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Re: [BioRDF] Comments from Christoph Grabmuller - annotation tool/ontology

From: Susanna-Assunta Sansone <sa.sansone@gmail.com>
Date: Tue, 09 Nov 2010 14:31:39 +0000
Message-ID: <4CD95B4B.2010209@gmail.com>
To: Jim McCusker <james.mccusker@yale.edu>
CC: Christoph Grabmuller <grabmuel@ebi.ac.uk>, mdmiller <mdmiller53@comcast.net>, "M. Scott Marshall" <mscottmarshall@gmail.com>, HCLS <public-semweb-lifesci@w3.org>
Hi Jim,
we are aware of your work, of course; one of the action from the last 
HCLS-SD call (on the isa to rdf conversion topic for the stem cell data 
scenario) was to communicate with you, also as Scott suggested. We do 
not use the limpopo, as isa tools already had their own set of parser, 
validator and converter (standalone) components.
We will come back to you on this soon - maybe starting a new thread to 
link the two subgroups's specific activities.


On 09/11/2010 13:42, Jim McCusker wrote:
> A direct conversion of csv to rdf usually results in a entity-per-line
> mapping. The magetab2rdf tool I made (at magetab2rdf.googlecode.com)
> does a conversion of the mage tab into an rdf representation that is a
> one to one mapping into the mage derivation graph and uses OBI et al
> for classes and properties. It should be easily extensible to ISA tab
> when Limpopo is extended to do the same.
> Jim
> On Tuesday, November 9, 2010, Susanna-Assunta Sansone
> <sa.sansone@gmail.com>  wrote:
>> Hi Christoph,
>> on the topic of annotation tool...
>> On 09/11/2010 10:09, Christoph Grabmuller wrote:
>> 3) I like the Excel to RDF converter, but it relies on the user
>> entering correct namespaces, names and database ids from various
>> places in a syntactically correct way. This requires knowledge of the
>> correct databases to choose and the 'correct' uri (many variants to
>> chose from).
>> If people just enter strings we are not all that far away from MAGE-TAB.
>> * i'm involved in an open source project, Annotare, that seeks to put a nice
>> UI on top of creating MAGE-TAB documents for a bench scientist.  part of
>> that is use of the NCBO tools to make it easy for the creator of the
>> document to go fetch the appropriate term from the appropriate
>> onotlogy/vocabulary.  version one has support for EFO built-in, one of the
>> main goals for version 2 is to make this much easier and much broader.
>> --mm
>> That looks like a very useful tool. Out of curiosity: how are the
>> ontologies/vocabularies loaded?
>> -cg
>> there is another set of annotation tools, ISA tools, that already support a variety of ontologies; these are accessed dynamically via BioPortal and OLS web services.
>> The tools convert into MAGE-Tab, but also Pride-XML and SRA-XML (SOFT is ongoing) and we have just start working with HCLS-SD subgroup (Sudeshna Das) to export in RDF.
>> Info and papers at: www.isa-tools.org; let me know if you intersted, can provide you with more info.
>> Thanks,
>> Susanna
>> -------------------------------------------------------------
>> Susanna-Assunta Sansone, PhD
>> Team Leader
>> Projects: www.isa-tools.org|www.mibbi.org|www.biosharing.org
>> University of Oxford            Tel: +44(0)1865 610622
>> Oxford e-Research Center        Fax: +44(0)1865 610612
>> 7 Keble Road, Oxford            skype: susanna-a.sansone
>> OX1 3QG, UK                     uk.linkedin.com/in/sasansone
>> -------------------------------------------------------------
Received on Tuesday, 9 November 2010 14:32:16 UTC

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