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[bioontology-support] extract "description" in Bio Portal

Eugene eugene at nextbio.com
Fri Oct 1 10:42:27 PDT 2010


Trish,

Use the MeSH browser to search that term. The following page will show: http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi

The page says that it should map to

Heptanoic Acids<http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Heptanoic+Acids>
Pyrroles<http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&term=Pyrroles>

But BioPortal doesn't map. It becomes floating.

Eugene

From: Trish Whetzel [mailto:whetzel at stanford.edu]
Sent: Friday, October 01, 2010 10:14 AM
To: Eugene
Cc: support at bioontology.org
Subject: Re: [bioontology-support] extract "description" in Bio Portal

Dear Eugene,

Can you provide more details on how you are getting the term "atorvastatin"?  For example, are you using the Get all terms web service, e.g. http://rest.bioontology.org/bioportal/virtual/ontology/1351/all?&pagesize=50&pagenum=1&email=example@example.org?  The output of the Get all terms web service and the Term web service for atorvastin, e .g. http://rest.bioontology.org/bioportal/virtual/ontology/1351/C065179?email=example@example.org  indicate that this term does not have any children terms [1].

Trish


[1]
<relations>
...
<entry>
<string>ChildCount</string>
<int>0</int>
</entry>


On Sep 22, 2010, at 2:17 PM, Eugene wrote:


Dear Sir or Madam,
One issue is some terms are floating, meaning the term has no parent. For example, atorvastatin has no parent --http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi.

Currently, we use the url to download -- http://rest.bioontology.org/bioportal/virtual/ontology/<onto<http://rest.bioontology.org/bioportal/virtual/ontology/%3conto>logyid>/<id>?email=example at example.org<mailto:?email=example at example.org>.

However, that URL requires the ID. But if a term has no parent, we don't know what the id of the term is without first knowing its parent ID. On the other hands, we don't know the name of the floating term. If we know, we can query by term to get the rest of info. But we don't know the name of the term.

Do you have idea how we can handle the case? We compared two MeSH versions which were all downloaded through BioPortal API, there are 5 times of size difference. In current version,atorvastatin has no parent, so all its children cannot be found.

Thanks

Eugene



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