Tutorial Examples

File:Tutorial Slides - T18.pdf

Sample Links

• http://rest.bioontology.org/bioportal/search/Melanoma/?ontologyids=1353
• http://rest.bioontology.org/bioportal/virtual/rootpath/1353/2092003
• http://rest.bioontology.org/bioportal/virtual/rdf/1353/2092003
• http://rest.bioontology.org/bioportal/virtual/ontology/1353/2092003

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• http://purl.bioontology.org/ontology/SNOMEDCT/2092003
• http://bioportal.bioontology.org/visualize/virtual/1353/2092003
• http://bioportal.bioontology.org/visualize/42789/2092003
• http://bioportal.bioontology.org/visualize/42789/?conceptid=2092003
• http://bioportal.bioontology.org/ontologies/42789#widgets

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• http://purl.bioontology.org/ontology/MSH/D008545
• http://bioportal.bioontology.org/visualize/39228/DOID:399
• http://rest.bioontology.org/bioportal/virtual/rootpath/1025/MP:0000929

Sample user needs

• I need to restrict user input to a certain value set

Create a value set with the needed terms, submit to BioPortal and then use the auto complete widget or the search service. If the value set is a subtree of an existing ontology, use the search service restricted to that sub branch.

e.g. http://rest.bioontology.org/bioportal/search/Melanoma?ontologyids=1353&subtreerootconceptid=108369006, searches for Melanoma under 'Neoplasm' in SNOMEDCT.

• I need to extract the disease branch from SNOMEDCT

Use the view extractor service or pick the desired root node and recursively call get child nodes; or pick the desired root node and get all paths to leaf terms from that node.

• I need to identify all terms mapped to UMLS CUI C0151779

Use the search service, search the properties of every term for C0151779. http://rest.bioontology.org/bioportal/search/C0151779?isexactmatch=1&includeproperties=1

• I need to code/annotate free-text with ontology terms

Use the Annotator service (at BioPortal or as a Virtual Machine at your institution); or make sure to use the auto complete widgets in the web forms at content acquisition time!