Action Items from call today

[Helen Parkinson]

Hi

here are my action items from the call today

1. MAGE-TAB->RDF, Lena requested details.

Code here: https://sourceforge.net/projects/limpopo/

Java Parser for MAGE-TAB developed by EBI, used by several groups.
Contact Tony Burdett tburdett@... for details. Tony estimates for
a simple RDF dump a few days work. Lena if you are interested in working
on this java code please contact Tony as he's already designed  with rdf
export in mind

2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn

https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
Pretty much all public MAGE-ML comes from AE and is available from
Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's
mage-ml importer, and non public data


3. EBI experimental factor ontology (EFO) slides, attached
see also www.ebi.ac.uk/efo

4. Noted that an RDF dump of atlas data and triple store access will be
useful, we'll announce when these are available

thanks

Helen

[Kei Cheung]

Thanks, Helen.

To make it more concrete. I've been thinking about some example queries
that I hope can be answered by the RDF data once converted. I wonder if
the following example quereis can be answered:

Retrieve a list of differentially expressed genes between different
brain regions (e.g., hippocampus and entorhinal cortex) for normally
aged human subjects.

Retrieve a list of differentially expressed genes for the same brain
region of normal human subjects and AD patients.

Using these lists of genes one can issue (federated) queries to retrieve
addtional information about the genes for various types of analyses
(e.g., GO term enrichment).

Just a thought.

Cheers,

-Kei



Helen Parkinson wrote:

> Hi
>
> here are my action items from the call today
>
> 1. MAGE-TAB->RDF, Lena requested details.
>
> Code here: https://sourceforge.net/projects/limpopo/
>
> Java Parser for MAGE-TAB developed by EBI, used by several groups.
> Contact Tony Burdett tburdett@... for details. Tony estimates
> for a simple RDF dump a few days work. Lena if you are interested in
> working on this java code please contact Tony as he's already
> designed  with rdf export in mind
>
> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>
> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
> Pretty much all public MAGE-ML comes from AE and is available from
> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's
> mage-ml importer, and non public data
>
>
> 3. EBI experimental factor ontology (EFO) slides, attached
> see also www.ebi.ac.uk/efo
>
> 4. Noted that an RDF dump of atlas data and triple store access will
> be useful, we'll announce when these are available
>
> thanks
>
> Helen
>
>
>

[mdmiller-2]

hi all,

on a different HCLS thread i saw this proposal from jeni tennison for
specifying a generic dataset, it might be a useful way to encode a list of
differentially expressed genes.  it looks like one could do this encoding on
the fly, so that the data itself at the source could be in whatever format
is natural.

http://sw.joanneum.at/scovo/schema.html

cheers,
michael

Michael Miller
mdmiller53@...

----- Original Message -----
From: "Kei Cheung" <kei.cheung@...>
To: "Helen Parkinson" <parkinson@...>
Cc: "HCLS" <public-semweb-lifesci@...>; "Tony Burdett"
<tburdett@...>
Sent: Wednesday, October 14, 2009 7:03 PM
Subject: Re: Action Items from call today

> Thanks, Helen.
>
> To make it more concrete. I've been thinking about some example queries
> that I hope can be answered by the RDF data once converted. I wonder if
> the following example quereis can be answered:
>
> Retrieve a list of differentially expressed genes between different brain
> regions (e.g., hippocampus and entorhinal cortex) for normally aged human
> subjects.
>
> Retrieve a list of differentially expressed genes for the same brain
> region of normal human subjects and AD patients.
>
> Using these lists of genes one can issue (federated) queries to retrieve
> addtional information about the genes for various types of analyses (e.g.,
> GO term enrichment).
>
> Just a thought.
>
> Cheers,
>
> -Kei
>
>
>
> Helen Parkinson wrote:
>
>> Hi
>>
>> here are my action items from the call today
>>
>> 1. MAGE-TAB->RDF, Lena requested details.
>>
>> Code here: https://sourceforge.net/projects/limpopo/
>>
>> Java Parser for MAGE-TAB developed by EBI, used by several groups.
>> Contact Tony Burdett tburdett@... for details. Tony estimates for a
>> simple RDF dump a few days work. Lena if you are interested in working on
>> this java code please contact Tony as he's already designed  with rdf
>> export in mind
>>
>> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>>
>> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
>> Pretty much all public MAGE-ML comes from AE and is available from
>> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's
>> mage-ml importer, and non public data
>>
>>
>> 3. EBI experimental factor ontology (EFO) slides, attached
>> see also www.ebi.ac.uk/efo
>>
>> 4. Noted that an RDF dump of atlas data and triple store access will be
>> useful, we'll announce when these are available
>>
>> thanks
>>
>> Helen
>>
>>
>>
>
>
>

[Kei Cheung]

Hi Michael et al,

Thanks for pointing to this generic approach of RDF representation of
datasets. A list of differentially expressed genes may be associated
with values such as P-values, fold-change, gene symbols, etc. Also, it's
important to capture metadata/provenance associated with the gene list.
This may include the type of statistical test (e.g., ANOVA) and the
array platform employed (e.g., Affymetrix U133A). This may be an
interesting discussion topic at the F2F meeting.

Cheers,

-Kei

mdmiller wrote:

> hi all,
>
> on a different HCLS thread i saw this proposal from jeni tennison for
> specifying a generic dataset, it might be a useful way to encode a
> list of differentially expressed genes.  it looks like one could do
> this encoding on the fly, so that the data itself at the source could
> be in whatever format is natural.
>
> http://sw.joanneum.at/scovo/schema.html
>
> cheers,
> michael
>
> Michael Miller
> mdmiller53@...
>
> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@...>
> To: "Helen Parkinson" <parkinson@...>
> Cc: "HCLS" <public-semweb-lifesci@...>; "Tony Burdett"
> <tburdett@...>
> Sent: Wednesday, October 14, 2009 7:03 PM
> Subject: Re: Action Items from call today
>
>
>> Thanks, Helen.
>>
>> To make it more concrete. I've been thinking about some example
>> queries that I hope can be answered by the RDF data once converted. I
>> wonder if the following example quereis can be answered:
>>
>> Retrieve a list of differentially expressed genes between different
>> brain regions (e.g., hippocampus and entorhinal cortex) for normally
>> aged human subjects.
>>
>> Retrieve a list of differentially expressed genes for the same brain
>> region of normal human subjects and AD patients.
>>
>> Using these lists of genes one can issue (federated) queries to
>> retrieve addtional information about the genes for various types of
>> analyses (e.g., GO term enrichment).
>>
>> Just a thought.
>>
>> Cheers,
>>
>> -Kei
>>
>>
>>
>> Helen Parkinson wrote:
>>
>>> Hi
>>>
>>> here are my action items from the call today
>>>
>>> 1. MAGE-TAB->RDF, Lena requested details.
>>>
>>> Code here: https://sourceforge.net/projects/limpopo/
>>>
>>> Java Parser for MAGE-TAB developed by EBI, used by several groups.
>>> Contact Tony Burdett tburdett@... for details. Tony estimates
>>> for a simple RDF dump a few days work. Lena if you are interested in
>>> working on this java code please contact Tony as he's already
>>> designed  with rdf export in mind
>>>
>>> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>>>
>>> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
>>> Pretty much all public MAGE-ML comes from AE and is available from
>>> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's
>>> mage-ml importer, and non public data
>>>
>>>
>>> 3. EBI experimental factor ontology (EFO) slides, attached
>>> see also www.ebi.ac.uk/efo
>>>
>>> 4. Noted that an RDF dump of atlas data and triple store access will
>>> be useful, we'll announce when these are available
>>>
>>> thanks
>>>
>>> Helen
>>>
>>>
>>>
>>
>>
>>
>
>
>
>

[mdmiller-2]

hi kei,

yes, the proposal for specifying the dataset seemed to allow rich
annotation, one reason i liked it.

the piece i find missing is this.  not being a biologist or statistician i
can't offer much help (my strength is software).

once a large group of individuals have been part of a GWAS (perhaps as part
of a clinical trial) and a marker based on a gene expression signature over
n genes has been determined, presumably that would be published as the set
of n genes and some averaged measure of up regulation or down regulation per
gene based on averaging that group of individuals and an outcome such as bad
prognosis or good prognosis associated with the marker.  now if a new
individual has a gene expression profile, how will the expression of this
individual's genes be compared against the marker to determine which group
the individual falls into?

(there are other scenarios, such as multiple markers associated with
different outcomes but the above seems the simplest case.)

look forward to meeting you and the others at the F2F next week.

cheers,
michael

Michael Miller
mdmiller53@...

----- Original Message -----
From: "Kei Cheung" <kei.cheung@...>
To: "mdmiller" <mdmiller53@...>
Cc: "Helen Parkinson" <parkinson@...>; "HCLS"
<public-semweb-lifesci@...>; "Tony Burdett" <tburdett@...>
Sent: Thursday, October 29, 2009 1:43 PM
Subject: Re: Action Items from call today

> Hi Michael et al,
>
> Thanks for pointing to this generic approach of RDF representation of
> datasets. A list of differentially expressed genes may be associated with
> values such as P-values, fold-change, gene symbols, etc. Also, it's
> important to capture metadata/provenance associated with the gene list.
> This may include the type of statistical test (e.g., ANOVA) and the array
> platform employed (e.g., Affymetrix U133A). This may be an interesting
> discussion topic at the F2F meeting.
>
> Cheers,
>
> -Kei
>
> mdmiller wrote:
>> hi all,
>>
>> on a different HCLS thread i saw this proposal from jeni tennison for
>> specifying a generic dataset, it might be a useful way to encode a list
>> of differentially expressed genes.  it looks like one could do this
>> encoding on the fly, so that the data itself at the source could be in
>> whatever format is natural.
>>
>> http://sw.joanneum.at/scovo/schema.html
>>
>> cheers,
>> michael
>>
>> Michael Miller
>> mdmiller53@...
>>
>> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@...>
>> To: "Helen Parkinson" <parkinson@...>
>> Cc: "HCLS" <public-semweb-lifesci@...>; "Tony Burdett"
>> <tburdett@...>
>> Sent: Wednesday, October 14, 2009 7:03 PM
>> Subject: Re: Action Items from call today
>>
>>
>>> Thanks, Helen.
>>>
>>> To make it more concrete. I've been thinking about some example queries
>>> that I hope can be answered by the RDF data once converted. I wonder if
>>> the following example quereis can be answered:
>>>
>>> Retrieve a list of differentially expressed genes between different
>>> brain regions (e.g., hippocampus and entorhinal cortex) for normally
>>> aged human subjects.
>>>
>>> Retrieve a list of differentially expressed genes for the same brain
>>> region of normal human subjects and AD patients.
>>>
>>> Using these lists of genes one can issue (federated) queries to retrieve
>>> addtional information about the genes for various types of analyses
>>> (e.g., GO term enrichment).
>>>
>>> Just a thought.
>>>
>>> Cheers,
>>>
>>> -Kei
>>>
>>>
>>>
>>> Helen Parkinson wrote:
>>>
>>>> Hi
>>>>
>>>> here are my action items from the call today
>>>>
>>>> 1. MAGE-TAB->RDF, Lena requested details.
>>>>
>>>> Code here: https://sourceforge.net/projects/limpopo/
>>>>
>>>> Java Parser for MAGE-TAB developed by EBI, used by several groups.
>>>> Contact Tony Burdett tburdett@... for details. Tony estimates for
>>>> a simple RDF dump a few days work. Lena if you are interested in
>>>> working on this java code please contact Tony as he's already designed
>>>> with rdf export in mind
>>>>
>>>> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>>>>
>>>> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
>>>> Pretty much all public MAGE-ML comes from AE and is available from
>>>> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's
>>>> mage-ml importer, and non public data
>>>>
>>>>
>>>> 3. EBI experimental factor ontology (EFO) slides, attached
>>>> see also www.ebi.ac.uk/efo
>>>>
>>>> 4. Noted that an RDF dump of atlas data and triple store access will be
>>>> useful, we'll announce when these are available
>>>>
>>>> thanks
>>>>
>>>> Helen
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>>
>>
>
>
>

[Jim McCusker-2]

Hi all, I have a quick bit of input about MAGE-TAB->RDF (which is something that I'm rather interested in).

On Tue, Oct 13, 2009 at 1:00 AM, Helen Parkinson <parkinson@...> wrote:

here are my action items from the call today

1. MAGE-TAB->RDF, Lena requested details.

Code here: https://sourceforge.net/projects/limpopo/

Java Parser for MAGE-TAB developed by EBI, used by several groups. Contact Tony Burdett tburdett@... for details. Tony estimates for a simple RDF dump a few days work. Lena if you are interested in working on this java code please contact Tony as he's already designed  with rdf export in mind

I have been experimenting with ftp://smd-ftp.stanford.edu/smd/transfers/magetab/, which is the "canonical" magetab parser, and includes an object model. I have been attempting to annotate the data model with Sesame Elmo annotations to produce a useful RDF graph from the parsed object graph. I have only made some progress on this, as the its use of custom collection subclasses confuses the Elmo mapping code.

If Limpopo is separate from the parser that I'm working on, and has an easier-to-work-with object model, I can possibly make some good progress on this in a short period of time. Glancing at the code from Limpopo, the object model seems very different, and can possibly be used by Elmo to generate RDF.

If I use this route, is this something that would be interesting to the group?

Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@... | [phone]
http://krauthammerlab.med.yale.edu

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mccusj@...
http://tw.rpi.edu

[Helen Parkinson]

Jim

Stanford are now using the limpopo parser as well, the cannonical one
has been replaced by this. Limpopo is used by at least 3 groups EBI,
SMD, and MeV and is tested, I'd go with this,

thanks

Helen

Jim McCusker wrote:

> Hi all, I have a quick bit of input about MAGE-TAB->RDF (which is
> something that I'm rather interested in).
>
> On Tue, Oct 13, 2009 at 1:00 AM, Helen Parkinson <parkinson@...
> <mailto:parkinson@...>> wrote:
>
>     here are my action items from the call today
>
>     1. MAGE-TAB->RDF, Lena requested details.
>
>     Code here: https://sourceforge.net/projects/limpopo/
>
>     Java Parser for MAGE-TAB developed by EBI, used by several groups.
>     Contact Tony Burdett tburdett@...
>     <mailto:tburdett@...> for details. Tony estimates for a
>     simple RDF dump a few days work. Lena if you are interested in
>     working on this java code please contact Tony as he's already
>     designed  with rdf export in mind
>
>
> I have been experimenting with
> ftp://smd-ftp.stanford.edu/smd/transfers/magetab/, which is the
> "canonical" magetab parser, and includes an object model. I have been
> attempting to annotate the data model with Sesame Elmo annotations to
> produce a useful RDF graph from the parsed object graph. I have only
> made some progress on this, as the its use of custom collection
> subclasses confuses the Elmo mapping code.
>
> If Limpopo is separate from the parser that I'm working on, and has an
> easier-to-work-with object model, I can possibly make some good
> progress on this in a short period of time. Glancing at the code from
> Limpopo, the object model seems very different, and can possibly be
> used by Elmo to generate RDF.
>
> If I use this route, is this something that would be interesting to
> the group?
>
> Jim
> --
> Jim McCusker
> Programmer Analyst
> Krauthammer Lab, Pathology Informatics
> Yale School of Medicine
> james.mccusker@... <mailto:james.mccusker@...> | [phone]
> http://krauthammerlab.med.yale.edu
>
> PhD Student
> Tetherless World Constellation
> Rensselaer Polytechnic Institute
> mccusj@... <mailto:mccusj@...>
> http://tw.rpi.edu

[Kei Cheung]

Hi Jim, Helen, et al,

If Limpopo has been used by multiple microarray data providers, it
should be more robust and useful to the microarray use case.

-Kei

Helen Parkinson wrote:

> Jim
>
> Stanford are now using the limpopo parser as well, the cannonical one
> has been replaced by this. Limpopo is used by at least 3 groups EBI,
> SMD, and MeV and is tested, I'd go with this,
>
> thanks
>
> Helen
>
> Jim McCusker wrote:
>
>> Hi all, I have a quick bit of input about MAGE-TAB->RDF (which is
>> something that I'm rather interested in).
>>
>> On Tue, Oct 13, 2009 at 1:00 AM, Helen Parkinson <parkinson@...
>> <mailto:parkinson@...>> wrote:
>>
>>     here are my action items from the call today
>>
>>     1. MAGE-TAB->RDF, Lena requested details.
>>
>>     Code here: https://sourceforge.net/projects/limpopo/
>>
>>     Java Parser for MAGE-TAB developed by EBI, used by several groups.
>>     Contact Tony Burdett tburdett@...
>>     <mailto:tburdett@...> for details. Tony estimates for a
>>     simple RDF dump a few days work. Lena if you are interested in
>>     working on this java code please contact Tony as he's already
>>     designed  with rdf export in mind
>>
>>
>> I have been experimenting with
>> ftp://smd-ftp.stanford.edu/smd/transfers/magetab/, which is the
>> "canonical" magetab parser, and includes an object model. I have been
>> attempting to annotate the data model with Sesame Elmo annotations to
>> produce a useful RDF graph from the parsed object graph. I have only
>> made some progress on this, as the its use of custom collection
>> subclasses confuses the Elmo mapping code.
>>
>> If Limpopo is separate from the parser that I'm working on, and has
>> an easier-to-work-with object model, I can possibly make some good
>> progress on this in a short period of time. Glancing at the code from
>> Limpopo, the object model seems very different, and can possibly be
>> used by Elmo to generate RDF.
>>
>> If I use this route, is this something that would be interesting to
>> the group?
>>
>> Jim
>> --
>> Jim McCusker
>> Programmer Analyst
>> Krauthammer Lab, Pathology Informatics
>> Yale School of Medicine
>> james.mccusker@... <mailto:james.mccusker@...> | (203)
>> 785-6330
>> http://krauthammerlab.med.yale.edu
>>
>> PhD Student
>> Tetherless World Constellation
>> Rensselaer Polytechnic Institute
>> mccusj@... <mailto:mccusj@...>
>> http://tw.rpi.edu
>
>

[Kei Cheung]

Hi Michael,

Thanks for sharing your experience with your GWAS project. The thing
with marker identification and prediction is that it involves a series
of possibly iteratirve analyses. The resulting gene lists are really the
products of these analyses. Therefore, it is important to capture the
context of these gene lists. See you and others at the F2F.

Cheers,

-Kei

dmiller wrote:

> hi kei,
>
> yes, the proposal for specifying the dataset seemed to allow rich
> annotation, one reason i liked it.
>
> the piece i find missing is this.  not being a biologist or
> statistician i can't offer much help (my strength is software).
>
> once a large group of individuals have been part of a GWAS (perhaps as
> part of a clinical trial) and a marker based on a gene expression
> signature over n genes has been determined, presumably that would be
> published as the set of n genes and some averaged measure of up
> regulation or down regulation per gene based on averaging that group
> of individuals and an outcome such as bad prognosis or good prognosis
> associated with the marker.  now if a new individual has a gene
> expression profile, how will the expression of this individual's genes
> be compared against the marker to determine which group the individual
> falls into?
>
> (there are other scenarios, such as multiple markers associated with
> different outcomes but the above seems the simplest case.)
>
> look forward to meeting you and the others at the F2F next week.
>
> cheers,
> michael
>
> Michael Miller
> mdmiller53@...
>
> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@...>
> To: "mdmiller" <mdmiller53@...>
> Cc: "Helen Parkinson" <parkinson@...>; "HCLS"
> <public-semweb-lifesci@...>; "Tony Burdett" <tburdett@...>
> Sent: Thursday, October 29, 2009 1:43 PM
> Subject: Re: Action Items from call today
>
>
>> Hi Michael et al,
>>
>> Thanks for pointing to this generic approach of RDF representation of
>> datasets. A list of differentially expressed genes may be associated
>> with values such as P-values, fold-change, gene symbols, etc. Also,
>> it's important to capture metadata/provenance associated with the
>> gene list. This may include the type of statistical test (e.g.,
>> ANOVA) and the array platform employed (e.g., Affymetrix U133A). This
>> may be an interesting discussion topic at the F2F meeting.
>>
>> Cheers,
>>
>> -Kei
>>
>> mdmiller wrote:
>>
>>> hi all,
>>>
>>> on a different HCLS thread i saw this proposal from jeni tennison
>>> for specifying a generic dataset, it might be a useful way to encode
>>> a list of differentially expressed genes.  it looks like one could
>>> do this encoding on the fly, so that the data itself at the source
>>> could be in whatever format is natural.
>>>
>>> http://sw.joanneum.at/scovo/schema.html
>>>
>>> cheers,
>>> michael
>>>
>>> Michael Miller
>>> mdmiller53@...
>>>
>>> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@...>
>>> To: "Helen Parkinson" <parkinson@...>
>>> Cc: "HCLS" <public-semweb-lifesci@...>; "Tony Burdett"
>>> <tburdett@...>
>>> Sent: Wednesday, October 14, 2009 7:03 PM
>>> Subject: Re: Action Items from call today
>>>
>>>
>>>> Thanks, Helen.
>>>>
>>>> To make it more concrete. I've been thinking about some example
>>>> queries that I hope can be answered by the RDF data once converted.
>>>> I wonder if the following example quereis can be answered:
>>>>
>>>> Retrieve a list of differentially expressed genes between different
>>>> brain regions (e.g., hippocampus and entorhinal cortex) for
>>>> normally aged human subjects.
>>>>
>>>> Retrieve a list of differentially expressed genes for the same
>>>> brain region of normal human subjects and AD patients.
>>>>
>>>> Using these lists of genes one can issue (federated) queries to
>>>> retrieve addtional information about the genes for various types of
>>>> analyses (e.g., GO term enrichment).
>>>>
>>>> Just a thought.
>>>>
>>>> Cheers,
>>>>
>>>> -Kei
>>>>
>>>>
>>>>
>>>> Helen Parkinson wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> here are my action items from the call today
>>>>>
>>>>> 1. MAGE-TAB->RDF, Lena requested details.
>>>>>
>>>>> Code here: https://sourceforge.net/projects/limpopo/
>>>>>
>>>>> Java Parser for MAGE-TAB developed by EBI, used by several groups.
>>>>> Contact Tony Burdett tburdett@... for details. Tony
>>>>> estimates for a simple RDF dump a few days work. Lena if you are
>>>>> interested in working on this java code please contact Tony as
>>>>> he's already designed with rdf export in mind
>>>>>
>>>>> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>>>>>
>>>>> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
>>>>> Pretty much all public MAGE-ML comes from AE and is available from
>>>>> Arrayexpress ftp dirs as mage-tab already. Exceptions are
>>>>> Rosetta's mage-ml importer, and non public data
>>>>>
>>>>>
>>>>> 3. EBI experimental factor ontology (EFO) slides, attached
>>>>> see also www.ebi.ac.uk/efo
>>>>>
>>>>> 4. Noted that an RDF dump of atlas data and triple store access
>>>>> will be useful, we'll announce when these are available
>>>>>
>>>>> thanks
>>>>>
>>>>> Helen
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
>

[Jun Zhao-2]

Hello Michael,

Sorry I didn't see this email from you since I have been traveling.

I am aware of the scovo vocabulary. Actually scovo is used in the voiD
[1] vocabulary to describe statistics about data and I am one member of
the voiD working group. Although scovo is a well-designed model to serve
its purpose, we have found that it is quite difficult to query for
datasets using this vocabulary. Hence, in the current voiD working
group, proposing an alternative model to describe statistics of datasets
has been a high priority. We are planning to release voiD2.0 including a
new statistics model around Christmas. It would be nice if I can gather
more user requirements from you and people on this list.:)

[1] http://rdfs.org/ns/void-guide

Best,

Jun

mdmiller wrote:

> hi all,
>
> on a different HCLS thread i saw this proposal from jeni tennison for
> specifying a generic dataset, it might be a useful way to encode a list of
> differentially expressed genes.  it looks like one could do this encoding on
> the fly, so that the data itself at the source could be in whatever format
> is natural.
>
> http://sw.joanneum.at/scovo/schema.html
>
> cheers,
> michael
>
> Michael Miller
> mdmiller53@...
>
> ----- Original Message -----
> From: "Kei Cheung" <kei.cheung@...>
> To: "Helen Parkinson" <parkinson@...>
> Cc: "HCLS" <public-semweb-lifesci@...>; "Tony Burdett"
> <tburdett@...>
> Sent: Wednesday, October 14, 2009 7:03 PM
> Subject: Re: Action Items from call today
>
>
>> Thanks, Helen.
>>
>> To make it more concrete. I've been thinking about some example queries
>> that I hope can be answered by the RDF data once converted. I wonder if
>> the following example quereis can be answered:
>>
>> Retrieve a list of differentially expressed genes between different brain
>> regions (e.g., hippocampus and entorhinal cortex) for normally aged human
>> subjects.
>>
>> Retrieve a list of differentially expressed genes for the same brain
>> region of normal human subjects and AD patients.
>>
>> Using these lists of genes one can issue (federated) queries to retrieve
>> addtional information about the genes for various types of analyses (e.g.,
>> GO term enrichment).
>>
>> Just a thought.
>>
>> Cheers,
>>
>> -Kei
>>
>>
>>
>> Helen Parkinson wrote:
>>
>>> Hi
>>>
>>> here are my action items from the call today
>>>
>>> 1. MAGE-TAB->RDF, Lena requested details.
>>>
>>> Code here: https://sourceforge.net/projects/limpopo/
>>>
>>> Java Parser for MAGE-TAB developed by EBI, used by several groups.
>>> Contact Tony Burdett tburdett@... for details. Tony estimates for a
>>> simple RDF dump a few days work. Lena if you are interested in working on
>>> this java code please contact Tony as he's already designed  with rdf
>>> export in mind
>>>
>>> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>>>
>>> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
>>> Pretty much all public MAGE-ML comes from AE and is available from
>>> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's
>>> mage-ml importer, and non public data
>>>
>>>
>>> 3. EBI experimental factor ontology (EFO) slides, attached
>>> see also www.ebi.ac.uk/efo
>>>
>>> 4. Noted that an RDF dump of atlas data and triple store access will be
>>> useful, we'll announce when these are available
>>>
>>> thanks
>>>
>>> Helen
>>>
>>>
>>>
>>
>>
>
>
>
>

[Kei Cheung]

Hi Jun et al,

The following gene list:

http://public.tgen.org/tgen.org/supplementarydata/neurogenomics/supplementarydata/brain_regions/PCA1_0_98_correlation.xls

was gereated using the Principal components analysis (PCA). It is an
annotated list of 102 genes showing at least a 0.98 correlation to PCA1
(first principal component). This is part of the following paper:

http://www.ncbi.nlm.nih.gov/pubmed/17077275?dopt=Abstract

I'm airport t to the airport now ...

Cheers,

-Kei

Jun Zhao wrote:

> Hello Michael,
>
> Sorry I didn't see this email from you since I have been traveling.
>
> I am aware of the scovo vocabulary. Actually scovo is used in the voiD
> [1] vocabulary to describe statistics about data and I am one member
> of the voiD working group. Although scovo is a well-designed model to
> serve its purpose, we have found that it is quite difficult to query
> for datasets using this vocabulary. Hence, in the current voiD working
> group, proposing an alternative model to describe statistics of
> datasets has been a high priority. We are planning to release voiD2.0
> including a new statistics model around Christmas. It would be nice if
> I can gather more user requirements from you and people on this list.:)
>
> [1] http://rdfs.org/ns/void-guide
>
> Best,
>
> Jun
>
> mdmiller wrote:
>
>> hi all,
>>
>> on a different HCLS thread i saw this proposal from jeni tennison for
>> specifying a generic dataset, it might be a useful way to encode a
>> list of differentially expressed genes.  it looks like one could do
>> this encoding on the fly, so that the data itself at the source could
>> be in whatever format is natural.
>>
>> http://sw.joanneum.at/scovo/schema.html
>>
>> cheers,
>> michael
>>
>> Michael Miller
>> mdmiller53@...
>>
>> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@...>
>> To: "Helen Parkinson" <parkinson@...>
>> Cc: "HCLS" <public-semweb-lifesci@...>; "Tony Burdett"
>> <tburdett@...>
>> Sent: Wednesday, October 14, 2009 7:03 PM
>> Subject: Re: Action Items from call today
>>
>>
>>> Thanks, Helen.
>>>
>>> To make it more concrete. I've been thinking about some example
>>> queries that I hope can be answered by the RDF data once converted.
>>> I wonder if the following example quereis can be answered:
>>>
>>> Retrieve a list of differentially expressed genes between different
>>> brain regions (e.g., hippocampus and entorhinal cortex) for normally
>>> aged human subjects.
>>>
>>> Retrieve a list of differentially expressed genes for the same brain
>>> region of normal human subjects and AD patients.
>>>
>>> Using these lists of genes one can issue (federated) queries to
>>> retrieve addtional information about the genes for various types of
>>> analyses (e.g., GO term enrichment).
>>>
>>> Just a thought.
>>>
>>> Cheers,
>>>
>>> -Kei
>>>
>>>
>>>
>>> Helen Parkinson wrote:
>>>
>>>> Hi
>>>>
>>>> here are my action items from the call today
>>>>
>>>> 1. MAGE-TAB->RDF, Lena requested details.
>>>>
>>>> Code here: https://sourceforge.net/projects/limpopo/
>>>>
>>>> Java Parser for MAGE-TAB developed by EBI, used by several groups.
>>>> Contact Tony Burdett tburdett@... for details. Tony estimates
>>>> for a simple RDF dump a few days work. Lena if you are interested
>>>> in working on this java code please contact Tony as he's already
>>>> designed  with rdf export in mind
>>>>
>>>> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>>>>
>>>> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
>>>> Pretty much all public MAGE-ML comes from AE and is available from
>>>> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's
>>>> mage-ml importer, and non public data
>>>>
>>>>
>>>> 3. EBI experimental factor ontology (EFO) slides, attached
>>>> see also www.ebi.ac.uk/efo
>>>>
>>>> 4. Noted that an RDF dump of atlas data and triple store access
>>>> will be useful, we'll announce when these are available
>>>>
>>>> thanks
>>>>
>>>> Helen
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>>
>
>