New webservice from 14 June 2018: the queries slightly changed, have been largely extended. See the examples below.
The webservice implements a very simple REST style API, you can make requests by the HTTP protocol (browser, wget, curl or whatever). After defining the query type and optionally a set of molecular entities (proteins) you can add further GET parameters encoded in the URL.
The webservice currently recognizes 7 types of queries:
The query types
about have not been
implemented yet in the new webservice.
The instance of the
pypath webserver running at the domain
https://omnipathdb.org/, serves not only the OmniPath data but also other
datasets. Each of them has a short name what you can use in the queries
omnipath: the OmniPath data as defined in the paper, an arbitrary optimum between coverage and quality
pathwayextra: activity flow interactions without literature reference
kinaseextra: enzyme-substrate interactions without literature reference
ligrecextra: ligand-receptor interactions without literature reference
dorothea: transcription factor (TF)-target interactions from DoRothEA
tf_target: transcription factor (TF)-target interactions from other sources
mirnatarget: miRNA-mRNA and TF-miRNA interactions
TF-target interactions from DoRothEA, a large collection additional enzyme-substrate interactions, and literature curated miRNA-mRNA interacions combined from 4 databases.
Mouse and rat
Except the miRNA interactions all interactions are available for human, mouse
and rat. The rodent data has been translated from human using the NCBI
Homologene database. Many human proteins do not have known homolog in rodents
hence rodent datasets are smaller than their human counterparts. Note, if you
work with mouse omics data you might do better to translate your dataset to
human (for example using the
pypath.homology module) and use human
A request without any parameter provides the main webpage:
info returns a HTML page with comprehensive information about the
resources. The list here should be and will be updated as currently OmniPath
includes much more databases:
Molecular interaction network
interactions query accepts some parameters and returns interactions in
tabular format. This example returns all interactions of EGFR (P00533), with
sources and references listed.
By default only the OmniPath dataset used, to include any other dataset you have to set additional parameters. For example to query the transcriptional regulators of EGFR:
The DoRothEA database assigns confidence levels to the interactions. You might want to select only the highest confidence, A category:
Show the transcriptional targets of Smad2 homology translated to rat including the confidence levels from TF Regulons:
Query interactions from PhosphoNetworks which is part of the kinaseextra dataset:
Get the interactions from Signor, SPIKE and SignaLink3:
All interactions of MAP1LC3B:
partners queries the interaction where either the source or the
arget is among the partners. If you set the
source_target parameter to
AND both the source and the target must be in the queried set:
As you see above you can use UniProt IDs and Gene Symbols in the queries and also mix them. Get the miRNA regulating NOTCH1:
Note: with the exception of mandatory fields and genesymbols, the columns appear exactly in the order you provided in your query.
Another query type available is
ptms which provides enzyme-substrate
interactions. It is very similar to the
Is there any ubiquitination reaction?
And acetylation in mouse?
Rat interactions, both directly from rat and homology translated from human, from the PhosphoSite database:
complexes query provides a comprehensive database of more than 22,000
protein complexes. For example, to query all complexes from CORUM and PDB
containing MTOR (P42345):
annotations query provides a large variety of data about proteins,
complexes and in the future other kinds of molecules. For example an
annotation can tell if a protein is a kinase, or if it is expressed in the
hearth muscle. These data come from dozens of databases and each kind of
annotation record contains different fields. Because of this here we have
record_id field which is unique within the records of each database.
Each row contains one key value pair and you need to use the
to connect the related key-value pairs. You can easily do this with
dplyr in R or
pandas in Python. An example to query the pathway
annotations from SignaLink:
Or the tissue expression of BMP7 from Human Protein Atlas:
Roles in inter-cellular communication
Another query type is the
intercell, providing information about the
roles in inter-cellular signaling. E.g. if a protein is a ligand, a receptor,
an extracellular matrix (ECM) component, etc. The proteins and protein
complexes are classified into categories. The categories are defined by a
number of attributes:
- aspect: funtional (e.g. ion channel) or locational (e.g. plasma membrane transmembrane).
- scope: generic (e.g. ligand) or specific (e.g. interleukin)
- source: resource specific (from one resource) or composite (combined from more resources)
- causality: transmitter (delivering signal from the expressing cell) or receiver (receiving signal into the expressing cell) or both
- topology: major localization categories derived from the locational categories: plasma membrane transmembrane or peripheral or secreted
The intercell database defines 25 functional and 10 locational generic, composite categories. The number of specific categories is above 1,000.
You can use all these attributes in your queries, see the exact keys and values at https://omnipathdb.org/queries/intercell
Some example queries:
All the resource specific functional classes for one protein:
A list of all ECM proteins:
Exploring possible parameters
Sometimes the names and values of the query parameters are not intuitive,
even though in many cases the server accepts multiple alternatives. To see
the possible parameters with all possible values you can use the
query type. The server checks the parameter names and values exactly against
these rules and if any of them don't match you will get an error message
instead of reply. To see the parameters for the