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[bioontology-support] BioPortal database and annotate results not in sync

Michael Dorf mdorf at
Wed Jul 7 09:01:42 PDT 2010


I don't have the exact date when this ontology becomes available, but the 
population IS in progress now and should be completed in the next couple of 

Emily, we will notify you as soon as Cell Cycle Ontology becomes available.



-----Original Message-----
From: Trish Whetzel [mailto:whetzel at]
Sent: Tuesday, July 06, 2010 5:50 PM
To: Emily Howe; Michael Dorf
Cc: Corey Powell; Sean Mooney; Uday Evani; support at
Subject: Re: BioPortal database and annotate results not in sync

Hi Emily,

The four individual, species-specific Cell Cycle ontologies are now
represented as one ontology named Cell Cycle Ontology on BioPortal 
).  However, the ontology data for the Annotator does not yet reflect
this change and lists the four individual, species-specific
ontologies. Updating this data for the Annotator is in progress. Misha
can provide more details on this timeline.

As for a workaround, replacing the value for the virtual ontology
identifier '1075' with the virtual ontology identifier for the new
entry for the Cell Cycle Ontology '1507' in the URL below will result
in a URL that can be resolved, e.g.


On Jul 6, 2010, at 12:05 PM, Emily Howe wrote:

> Hi Trish,
> I have noticed the results returned from the annotator appear to be
> out of sync with the rest of the bioportal databases.
> The specific problem is with Cell Cycle Ontology.
> When I browse all ontologies for Cell Cycle Ontology the ontology ID
> is 1507
> Results from the Annotator return results for Cell Cycle Ontology
> (H. sapiens) with the following link 
>  which can no longer be found.
> Is this a known error?   Are there any workarounds or when is this
> expected to be fixed?
> Thanks
> Emily
> Below is the sample text I was using.
> Overall, there is a total of three main and important steps to the
> biosynthesis of penicillin G (benzylpenicillin)
>    * The first step in the biosynthesis of penicillin G is the
> condensation of three amino acids L-α-aminoadipic acid, L-cysteine,
> L-valine into a tripeptide.[7][8][9] Before condensing into a
> tripeptide, the amino acid L-valine will undergo epimerization and
> become D-valine.[10][11] After the condensation, the tripeptide is
> named δ-(L-α-aminoadipyl)-L-cysteine-D-valine, which is also known
> as ACV. While this reaction occurs, we must add in a required
> catalytic enzyme ACVS, which is also known as δ-(L-α-aminoadipyl)-L-
> cysteine-D-valine synthetase. This catalytic enzyme ACVs is required
> for the activation of the three amino acids before condensation and
> the epimerization of transforming L-valine to D-valine.
>    * The second step in the biosynthesis of penicillin G is to use
> an enzyme to change ACV into isopenicillin N. The enzyme is
> isopenicillin N synthase with the gene pcbC enclosed. The tripeptide
> on the ACV will then undergo oxidation, which then allows a ring
> closure so that a bicyclic ring is formed.[7][8] Isopenicillin N is
> a very weak intermediate because it does not show much antibiotic
> activity.[10]
>    * The Last step in the biosynthesis of penicillin G is the
> exchange the side-chain group so that isopenicillin N will become
> penicillin G. Through the catalytic coenzyme isopenicillin N
> acyltransferase (IAT), the alpha-aminoadipyl side-chain of
> isopenicillin N is removed and exchanged for a phenylacetyl side-
> chain. This reaction is encoded by the gene penDE, which is unique
> in the process of obtaining penicillins.[7]

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