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Re: HCLSig July 6 Teleconference Agenda

From: William Bug <William.Bug@DrexelMed.edu>
Date: Thu, 6 Jul 2006 06:16:15 -0400
Message-Id: <487D7B66-8420-4DF9-BCB6-77E78A5BE49E@DrexelMed.edu>
Cc: public-semweb-lifesci@w3.org
To: "AJ Chen" <canovaj@gmail.com>
This sound like excellent, focused objectives, AJ.

We've focused a lot on these issues on both the BIRN Ontology Task  
Force, as well as the working groups associated with developing a  
BIRN-wide XML Schema for data representation (XCEDE) and the work  
done to register all local site databases with the BIRN Mediator.

Based on that work, I'd like to follow Eric N's penchant for  
"strawmen" and propose the following amendments to the Proposed  
Classes to give focus to the discussion:

Project
	Study
		Hypothesis
		Objective
		Study_design
			Correlative_study
			Descriptive_study
			Experiment_study
			Cardinal_part_of_design
				Cardinal_part_of_protocol
					Cardinal_part_of_value
						Cardinal_part_of_qualitative_value
							intensity
							quality
						Cardinal_part_of_quantitative_value
							Confidence_level
							Numerical_value
							Unit
						Dimension
					Datum
						Measured_value
						Reported_value
						Set_parameter_value
					Order
					Parameter
						Stimulus_paramter_value
		Study_population
			Subject_group (N >= 1)
				Experimental_group
				Normal_control_group
				Sham_control_group
		Study_Executor_Group
			Study_Executor (each with an institutional affiliation - e.g.,   
Institution or  Institution/Dept. or Institution/Dept./Lab)
				Co_investigator
				Collaborator
				Data_analyzer
				Experimenter
				Instrument_operator
				Principle_investigator
				Project_leader
				Software_engineer
		Study_factor
			Dependent_factor
			Independent_factor
				Dose_effect
				Genetic_manipulation_effect
				Sex_effect
		Session
			Experiment
				Hypothesis
				Objective
				Protocol
					Analysis_protocol
					Specimen_preparation_protocol
						Fixation_protocol
							Consumables
								Reagent
									Fixative
						Contrast_enhancement_protocol
							Consumables
								Reagent
									Contrast_agent
										Molecular_probe
										Histological_indicator
						Isoloation_protocol
							Tissue_disection_protocol
							Cell_isoloation_protocol
							Molecular_isolation_protocol
					Assay_protocol (e.g., 'imaging_assay_protocol',  
'biochemical_assay_protocol', etc.)
						Instrument
							Instrument_fixed_property
							Instrument_variable_property
								variable_property_setting
							Cardinal_part_of_instrument
								part_fixed_property
								part_variable_property
									variable_property_setting
						Consumables
							Reagent
								Molecular_probe
									Dna_specific_probe
									Rna_specific_probe
									Protein_specific_probe
										Antibody
											Monoclonal_antibody
											Polyclonal_antibody
										Toxin
											Phallodin
											TTX
											alpha-Conotoxin
								Growth_substrate
									Surface_later_substrate
										Polylysine
									Matrix_substrate
							Container
								Tube_container
									Centrifuge_tube
									Test_tube
								Culture_container
									Culture_dish
										Multiwell_culture_dish
									Culture_bottle
								Transfer_container
									pipette
										micro_pipette_tube
										micro_pipette_tip
						Environmental_condition
							Temperature
							Pressure
							Temporal_value
								Time_point
									Calendar_date
									Time
								Duration
							Medical_history (I know this is a HUGE category.  Consider  
this just a placeholder)
				Study_entity
					Study_organism
						tissue
							cell
								molecule
				Study_sample
					Body_substance
					Cardinal_part_of_body
						Whole_organ
							Cardinal_part_of_organ
								Whole_cell
									Cardinal_part_of_cell
					Part_of_study_sample
						Dissected_study_sample
							Gross_dissected_study_sample
							Microdissected_study_sample
								Laser_captured_study_sample
						Section_of_study_sample
							Tissue_section
						Isolated_study_sample_molecule
							LC_isolated
							HPLC_isolated
							Gel_isolated
							Dialysis_isolated
				Study_measurement
		Study_report
			Data_manipulation
				Data_normalization
				Data_binning
				Data_reduction
				Data_analysis
			Conclusion



NOTES:
	1) The hierarchy mixes mereological ("parthood") relations with  
class relations - e.g., 'Gene_specific_probe', 'Study_executor',  
'Subject_group', 'Isoloated_study_sample_molecule',  
'Microdissected_study_sample', etc..  This admittedly messy  
representation provides a better sense of how the pieces fit together  
than a pure 'is_a' graph.
		* this hierarchy is not meant to be a formal specification but  
rather just a means for thinking about these related objects.  This  
is especially true given the formal type of mereological relations  
represented here differ across the hierarchy.  For instance, a  
'Calendar_date' is a 'part_of' a 'Time_point' in a way that  
fundamentally differs from the way a 'Data_analyzer' is a 'part_of' a  
'Study'
		* Since this is not a pure CLASS view of the entities, there is  
some redundancy.  For instance, both a 'Study' and it's constituent  
'Experiments' may have non-identical 'Objectives' and 'Hypotheses'.   
Having said that, there must be a way (e.g., via DL) to link an  
experiment's hypotheses to those of the overall study.  If not, there  
would be no way to use the results from the collection of   
experiments to provide a means of addressing the overall study  
hypothesis.

	2) Alan and others working on FuGO should correct me if I'm wrong  
here, but many - if not eventually ALL - entities from 'Project' on  
down will likely be in FuGO.  Right now, FuGO's scope is fixed on  
describing investigational continuants and occurrents associated with  
gene/protein expression studies.  Even so, nearly all of the entities  
represented here are needed to formally specify the details of  
various types of gene/protein expression studies.  With that in mind,  
it should be said the 'Instrument' category here is very much a  
cipher of what you will find in FuGO.

	3) The terms listed here are culled from the lexicon we are  
compiling in BIRN used to describe all the various types of  
experiments performed by BIRN associated labs.  Most that appear here  
have in fact been derived from FuGO, but also some from UMLS, some  
from FMA, some from PaTO, and some we've assembled ourselves on the  
BIRN Ontology Task Force.  Since this is just a 'strawman' where we'd  
probably like to stick to high-level universals (as AJ started with),  
if left out a lot of details we do cover in BIRNLex.  As the majority  
of studies being collated in BIRN have an imaging component, we have  
a lot - and expect to do a lot more - formally specifying imaging  
devices - EM, LM, and MRI of various sorts.  We also have to deal  
with neurological, behavioral, and cognitive assessment assays.  None  
of this is included here for clarity sake.
	
	4) Granularity coverage is somewhat ad hoc (again, this is just a  
'strawman').

	5) This 'view' of scientific study landscape is very much influenced  
by the formalism being put forth via the OBO group to:
			a) use PaTO to formally describe all observations about the  
biological entities being studied as phenotypic attributes;
			b) use FuGO for formal specification of details regarding  
experimental provenance of the observations being made - details  
specifically about assays, instruments, and reagents;
			c) use other ontologies to specify anatomical entities (FMA - or  
in the case of BIRN, NeuroFMA), molecular entities (Sequence  
Ontology, RNA Ontology, GO, ChEBI), cellular & subcelluar entities  
(GO & Cell Type Ontology), etc.
		Note that all of this information - the more formally abstract  
ontological info - as well as the knowledge maps built linking  
instance data into the ontologies - can be represented via RDF/OWL -  
with the current limit of not being able to deal well with linking  
entities through time (my understanding is this is being addressed  
via W3C standards efforts).

	6) Though this view is more grounded in the physical world than much  
of what is presented in SWAN, I see it as complimentary, and would  
hope to see both approaches to formally describing self-published  
scientific observations to work quite synergistically together.

Cheers,
Bill




On Jul 6, 2006, at 3:44 AM, AJ Chen wrote:

> To prime for tomorrow's HCLS conference call, I'd like to briefly  
> list the objectives, use cases and requirements for the scientific  
> publishing task. Hope there will be a real debate on them.
>
> Objectives:
>
> 1. To develop a general-purpose ontology for self-publishing single  
> experiment in RDF format
>
> 2. Current focus: data sharing and discovery on the web by all  
> researchers
> Main use cases:
>
> 1. Any researcher can publish experiment data as single unit of  
> experiment in RDF.
>
> 2. New web publishing tools can be developed to support the ontology.
>
> 3. New search engines can be developed to aggregate all of the  
> published experiment information.
>
> 4. Anyone can use the new search engines to find all experiments  
> available on the web.
>
> Requirements:
>
> 1. General terms to be used in all research areas (not just bio and  
> med)
>
> 2. Proposed classes:
>
>             experiment
>
>             project
>
>             protocol
>
>             product
>
>             researcher
>
>             group
>
>             organization
>
> -AJ
>
>
> On 7/5/06, Eric Neumann <eneumann@teranode.com> wrote:
>
> Planned July 6 HCLSig Teleconference Agenda:
> Time: 11:00 am EDT July 6, 2006 in America/New York for a duration  
> of 1
> hour
> Phone: tel:+1-617-761-6200 (Zakim) conference #4257 (HCLS)
> irc://irc.w3.org:6665/hcls
> Chairs: Eric Neumann, Tonya Hongsermeier
>
> Agenda:
> a) Convene, take roll, review record
> b) Propose next HCLS call July, 20, 2006, nominate a scribe
> c) Introductions - New participants since last call
> d) Discussion on Scientific Publishing of Experiments - AJ Chen
>  	- see:  http://esw.w3.org/topic/HCLS/ScientificPublishingTaskForce
> e ) BioRDF Update
> 	- Next steps for life science URI's
> 	- see Sean Martin's post:  http://lists.w3.org/Archives/Public/ 
> public-semweb-lifesci/2006Jun/0210.html
>  	- also on wiki discussion:  http://esw.w3.org/topic/ 
> HCLSIG_BioRDF_Subgroup/LSID_URN_URI
> f) F2F planning: Target date: Oct 3, 2006
> g) ISWC HCLS Workshop: Task Force contributions
>
>
> Eric Neumann, Tonya Hongsermeier, co-chairs, W3C Healthcare and Life
> Sciences
>

Bill Bug
Senior Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu







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Received on Thursday, 6 July 2006 10:24:45 GMT

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