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Re: Minutes for Scientific Discourse call

From: <jiezheng@pcbi.upenn.edu>
Date: Wed, 24 Mar 2010 21:07:24 -0400
Message-ID: <20100324210724.61k13b8zhkdu2o8k@mail.pcbi.upenn.edu>
To: Helen Parkinson <parkinson@ebi.ac.uk>
Cc: Michael Miller <mmiller@teranode.com>, "M. Scott Marshall" <marshall@science.uva.nl>, HCLS <public-semweb-lifesci@w3.org>
Hi All,

I have made the mapping between MO and OBI/OBO ontologies and posted 
the mapping
files on MGED ontology page. You can find the links in the mapping section of
page
http://mged.sourceforge.net/ontologies/MGEDontology.php

The mapping were made based on the definition. We found it should be more
accurate to map the terms based on how they were used in the MAGE-TAB files.
This work is in progress. I will update the MO to OBI mapping file soon and
distribute the link.

Thanks,

Jie


Quoting Helen Parkinson <parkinson@ebi.ac.uk>:

> Hi all,
>
> let me clarify. OBI is at release 1.0
>
> 1. EFO imports parts of OBI that we need for ArrayExpress, we will 
> continue to use EFO in ArrayExpress, as it has added terms and 
> relations between terms that exist nowhere else - cell types, to cell 
> lines for example. And it has some terms that are imported from e.g. 
> the cell type ontologu EFO is an application ontology and will 
> persist as we need it in our GUIs. You can see our paper on this here:
>
> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq099
>
> 2. Where we import terms from OBI - or any other ontology we retain 
> their namespace as recommended by OBI foundry. As more terms are in 
> OBI we will import them.
>
> 3. My colleague Jie Zheng is in the process of mapping MO to OBI and 
> when this is complete we will import more terms from OBI into EFO, 
> but EFO will still be used for the foreseeable future by 
> ArrayExpress. You can think of EFO as an application ontology, or 
> view on OBI and many other ontologies.
>
> 4. Where ontology terms imported into EFO have an authoritative 
> source e.g. Chebi we use their namespace and where they are from non 
> authoritative sources, for example there is no obo foundry ontology 
> and many competing ontologies we assign our own ids and will continue 
> to do so
>
> Happy to answer any questions.
>
> best regards
>
> Helen
>
>
>
>
>
> Michael Miller wrote:
>> hi all,
>>
>> some comments on the minutes.
>>
>> "Possible overlaps with EFO ontology from EBI and OBI"
>>
>> if i understand correctly, EFO was created because OBI was not finalized
>> yet and ArrayExpress at EBI is a live gene expression data repository and
>> the curators needed an ontology they could use.  i believe their plan is
>> to move to OBI or update EFO to reflect the relationship of terms in EFO
>> to terms in OBI.
>>
>> "MGED may be part of OBI now"
>>
>> MGED (www.mged.org) is a non-profit organization.  What is being referred
>> to as MGED on the HCLS web site is a predecessor to OBI which should be
>> called the MGED Ontology, also referred to as MO, that came out of an MGED
>> effort.  OBI is to replace MO.
>>
>> cheers,
>> michael
>>
>> Michael Miller
>> Principal Software Developer
>> www.teranode.com
>>
>>
>>> -----Original Message-----
>>> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
>>> lifesci-request@w3.org] On Behalf Of M. Scott Marshall
>>> Sent: Wednesday, March 24, 2010 12:31 PM
>>> To: HCLS
>>> Subject: Minutes for Scientific Discourse call
>>>
>>> Minutes for the Scientific Discourse call last Monday can be found at:
>>> http://www.w3.org/2010/03/22-hcls-minutes.html
>>>
>>> Sudeshna has distilled them nicely onto the wiki:
>>> http://esw.w3.org/HCLSIG/SWANSIOC/Meetings/2010-3-22_Conference_Call
>>>
>>> Cheers,
>>> Scott
>>>
>
Received on Wednesday, 31 March 2010 08:48:21 GMT

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