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