[MOBY-l] MobyXMLObject.pm question...

[Michael Jensen]

I have been trying to use the MobyXMLObject.pm as Ken suggested, but am 
having a few problems beyond the samples used. I am trying to combine 
the two pubmed services by piping the PMIDs from SearchPubmed to 
getting Medline output from getPubmed. I have been trying to get 
MobyXMLObject.pm to work with SearchPubmed but it doesn't want to work, 
returning nothing except for the webservice. I think the problem might 
be that the output has <Simple> tags instead of <moby:Simple> like so:

<moby:queryResponse>
	<Simple>
		<moby:Object namespace='PMID' id="14607285">
  		</moby:Object>
	</Simple>
</moby:queryResponse>

as opposed to the XML from the test xml found on Ken's learning site.

<moby:queryInput>
	<moby:Simple>	
		<moby:GenericSequence namespace='AGI_LocusCode' id='At3g19yyy'>
			<moby:Integer namespace='' id='' 
articleName='Length'>4</moby:Integer>
			<moby:String namespace='' id='' 
articleName='SequenceString'>MGGC</moby:String>
		</moby:GenericSequence>
	</moby:Simple>
</moby:queryInput>

I tried to slowly put in the results from SearchPubmed into the test 
xml script from Ken's site, and I can get a result as long as I keep a 
<moby:queryInput> from the example script along with a 
<moby:queryResponse> from the results of SearchPubmed (just copied and 
pasted). The mobyxmltest.pl file attached here is the one referred to 
just now, and the pubmed_combined.pl is my other attempt at using 
SearchPubmed to list the PMIDs (so next I can feed those into 
getPubmed).

I am not sure if I am just missing something obvious or what, but I 
have tried a lot of different things to understand how to get the 
elements I need. Any help would be greatly appreciated! Thanks!

(I tried posting this a few days ago, but never went through?)


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