microarray-ontol-digest    Wednesday, July 3 2002    Volume 01 : Number 026




----------------------------------------------------------------------

Date: Sun, 2 Jun 2002 17:29:27 -0400
From: Chris Stoeckert <stoeckrt@SNOWBALL.pcbi.upenn.edu>
Subject: Re: [microarray-ontol] cancer disease descriptions

Hi Helen,
What does "histology1" mean? Is this like a leukemia classification 
(e.g., M6) based on a histology atlas (e.g., 
http://www.meds.com/leukemia/atlas/acute_leukemia.html)? This may be 
covered by DiseaseState. I guess it could also be used for OrganismPart 
where you have anatomical atlases. I think if we want this information 
as a source for describing existing BiosourceProperties then I don't 
think we need to add a Histology class. However, if we want a class to 
capture images and their interpretations, we could add one for that but 
not as an OntologyEntry.

I also don't know enough about disease grade to really say. Are we 
pointing to an external resource that lists different disease grades or 
are these a measurement that we can associate with DiseaseState? Or 
something else?

I'd like to hear more feedback from the group about tissue. If you had a 
good ontology or hierarchical c.v. to refer to then by picking the 
tissue of interest you've automatically established what organ and body 
part you are in by virtue of the hierarchy. You also know what cell 
types are present but not necessarily which one is of interest. Thus it 
makes sense to have a CellType and a TargetedCellType as this allows you 
to specify "lung" and "fibroblast" as opposed to "skin" and 
"fibroblast." Some c.v.s distinguish these too (with distinct IDs) but 
there is a move to have orthogonal vocabularies for organ/tissue, cell 
type, and developmental stage that can be combined. So we should 
certainly have these 3. Does anyone know if there is a separate body 
part orthogonal vocabulary planned as well that would allow distinctions 
between geographical anatomical descriptions (e.g., "head") from 
systemic description (e.g., "nervous system" - I would consider 
organ/tissue to be included in this)? In summary, I say let's follow 
what's going on with the GOBO or PATO plans - one class for each 
orthogonal vocabulary.

Cheers,
Chris

On Tuesday, May 28, 2002, at 11:10 AM, Helen Parkinson wrote:

> Hi Chris and John et al.,
>
> I have just received a MAGE-ML sample submission from John
> Yost NCI's annotation tool/database, this has the following
> OntologyEntries:
>
> <OntologyEntry category="histology" value="'histology1'"/>
> <OntologyEntry category="disease_grade" value="'grade'"/>
> <OntologyEntry category="tissue" value="'tissue 1'"/>
>
> currently we have
> %BiosourceOntologyEntry
>  %DiseaseState
>  %ClinicalInformation, are these adequate?
>
> The tissue type one is already under discussion, I am
> supposing that if NCI are generating this type of annotation
> they want to/already use these.
>
> Should these be defined and added to the ontology, and would
> anyone esp. cancer biologists like to comment?
>
> Helen
>

------------------------------

Date: Mon, 3 Jun 2002 13:38:16 -0400
From: Martin Ringwald <ringwald@informatics.jax.org>
Subject: Re: [microarray-ontol] tissues, etc.

Chris,

As to the tissue question, I basically agree with you. I am quite 
happy with the idea that OrganismPart covers everything except the 
cellular level. Organs have many substructures which one would not 
call a tissue. In other cases it will be difficult to decide if one 
should refer to that anatomical structure as a tissue or not. (It 
might be helpful to have tissue types that are assigned as attributes 
to tissues. We are currently looking into this option. However, 
attributes are a different issue altogether).

Along the same lines, one could argue that cells are part of tissues 
and, therefore, should be represented in the same hierarchical 
system. We tried to do this with the mouse anatomy but realized that 
this is not practical. The hierarchies would become huge, there is a 
danger of missing hierarchical levels, and it would be very difficult 
to describe each level in a complete and consistent manner. 
Therefore, we decided to develop a separate cell type ontology. We 
plan to record what cell types can occur in what organs/tissues.

Bruce raised important points in a previous email. You want to be 
able to break down the anatomy in different ways. Breakdown according 
to anatomic region or physiological system is a very good example. We 
try to achieve this by using a DAG structure for the anatomical 
vocabulary, i.e. by allowing multiple parents for a given anatomical 
structure. In this way we can represent in a normalized, i.e. 
non-redundant, fashion the fact that anatomical structures can be 
part of different physiological systems and body parts. However, 
building appropriate intersections between systemic and "geometric" 
hierarchies is tricky, in particular at more detailed levels. So, I 
am not yet sure if we will have to resort, at some point or in some 
instances, to combinatorial descriptions. For now, we try to 
represent everything in one DAG.

There is a different set of geometric descriptors that are truly 
orthogonal and can be applied to many anatomical structures using 
combinatorial descriptions:

Anterior (rostral)
Posterior (caudal)
Dorsal
Ventral
Lateral
Medial
Proximal
Distal
Central
Peripheral

We plan to implement this capability for the description of 
expression patterns in GXD.

Hope this helps,

Martin









>
>I'd like to hear more feedback from the group about tissue. If you 
>had a good ontology or hierarchical c.v. to refer to then by picking 
>the tissue of interest you've automatically established what organ 
>and body part you are in by virtue of the hierarchy. You also know 
>what cell types are present but not necessarily which one is of 
>interest. Thus it makes sense to have a CellType and a 
>TargetedCellType as this allows you to specify "lung" and 
>"fibroblast" as opposed to "skin" and "fibroblast." Some c.v.s 
>distinguish these too (with distinct IDs) but there is a move to 
>have orthogonal vocabularies for organ/tissue, cell type, and 
>developmental stage that can be combined. So we should certainly 
>have these 3. Does anyone know if there is a separate body part 
>orthogonal vocabulary planned as well that would allow distinctions 
>between geographical anatomical descriptions (e.g., "head") from 
>systemic description (e.g., "nervous system" - I would consider 
>organ/tissue to be included in this)? In summary, I say let's follow 
>what's going on with the GOBO or PATO plans - one class for each 
>orthogonal vocabulary.
>
>Cheers,
>Chris
>

------------------------------

Date: Mon, 3 Jun 2002 21:17:38 -0400
From: Chris Stoeckert <stoeckrt@SNOWBALL.pcbi.upenn.edu>
Subject: [microarray-ontol] ISMB Birds of Feather

Dear Group,
For those of you attending ISMB 2002 in Edmonton, Canada, I am arranging 
a "Birds of a Feather" room so that we can have an Ontology Working 
Group meeting. I have requested August 7th from 10 - 11 AM.
Will let you know when that is confirmed.

Cheers,
Chris

------------------------------

Date: Tue, 4 Jun 2002 06:49:50 +0100 (BST)
From: "Uli Buchholz" <u.buchholz@genescan.com>
Subject: [microarray-ontol] Date: Tue, 4 Jun 2002 07:50:40 +0200

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------------------------------

Date: 04 Jun 2002 09:57:51 -0600
From: jason@openinformatics.com (Jason E. Stewart)
Subject: Re: [microarray-ontol] Date: Tue, 4 Jun 2002 07:50:40 +0200

Hey Chris,

I run all the mged MAGE related lists out of SourceForge. This makes
it a lot easier for users to subscribe and unsubscribe themselves via
their WWW browser.

If you'd like to move the ontology list over, I can set it up and make
you the moderator.

jas.

"Uli Buchholz" <u.buchholz@genescan.com> writes:

> remove u.buchholz@genescan.com

------------------------------

Date: Tue, 4 Jun 2002 17:30:09 -0400
From: Chris Stoeckert <stoeckrt@SNOWBALL.pcbi.upenn.edu>
Subject: [microarray-ontol] abstract for ISMB Bio-Ontologies meeting

Dear Group,
I would like to present our work at the Bio-Ontologies special interests 
group meeting at ISMB (http://img.cs.man.ac.uk/stevens/meeting02/) and 
have prepared this abstract. Please let me know if you have any comments 
or suggestions.
Thanks,
Chris

The MGED Ontology Is An Experimental Ontology
  and the MGED Ontology Working Group

The mission of the Microarray Gene Expression Data (MGED, 1) society is 
to establish standards for the representation and exchange of 
information about experiments in the domain of functional genomics. As 
implied by the name, MGED was formed with an initial focus on 
experiments involving microarray technology. In microarray experiments, 
the expression or activity of many genes or proteins is simultaneously 
monitored through their interactions with arrays of nucleic acids or 
proteins.  Such experiments are performed on a wide variety of organisms 
for a wide variety of reasons such as understanding the growth of 
bacteria, examining the response of plants to treatments, and the 
classification of tumor biopsies from patients. Despite the diversity of 
applications, there are common concepts used and a common need to 
capture experimental information in a standardized manner. Based on the 
participation of hundreds of investigators from around the world, a 
common set of concepts for microarray experiments was established as the 
MIAME (mimimum information about a microarray experiment) guideline (2). 
These concepts have been organized into an object model for the purpose 
of generating a standard document format to facilitate data exchange. 
The MAGE (microarray gene expression) object model has been accepted by 
the OMG (object management group) as a standard (3). However, neither 
the MIAME guideline or the MAGE object model provide the details or 
terms needed to create instances of microarray experiments especially in 
the areas of describing the biological sample and its manipulation for 
study. Indeed, in such areas it was planned that an ontology be 
generated to further structure information about the microarray 
experiment.

In building the MGED ontology, it was recognized that it would be 
impractical to cover all the different types of experiments on all the 
different types of organisms by listing and defining all the types of 
organisms, their anatomies, their developmental stages, their diseases, 
the compounds used to treat them, etc. If such listings already existed, 
then it would be a duplication of effort to transfer them into our 
ontology. If multiple listings for the same information (e.g., human 
disease) existed, then we would have to make decisions as to which was 
best causing endless debate. If listings for certain species didn’t 
exist then we would be at a loss until finding the time, resources, and 
expertise to generate them. Our solution was to create a framework for 
describing microarray experiments with an initial focus on the 
biological sample and its manipulation. This framework would specify in 
greater detail than MIAME or MAGE the different types of information to 
be captured. For concepts such as  “Sex” or “Age” that are common for 
many species, we could provide a manageable listing of controlled terms. 
For concepts such as “OrganismPart” or “DiseaseState”  that are 
species-specific, we created an “OntologyEntry” concept that referenced 
an external resource.

The MGED ontology has been built using OILed (4) allowing us to export 
documents in DAML, rdfs, and to generate html pages for browsing (5). It 
is a work in progress that needs additional instances and particularly 
needs constraints to be added. The ontology currently covers the 
experimental sample and we have begun capturing the experimental design 
as well. The primary application of the ontology will be to develop 
forms for entering information into databases and consequently allowing 
queries taking advantage of the structure provided by the ontology. The 
application of an ontology of experimental conditions (which is what the 
MGED ontology represents) extends beyond the domain of microarray 
experiments. As such, it is important to coordinate efforts with other 
ontology efforts such as GOBO (global open biological ontologies, 6) so 
that the language of functional genomics can be understood and processed.

1. http://www.mged.org
2.Brazma et al (2001) Nature Genetics 29:365-371
3. 
http://www.omg.org/techprocess/meetings/schedule/Gene_Expression_RFP.html
4. http://oiled.man.ac.uk/
5. http://www.cbil.upenn.edu/Ontology/MGED_ontology.html
6. http://www.geneontology.org/doc/gobo.html

------------------------------

Date: Wed, 05 Jun 2002 15:58:05 -0400
From: Bruce Aronow <bruce.aronow@chmcc.org>
Subject: Re: [microarray-ontol] tissues, etc.

Let me take a hack at an example..

description:  left ventricle
is a tissue
is a muscle
part of circulatory system
part of heart
part of thoracic cavity
contains myocardial cells
contains endocardial cells
contains axons
contains neuromuscular junctions
contains endothelial cells
has properties of excitability
has properties of contractility


need to go to meeting, but see what you guys think...

best,
Bruce





Martin Ringwald wrote:

> Chris,
>
> As to the tissue question, I basically agree with you. I am quite
> happy with the idea that OrganismPart covers everything except the
> cellular level. Organs have many substructures which one would not
> call a tissue. In other cases it will be difficult to decide if one
> should refer to that anatomical structure as a tissue or not. (It
> might be helpful to have tissue types that are assigned as attributes
> to tissues. We are currently looking into this option. However,
> attributes are a different issue altogether).
>
> Along the same lines, one could argue that cells are part of tissues
> and, therefore, should be represented in the same hierarchical
> system. We tried to do this with the mouse anatomy but realized that
> this is not practical. The hierarchies would become huge, there is a
> danger of missing hierarchical levels, and it would be very difficult
> to describe each level in a complete and consistent manner.
> Therefore, we decided to develop a separate cell type ontology. We
> plan to record what cell types can occur in what organs/tissues.
>
> Bruce raised important points in a previous email. You want to be
> able to break down the anatomy in different ways. Breakdown according
> to anatomic region or physiological system is a very good example. We
> try to achieve this by using a DAG structure for the anatomical
> vocabulary, i.e. by allowing multiple parents for a given anatomical
> structure. In this way we can represent in a normalized, i.e.
> non-redundant, fashion the fact that anatomical structures can be
> part of different physiological systems and body parts. However,
> building appropriate intersections between systemic and "geometric"
> hierarchies is tricky, in particular at more detailed levels. So, I
> am not yet sure if we will have to resort, at some point or in some
> instances, to combinatorial descriptions. For now, we try to
> represent everything in one DAG.
>
> There is a different set of geometric descriptors that are truly
> orthogonal and can be applied to many anatomical structures using
> combinatorial descriptions:
>
> Anterior (rostral)
> Posterior (caudal)
> Dorsal
> Ventral
> Lateral
> Medial
> Proximal
> Distal
> Central
> Peripheral
>
> We plan to implement this capability for the description of
> expression patterns in GXD.
>
> Hope this helps,
>
> Martin
>
> >
> >I'd like to hear more feedback from the group about tissue. If you
> >had a good ontology or hierarchical c.v. to refer to then by picking
> >the tissue of interest you've automatically established what organ
> >and body part you are in by virtue of the hierarchy. You also know
> >what cell types are present but not necessarily which one is of
> >interest. Thus it makes sense to have a CellType and a
> >TargetedCellType as this allows you to specify "lung" and
> >"fibroblast" as opposed to "skin" and "fibroblast." Some c.v.s
> >distinguish these too (with distinct IDs) but there is a move to
> >have orthogonal vocabularies for organ/tissue, cell type, and
> >developmental stage that can be combined. So we should certainly
> >have these 3. Does anyone know if there is a separate body part
> >orthogonal vocabulary planned as well that would allow distinctions
> >between geographical anatomical descriptions (e.g., "head") from
> >systemic description (e.g., "nervous system" - I would consider
> >organ/tissue to be included in this)? In summary, I say let's follow
> >what's going on with the GOBO or PATO plans - one class for each
> >orthogonal vocabulary.
> >
> >Cheers,
> >Chris
> >

------------------------------

Date: Wed, 5 Jun 2002 16:19:52 -0400
From: Chris Stoeckert <stoeckrt@SNOWBALL.pcbi.upenn.edu>
Subject: Re: [microarray-ontol] tissues, etc.

Right. For ontologies like this, we would just point to "left ventricle" 
as the BiosourceOntologyEntry for OrganismPart and all would be clear 
(TissueType would not be necessary).

Chris

On Wednesday, June 5, 2002, at 03:58 PM, Bruce Aronow wrote:

> Let me take a hack at an example..
>
> description:  left ventricle
> is a tissue
> is a muscle
> part of circulatory system
> part of heart
> part of thoracic cavity
> contains myocardial cells
> contains endocardial cells
> contains axons
> contains neuromuscular junctions
> contains endothelial cells
> has properties of excitability
> has properties of contractility
>
>
> need to go to meeting, but see what you guys think...
>
> best,
> Bruce
>
>
>
>
>
> Martin Ringwald wrote:
>
>> Chris,
>>
>> As to the tissue question, I basically agree with you. I am quite
>> happy with the idea that OrganismPart covers everything except the
>> cellular level. Organs have many substructures which one would not
>> call a tissue. In other cases it will be difficult to decide if one
>> should refer to that anatomical structure as a tissue or not. (It
>> might be helpful to have tissue types that are assigned as attributes
>> to tissues. We are currently looking into this option. However,
>> attributes are a different issue altogether).
>>
>> Along the same lines, one could argue that cells are part of tissues
>> and, therefore, should be represented in the same hierarchical
>> system. We tried to do this with the mouse anatomy but realized that
>> this is not practical. The hierarchies would become huge, there is a
>> danger of missing hierarchical levels, and it would be very difficult
>> to describe each level in a complete and consistent manner.
>> Therefore, we decided to develop a separate cell type ontology. We
>> plan to record what cell types can occur in what organs/tissues.
>>
>> Bruce raised important points in a previous email. You want to be
>> able to break down the anatomy in different ways. Breakdown according
>> to anatomic region or physiological system is a very good example. We
>> try to achieve this by using a DAG structure for the anatomical
>> vocabulary, i.e. by allowing multiple parents for a given anatomical
>> structure. In this way we can represent in a normalized, i.e.
>> non-redundant, fashion the fact that anatomical structures can be
>> part of different physiological systems and body parts. However,
>> building appropriate intersections between systemic and "geometric"
>> hierarchies is tricky, in particular at more detailed levels. So, I
>> am not yet sure if we will have to resort, at some point or in some
>> instances, to combinatorial descriptions. For now, we try to
>> represent everything in one DAG.
>>
>> There is a different set of geometric descriptors that are truly
>> orthogonal and can be applied to many anatomical structures using
>> combinatorial descriptions:
>>
>> Anterior (rostral)
>> Posterior (caudal)
>> Dorsal
>> Ventral
>> Lateral
>> Medial
>> Proximal
>> Distal
>> Central
>> Peripheral
>>
>> We plan to implement this capability for the description of
>> expression patterns in GXD.
>>
>> Hope this helps,
>>
>> Martin
>>
>>>
>>> I'd like to hear more feedback from the group about tissue. If you
>>> had a good ontology or hierarchical c.v. to refer to then by picking
>>> the tissue of interest you've automatically established what organ
>>> and body part you are in by virtue of the hierarchy. You also know
>>> what cell types are present but not necessarily which one is of
>>> interest. Thus it makes sense to have a CellType and a
>>> TargetedCellType as this allows you to specify "lung" and
>>> "fibroblast" as opposed to "skin" and "fibroblast." Some c.v.s
>>> distinguish these too (with distinct IDs) but there is a move to
>>> have orthogonal vocabularies for organ/tissue, cell type, and
>>> developmental stage that can be combined. So we should certainly
>>> have these 3. Does anyone know if there is a separate body part
>>> orthogonal vocabulary planned as well that would allow distinctions
>>> between geographical anatomical descriptions (e.g., "head") from
>>> systemic description (e.g., "nervous system" - I would consider
>>> organ/tissue to be included in this)? In summary, I say let's follow
>>> what's going on with the GOBO or PATO plans - one class for each
>>> orthogonal vocabulary.
>>>
>>> Cheers,
>>> Chris
>>>
>

------------------------------

Date: Wed, 5 Jun 2002 16:48:37 -0400
From: Martin Ringwald <ringwald@informatics.jax.org>
Subject: Re: [microarray-ontol] tissues, etc.

Yes, I agree. -- Martin



>Right. For ontologies like this, we would just point to "left 
>ventricle" as the BiosourceOntologyEntry for OrganismPart and all 
>would be clear (TissueType would not be necessary).
>
>Chris
>
>On Wednesday, June 5, 2002, at 03:58 PM, Bruce Aronow wrote:
>
>>Let me take a hack at an example..
>>
>>description:  left ventricle
>>is a tissue
>>is a muscle
>>part of circulatory system
>>part of heart
>>part of thoracic cavity
>>contains myocardial cells
>>contains endocardial cells
>>contains axons
>>contains neuromuscular junctions
>>contains endothelial cells
>>has properties of excitability
>>has properties of contractility
>>
>>
>>need to go to meeting, but see what you guys think...
>>
>>best,
>>Bruce
>>
>>
>>
>>
>>
>>Martin Ringwald wrote:
>>
>>>Chris,
>>>
>>>As to the tissue question, I basically agree with you. I am quite
>>>happy with the idea that OrganismPart covers everything except the
>>>cellular level. Organs have many substructures which one would not
>>>call a tissue. In other cases it will be difficult to decide if one
>>>should refer to that anatomical structure as a tissue or not. (It
>>>might be helpful to have tissue types that are assigned as attributes
>>>to tissues. We are currently looking into this option. However,
>>>attributes are a different issue altogether).
>>>
>>>Along the same lines, one could argue that cells are part of tissues
>>>and, therefore, should be represented in the same hierarchical
>>>system. We tried to do this with the mouse anatomy but realized that
>>>this is not practical. The hierarchies would become huge, there is a
>>>danger of missing hierarchical levels, and it would be very difficult
>>>to describe each level in a complete and consistent manner.
>>>Therefore, we decided to develop a separate cell type ontology. We
>>>plan to record what cell types can occur in what organs/tissues.
>>>
>>>Bruce raised important points in a previous email. You want to be
>>>able to break down the anatomy in different ways. Breakdown according
>>>to anatomic region or physiological system is a very good example. We
>>>try to achieve this by using a DAG structure for the anatomical
>>>vocabulary, i.e. by allowing multiple parents for a given anatomical
>>>structure. In this way we can represent in a normalized, i.e.
>>>non-redundant, fashion the fact that anatomical structures can be
>>>part of different physiological systems and body parts. However,
>>>building appropriate intersections between systemic and "geometric"
>>>hierarchies is tricky, in particular at more detailed levels. So, I
>>>am not yet sure if we will have to resort, at some point or in some
>>>instances, to combinatorial descriptions. For now, we try to
>>>represent everything in one DAG.
>>>
>>>There is a different set of geometric descriptors that are truly
>>>orthogonal and can be applied to many anatomical structures using
>>>combinatorial descriptions:
>>>
>>>Anterior (rostral)
>>>Posterior (caudal)
>>>Dorsal
>>>Ventral
>>>Lateral
>>>Medial
>>>Proximal
>>>Distal
>>>Central
>>>Peripheral
>>>
>>>We plan to implement this capability for the description of
>>>expression patterns in GXD.
>>>
>>>Hope this helps,
>>>
>>>Martin
>>>
>>>>
>>>>I'd like to hear more feedback from the group about tissue. If you
>>>>had a good ontology or hierarchical c.v. to refer to then by picking
>>>>the tissue of interest you've automatically established what organ
>>>>and body part you are in by virtue of the hierarchy. You also know
>>>>what cell types are present but not necessarily which one is of
>>>>interest. Thus it makes sense to have a CellType and a
>>>>TargetedCellType as this allows you to specify "lung" and
>>>>"fibroblast" as opposed to "skin" and "fibroblast." Some c.v.s
>>>>distinguish these too (with distinct IDs) but there is a move to
>>>>have orthogonal vocabularies for organ/tissue, cell type, and
>>>>developmental stage that can be combined. So we should certainly
>>>>have these 3. Does anyone know if there is a separate body part
>>>>orthogonal vocabulary planned as well that would allow distinctions
>>>>between geographical anatomical descriptions (e.g., "head") from
>>>>systemic description (e.g., "nervous system" - I would consider
>>>>organ/tissue to be included in this)? In summary, I say let's follow
>>>>what's going on with the GOBO or PATO plans - one class for each
>>>>orthogonal vocabulary.
>>>>
>>>>Cheers,
>>>>Chris

------------------------------

Date: Thu, 6 Jun 2002 12:32:03 -0400
From: Chris Stoeckert <stoeckrt@SNOWBALL.pcbi.upenn.edu>
Subject: [microarray-ontol] news

Two announcements.
1. The next Ontology Working Group meeting will be held as part of ISMB 
2002 in Salon 19 at the Shaw Conference Centre on August 7 from 10 - 11 
a.m as part of the Birds of a Feather program. Hope to see you there.
2. John Matese has pasted together a picture of the class tree structure 
for the ontology that I have posted at 
http://www.cbil.upenn.edu/Ontology/biomaterial_1.4.jpg.

Cheers,
Chris

------------------------------

Date: Mon, 10 Jun 2002 15:02:53 +0100
From: Helen Parkinson <parkinson@ebi.ac.uk>
Subject: [microarray-ontol] Fifth Annual Bio-Ontologies Meeting @ ISMB

Fifth Annual Bio-Ontologies Meeting

A Semantic Web of Bioinformatics Resources

8 August 2002

We would like to invite you to the fifth Annual
Bio-Ontologies Meeting 
(Bio-Ontologies 2002), on August 8th in Edmonton,
Canada. This is immediately after the ISMB-02 August 3-7 in
Edmonton. 
registration is available via http://www.ismb02/org.

This is usually a lively meeting; so submit abstracts and
register as soon 
as possible. We usually have a large crowd (10% of ISMB
attendees in the 
last two years), so come along to hear the latest
developments in the 
exciting world of bio-ontologies.

The meeting details may be found via 
http://www.cs.man.ac.uk/~stevensr/meeting02/ and any queries
can be 
directed to robert.stevens@cs.man.ac.uk.

Topics that will be discussed at the meeting will include,
but not be 
limited to:

*      Presentation of ontologies for describing the content
of 
bioinformatics resources accessible on the Web;
*     Presentation of ontologies for describing
bioinformatics services 
available on the Web;
*     Exploitation of ontologically mark-up data and
services;
*     Applications that use bio-ontologies to support the
work of biologists;
*     Improving the collaboration between biologists
developing ontology 
content and computer scientists who can provide
      ontology infra-structure;
*     Ontologies produced by members from various genomics
and life-science 
efforts.

Please submit two page abstracts (approximately 1000 words)
to 
robert.stevens@cs.man.ac.uk by the end of June 2002. These
abstracts will be
reviewed by a small programme committee. There will be three
kinds of talk 
at the day-long meeting:

    1.A key-note address ;
    2.A selection of 25 minute long-talks;
    3.A selection of 10 minute short-talks.
Dr. Robert Stevens
Bioinformatics lecturer
Department of Computer Science
Kilburn building
University of Manchester
Oxford Road
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Date: Wed, 3 Jul 2002 11:05:28 -0400
From: Chris Stoeckert <stoeckrt@SNOWBALL.pcbi.upenn.edu>
Subject: [microarray-ontol] new classes

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Hi All,
I'm finally getting around to adding some more resources that Susanna 
has sent and relevant ones from the GOBO site 
(http://www.geneontology.org/doc/gobo.html).

I propose that we create a new class under BioSourceOntologyEntry for 
histology (see http://histology.nih.gov/ for human, mouse, rat). Rather 
than call it histology we might generalize it a bit more to include 
other types of atlases. In fact we couyld call it "Atlas" Definition: 
Annotated images of organisms and their parts.

I also propose that we create a new subclass to 
IndividualGeneticCharacteristics for traits and phenotypes (see 
http://www.gramene.org/plant_ontology/trait.ontology). Let's call it 
"PhysicalCharacteristics" after GOBO but restrict it to phenotype and 
traits and not include pathology and disease.

- --Apple-Mail-4-156888441
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	charset=US-ASCII

Hi All,

I'm finally getting around to adding some more resources that Susanna
has sent and relevant ones from the GOBO site
(http://www.geneontology.org/doc/gobo.html). 


I propose that we create a new class under BioSourceOntologyEntry for
histology (see
<underline><color><param>1A1A,1A1A,FFFF</param>http://histology.nih.gov/</color></underline>
for human, mouse, rat). Rather than call it histology we might
generalize it a bit more to include other types of atlases. In fact we
couyld call it "Atlas" Definition: Annotated images of organisms and
their parts.


I also propose that we create a new subclass to
IndividualGeneticCharacteristics for traits and phenotypes (see
http://www.gramene.org/plant_ontology/trait.ontology). Let's call it
"PhysicalCharacteristics" after GOBO but restrict it to phenotype and
traits and not include pathology and disease.
- --Apple-Mail-4-156888441--

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End of microarray-ontol-digest V1 #26
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