Network data from OmniPath

Marton Olbei

10/12/2020

In this tutorial we show you how to query interactions from one of the many resources included in OmniPath, customize the data by interaction types, and further quality controls.

We'll start by importing libraries, first omnipath, and pandas for data wrangling.

import omnipath as op
import pandas as pd

OmniPath contains many resources we can choose to collate our desired network from. To browse the list available resources call the op.interactions.AllInteractions.resources() function.

op.interactions.AllInteractions.resources()

('ABS',
 'ACSN',
 'ACSN_SignaLink3',
 'ARACNe-GTEx_DoRothEA',
 'ARN',
 'Adhesome',
 'AlzPathway',
 'BEL-Large-Corpus_ProtMapper',
 'Baccin2019',
 'BioGRID',
 'BioGRID_ICELLNET',
 'CA1',
 'CancerCellMap',
 'CellPhoneDB',
 'CellPhoneDB_ICELLNET',
 'DEPOD',
 'DIP',
 'DOMINO',
 'DeathDomain',
 'Dinarello2013_ICELLNET',
 'DoRothEA',
 'DoRothEA-reviews_DoRothEA',
 'ELM',
 'EMBRACE',
 'ENCODE-distal',
 'ENCODE-proximal',
 'ENCODE_tf-mirna',
 'FANTOM4_DoRothEA',
 'Fantom5_LRdb',
 'GO-lig-rec_ICELLNET',
 'Guide2Pharma',
 'Guide2Pharma_CellPhoneDB',
 'Guide2Pharma_ICELLNET',
 'Guide2Pharma_LRdb',
 'HOCOMOCO_DoRothEA',
 'HPMR',
 'HPMR_ICELLNET',
 'HPMR_LRdb',
 'HPRD',
 'HPRD-phos',
 'HPRD_KEA',
 'HPRD_LRdb',
 'HPRD_MIMP',
 'HTRIdb',
 'HTRIdb_DoRothEA',
 'HuRI',
 'I2D_CellPhoneDB',
 'ICELLNET',
 'IMEx_CellPhoneDB',
 'InnateDB',
 'InnateDB-All_CellPhoneDB',
 'InnateDB_CellPhoneDB',
 'InnateDB_ICELLNET',
 'InnateDB_SignaLink3',
 'IntAct',
 'IntAct_CellPhoneDB',
 'IntAct_DoRothEA',
 'JASPAR_DoRothEA',
 'KEA',
 'KEGG-MEDICUS',
 'Kinexus_KEA',
 'Kirouac2010',
 'Kirouac2010_ICELLNET',
 'LMPID',
 'LRdb',
 'Li2012',
 'Lit-BM-17',
 'LncRNADisease',
 'MIMP',
 'MINT_CellPhoneDB',
 'MPPI',
 'Macrophage',
 'Macrophage_ICELLNET',
 'MatrixDB',
 'MatrixDB_CellPhoneDB',
 'NCI-PID_ProtMapper',
 'NFIRegulomeDB_DoRothEA',
 'NRF2ome',
 'NetPath',
 'NetworKIN_KEA',
 'ORegAnno',
 'ORegAnno_DoRothEA',
 'PAZAR',
 'PAZAR_DoRothEA',
 'PhosphoNetworks',
 'PhosphoPoint',
 'PhosphoSite',
 'PhosphoSite_KEA',
 'PhosphoSite_MIMP',
 'PhosphoSite_ProtMapper',
 'PhosphoSite_noref',
 'ProtMapper',
 'REACH_ProtMapper',
 'RLIMS-P_ProtMapper',
 'Ramilowski2015',
 'Ramilowski2015_Baccin2019',
 'Ramilowski2015_ICELLNET',
 'ReMap_DoRothEA',
 'Reactome_ICELLNET',
 'Reactome_LRdb',
 'Reactome_ProtMapper',
 'Reactome_SignaLink3',
 'RegNetwork_DoRothEA',
 'SIGNOR',
 'SIGNOR_ICELLNET',
 'SIGNOR_ProtMapper',
 'SPIKE',
 'SPIKE_ICELLNET',
 'STRING_ICELLNET',
 'SignaLink3',
 'SignaLink3_ICELLNET',
 'Sparser_ProtMapper',
 'TCRcuration_SignaLink3',
 'TFactS_DoRothEA',
 'TFe_DoRothEA',
 'TRED_DoRothEA',
 'TRIP',
 'TRRD_DoRothEA',
 'TRRUST_DoRothEA',
 'TransmiR',
 'UniProt_CellPhoneDB',
 'UniProt_LRdb',
 'Wang',
 'dbPTM',
 'iPTMnet',
 'iTALK',
 'lncrnadb',
 'miR2Disease',
 'miRDeathDB',
 'miRTarBase',
 'miRecords',
 'ncRDeathDB',
 'phosphoELM',
 'phosphoELM_KEA',
 'phosphoELM_MIMP')

OmniPath can serve multiple kinds of interactions, based on the quality of the interactors or the interactions themselves:

• post_translational i.e. physical interactions of proteins, protein-protein interactions (or PPIs)
• transcriptional i.e. gene regulatory interactions
• post_transcriptional i.e. miRNA-mRNA interactions
• mirna_transcriptional i.e. transcriptional regulation of miRNA genes

In the following code blocks we are going to query all of them, and show the URLS these queries generate, through which the data is also accessible, through a browser.

First, let's take a look at PPI interactions.

URL: https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic

By default, this query returns data from the omnipath dataset, which means literature curated activity flow (directed, signed interactions in most cases, curation effort).

interactions = op.interactions.PostTranslational.get()
interactions
#
#RecursionError: maximum recursion depth exceeded

---------------------------------------------------------------------------
RecursionError                            Traceback (most recent call last)
<ipython-input-20-69bc68e6b6bc> in <module>
----> 1 interactions = op.interactions.PostTranslational.get()
      2 interactions
      3 #
      4 #RecursionError: maximum recursion depth exceeded

~/miniconda3/lib/python3.7/site-packages/omnipath/_core/requests/_utils.py in wrapper(wrapped, _instance, args, kwargs)
    102     @wrapt.decorator(adapter=wrapt.adapter_factory(argspec_factory))
    103     def wrapper(wrapped, _instance, args, kwargs):
--> 104         return wrapped(*args, **kwargs)
    105 
    106     if hasattr(clazz, "get") and not hasattr(clazz.get, "__wrapped__"):

~/miniconda3/lib/python3.7/site-packages/omnipath/_core/requests/interactions/_interactions.py in get(cls, exclude, **kwargs)
    432         %(get.returns)s
    433         """
--> 434         return cls(exclude=exclude).get(**kwargs)
    435 
    436 

... last 2 frames repeated, from the frame below ...

~/miniconda3/lib/python3.7/site-packages/omnipath/_core/requests/_utils.py in wrapper(wrapped, _instance, args, kwargs)
    102     @wrapt.decorator(adapter=wrapt.adapter_factory(argspec_factory))
    103     def wrapper(wrapped, _instance, args, kwargs):
--> 104         return wrapped(*args, **kwargs)
    105 
    106     if hasattr(clazz, "get") and not hasattr(clazz.get, "__wrapped__"):

RecursionError: maximum recursion depth exceeded

We can include interactions without explicit literature references as well, by including the extra datasets pathwayextra, kinaseextra, or ligrecextra.

To get just one of these extra sets, one can call the specific function for it:

URL https://omnipathdb.org/interactions?genesymbols=yes&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic

interactions_pathwayextra = op.interactions.PathwayExtra.get()
interactions_pathwayextra

	source	target	is_directed	is_stimulation	is_inhibition	consensus_direction	consensus_stimulation	consensus_inhibition	dip_url	curation_effort	references	sources	references_stripped	n_references	n_sources	n_primary_sources
0	P48995	Q13255	True	False	True	False	False	False	None	0	NaN	Wang	None	None	1	1
1	Q13255	P48995	True	True	False	True	True	False	None	1	TRIP:14614461	TRIP	14614461	1	1	1
2	P20591	Q9Y210	True	True	False	True	True	False	None	3	HPRD:15757897;Lit-BM-17:15757897;TRIP:15757897	HPRD;Lit-BM-17;TRIP;Wang	15757897	1	4	4
3	O60500	Q9Y210	True	True	False	True	True	False	None	2	TRIP:15924139;TRIP:22155451	TRIP;Wang	15924139;22155451	2	2	2
4	Q13976	Q9Y210	True	False	True	True	False	True	None	5	PhosphoSite:19961855;PhosphoSite:23645677;Prot...	MIMP;PhosphoSite;PhosphoSite_MIMP;PhosphoSite_...	18617565;19961855;21402151;23645677;24740790	5	9	4
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
41812	P52789	Q07812	True	False	True	True	False	True	None	0	NaN	KEGG-MEDICUS	None	None	1	1
41813	O15264	Q96BA8	True	True	False	True	True	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1
41814	COMPLEX:P49023_Q05397_Q13418	COMPLEX:O43707_P18206_Q9Y4G6	True	True	False	True	True	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1
41815	COMPLEX:P29466_Q96P20_Q9ULZ3	P01584	True	True	False	True	True	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1
41816	Q02750	O15264	True	True	False	False	False	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1

41817 rows × 16 columns

interactions_pathwayextra_citations = interactions_pathwayextra[
    interactions_pathwayextra['curation_effort'] >= 7
]
interactions_pathwayextra_citations

	source	target	is_directed	is_stimulation	is_inhibition	consensus_direction	consensus_stimulation	consensus_inhibition	dip_url	curation_effort	references	sources	references_stripped	n_references	n_sources	n_primary_sources
7	P12931	Q8NER1	True	True	False	True	True	False	None	8	PhosphoSite:16319926;ProtMapper:16319926;ProtM...	MIMP;NCI-PID_ProtMapper;PhosphoSite;PhosphoSit...	15084474;16319926;17582331;24717323;25970319;3...	6	10	5
14	P49137	Q16539	True	True	False	False	False	False	None	24	BioGRID:17395714;ELM:23047924;ELM:25255283;HPR...	BioGRID;ELM;HPRD;InnateDB;IntAct;Lit-BM-17;Pho...	10581204;10922375;11042204;17255097;17395714;2...	18	8	8
15	Q16539	P49137	True	True	False	True	True	False	None	60	ACSN:11274345;ACSN:12738796;ACSN:15187187;ACSN...	ACSN;BEL-Large-Corpus_ProtMapper;BioGRID;CA1;E...	10581204;10922375;11042204;11274345;11551945;1...	34	35	23
16	O60674	P19235	True	True	False	True	True	False	None	19	BioGRID:8343951;HPRD-phos:12441334;HPRD:117795...	BEL-Large-Corpus_ProtMapper;BioGRID;HPRD;HPRD-...	10579919;10660611;11443118;11779507;12027890;1...	12	20	12
17	P19235	O60674	True	True	False	False	False	False	None	8	BioGRID:8343951;HPRD:11779507;HPRD:12441334;HP...	BioGRID;HPRD;SignaLink3;Wang	11779507;12441334;18160720;23331499;8343951	5	4	4
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
40511	Q16665	P17948	True	True	False	True	True	False	None	15	ACSN:10403805;ACSN:11528470;ACSN:11566883;ACSN...	ACSN;Wang	10403805;11528470;11566883;12080085;12829734;1...	15	2	2
40573	P27540	Q15672	True	True	False	True	True	False	None	21	ACSN:10403805;ACSN:11566883;ACSN:12080085;ACSN...	ACSN;Wang	10403805;11566883;12080085;12829734;13130303;1...	21	2	2
40743	Q9UJX5	O95997	True	True	True	True	True	False	None	19	ACSN:10477750;ACSN:11402067;ACSN:11535616;ACSN...	ACSN;Wang	10477750;11402067;11535616;12640463;15024386;1...	19	2	2
41009	Q9UJU2	O43623	True	True	False	True	True	False	None	19	ACSN:11955436;ACSN:11967263;ACSN:12051714;ACSN...	ACSN;Wang	11955436;11967263;12051714;12490555;14623871;1...	19	2	2
41050	P49841	Q00534	True	False	True	True	False	True	None	13	ACSN:10385618;ACSN:10486203;ACSN:11124803;ACSN...	ACSN;Wang	10385618;10486203;11124803;11152665;12459251;1...	13	2	2

3426 rows × 16 columns

We can use these properties to further specify our queries, for example on curation effort. The curation_effort value we filtered our query on shows the unique database - citation pairs, i.e. how many times was an interaction described in a paper and mentioned in a database.

To get all PPI interactions call interactions.AllInteractions. By default only directed interactions are included, but we can include a flag to import undirected interactions as well.

URL: https://omnipathdb.org/interactions?genesymbols=yes&fields=sources,references&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&directed=no

op.interactions.AllInteractions.get(directed = False, organism = 'human')

/Users/olbeim/miniconda3/lib/python3.7/site-packages/omnipath/_core/requests/interactions/_interactions.py:377: DtypeWarning: Columns (8) have mixed types.Specify dtype option on import or set low_memory=False.
  return cls(include, exclude=exclude)._get(**kwargs)

	source	target	is_directed	is_stimulation	is_inhibition	consensus_direction	consensus_stimulation	consensus_inhibition	dip_url	curation_effort	references	sources	type	references_stripped	n_references	n_sources	n_primary_sources
0	P0DP24	P48995	True	False	True	True	False	True	None	3	TRIP:11290752;TRIP:11983166;TRIP:12601176	TRIP	post_translational	11290752;11983166;12601176	3	1	1
1	Q03135	P48995	True	True	False	True	True	False	http://dip.doe-mbi.ucla.edu/dip/DIPview.cgi?IK...	13	DIP:19897728;HPRD:12732636;IntAct:19897728;Lit...	DIP;HPRD;IntAct;Lit-BM-17;TRIP	post_translational	10980191;12732636;14551243;16822931;18430726;1...	8	5	5
2	P14416	P48995	True	True	False	True	True	False	None	1	TRIP:18261457	TRIP	post_translational	18261457	1	1	1
3	Q02790	P48995	True	False	True	True	False	True	None	3	TRIP:15199065;TRIP:19945390;TRIP:23228564	TRIP	post_translational	15199065;19945390;23228564	3	1	1
4	P48995	Q86YM7	False	False	False	False	False	False	None	4	HPRD:14505576;TRIP:14505576;TRIP:16905188;TRIP...	HPRD;TRIP	post_translational	14505576;16905188;22506990	3	2	2
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
176859	UCA1	P49715	True	False	False	False	False	False	None	1	ncRDeathDB:24648007	ncRDeathDB	lncrna_post_transcriptional	24648007	1	1	1
176860	UCA1	Q16665	True	False	False	False	False	False	None	1	ncRDeathDB:24737584	ncRDeathDB	lncrna_post_transcriptional	24737584	1	1	1
176861	URH	Q9NYL2	True	False	False	False	False	False	None	1	ncRDeathDB:25013376	ncRDeathDB	lncrna_post_transcriptional	25013376	1	1	1
176862	Xist	P26358	True	False	False	False	False	False	None	1	ncRDeathDB:8769643	ncRDeathDB	lncrna_post_transcriptional	8769643	1	1	1
176863	Xist	Q01860	True	False	False	False	False	False	None	1	ncRDeathDB:24945968	ncRDeathDB	lncrna_post_transcriptional	24945968	1	1	1

176864 rows × 17 columns

The other interaction types have their own built-in functions as well. This query accesses interactions from DoRothEA, from confidence levels A to D, from highest to lowest. It is set to pull out A and B by default, but naturally we can extend it.

URL: https://omnipathdb.org/interactions?genesymbols=yes&fields=sources,references&datasets=dorothea,tf_target&dorothea_levels=A,B,C,D

op.interactions.Transcriptional.get(dorothea_levels = ["A","B","C"], organism = 'human')

	source	target	is_directed	is_stimulation	is_inhibition	consensus_direction	consensus_stimulation	consensus_inhibition	dip_url	curation_effort	references	sources	references_stripped	n_references	n_sources	n_primary_sources
0	Q9H2P0	Q6VMQ6	True	False	False	False	False	False	None	0	NaN	ARACNe-GTEx_DoRothEA;ReMap_DoRothEA	None	None	2	0
1	Q9H2P0	Q13627	True	False	False	False	False	False	None	0	NaN	ARACNe-GTEx_DoRothEA;ReMap_DoRothEA	None	None	2	0
2	Q9H2P0	Q9UKI8	True	False	False	False	False	False	None	0	NaN	ARACNe-GTEx_DoRothEA;ReMap_DoRothEA	None	None	2	0
3	Q9H2P0	Q5VZL5	True	False	False	False	False	False	None	0	NaN	ARACNe-GTEx_DoRothEA;ReMap_DoRothEA	None	None	2	0
4	P35869	Q53QZ3	True	False	False	False	False	False	None	0	NaN	ARACNe-GTEx_DoRothEA;ReMap_DoRothEA	None	None	2	0
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
90135	COMPLEX:P15336	P12004	True	True	False	True	True	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1
90136	COMPLEX:P01106_Q92993_Q9Y4A5	P30279	True	True	False	True	True	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1
90137	COMPLEX:O00268_Q8TEY5	Q9UBK2	True	True	False	True	True	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1
90138	Q14934	P35354	True	True	False	True	True	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1
90139	COMPLEX:P03372_Q15596	P08727	True	True	False	True	True	False	None	0	NaN	KEGG-MEDICUS	None	None	1	1

90140 rows × 16 columns

To access post_transcriptional and mirna_transcriptional interactions, we can utilise their respective functions, or call the corresponding URLs:

• miRNA - mRNA https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic

• TF - miRNA: https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic

op.interactions.TFmiRNA.get()

	source	target	is_directed	is_stimulation	is_inhibition	consensus_direction	consensus_stimulation	consensus_inhibition	dip_url	curation_effort	references	sources	references_stripped	n_references	n_sources	n_primary_sources
0	Q9UKV8	MIMAT0000646	True	False	True	True	False	True	None	1	TransmiR:24263100	TransmiR	24263100	1	1	1
1	Q9UKV8	MIMAT0004658	True	False	True	True	False	True	None	1	TransmiR:24263100	TransmiR	24263100	1	1	1
2	P35869	MIMAT0004672	True	True	False	True	True	False	None	1	TransmiR:24798859	TransmiR	24798859	1	1	1
3	P35869	MIMAT0000680	True	True	False	True	True	False	None	1	TransmiR:24798859	TransmiR	24798859	1	1	1
4	P35869	MIMAT0004594	True	True	False	True	True	False	None	2	TransmiR:25617893;TransmiR:26377202	TransmiR	25617893;26377202	2	1	1
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
4974	Q15545	MIMAT0000075	True	False	False	False	False	False	None	0	NaN	ENCODE_tf-mirna	None	None	1	0
4975	O60216	MIMAT0005867	True	False	False	False	False	False	None	0	NaN	ENCODE_tf-mirna	None	None	1	0
4976	P23511	MIMAT0003308	True	False	False	False	False	False	None	0	NaN	ENCODE_tf-mirna	None	None	1	0
4977	P15408	MIMAT0005867	True	False	False	False	False	False	None	0	NaN	ENCODE_tf-mirna	None	None	1	0
4978	Q12824	MIMAT0004491	True	False	False	False	False	False	None	0	NaN	ENCODE_tf-mirna	None	None	1	0

4979 rows × 16 columns

op.interactions.miRNA.get()

	source	target	is_directed	is_stimulation	is_inhibition	consensus_direction	consensus_stimulation	consensus_inhibition	dip_url	curation_effort	references	sources	references_stripped	n_references	n_sources	n_primary_sources
0	MIMAT0000062	P01116	True	False	False	False	False	False	None	5	miRTarBase:15766527;miRTarBase:16651716;miRTar...	miR2Disease;miRTarBase;miRecords;ncRDeathDB	15766527;16651716;20033209;24092860	4	4	4
1	MIMAT0000062	P52926	True	False	False	False	False	False	None	9	miRTarBase:17322030;miRTarBase:17600087;miRTar...	miR2Disease;miRTarBase;miRecords;ncRDeathDB	17322030;17554199;17600087;18083101;18413822;1...	8	4	4
2	MIMAT0000062	P10415	True	False	False	False	False	False	None	0	NaN	miR2Disease	None	None	1	1
3	MIMAT0000062	P01106	True	False	False	False	False	False	None	2	miRTarBase:16651716;miRTarBase:20033209	miR2Disease;miRTarBase	16651716;20033209	2	2	2
4	MIMAT0000062	P30304	True	False	False	False	False	False	None	0	NaN	miR2Disease	None	None	1	1
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
8273	MIMAT0000617	Q13526	True	False	False	False	False	False	None	1	miRTarBase:24786790	miRTarBase	24786790	1	1	1
8274	MIMAT0000451	Q9NSE2	True	False	False	False	False	False	None	1	miRTarBase:23723424	miRTarBase	23723424	1	1	1
8275	MIMAT0000416	Q12797	True	False	False	False	False	False	None	1	miRTarBase:23723006	miRTarBase	23723006	1	1	1
8276	MIMAT0000449	Q96LI5	True	False	False	False	False	False	None	1	miRTarBase:23591815	miRTarBase	23591815	1	1	1
8277	MIMAT0000256	O14746	True	False	False	False	False	False	None	1	miRTarBase:25444904	miRTarBase	25444904	1	1	1

8278 rows × 16 columns

In this tutorial we learned:

• The various interaction types in OmniPath
• The differences between the encoded interaction types
• How to access and query these interaction types