Programmatic Access To Biological Databases (Perl). 1 October 2012

1. Community effort to provide molecular
interaction data
PSI-MI & PSICQUIC
Programmatic Access To Biological Databases (Perl)
1 – 4 October 2012
Marine Dumousseau, Noemi Del Toro Ayllon and Rafael C. Jimenez
marine@ebi.ac.uk, ntoro@ebi.ac.uk and rafael@ebi.ac.uk

2. PSI-MI
Data format
Data distribution
Control vocabulary
Reporting guidelines
Standard format
Tools
PSICQUIC
PSI-MI CV
MIMIx
PSI-MI XML
PSI-MITAB
XML Java API
MITAB Java API
XMLMakerFlattener
Semantic Validator
RPsiXML (Bioconductor)
PSI Excel Sheet submission
PSI Web Form submission
Servers
Registry
Clients
PSISCORE Servers
Registry
Clients
IMEx
TOC
Data distribution best practices
1
2
3
4
5
6

3. • Proteomics Standards Initiative
• Work group of the Human Proteome Organization
• Defines community standards for data in proteomics
• … facilitating data comparison, exchange and verification
PSI
3

4. PSI-MI
• Work group of the Proteomics Standards Initiative
• Community coordination to ensure deposition of
Molecular Interaction data in public repositories
• Concentrating on …
• Annotation and representation of published MI data
• Accessibility of MI data to the user community
http://www.psidev.info/MI

5. 13/12/2018
5
http://psidev.info/

6. PSI-MI
Data format
Data distribution
Control vocabulary
Reporting guidelines
Standard format
Tools
PSICQUIC
PSI-MI CV
MIMIx
PSI-MI XML
PSI-MITAB
XML Java API
MITAB Java API
XMLMakerFlattener
Semantic Validator
RPsiXML (Bioconductor)
PSI Excel Sheet submission
PSI Web Form submission
Servers
Registry
Clients
PSISCORE Servers
Registry
Clients
IMEx
TOC
Data distribution best practices

7. PSI-MI
Data format/schema
Data distribution
Control vocabulary
MIAPE
Reporting guideline
PSI-MI XML
PSI-MITAB
PSICQUIC
MIMIx
IMEx
PSI-MI CV
http://www.psidev.info/MI
Scoring
PSISCORE

8. PSI-MI format
• Community standard for Molecular Interactions
• Jointly developed by major data providers: BIND,
CellZome, DIP, GSK, HPRD, Hybrigenics, IntAct, MINT, MIPS, Serono,
U. Bielefeld, U. Bordeaux, U. Cambridge, and others
• Collecting and combining data from different sources
has become easier
• Standardized annotation through PSI-MI ontologies
• Tools from different organizations can be chained, e.g.
IntAct data in Cytoscape.
8
psi-mi/xml25 psi-mi/tab25

9. 9
PSI-MI 2.5 Standards
• Version 1.0 published in February 2004
The HUPO PSI Molecular Interaction Format - A community standard for the representation of
protein interaction data.Henning Hermjakob et al, Nature Biotechnology 2004, 22, 176-183.
• Version 2.5 published in October 2007

10. PSI-MI XML: A simplified view of the schema
Participant Participant Participant
Interactor Interactor
Feature
RangeRange
Feature
Experiment
Entry
EntrySet
Interaction Interaction
XML specification: http://code.google.com/p/psimi/wiki/PsimiXMLSpecifications
Schema view: http://psidev.sourceforge.net/molecular_interactions/rel25/doc/
Schema: http://psidev.sourceforge.net/mi/rel25/src/MIF25.xsd
General docuemntation: http://www.psidev.info/node/60#overlay-context=node/60

11. “Compact” format
Interaction
Interaction
experimentDescription id=“1”
experimentDescription id=“2”
experimentRef=“1”
interactor id=“3”
interactor id=“4”
Participant id=“5”
interactorRef=“3”
Participant id=“6”
interactorRef=“4”
Interaction id=“7”
Interaction id=“8”
“Expanded” formatPSI-MI XML

12. PSI-MI XML
“Compact” format

13. PSI-MI XML
“Expanded” format

14. PSI-MITAB
• Released at the same time that PSI-MI XML 2.5
• Aimed at users that are more comfortable with Excel
• Only provides binary interactions
• Latest version: PSI-MI TAB 2.7
14
psi-mi/tab27
PSI-MI TAB 2.5: http://code.google.com/p/psimi/wiki/PsimiTabFormat
PSI-MI TAB 2.7: http://code.google.com/p/psimi/wiki/PsimiTab27Format
General information: http://www.psidev.info/groups/molecular-interactions

15. 15
Standard columns (15):
• ID(s) interactor A & B
• Alt. ID(s) interactor A & B
• Alias(es) interactor A & B
• Interaction detection method(s)
• Publication 1st author(s)
• Publication Identifier(s)
• Taxid interactor A & B
• Interaction type(s)
• Source database(s)
• Interaction identifier(s)
• Confidence value(s)
PSI-MITAB 2.5 columns
15
v2.5

16. 16
Standard columns (15):
• ID(s) interactor A & B
• Alt. ID(s) interactor A & B
• Alias(es) interactor A & B
• Interaction detection method(s)
• Publication 1st author(s)
• Publication Identifier(s)
• Taxid interactor A & B
• Interaction type(s)
• Source database(s)
• Interaction identifier(s)
• Confidence value(s)
Standard columns (21):
• Complex expansion
• Biological role A & B
• Experimental role A & B
• Interactor type A & B
• Xrefs A, B & Int.
• Annotations A, B & Int.
• Host organism
• Parameters Int.
• Created
• Updated
• CheckSum A, B & Int.
• Negative
Standard columns (4):
• Binding feature A & B
• Stoichiometry A & B
v2.5 v2.6 v2.7
15 36 40
PSI-MITAB 2.7 columns
+ +

17. PSI-MI format: Tools
• XML Java API (PSI-MI XML 2.5 Java Parser)
• Parse “PSI-MI XML”
• Create “PSI-MI XML”
• MITAB Java API (PSI-MITAB 2.5 Java Parser)
• Parse “PSI-MITAB”
• Create “PSI-MITAB”
• XMLMakerFlattener
• “PSI MI XML” to “Tab-delimited format”
• “Tab-delimited format” to “PSI MI XML”
• XML Validator
• Semantic and syntactic consistency
• XML transformation:
• MIF25_view.xsl “XML” to “HTML”
• MIF25_compact.xsl PSI-MI XML “expanded” to “compact”
• MIF25_expand.xsl PSI-MI XML “compact” to “expanded”
17
More information: http://www.psidev.info/mif#tools

18. Data submission tools
PSI-MI XML files
PSI Excel Sheet
PSI Web Form
More information: http://www.psidev.info/mif#tools

19. PSI-MI
Data format
Data distribution
Control vocabulary
Reporting guidelines
Standard format
Tools
PSICQUIC
PSI-MI CV
MIMIx
PSI-MI XML
PSI-MITAB
XML Java API
MITAB Java API
XMLMakerFlattener
Semantic Validator
RPsiXML (Bioconductor)
PSI Excel Sheet submission
PSI Web Form submission
Servers
Registry
Clients
PSISCORE Servers
Registry
Clients
IMEx
TOC
Data distribution best practices

20. 20
• OLS Makes available OBO controlled vocabularies
• Web site allows for searching and browsing their
hierarchy
• Programmatic access though SOAP web services
PSI-MI CV in the Ontology Lookup Service

21. Control vocabulary: PSI-MI CV
• Ontology browser: http://www.ebi.ac.uk/ontology-lookup

22. PSI-MI
Data format
Data distribution
Control vocabulary
Reporting guidelines
Standard format
Tools
PSICQUIC
PSI-MI CV
MIMIx
PSI-MI XML
PSI-MITAB
XML Java API
MITAB Java API
XMLMakerFlattener
Semantic Validator
RPsiXML (Bioconductor)
PSI Excel Sheet submission
PSI Web Form submission
Servers
Registry
Clients
PSISCORE Servers
Registry
Clients
IMEx
TOC
Data distribution best practices

23. MIMIx
• Minimum information guideline for reporting molecular interactions
• 1. Manuscript information
• 2. Experiment
• 3. Interaction
• 4. Confidence
http://www.nature.com/nbt/journal/v25/n8/full/nbt1324.html

24. IMEx
13/12/2018
24
http://onlinelibrary.wiley.com/doi/10.1002/pmic.200700286/abstract

25. Data distribution best practices
13/12/2018
25
http://code.google.com/p/psicquic/wiki/DataDistributionBestPractices

26. PSI-MI
Data format
Data distribution
Control vocabulary
Reporting guidelines
Standard format
Tools
PSICQUIC
PSI-MI CV
MIMIx
PSI-MI XML
PSI-MITAB
XML Java API
MITAB Java API
XMLMakerFlattener
Semantic Validator
RPsiXML (Bioconductor)
PSI Excel Sheet submission
PSI Web Form submission
Servers
Registry
Clients
PSISCORE Servers
Registry
Clients
IMEx
TOC
Data distribution best practices

27. Data distribution: PSICQUIC
• Proteomics Standards Initiative Common QUery InterfaCe.
• Community effort to standardise the way to access and retrieve data
from Molecular Interaction databases.
• Widely implemented by independent interaction data resources.
• Based on the PSI standard formats (PSI-MI XML and MITAB)
• Not limited to protein-protein interactions, also e.g.
• Drug-target interactions
• Simplified pathway data
• A registry listing resources implementing PSICQUIC
• Documentation: http://psicquic.googlecode.com

28. Published in 2011
http://www.ncbi.nlm.nih.gov/pubmed/21716279

29. APID
416,124
612,785
362,355
268,920
1,465,119
845
132,490
24,268
74,861
15,844
107,619
26,045,661
Around
150 million
binary interactions
available using
PSICQUIC*
208,55839,367
192,961
(*) As of February 2012
117
I2D
546

30. IntAct And PSICQUICBruno Aranda (baranda@ebi.ac.uk)
“The one Client to rule them all”

31. • Services
• IntAct
• Biogrid
• String
• ...
• Registry
• Clients
• PSICQUIC view
• Cytoscape
• …
13.12.201831
Service Oriented Architecture
query
PublishFind
PSICQUIC
Registry
DAS ClientsDAS ClientsPSICQUIC
Clients
Format
PSICQUIC
sources
PSICQUIC
sources
PSICQUIC
Services
MIQL
PSI-MI

32. PSIQUIC Proteomics Standard Initiative Common QUery InterfaCe
13/12/2018
32
PSICQUIC
Query Interactions
PSICQUIC
Registry
PSI-MIMIQL
Input Output
PSICQUIC
Service A
PSICQUIC
Service B
PSICQUIC
Service C
User View
Web Service System
application

33. PSICQUIC Registry
• It contains a list of the PSICQUIC services from different
providers.
• It is a web service itself, and it can be accessed remotely
using REST.
• Information can be found about the services, such as the
URLs to use, number of interactions provided, versioning,
tags, etc.

34. PSICQUIC Registry
• ~ 150 million interactions from 25 resources
• ~ 2.5 million interactions from 16 curated resources
http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS
(*) As of February 2012

35. Registry Tagging system
• The registry classifies the different services with tags.

36. PSICQUIC services
36
• PSICQUIC services are Web Services (REST & SOAP)
• Independent databases
• Adopting the same specification
• Implementing the same interface
• Same methods to query services
• Same format to provide results
PSICQUIC
serviceMIQL PSI-MI
input output
Query language Format

37. PSICQUIC REST specification
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http://code.google.com/p/psicquic/wiki/PsicquicSpec_1_2_Rest

38. PSICQUIC REST Query explained
http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/species:human?firstResult=0&maxResults=100
Example:

39. PSICQUIC REST queries
Bruno Aranda (baranda@ebi.ac.uk)
http://mint.bio.uniroma2.it/mint/psicquic/webservices/current/search/query/p53
http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/p53
http://www.ebi.ac.uk/Tools/webservices/psicquic/chembl/webservices/current/search/query/p53
1
2
3

40. MIQL: Molecular Interactions Query Language
• The Molecular Interactions Query Language (MIQL)
allows more powerful and flexible queries.
• It is the default query syntax for PSIQCUIC.
• Designed for fast and effective searches on PSI-MI
TAB files.
• All fields (columns) can be searched with specific
queries.
• MIQL is a consensus between the different
databases, so you should be able to use the same
query across different repositories.

41. MIQL
Bruno Aranda (baranda@ebi.ac.uk)

42. MIQL
…/query/specie:rat
…/query/brca AND rpa1
• Terms
• Fields
• Operands

43. PSICQUIC SOAP service
species:trypanosoma AND detmethod:’two hybrid’

44. SOAP Methods
• getByInteraction
Retrieves interactions by using an interaction AC.
• getByInteractionList
Retrieves interactions by using a list of interaction AC.
• getByInteractor
Retrieves interactions by using a participant identifier.
• getByInteractorList
Retrieves interactions by using a list of participant identifiers.
• getByQuery
Retrieves interactions by using a Molecular Interaction Query Language (MIQL)
query (full text searches)

45. SOAP Methods
Other metadata methods:
• getVersion
Returns the version of the web service implementation.
• getSupportedDbAcs
Returns the supported database identifiers
• getSupportedReturnTypes
Returns the list of available format types for the results.
• A limited number of interactions can be fetched. It is possible to retrieve
large datasets using pagination. Most methods have two additional
parameters:
•First result: Index for the first result to retrieve.
•Max results: Number of interactions returned per query.

46. Default formats
• The default formats are:
• PSI-MI XML 2.5.4 (psi-mi/xml25)
• PSI MITAB 2.5 (psi-mi/tab25)
• PSI MITAB 2.7 (psi-mi/tab27)
• Compressed MITAB (tab25-bin) – Only REST
• Count (count) – Only REST
• New formats will be included in the future (work in
progress):
• BioPAX (biopax)
• And other RDF formats (rdf-xml / rdf-n3 / rdf-n3-triple / rdf-turtle)
• (so it will be possible to use PSICQUIC in the semantic web!)

47. IntAct And PSICQUICBruno Aranda (baranda@ebi.ac.uk)
psi-mi/xml25
psi-mi/tab25
psi-mi/tab27

48. biopax

49. RDF/XML

50. RDF N3

51. PSICQUIC clients
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PSICQUIC view Cytoscape
www.ebi.ac.uk/Tools/webservices/psicquic/view
Web client
http://code.google.com/p/psicquic/wiki/CytoscapeClient
Desktop application

52. PSICQUIC view
• Simple and complex queries
• Link back to the original source for more details
• Clustering of queries across providers
• Visualization of graphical network
http://www.ebi.ac.uk/Tools/webservices/psicquic/view/

53. 53
PSICQUIC View: table view

54. 54
PSICQUIC View: clustering

55. PSICQUIC View: graphical network

56. Cytoscape PSICQUIC support
• Cytoscape 2.5
• Open “PSI-MI XML 1.0” files
• Cytoscape 2.7
• Open “PSI-MI XML 1.0” files
• Import interactions from PSICQUIC (plug-in)
• Cytoscape 3.0
• Open “PSI-MI TAB 2.5” files
• Import interactions from PSICQUIC (core)
• Merge/cluster PSICQUIC interactions
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56

57. Cytoscape 3.0 PSICQUIC import
13/12/2018
57
Thanks to ...
Keiichiro Ono
and the cytoscape team

58. 0.90
0.380.25
—0.63
0.45
0.71
0.40
0.11
PSICQUIC PSISCORE
Query Interactions
PSI-MI
0.90
0.380.25
—0.63
0.45
0.71
0.40
0.11
PSICQUIC
Registry
Confidence Scores
PSI-MIMIQL
PSISCORE
Registry
client
Input Input
Output Output
PSICQUIC
Service A
PSICQUIC
Service B
PSISCORE
Service D
PSISCORE
Service E
PSICQUIC
Service C
User View
Web Service System

59. PSISCORE registry
• 4 sources
• 14 scoring methods
http://code.google.com/p/psiscore/

60. PSISCORE client

61. PSI-MI
Data format
Data distribution
Control vocabulary
Reporting guidelines
Standard format
Tools
PSICQUIC
PSI-MI CV
MIMIx
PSI-MI XML
PSI-MITAB
XML Java API
MITAB Java API
XMLMakerFlattener
Semantic Validator
RPsiXML (Bioconductor)
PSI Excel Sheet submission
PSI Web Form submission
Servers
Registry
Clients
PSISCORE Servers
Registry
Clients
IMEx
TOC
Data distribution best practices

62. IMEx: The International Molecular Exchange Consortium
• Group of major public interaction data providers sharing
curation effort: DIP, IntAct, MINT, MPact, MatrixDB, MPIDB and BioGRID
• Independent molecular interaction resources
• Common curation standards for detailed curation
• Common data formats (PSI-MI XML, PSI-MITAB, PSICQUIC)
• Common accession number space
• Coordinated & non-redundant curation
• In production mode since February 2010
• Since 3/2009 supported by the European Commission
under PSIMEx, contract number FP7-HEALTH-2007-223411, with additional partners Vital-IT, Nature,
Wiley, BiaCore (GE), U. Maryland, CSIC, TU Munich, MIPS, SCBIT (Shanghai)
http://www.imexconsortium.org

63. IMEx website http://www.imexconsortium.org

64. PSICQUIC client: PSICQUIC view in IMEx
http://www.imexconsortium.org

65. Thank you!
13/12/2018
65
ProteomicsServicesTeam