I have the links between entities all squared away now. Actually, I had a
few bugs that I discovered through that process. However, the "About" page
seems to not support using "#" as being the same as "" for the root URI. See
http://linkeddata.uriburner.com/about/html/http://espresso.med.yale.edu/~
Jim McCusker wrote:
Hi all. I've think I've addressed the issues raised above. I have a
new example at:
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986.rdf
which is generated from the ArrayExpress IDF url. I have added the
foaf:primaryTopic p
Hi all. I've think I've addressed the issues raised above. I have a new
example at:
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986.rdf
which is generated from the ArrayExpress IDF url. I have added the
foaf:primaryTopic property as suggested, but I s
Jim McCusker wrote:
On Wed, Jan 6, 2010 at 11:07 AM, Kingsley Idehen
mailto:kide...@openlinksw.com>> wrote:
Quick request re. the RDF documents holding the RDF triples, you
need to add a relation that connects the RDF Documents to its
contents e.g., using one of the Topic oriented p
Sent: Wednesday, January 06, 2010 9:37 AM
To: Michael Miller
Cc: w3c semweb HCLS
Subject: Re: magetab2magerdf
On Wed, Jan 6, 2010 at 12:18 PM, Michael Miller
wrote:
"Unless I have a bug, ..."
pretty sure you do, especially since there is no 'Array Data Matrix
File' column in
32722.txt
E-MEXP-986-raw-data-1321832716.txt
E-MEXP-986-raw-data-1321832734.txt
and
Derived Array Data Matrix File
E-MEXP-986-processed-data-1343528010.txt
E-MEXP-986-processed-data-1343528012.txt
E-MEXP-986-processed-data-1343528010.txt
E-MEXP-986-processed-data-1343528012.txt
I used
http://mageta
7;m
missing something.
cheers,
michael
From: Jim McCusker [mailto:james.mccus...@yale.edu]
Sent: Wednesday, January 06, 2010 9:09 AM
To: Michael Miller
Cc: Helena Deus; w3c semweb HCLS
Subject: Re: magetab2magerdf
On Wed, Jan 6, 2010 at 11:55 AM, Michael Miller
wrote:
but the prob
On Wed, Jan 6, 2010 at 11:07 AM, Kingsley Idehen wrote:
> Quick request re. the RDF documents holding the RDF triples, you need to
> add a relation that connects the RDF Documents to its contents e.g., using
> one of the Topic oriented properties from Dublic Core, FOAF, Bibliographic
> Ontology et
On Wed, Jan 6, 2010 at 11:55 AM, Michael Miller wrote:
> but the problem seems to be that ArrayDataMatrix is referencing the
> 'Derived Array Data Matrix File' column (which is different than a 'Array
> Data Matrix File' column) when it should be referencing the 'Array Data
> File' column, there
3.org
[mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of Helena Deus
Sent: Wednesday, January 06, 2010 8:09 AM
To: Jim McCusker
Cc: w3c semweb HCLS
Subject: Re: magetab2magerdf
Hi Jim,
This is great! I noticed you already add the links both to the raw data
files and the processed da
On Wed, Jan 6, 2010 at 11:08 AM, Helena Deus wrote:
> Hi Jim,
>
> This is great! I noticed you already add the links both to the raw data
> files and the processed data files, am I right in assuming this data comes
> from the SDRF?
>
Yes, these are comments embedded in SDRF, and the nodes for th
e, Dec 8, 2009 at 8:05 AM, Jim McCusker wrote:
> I'm distinguishing between magetab2rdf (raw conversion of magetab into
> an RDF structure) and magetab2magerdf (conversion of magetab into an
> RDF-based MAGE-OM structure) here. My purposes and goals require a
> magetab2magerdf approach,
he time to correct this.
cheers,
michael
- Original Message -
*From:* Jim McCusker <mailto:james.mccus...@yale.edu>
*To:* w3c semweb HCLS <mailto:public-semweb-lifesci@w3.org>
*Sent:* Tuesday, January 05, 2010 10:43 PM
*Subject:* Re: magetab2magerdf
I h
s.
cheers,
michael
- Original Message -
From: Jim McCusker
To: w3c semweb HCLS
Sent: Tuesday, January 05, 2010 10:43 PM
Subject: Re: magetab2magerdf
I have checked in a first (complete) cut for magetab2magerdf 0.9a. Everything
should be there, both IDF and SDRF, but I have
I have checked in a first (complete) cut for magetab2magerdf 0.9a.
Everything should be there, both IDF and SDRF, but I haven't tested against
a wide range of files yet. This is alpha software.
*Features:
*
- Conversion of nearly all (see known issues) data from IDF and SDRF
MAGE-TAB
;
>
>
>
> *From:* public-semweb-lifesci-requ...@w3.org [mailto:
> public-semweb-lifesci-requ...@w3.org] *On Behalf Of *Jim McCusker
> *Sent:* Tuesday, January 05, 2010 3:10 PM
> *To:* mdmiller; w3c semweb HCLS
> *Subject:* Re: magetab2magerdf
>
>
>
> For w
www.mged.org
>> [2] https://sourceforge.net/projects/limpopo/
>> [3] http://bioinformatics.oxfordjournals.org/cgi/content/full/25/2/279
>>
>> - Original Message - From: "Kei Cheung"
>> To: "mdmiller"
>> Cc: "Jim McCusker&quo
ontent/full/25/2/279
- Original Message - From: "Kei Cheung"
To: "mdmiller"
Cc: "Jim McCusker" ; "w3c semweb HCLS"
Sent: Sunday, December 13, 2009 6:34 PM
Subject: Re: magetab2magerdf
Hi Jim, Michael,
The following paper describes how to convert mage-tab
mpopo/
[3] http://bioinformatics.oxfordjournals.org/cgi/content/full/25/2/279
- Original Message -
From: "Kei Cheung"
To: "mdmiller"
Cc: "Jim McCusker" ; "w3c semweb HCLS"
Sent: Sunday, December 13, 2009 6:34 PM
Subject: Re: magetab2magerdf
Hi Jim, Michael,
The fo
Hi Kei,
correct, and just to clarify this
> ...if people are doing micorarray experiments only, MAGE-TAB and
ISA-TAB are essentially the same.
meaning that both can be used as fullfil the same reporting needs, but
their syntax is different.
Regards,
Susanna
Kei Cheung wrote:
Hi Susanna,
Th
Hi Susanna,
Thanks for the information. If I understand it correctly, ISA-TAB can be
used for different types of experiments (e.g., microarray, deep
sequencing, and mass spectrometry), while MAGE-TAB is designed for
microarray experiments only. However, if people are doing micorarray
experime
;w3c semweb HCLS"
Sent: Tuesday, December 08, 2009 6:05 AM
Subject: magetab2magerdf
I'm distinguishing between magetab2rdf (raw conversion of magetab into
an RDF structure) and magetab2magerdf (conversion of magetab into an
RDF-based MAGE-OM structure) here. My purposes and goals requi
,
looks like you're making great progress. i have a few comments
in-line below.
cheers,
michael
- Original Message - From: "Jim McCusker"
To: "w3c semweb HCLS"
Sent: Tuesday, December 08, 2009 6:05 AM
Subject: magetab2magerdf
I'm distinguishing betwe
On Wed, Dec 9, 2009 at 9:44 AM, mdmiller wrote:
> - Original Message - From: "Jim McCusker"
>> The URI for the MGED Ontology is
>> http://mged.sourceforge.net/ontologies/MGEDontology.owl, but has been
>> set to http://mged.sourceforge.net/ontologies/MGEDontology.php in the
>> IDF. The ac
hi jim,
looks like you're making great progress. i have a few comments in-line
below.
cheers,
michael
- Original Message -
From: "Jim McCusker"
To: "w3c semweb HCLS"
Sent: Tuesday, December 08, 2009 6:05 AM
Subject: magetab2magerdf
I'm distingui
I'm distinguishing between magetab2rdf (raw conversion of magetab into
an RDF structure) and magetab2magerdf (conversion of magetab into an
RDF-based MAGE-OM structure) here. My purposes and goals require a
magetab2magerdf approach, so that's what I've been working on.
I have chec
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