Difference between revisions of "Tutorial Examples"
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| − | Sample Links | + | [http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/lib/exe/fetch.php?id=test&cache=cache&media=ontology_services_from_ncbo.ppt Tutorial Slides] |
| + | |||
| + | '''Sample Links''' | ||
* http://rest.bioontology.org/bioportal/search/Melanoma/?ontologyids=1353 | * http://rest.bioontology.org/bioportal/search/Melanoma/?ontologyids=1353 | ||
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* http://rest.bioontology.org/bioportal/virtual/rdf/1353/2092003 | * http://rest.bioontology.org/bioportal/virtual/rdf/1353/2092003 | ||
* http://rest.bioontology.org/bioportal/virtual/ontology/1353/2092003 | * http://rest.bioontology.org/bioportal/virtual/ontology/1353/2092003 | ||
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| + | ---- | ||
* http://purl.bioontology.org/ontology/SNOMEDCT/2092003 | * http://purl.bioontology.org/ontology/SNOMEDCT/2092003 | ||
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* http://bioportal.bioontology.org/visualize/42789/?conceptid=2092003 | * http://bioportal.bioontology.org/visualize/42789/?conceptid=2092003 | ||
* http://bioportal.bioontology.org/ontologies/42789#widgets | * http://bioportal.bioontology.org/ontologies/42789#widgets | ||
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| + | ---- | ||
* http://purl.bioontology.org/ontology/MSH/D008545 | * http://purl.bioontology.org/ontology/MSH/D008545 | ||
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* http://rest.bioontology.org/bioportal/virtual/rootpath/1025/MP:0000929 | * http://rest.bioontology.org/bioportal/virtual/rootpath/1025/MP:0000929 | ||
| − | Sample user needs | + | '''Sample user needs''' |
* I need to restrict user input to a certain value set | * 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. | 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 | * I need to extract the disease branch from SNOMEDCT | ||
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Use the search service, search the properties of every term for 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 | * 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! | 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! | ||
| + | |||
| + | |||
| + | API-Key for Tutorial: 24e037b6-54e0-11e0-9d7b-005056aa331[SIX] | ||
Latest revision as of 07:05, 27 July 2011
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
- 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
- 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!
API-Key for Tutorial: 24e037b6-54e0-11e0-9d7b-005056aa331[SIX]