Web Services and Development of Semantic Applications

Transcription

1 Web Services and Development of Semantic Applications Trish Whetzel Outreach Coordinator THE NATIONAL CENTER FOR BIOMEDICAL ONTOLOGY

2 Na#onal Center for Biomedical Ontology Mission To create software for the application of ontologies in biomedical science and clinical care NCBO Partners Stanford University - Dr. Mark A. Musen Mayo Clinic - Dr. Christopher G. Chute University of Buffalo - Dr. Barry Smith University of Victoria - Dr. Margaret-Anne Storey

3 Na5onal Centers for Biomedical Compu5ng (h<p://

4 NCBO Key Ac#vi#es We create and maintain a library of biomedical ontologies We build tools and Web services to enable the use of ontologies We collaborate with scientific communities that develop and use ontologies

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6 Links of Interest h<p:// SWAT4LS_Tutorial

7 Outline Learning Objec#ves REST Web services BioPortal NCBO Web Services BioPortal SPARQL Endpoint

8 Learning Objec#ves Learn what Web services are available from NCBO Learn how to programma#cally use these Web services Learn how to combine these Web services to perform tasks

9 REST Web Services Accessed via HTTP h<p://rest.bioontology.org/{parameters} Each unique URL is a representa#on of some object Opera#ons include GET, POST, PUT, DELETE Lightweight, easy to build

10 User Interface Code Browser Web Services

11 Outline REST Web services BioPortal NCBO Web Services BioPortal SPARQL Endpoint

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13 Outline REST Web services BioPortal NCBO Web Services BioPortal SPARQL Endpoint

14 Ontology Services Views Search Traverse Comment Download h<p://rest.bioontology.org Mapping Services Widgets Annota5on Create Upload Download Tree- view Auto- complete Graph- view Term recogni5on Data Access Fetch data annotated with a given term h<p://bioportal.bioontology.org

15 ONTOLOGY WEB SERVICES Accessing, browsing, searching and traversing ontologies in Your applica#on

16 Ontology Web Services List All Ontologies List all ontologies in BioPortal Documenta#on: h<p://bit.ly/sxl2qi GoogleDoc Excel example: h<p://bit.ly/ncbo- list- all- ontologies

17 Ontology version id One ontology id has many ontology version ids Ontology id

18 Ontology Web Services cont. Search Search by term or term iden#fier across all ontologies in BioPortal Documenta#on: h<p://bit.ly/tmdkr6 Example clients Java: h<p://bit.ly/<tb1g Perl: h<p://bit.ly/spxc2x

19 Ontology Web Services cont. Term get details about a term including it s defini#on, synonyms, URI, super- and sub- classes, and other proper#es h<p://bit.ly/teedbd Hierarchy get parent, children, and sibling terms h<p://bit.ly/tpzm75

20 RightField

21 ECG Gadget

22 ISAcreator

23 DOG4DAG Ontology Genera#on Tool for OBO- Edit and Protégé

24 Word Add- in

25 cgmdr

26 openmdr

27 elemap

28 BioPortal Import Plugin BioPortal_Import_Plugin

29 NOTES WEB SERVICES Propose new terms and comment on ontologies

30 Notes Web Service Add terms proposals and comments on ontology terms Documenta#on: h<p:// Ontology_Notes

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32 WebProtégé

33 VIEWS Custom subset of large ontologies

34 Views and Value Sets Users can submit their own deriva#ves of BioPortal ontologies these which become first- class objects in BioPortal and can be used as all other Web services

35 Views in BioPortal

36 Views and Value Sets View Extrac#on Web service Given a root node term, extracts all child terms h<p://bit.ly/uxeh2s Access directly from Protégé via the BioPortal Import plugin h<p://protegewiki.stanford.edu/wiki/ BioPortal_Import_Plugin

37 MAPPING WEB SERVICES Using NCBO technology to integrate terminologies and ontologies

38 Mappings Root R Term-1 Term-2 t1 t2 Term-2 t1 Term-3 Term-4 t3 t4 Term-5 t5 Term-5 t5 t6 t7 Ontology A Ontology B Upload or Download mapping subsets

39 Mappings Mappings Web service Documenta#on: h<p:// BioPortal_Mappings_Service Func#ons Get Create/Upload Example Perl client to Get mappings: h<p://bit.ly/tdkpqd

40 WIDGETS Using NCBO technology on your web pages

41 Widgets Form auto- complete auto- complete func#on and can return term URI, term ID or term name Jump To auto- complete func#on to select term and Jump To BioPortal to view term details Visualize widget view the ontology structure and rela#ons Tree widget view the ontology tree Code for widgets is available on BioPortal

42 Widgets Form auto-complete Jump To RSS feed

43 Widgets Visualization Tree widget

44 RedFly

45 Radiological Society of North America

46 GMiner

47 Knowledge Egg

48 ANNOTATOR WEB SERVICE Using Ontologies to Annotate Your Data

49 Annotator: The Basic Idea Tag textual metadata with ontology terms

50 Annotator Workflow

51 Annotator Web Service Tag free text with ontology terms Documenta#on: h<p:// Annotator_Web_service Example clients: Perl: h<p://bit.ly/vkypcp Java: h<p://bit.ly/rrfokd

52 Gene Wiki Annotator

53 Sta#s#cal Tracking of Ontological Phrases (STOP)

54 Ontological Discovery Environment

55 STRIDE

56 DATA SERVICE Using Ontologies to Access Public Data

57 Resource Index: The Basic Idea The index can be used for Search Data mining

58 Resources index: Example

59 Data Access Resource Index Web service Documenta#on: h<p:// Resource_Index

60 ODiSSea

61 BioPortal SPARQL Endpoint Documenta#on: h<p:// SPARQL_BioPortal Query interface: h<p://alphasparql.bioontology.org/ Example queries: h<p://alphasparql.bioontology.org/examples Sample code: h<ps://github.com/ncbo/sparql- code- examples

62 Thank you! Web service documenta#on: h<p:// NCBO_REST_services Keep in touch NCBO Announce mailing list: h<p://bit.ly/oslzng Somware support: Facebook and LinkedIn Ques#ons: