IntAct

IntAct#

IntAct[1] is another one of the most widely-used databases that catalogues protein-protein interactions.

TMKit offers an interface, tmkit.ppi, to access the database. In this tutorial, we will show how we can use this database in Python, starting from downloading it.

Example usage#

First, let’s download the IntAct database. In the example dataset, there is a folder called ppi. The path is ./data/ppi/, which is the place where we suggest users to manage the data used and generated. We can choose either a specific version or the most recent version of the database. Using current, we can download the most recent version. Then we can save it in ./data/ppi/ through parameter sv_fp.

You should have a file called intact.zip after downloading. The tmk.ppi.download_intact_db function will automatically decompress it as intact.txt.

import tmkit as tmk

tmk.ppi.download_intact_db(
    version='current',
    sv_fp='./data/ppi/',
)

Then, using the following codes, you can access the database. The data/ppi/intact.txt is the IntAct database. The tmk.ppi.read_intact_db function will extract a subset of it containing only protein interactors A and B (#ID(s) interactor A and ID(s) interactor B).

Importantly, this function will save the subset as in interA_B.intact in ./data/ppi/interA_B.intact.

import tmkit as tmk

df = tmk.ppi.read_intact_db(
    intact_fpn='./data/ppi/intact.txt',
    extract_ids=[
        '#ID(s) interactor A',
        'ID(s) interactor B',
    ],
    sv_fpn='data/ppi/interA_B.intact',
)
print(df)

Attributes#

Attribute

Description

version

version of a BioGRID database, for example, 4.4.212.

intact_fpn

path where a IntAct database is placed

sv_fp

path to where you want to save files

extract_ids

a list that can include more than one feature, such as #ID(s) interactor A and ID(s) interactor B.

See also

Please see here for better understanding the file-naming system.

Output#

Finally, you will see the following output, which shows 42 features in IntAct, for example Taxid interactor A. You can extract each of the feature in Python, e.g., df['ID(s) interactor B'].

======>reading IntAct...
======>IntAct features are:
=========>No.1: #ID(s) interactor A
=========>No.2: ID(s) interactor B
=========>No.3: Alt. ID(s) interactor A
=========>No.4: Alt. ID(s) interactor B
=========>No.5: Alias(es) interactor A
=========>No.6: Alias(es) interactor B
=========>No.7: Interaction detection method(s)
=========>No.8: Publication 1st author(s)
=========>No.9: Publication Identifier(s)
=========>No.10: Taxid interactor A
=========>No.11: Taxid interactor B
=========>No.12: Interaction type(s)
=========>No.13: Source database(s)
=========>No.14: Interaction identifier(s)
=========>No.15: Confidence value(s)
=========>No.16: Expansion method(s)
=========>No.17: Biological role(s) interactor A
=========>No.18: Biological role(s) interactor B
=========>No.19: Experimental role(s) interactor A
=========>No.20: Experimental role(s) interactor B
=========>No.21: Type(s) interactor A
=========>No.22: Type(s) interactor B
=========>No.23: Xref(s) interactor A
=========>No.24: Xref(s) interactor B
=========>No.25: Interaction Xref(s)
=========>No.26: Annotation(s) interactor A
=========>No.27: Annotation(s) interactor B
=========>No.28: Interaction annotation(s)
=========>No.29: Host organism(s)
=========>No.30: Interaction parameter(s)
=========>No.31: Creation date
=========>No.32: Update date
=========>No.33: Checksum(s) interactor A
=========>No.34: Checksum(s) interactor B
=========>No.35: Interaction Checksum(s)
=========>No.36: Negative
=========>No.37: Feature(s) interactor A
=========>No.38: Feature(s) interactor B
=========>No.39: Stoichiometry(s) interactor A
=========>No.40: Stoichiometry(s) interactor B
=========>No.41: Identification method participant A
=========>No.42: Identification method participant B
======>The file is saved.
        #ID(s) interactor A ID(s) interactor B
0                    P49418             O43426
1          intact:EB7121639             P49418
2          intact:EB7121654             P49418
3          intact:EB7121715             P49418
4                    P49418   intact:EB7121765
...                     ...                ...
1262938              Q80TR1             Q9WTS4
1262939              Q92556             P07355
1262940              Q92556             Q14185
1262941              Q92556             P07355
1262942              Q92556             P07355

[1262943 rows x 2 columns]
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