W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > November 2010

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

From: Susanna-Assunta Sansone <sa.sansone@gmail.com>
Date: Tue, 09 Nov 2010 12:07:12 +0000
Message-ID: <4CD93970.4000208@gmail.com>
To: Christoph Grabmuller <grabmuel@ebi.ac.uk>
CC: mdmiller <mdmiller53@comcast.net>, "M. Scott Marshall" <mscottmarshall@gmail.com>, HCLS <public-semweb-lifesci@w3.org>
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 12:11:36 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:01:00 GMT