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[bioontology-support] MeSH 2009_2009_02_13 in BioPortal via REST Services

David Hummel david_hummel at hms.harvard.edu
Fri Dec 11 13:36:44 PST 2009


Hello,

For various projects, we are trying to leverage the REST services
described here:

http://www.bioontology.org/wiki/index.php/NCBO_REST_services

It appears that there is a problem with many of the available calls
(and it turns out the most potentially useful ones for us) when
targeting the MeSH ontology.

According to the "all ontologies" call:

http://rest.bioontology.org/bioportal/ontologies?email=example@example.org

MeSH should have ontologyId=1351 and ontologyVersionId=40401, and this
does appear to be the case since the following calls seem to work:

"term":
http://rest.bioontology.org/bioportal/concepts/40401/D005796?email=example@example.org
http://rest.bioontology.org/bioportal/virtual/ontology/1351/D005796?email=example@example.org

"all root terms":
http://rest.bioontology.org/bioportal/concepts/40401/root?email=example@example.org

However, the following calls all return errors:

"all terms":
http://rest.bioontology.org/bioportal/concepts/40401/all?email=example@example.org
http://rest.bioontology.org/bioportal/virtual/ontology/1351/all?email=example@example.org

"parents":
http://rest.bioontology.org/bioportal/virtual/parents/1351/D005796?email=example@example.org
http://rest.bioontology.org/bioportal/concepts/parents/40401/D005796?email=example@example.org

"children":
http://rest.bioontology.org/bioportal/virtual/children/1351/D005796?email=example@example.org
http://rest.bioontology.org/bioportal/concepts/children/40401/D005796?email=example@example.org

"paths to roots":
http://rest.bioontology.org/bioportal/concepts/rootpath/40401/D005796?email=example@example.org
http://rest.bioontology.org/bioportal/virtual/rootpath/1351/D005796?email=example@example.org

"paths to leaves":
http://rest.bioontology.org/bioportal/concepts/leafpath/40401/D005796?email=example@example.org
http://rest.bioontology.org/bioportal/virtual/leafpath/1351/D005796?email=example@example.org

"siblings":
http://rest.bioontology.org/bioportal/concepts/siblings/40401/D005796?level=1&email=example@example.org
http://rest.bioontology.org/bioportal/virtual/siblings/1351/D005796?level=1&email=example@example.org

Thanks in advance for any information you can provide.

Sincerely,

--
David Hummel
Senior Software Engineer
Center for Biomedical Informatics
Countway Library of Medicine
Harvard Medical School
617-432-6863



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