BIOLOGICAL PATHWAYS AND THE SEMANTIC WEB

Transcription

1 BIOLOGICAL PATHWAYS AND THE SEMANTIC WEB Andra Waagmeester, Tina Kutmon, Egon Willighagen, and Alex Pico Univ. Maastricht, NL, and Gladstone Institutes, CA, USA

2 What we will talk about today Introduc*on to biological pathways Conversion to linked data Seman*c queries on pathways - - Break - - Building tools and resources Pathways in Open PHACTS

3 Gerhard Michal 1974

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5 hcp://

6 hcp://

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8 hcp://

9 XML format (BioPAX) RESTful web services HTML embed code

10 @prefix dc: cas: wprdf: foaf: < < a gpml:datanode, skos:concept, wp:geneproduct ; rdfs:isdefinedby gpml:datanode ; rdfs:label "CRHR1"@en ; dc:identifier < "1394"^^xsd:string ; dc:source "Entrez Gene"^^xsd:string ; dcterms:ispartof < WP4_r39380.ttl> ; gpml:centerx "340.0"^^xsd:float ;... XM RDF and SPARQL endpoint hcp://sparql.wikipathways.org

11 hcp://wikipathways.org

12 hcp://wikipathways.org

13 Converting WikiPathways to RDF

14 Overview Why linked data /RDF? How are the pathways available now? The WikiPathways RDF recipe?

15 5 stars Open Data

16 AIM: Collection of documents -> Web of interconneced pathway entities

17 Gene is_part_of Pathway1. Gene is_part_of Pathway2. Gene is_part_of PathwayN. Gene inside Membrane. Gene2 outside Membrane

18 List all gene products

19 List all intracellular geneproducts

20 Mapping knowledge as triples Gene is_part_of Pathway1. Gene is_part_of Pathway2. Gene is_part_of PathwayN. Gene inside Membrane. Gene2 outside Membrane

21 Putting the semantics in Triples Gene is_part_of Pathway1. v Pathway:WP1

22 Using prefixes to make it readable PREFIX ncbigene : < PREFIX dcterms: < PREFIX wp: < ncbigene:16971 dcterms:ispartof wp:wp1.

23 Pathway content Getting it through o Download it as GPML and text files (gene lists) o Download as image (PDF, PNG, JPG) Getting it through the Webservices ( Help:WikiPathways_Webservice) o listorganism, listpathways, list

24 Get a list of human genes from WikiPathways 1. List all Human Pathways (apiclient- >listpathways(human)) 2. Iterate over all pathways and filter for genes a. Get the pathway files (apiclient- >getpathwayas(gpml)) b. Load the xml document c. Extract the Genes from the pathway file 3. List the extracted genes

25 Webservice vs Api List all genes in WikiPathways $pathways = client->listpathways $pathways = $pathways->iterate { } SET $genes += $pathway->getgenes(); print $genes; SELECT DISTINCT * { }?gene is_a WP:gene.

26 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF. 8. Load RDF in triple store with sparql endpoint. 9. Query and federate along.

27 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF a. b. c. Open PHACTS Linked Data Cache 8. Query and federate along.

28 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF a. b. c. Open PHACTS Linked Data Cache 8. Query and federate along.

29 WikiPathways knowledge Pathway knowledge o Pathway elements (e.g. Interactions, GeneProducts Metabolites, Targets) o References to the literature o Datasource identifiers Curators knowledge o Author name Graphical information. o Coordinates of the position in drawn diagram

30 Identify and describe the different classes and pathways

31 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF a. b. c. Open PHACTS Linked Data Cache 8. Query and federate along.

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36 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF. 8. Load RDF in triple store with sparql endpoint. 9. Query and federate along.

37 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF a. b. c. Open PHACTS Linked Data Cache 8. Query and federate along.

38 create RDF with Jena // URI declarations String pathwayuri = " String geneuri = " String relationshipuri = " // Create an empty Model Model model = ModelFactory.createDefaultModel(); // Create a Resource for each family member, identified by their URI Resource wp1 = model.createresource(pathwayuri+"wp1"); Resource gene1 = model.createresource(geneuri+"16971"); Resource wp2 = model.createresource(pathwayuri+"wp2"); Resource gene2 = model.createresource(geneuri+"12311"); // and so on for other pathway Elements // Create properties for the different types of relationship to represent Property organism = model.createproperty(relationshipuri,"organism"); Property hasidentifier = model.createproperty(relationshipuri,"hasidentifier"); Property pathwayontology = model.createproperty(relationshipuri,"pathwayontology"); Property pathwayname = model.createproperty(relationshipuri,"pathwayname");

39 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF a. b. c. Open PHACTS Linked Data Cache 8. Query and federate along.

40 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF. 8. Load RDF in triple store with sparql endpoint. 9. Query and federate along.

41 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF a. b. c. Open PHACTS Linked Data Cache 8. Query and federate along.

42 WikiPathways identifiers In WikiPathways an identifier is set of a datasource and a identifier (a xref) Similar or identical pathway elements can have different identifiers o GeneProducts -> Ensembl or Uniprot o Metabolites -> Cas, InChI or ChemSpider ID o We need URI for identifiers.

43 IDENTIFIERS.ORG Providing resolvable persistent URIs. Based on Miriam ( on Miriam ( Textual Pathway identifiers (xrefs) converted to identifiers.org uri through the miriam api

44 Miriam and identifiers.org

45 Mapping of similar identifiers SKOS: Simple Knowledge Organization System ( o skos:mappingrelation o skos:closematch o skos:exactmatch o skos:broadmatch o skos:narrowmatch o skos:relatedmatch

46 IDENTIFIER MAPPING Data enrichment Query expansion Unified identifier conversion

47 DATA ENRICHMENT

48 UNIFIED IDENTIFIERS

49 QUERY EXPANSION

50 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF a. b. c. Open PHACTS Linked Data Cache 8. Query and federate along.

51 WP TO RDF CONVERSION 1. Get Pathway content (Gpml format) Download all pathway content at 2. Identify and describe the different pathway classes and properties a. GPML vocabulary b. WikiPathways Vocabulary 3. Link pathway classes and properties to external semantic descriptions a. Biopax level 3 b. Inspect related linked data sets c. Browse Linked Open Vocabularies d. Search Bioportal e. Use social media 4. Create RDF a. Jena Framework (java) b. Arc2 Framework (php) c. Xslt templates d. d2r e. Construct queries 5. Parse GPML2RDF 6. Create linksets for identity mapping 7. Publish RDF a. b. c. Open PHACTS Linked Data Cache 8. Query and federate along.

52 Step 9. Query and federate away prefix xsd: < prefix wprdf: < prefix dc: < prefix dcterms: < select distinct?pathway?wplabel?identifier?snp as?genewikisnp where {?s dcterms:ispartof?pathway.?s dc:identifier < dc:identifier?identifier.?s rdfs:label?wplabel.?s dc:source?source. SERVICE < {?gws dc:identifier?identifier.?gws rdf:type?gwtype.?gws < } }

53 Valuable resources Help:WikiPathways_Sparql_queries

54 TOOLS AND APPLICATIONS

55 Recap 1st session early afternoon about WikiPathways -> RDF conversion o o WikiPathways introduction RDF decisions late afternoon about applications, hands on and link to Open Phacts

56 Introduction WikiPathways SPARQL endpoint o Integration of pathway data in tools and databases Linked Open Data No parsing through GPML files Use only the parts you need!

57 Outline Use cases o Why using the SPARQL endpoint? Integration in workflows o What libraries are available for which programming language? Hands on session

58 USE CASES Why should we use the SPARQL endpoint? image source:

59 Data Integration image source:

60 image source: Data Integration

61 Data Integration Combined queries in the open linked data network Challenges: o o o Identifier mapping Ontologies RDF data resources

62 PathwayLoom Plugin for pathway editor PathVisio o o o Use existing knowledge to guide pathway creation Online resources for interaction data Searches for known interaction partners for a target element

63 PathwayLoom

64 Network Creation Get all interactions from all pathways to create one big interaction network Integrate other pathway databases through combined SPARQL queries Powerful network analysis possible

65 Alternative to web service Not replacement but alternative! Detailed queries possible without going through every GPML file Combine pathway data with other resources

66 Data and Code Curation Convenient tool to detect errors in data and code Examples: o Inconsistency in datasource naming o Data nodes with missing identifier or datasource o...

67 Data Reasoning/ Data Enrichment Currently no cellular location available Shapes in pathway diagram Extract cellular location based on location of the gene in the pathway diagram (inside the cell, on the membrane, outside the cell)

68 INTEGRATION IN WORKFLOWS How to connect to the WP SPARQL endpoint from different programming languages? image source:

69 Command Line Quick and easy querying with curl Unix systems curl -F "query=select * WHERE {?s?p?o} LIMIT 10" Image sources:

70 Command Line Quick and easy querying with curl Unix systems curl -F "query=select * WHERE {?s?p?o} LIMIT 10" Result: XML o W3C schema: DataAccess/rf1/result2.xsd Image sources:

71 Java & Jena Apache Jena: o jena.apache.org an API for reading, processing and writing RDF data in XML, N-triples and Turtle formats; an ontology API for handling OWL and RDFS ontologies; a rule-based inference engine for reasoning with RDF and OWL data sources; stores to allow large numbers of RDF triples to be efficiently stored on disk; a query engine compliant with the latest SPARQL specification servers to allow RDF data to be published to other applications using a variety of protocols, including SPARQL Image sources: java.jpg

72 Java & Jena Image sources: java.jpg

73 R & rrdf R/Bioconductor package: rrdf o install.packages("rrdf") library(rrdf) store = sparql.remote( " "SELECT * WHERE {?s?p?o} LIMIT 10" ) Image sources:

74 HANDS ON Try it out and play around image source:

75 Hands on Draw a pathway on WikiPathways o --> Help --> Tutorial SPARQL queries online o --> Help --> WikiPathways Sparql Queries Query from a programming language

76 Ideas Submit your queries, ideas and suggestions here: o --> Help --> WikiPathways Sparql Queries --> Submit ideas

77 WP Gene Sets Create a gene set for each pathway Only include genes that are annotated with a "Entrez Gene" identifier File format: GMT file Combined query with GeneWiki data

78 Image sources: WP Gene Sets

79 image source: DISCUSSION

80 Linking data What are the resources that you are working on? Can you think of ways to link them with WP? Other resources you would like to be linked to pathway data? e.g. expression data, annotation, interaction links,...

81 QUESTIONS & CONTACT image source:

82 Query: WP Gene Sets

83 The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement n , resources of which are composed of financial contribution from the European Union s Seventh Framework Programme (FP7/ ) and EFPIA companies in kind contribution and the NIH National Institute for General Medical Sciences (R01-GM100039)