

   From the main directory, execute

   cd main
   bash buildDB.sh

Additional options such as overwriting existing files, retaining intermediate files, or including user-provided data can be configured within the script.

Database Output

The built database is available in CSV and TSV formats, with the following columns:

• Serial Number — Unique identifier for each interaction
• Taxonomy ID (A/B) — NCBI Taxonomy identifier
• Organism (A/B) — Scientific species name
• UniProt ID (A/B) — UniProt protein identifier
• Protein Name (A/B) — UniProt protein name
• Interaction Type — Description of the interaction
• Ontology ID — Ontology identifier for the interaction
• Reference — Reference as provided by the source
• Database — Source database of the interaction

How to deposite data to the ISDB?

To submit data for inclusion in our system, please contact our team directly. For local incorporation of your own data, refer to Building ISDB Locally Building ISDB Locally instructions.

List of resources

The database can be built automatically. However, some resources need to be downloaded manually. This includes:

Database	#Species	#Species Pairs	#PPIs	Interaction Type	Batch Download	Database Type
BioGRID	86	260	1,905,211	✔	✔	M
IntAct	1,806	2,855	942,611	✔	✔	M
MINT	697	1,018	79,223	✔	✔	M
DIP	193	270	39,422	✔	✔	M
Signor	7	7	14,959	✔	✔	M
VirHostNet	331	465	41,422	✔	✔	HP/M
PHISTO	589	528	25,405	✔	X	HP/M
Interactomics	294	293	3,958	✔	✔	HP/M
BV-BRC	136,861	146,797	0	X	X	HP
EID2	12,428	17,927	0	✔	✔	HP
GMPD	1,562	5,525	0	X	X	HP
PHILM2Web	411	1,167	0	✔	X	HP
PHI-base	538	1,061	0	X	✔	HP
HPIDB	620	788	0	✔	✔	HP
GloBI	87,958	436,911	0	✔	✔	E
Bat Eco-Interactions	3,094	8,080	0	✔	X	E
SIAD	3,732	5,028	0	✔	✔	E
IWDB	593	3,440	0	X	✔	E
Web of Life database	172	1,050	0	X	✔	E
PIDA	598	757	0	X	✔	E
FGSCdb	19	15	0	✔	X	E

Cite

Mederer, M., Gautam, A., Kohlbacher, O., Lupas, A., Elhabashy, H. Interacting Species Database (ISDB): A Comprehensive Resource for Ecological Interactions at the Molecular Level. Manuscript under review.

Authors

• Michael Mederer
• Anupam Gautam
• Hadeer Elhabashy

Contact

If you have any questions or inquiries, please feel free to contact Hadeer Elhabashy at (Elhabashylab [@] gmail.com)

License

• The ISDB code in this repository is licensed under the MIT License.
• ⭐ If this tool helped your research, please consider starring the repository.

Shield:

• This ISDB database in the versions/ folder is licensed under a Creative Commons Attribution 4.0 International License.