ONSTR/NBSDC update

[Nikolic, Snezana]

Dear All,

I would like to send you a quick update about what is going on with ONSTR/NBSDC.

Dr. Singh has been on medical leave since November. She is recovering well now and, upon doctors approval, she expects that she will be able to return to work sometime in mid April.

In the meantime, I would like to give you a brief ontology work update:

- Reasoning results over different data sets using HermiT (standalone version, shell command line):

ONSTR_withTestData.owl, completed in 2-3 minutes or less depending on hardware resources. This file is available for download and testing at:

http://code.google.com/p/onstr/source/browse/data/testDataSets/ONSTR_withTestData.owl 

- Reasoning over real life data sets (the Kuvan study data, i.e., the KS data): still running slow (using one CPU). Files containing different numbers of data instances will be available at

http://code.google.com/p/onstr/source/browse/data/testDataSets/ 

So far, all reasoning tasks were attempted/done using HermiT (standalone version, shell command line), but I will try using Pellet (standalone) and see it that works better for us.

Ontology development plans (already in different stages or realization):

- Completing/revising/building ontology hierarchies covering positive screening results for hyperphenylalaninemia HPA and possibly one or more of other screened inherited metabolic diseases. Reasoning over small scale real life patient data set(s) collected via Emory newborn screening program.

- Representing in the ontology data items pertaining to developmental growth and linking them with dietary intakes. Reasoning over smaller set(s) of real life patient data collected during the long-term follow-up.

- Representing in the ontology links between the hyperphenylalaninemia (HPA) genotype/alleles, PAH enzyme activity measurements and HPA phenotype severity measurements.

We are planning to organize a meeting by the end of April (or first half of May) and I will be sending you timely notifications about meeting details.

If you have any questions, comments or advice please be free to contact me any time.

Again, thank you for your support and participation!

snez

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[Melanie Courtot]

Hi Snezana,

Thanks for the update, and good to hear all is going well on your side!

Which version of HermiT do you have, and what is your command line? I just tried classifying the file at http://code.google.com/p/onstr/source/browse/data/testDataSets/ONSTR_withTestData.owl on my machine and it doesn't go through :( (or at least not in an hour or so)
I only have a laptop (Mac OS X with a 2.4Ghz Intel Core i5 and 8GB of memory) - what kind of machine are you using?

Or alternatively, do you have an inferred version you could share?

Cheers,
Melanie

On 2014-02-27, at 12:45 PM, Nikolic, Snezana wrote:

> Dear All,
>
> I would like to send you a quick update about what is going on with ONSTR/NBSDC.
>
> Dr. Singh has been on medical leave since November. She is recovering well now and, upon doctors approval, she expects that she will be able to return to work sometime in mid April.
>
>
> In the meantime, I would like to give you a brief ontology work update:
> - Reasoning results over different data sets using HermiT (standalone version, shell command line):
> ONSTR_withTestData.owl, completed in 2-3 minutes or less depending on hardware resources. This file is available for download and testing at:
> http://code.google.com/p/onstr/source/browse/data/testDataSets/ONSTR_withTestData.owl
> - Reasoning over real life data sets (the Kuvan study data, i.e., the KS data): still running slow (using one CPU). Files containing different numbers of data instances will be available at
> http://code.google.com/p/onstr/source/browse/data/testDataSets/
>
> So far, all reasoning tasks were attempted/done using HermiT (standalone version, shell command line), but I will try using Pellet (standalone) and see it that works better for us.
>
> Ontology development plans (already in different stages or realization):
> - Completing/revising/building ontology hierarchies covering positive screening results for hyperphenylalaninemia HPA and possibly one or more of other screened inherited metabolic diseases. Reasoning over small scale real life patient data set(s) collected via Emory newborn screening program.
> - Representing in the ontology data items pertaining to developmental growth and linking them with dietary intakes. Reasoning over smaller set(s) of real life patient data collected during the long-term follow-up.
> - Representing in the ontology links between the hyperphenylalaninemia (HPA) genotype/alleles, PAH enzyme activity measurements and HPA phenotype severity measurements.
>
>
> We are planning to organize a meeting by the end of April (or first half of May) and I will be sending you timely notifications about meeting details.
>
> If you have any questions, comments or advice please be free to contact me any time.
>
> Again, thank you for your support and participation!
>
> snez
>
>
>

> This e-mail message (including any attachments) is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information. If the reader of this message is not the intended
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> or copying of this message (including any attachments) is strictly
> prohibited.
>
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
> original message (including attachments).
>

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