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MGED Ontology Working Group Document Archive


Summary from the OWG meeting held during ISMB02 in Edmonton, CA.(Courtesy of Helen Parkinson)

	MGED ontology working group meeting, ISMB Edmonton.
	--------------------------------------------------
	
	Present:
	Cary Miller from Larry Hunter's Group, Colorado
	Jun Ulat from Richard Bruskiewich's group, IRRI
	Jens Eberlein from Larry Hunters group creating a knowledge base for signal transduction pathways
	David OutteridgeB  University of Colorado, 
	Steffen Schulze-Kremer, RZPD
	Win Hide, SANBI
	Janet Kelso, SANBI
	Ron Taylor University Colorado.
	Johan, SANBI
	Francis Ouellette, UBC
	Joanne Luciano, Harvard 
	
	All present agreed to sign up for the email list, Chris to take care of this and send out the URL for the web pages. Note not via www.mged.org as the domain name has expired. Though is being fixed.
	
	Chris:
	Introduced MAGE, MIAME, MGED and outlined the evolution of the ontology and motivation for it's development.
	Briefly: Concepts from MIAME structure from MAGE.
	A general framework for Microarray experiments and a place to find resources refor organism specific terms. These can all be found on the website with a brief description. People are free to add resources to this list via the mged list, either their own or other's resources.
	
	Question was asked about how MGED ontology relates to the gene ontology. Chris explained that GO attenpts to describe gene products, MGED ontology attempts to describe initially Biomaterial, the starting sample for a microarray experiment, and recently experimental framework. Both of these areas are applicable outside the area of microarrays, though this was not the primary motivation. Also the MGED ontology points out at external ontology resources, where they exist.
	
	
	Question from Jens: Do we provide inter-ontology mapping?
	Chris: not trying to impose a set of terms or do a mapping.
	Helen: not species specific and not prescritive about one ontology vs another.
	Chris: Very few cases where there are directly competing ontologies.
	Helen: where these are used in the context of the database, then we ask for a source and or a defintion if an existing ontology is not used.
	
	David Outteridge: How is the ontology accessed and implemented. How does he go about adding a term? Is this controlled? Is there an interface that demands the justification of terms. What are the ways we plan to encourage use of these terms. Possible to have 20 terms for the same thing.
	
	Chris:
	Most cases not many places that can actually get terms, and these can be added into interfaces, eg MIAMExpress and this will make annotation esier.
	
	We do have a sourceforge resource, but there have been a limited number of people actually working on the ontology and the mailimg list exists as a discussion forum to develop the ontology and form subclasses and add instances. New versions of the ontology are posted on the website. Major changes are advertised through the lists (not the addition of instances, usually changes that affect class relationships).
	
	Chris: Where we fit in with GO and GOBO.
	MGED ontology describes an expt framework, applicable in general, sample construction etc. This is our contribution to the ontology effort, we use external ontologies to describe biomaterials. We plan to talk to other ontology developers at the SOFG meeting in Hinxton in November to see how we can develop this further.
	
	Steffen: Who is adding terms? Where is it available?
	Helen and Chris at present are the most active, others interact via the list.
	
	Chris is vis as an html page, also DAML, rdfs from MGED ontology pages and CVS @ sourceforge. If we get more users we will make greater us of sourceforge (sensu GO) but at present has not been needed.
	
	Steffen: what about MIAMExpress?
	Helen: MIAMExpress (from the EBI) due for a September release, is using the ontology terms where possible. There are also other tools to annotate expts that we hope will use the ontology eg BASE, MADAM, TIGR's microarray data manager.
	
	CHRIS: asked those present about their motivation for attending the working group and what sort of usage theyt envisaged.
	
	Ron: Database developer forB  microarray data for a neuroscience consortium. Their current entry screens are hard to integrate, interested in MIAMExpress and using as expt annotation system.
	
	Jens: Ontology builder for signal transduction pathways, interested in MGED as also uses concepts like disease.
	
	Ron: There is another ontologist George AcquaahMensah working in Colorado who is generating an ontology to describe pharmamco genomics in mouse model. Has the concepts exexpt systems. There is a plan to merge this and Jen's ontologies and have new ahardware for that
	
	Chris: U Penn working on microarray expts for human and mouse, have clinical studies.
	Helen: problems with ILSI, user education, lack of a single onbtology eg for toxicology.
	
	Janet: building an ontology for annotation for EST libraries. Describes anatomy,
	cell type, prep method, pathology, started 18 months ago, very few people publicly doing that at that time and now want to start integrating.
	
	Ron: Jens and Georges starting point was Peter Karp's EcoCyc ontology and Andre Razetsky's paper in Bioinformatics. These are geared towards signal transduction. Does MGED incorporate these? These describe a domain and describe molecular events. Things that assign proteins/events to.
	
	CHRIS: MGED focus is on descript expt and sample and not the way that molecules interact.
	
	Jens: do we have a hypothesis?
	Chris: we are working on initially sample descriptions, now moving to study design, brings all assays together in an experimental design. Not our remit to provide annotations for gene products and pathways, though some concepts are shared. Now extending the model to encompass all areas of microarray including, quantification, processing and analysis.
	
	Helen: MGED has dataprocessing working group and we will work with them on this part of the ontology.
	
	Jun, from IRII. Part of the plant community IRII, currently trying to integrateseveral IRII databases for areas of crop research. Data from molecular level to field studies, plant trials, unite molcular studies, desiging a LIMS system for microarray. Working with GRAMENE to define ontologies for plants. Getting microarray lab working, currently performing preliminary expts, target to be fully operational for next year. Get data in db and make it human readable. Taking a look at the MIAMExpress forms as a way to annotate their data.
	
	Helen: EBI is committed to a project- CAGE, compendium of A.thaliana gene expression, we are fundedB  to develop a plant specific interface so suggest that may wantto talk to us about that on development of plant specific interface.
	
	Joanne, from Biopathways SIG.
	Prev worked with Eric Neumann, on developing an ontology based around Huntingdons(?)
	Chris: does it reach out to external ontologies
	
	Joanne: Trying to incorporate data from Fred Hutch Cancer Centre, data includes clinical observations, using MESH terms. Also database integration of microarrays, different protocols etc and multi level expts. Project funding stopped so now has in interest, also in biopathways context.
	
	Steffen.
	Member of MGED, currently working on db structure, ways to MIAME compliant data and implement mage-ml inport/export. Plans: Enter ontology development after the db import export is achieved. Also working to annotate clones supplied by RZPD with GO terms. Also has a Phd student (Jacob), ontol integration for database. Has developed a tool that allows you to describe your db in terms of the existing ontology, then use to fan out query to other db based on the ontology. Possible to add to the ontology if insufficient to describe your ontology.
	Now a non profit.
	
	David Outteridge, general interest, user of an ontology, new, info seeking.
	Few questions: ontol construction details , screening what goes into it, concerns usability in general. Q. maturity of what is required, status of ontologies and how they fit together.
	
	Chris: Ontologies is a mature field esp. in business area, now being applied to biology. Application in biology is an active research area and is also needed both in terms of MGED and other high throughput technologies. In the course of this project want to learn, make it interesting for those developing, not a research project in itslef.. Within the framework that we have developed with the tools we are using, can have constraints in the form of axioms, possibility to develop.
	
	Cary Miller Colorado, analysis of microarays, use of ontologies to describe arays.
	
	Conclusions:
	Chris: Thanks for coming, please get involved, more details at the Bioontologies day. 

Documents resulting from the first meeting and subsequent email postings

Summary of task and goals (M. Bittner)
	Ontologies for sample source and treatment
	description.
	
	Ontologies should be used for sample source and
	treatment description (e.g., organism, development
	stage, tissue, cell line type, cell line, treatment
	type) where possible. In particular, we use
	collections of categories, each of which have their
	own controlled vocabularies, where the categories are
	themselves organised, e.g., as a tree.
	
	  1. Universally accepted ontologies or standard
	vocabularies currently do not exist, except for
	description of species (Taxonomy database).
	Ontologies for developmental stages and tissues
	are relatively well described for some organisms,
	mouse and fruit fly in particular.
	  2. A working group was established to consider where
	introduction of an ontology is possible, and ways
	achieving this. It is not feasible for the
	working group to develop the final ontology for
	any new category of sample description, but
	rather to
	   * identify categories which should be included
		 in sample source and treatment description;
	   * identify and review relevant ontologies
		 developed by independent groups;
	   * identify the subset of required categories
		 that can be covered by incorporating and
		 adapting available ontologies, and identify
		 provisional means of handling remaining
		 categories;
	   * document issues pertinent to use of other
		 ontologies, and issues and possible
		 approaches for fuller treatment of
		 provisionally handled categories. The
		 identification of high level categories and
		 nodes where controlled vocabularies are
		 possible will be considered for these latter
		 categories.
	  3. Recommendations from this working-group will
	reflect on the minimum information definition and
	on data exchange standard.
	

Documents resulting from the second meeting

Ontology working group's Biological Sample description.
  • Diagram
  • Concepts:
    	SAMPLE
    	Species (strain/cultivar, name..identifier..label)
    	Genotype  (mutants, transgenics, sex, ploidy, transfected-stable, transient transfection, epigenetic, heterogeneity
    	Developmental Stage  (embryological, age, morphology, synchronized for cell cycle....)
    	Environment (culturing conditions, nutrients, temperature, passage number, media, density, contamination/purity, co-culture, host)
    	Anatomy (tissue/organ, cellular composition-homogeneity
    	Pathology (clinical history, pathological staging
    	History (treated for mycoplasma, family history, dead or alive, time of day at sampling
    	Treatment (chemical, physical, behavioral, time after treatment
    	Behavior (growth rate, neurological
    	Phenotype (
    	Description (race, size...
    	Source (donor, provider, owner, where it came from -geographic location,
    		(commercial/other) source, availability, catalog #,
    	In vivo/in vitro
    	Infection
    	Quality (purity, 
    	Physio-chemical composition of the sample
    	Amount  (# of cells
    	Cell lines from multi-cellular organism
    	
    	
    	ALTERNATIVE TREES
    	SAMPLE INTO BIOLOGICAL/NON-BIOLOGICAL
    	BIOLOGICAL INTO WHOLE ORGANISM/PARTS/ PRIMARY CELLS/CELL LINES
    	
  • Structured Concepts (OWG plus additional structuring by M.Bittner, W. Liebermeister, C.Stoeckert):
    	BIOLOGICAL SOURCE: SAMPLE
    	
    		 PROVIDER (adminstrative provider, commercial/other source, availability, catalog #)
    	
    		 TAXONOMY
    	
    			  STRAIN/CULTIVAR (properties of a collection of individuals, group identifier)
    	 
    				   GENOTYPE
    						mutants, transgenics, sex, ploidy, transfected-stable, 
    						transient transfection, epigenetic, heterogeneity
    	
    				   INDIVIDUAL		
    					Name, identifier/clinical tag, label
    					
    						ANATOMY
    	
    							 TISSUE/ORGAN (cellular composition-homogeneity)
    	
    								  CELL 
    									   purified from primary tissue
    	
    								  CELL LINE
    	
    						DEVELOPMENTAL STAGE
    							 embryological, age, morphology, synchronized for cell cycle...
    	 
    		 PHENOTYPE 
    	
    			  BEHAVIOR
    	
    			  PATHOLOGY
    			   clinical history 
    				   pathological staging
    	
    		 HISTORY/DEFINED PROPERTIES
    			  culturing conditions/media nutrients, temperature, co-culture, 
    			  host, passage number, treated for mycoplasma, density, 
    			  contamination/purity, infection, family history, 
    			  time of day at sampling, pre or post mortem at sampling, 
    			  Physio-chemical composition of the sample, amount of material, # of cells
    	
    			  ENVIRONMENT 
    				   where it came from -geographic location
    				   in vivo
    				   in vitro
    				   in situ (xenografts)
    	
    			  TREATMENT
    				   agents (drugs, chemicals, biochemicals, physical) 
    				   time after treatment 
    				   behavioral stimulus 
    	

Last updated Aug 26, 2002

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