NCOR Wiki - User contributions [en]

Clinical Terminology Shock and Awe

2016-04-07T18:36:09Z

Alan Ruttenberg: /* Participants */

Fifth Annual Workshop of the Clinical and Translational Science Ontology Group

'''Date''': September 7-8, 2016

'''Venue''': Ramada Hotel, Amherst, NY

'''Rationale''': The CTSA Program has always emphasized the need for data standards to promote sharing and comparison of data across the CTSA Consortium and beyond. Yet creation and adoption of such standards is still painfully slow. Urgent action remains necessary. History shows the high value of standard terms, definitions, and symbols (i.e. ontology) to science. But the creation and adoption of such standards often takes decades. Translational science requires a consistent set of standard ontologies spanning all scales, from molecule to organism to population. But clinical terminologies at the macroscale – such as SNOMED and ICD – inhibit translational science. They are inconsistent with successful micro-scale ontologies such as the Gene Ontology, and they also cannot change rapidly with the advance of science. Translational science must settle on standards that evolve in a way that is closely tied to scientific advance. In the case of chemical symbols and SI Units adoption proceeded in three overlapping stages. First came widespread recognition and understanding of the problem. Second, influential stakeholders helped to develop, test, and select appropriate standards. Third, once scientifically useful standards emerged, the community enforced them via peer review. How can we accelerate progress on clinical ontologies through all three stages? How, in other words, can we create and implement standard clinical ontologies that are open and sufficiently well disseminated to achieve consortium-wide adoption?

This workshop will convene stakeholders interested in identifying ways to harmonize clinical terminology resources with their counterparts at the molecular level. A consistent framework for ontologies that enable interoperability of systems, compatibility of data, and research reproducibility is the vision. Furthermore, we will address additional issues with clinical terminologies as they currently exist, specifically the problem that even professional coding with them has poor inter-coder reliability. This situation degrades the quality of terminology-encoded data below acceptable research standards. Lastly, we believe confusing and incoherent terminologies are a barrier to end-user usability of resources like EHRs and the data they produce.

'''Goals''': The [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group Clinical and Translational Science Ontology Group] was established in 2012 to leverage the use of common ontologies to support different aspects of information-driven clinical and translational research. The focus of this meeting is to explore new and existing uses of common ontologies to support creation, sharing, and analysis of clinical data.

Like its predecessors in the [http://ncorwiki.buffalo.edu/index.php/Clinical_and_Translational_Science_Ontology_Group#Annual_Workshops series], this meeting is designed to bring together clinical and translational scientists from across the CTSA Consortium who are interested in using ontologies to promote discoverability and interoperability of biomedical data.

Specific themes will include:

*Advancing reproducibility of clinical and translational research (BFO, OBI, LOINC)

*Advancing EHR interoperability (addressing SNOMED / CCD and meaningful use regulations whereby SNOMED CT is required for recording problem list and smoking status, and CCD is required for care summary)

*Improving EHR data usability

*Improving SNOMED / CCD / c-CDA usability

*Advancing interoperability of clinical data generally and of EHR data in particular

*Improving EHR usability in the clinic

*i2b2, PCORnet, OMOP and other approaches to clinical data sharing

Persons interested in attending or in presenting at the meeting should write to [mailto:phismith@buffalo.edu Barry Smith].

== Schedule ==

Wednesday, September 7

8:00am Registration and Breakfast

6:00pm Dinner

Thursday, September 8

8:00am Registration and Breakfast

4:00pm Close

== Sponsors ==

Department of Biomedical Informatics, University at Buffalo

National Center for Ontological Research, Buffalo

==Organizing Committee==

Barry Smith (University at Buffalo)

William Hogan (University of Florida)

== Participants ==

Jonathan Bona (Buffalo)

Mathias Brochhausen (Arkansas)

Werner Ceusters (Buffalo)

Alexander Diehl (Buffalo)

Willian Duncan (Buffalo)

Peter Elkin (Buffalo)

Fernanda Farinelli (Minas Gerais, Brazil)

Yongqun "Oliver" He (Ann Arbor)

William Hogan (Gainesville)

Mark Jensen (United Nations Environment Programme)

Edison Ong (Ann Arbor)

Rasmus Rosenberg Larsen (Buffalo)

Øystein Nytro (Trondheim, Norway)

Jihad Obeid (Charleston)

Jose Parente de Oliveira (ITA, Brazil)

Alan Ruttenberg (Buffalo)

Stefan Schulz (Graz, Austria)

Barry Smith (Buffalo)

Dagobert Soergel (Buffalo)

OBI ontology

2014-10-11T10:25:54Z

Alan Ruttenberg: Created page with 'OBI is the Ontology for Biomedical Investigations <h1>The OBI WIKI is down for the moment due to hardware issues with the host. For now see [http://web.archive.org/web/201403...'

OBI is the Ontology for Biomedical Investigations

<h1>The OBI WIKI is down for the moment due to hardware issues with the host. For now see [http://web.archive.org/web/20140304094644/http://obi-ontology.org/page/Main_Page a recent version] at the Internet Archive</h1>

We apologize for the inconvenience

Ontology and Imaging Informatics

2014-05-28T14:05:47Z

Alan Ruttenberg: /* Schedule: Workshop */

'''Third Clinical and Translational Science Ontology Workshop'''

*Tutorial: June 23, 2014
*Workshop: June 24-25, 2014

*Venue: [http://www.ramadahotelamherst.com/ Ramada Inn Hotel and Conference Center, Amherst, NY 14068]. For logistics details, including access to special hotel room rate, please contact [mailto:sgsmith2@buffalo.edu Sandra Smith].

_______________________________________________________________________________________________________________

'''THIS MEETING IS NOW CLOSED TO FURTHER PARTICIPANTS'''

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

==Goals==

The goal of this meeting is to advance discoverability, interoperability and combinability of biomedical imaging data. It consists of a tutorial providing an introduction to imaging ontology, followed by two days of presentation and discussion of major contributions to biomedical imaging in radiology and digital pathology.

- Day 0 of the workshop will consist in a tutorial providing an introduction to biomedical imaging ontology.

- Day 1 of the workshop will consist in an overview of major contributions to biomedical imaging in radiology and digital pathology with a view towards coordination and exchange of ideas.

- Day 2 will focus on the creation and review of a draft Biomedical Image Ontology and explore how ontology can contribute to the coordination of research across the CTSA consortium with a special reference to digital histopathology imaging.

== '''Schedule: Tutorial''' ==

Monday, June 23

'''Tutorial'''

10:00 Registration

10:30 [http://www.ccmb.med.umich.edu/node/192 Ulysses Balis] (Michigan): Introduction to Imaging Informatics: The Problem of Image Data Interoperability

12:30 Lunch

13:30 [http://ontology.buffalo.edu/smith Barry Smith] (Buffalo): Introduction to Ontology for Imaging Informatics

15:00 Break

15:30 [http://dbmi.uams.edu/faculty/william-r-hogan-m-d/ William Hogan] (Arkansas): Ontology in the CTSA Consortium

== '''Schedule: Workshop''' ==

Tuesday, June 24

 Morning 

:8:30 Breakfast and Registration

:9:00 Participant Introductions

:9:15 Keynote Address: [http://www.stanford.edu/~rubin/ '''Daniel Rubin]: Imaging Big Data'''
::Driving use cases for imaging in the era of Big Data
::The central role of imaging ontology
::Example projects using ontologies
::[[Abstract]]

:10:15 Break

:10:30 '''[http://www.dbmi.pitt.edu/person/michael-j-becich-md-phd Michael J. Becich]: An Overview of Standards and Initiatives in Digital Pathology'''

:11:15 '''[http://www.mcw.edu/radiology/faculty/CharlesKahn.htm Charles Kahn]: Radiology Gamuts Ontology: Differential Diagnosis in Radiology'''

:12:00 Lunch

 Afternoon 

:13:00 '''[https://www.linkedin.com/pub/michael-calhoun/19/36a/567 Michael Calhoun] and [http://www.irp.nia.nih.gov/branches/irp/igoldberg.htm Ilya Goldberg]: Image Language Processing and Encoding'''

:13:40 '''[https://medicis.univ-rennes1.fr/members/bernard.gibaud/index Bernard Gibaud]: Ontology of Imaging Datasets as a Prerequisite for Ontologies of Imaging Biomarkers'''

:14:20 :'''[http://knocean.com/ James Overton] and Heiner Overkampf: Expressing Medical Image Measurements using the Ontology for Biomedical Investigations'''

:15:00 Break

:15:20 '''[http://www.becklab.org Andrew H. Beck]: Imaging Informatics and Ontologies for the Development and Dissemination of Integrative Cancer Diagnostics'''

:16:00 '''[http://www.hcklab.org/ Paolo Ciccarese]: Interoperable Biomedical Image Annotations. Describing and Linking Biomedical Images through Open Annotation and Domain Ontologies'''

:16:40 '''[https://www.linkedin.com/pub/anna-maria-masci/11/a74/a55 Anna Maria Masci]: Immunological Images and the ImmPort Database and Analysis Portal'''

:17:20 '''[http://medicine.buffalo.edu/faculty/profile.html?ubit=addiehl Alexander Diehl]: The NIF / ImmPort Antibody Registries: Benefits of Consistent Naming'''

:18:00 '''Reception and Dinner''' sponsored by the University at Buffalo [http://wings.buffalo.edu/smbs/biomedicalinformatics/ Department of Biomedical Informatics]

Wednesday, June 25

 Morning 

:8:30 Breakfast

:9:00 Practical sessions devoted to creating a strategy to promote comparability and queryability of biomedical image data in general and digital pathology imaging data in particular

Sessions will include:

:'''[https://www.linkedin.com/in/alanruttenberg Alan Ruttenberg]: Queryathon''' This session is targeted to participants with imaging data. The goal is to develop a set of competency questions to help assess progress on a imaging ontology. If we don't document the purpose for which we are building an ontology then we won't be able to assess whether what we've built is fit for purpose. The competency questions we will be looking for will be questions participants want to be able to ask of their data for which they think the data suffice to answer the questions but which can't be effectively asked with current approaches to image representation.

:'''[http://ontology.buffalo.edu/smith Barry Smith]: An Ontology Framework for Biomedical Imaging'''

:'''[http://medicine.osu.edu/bmi/people/metin_gurcan/pages/index.aspx Metin N. Gurcan], [http://engineering.case.edu/centers/ccipd/ Anant Madabhushi] and [http://medicine.buffalo.edu/faculty/profile.html?ubit=johntoma John Tomaszewski]: Histopathological Image Analysis (HIMA) and Ontology'''

:10:30-10:45 Break

:'''[https://www.linkedin.com/profile/view?id=106844090&authType=NAME_SEARCH&authToken=byF1&locale=en_US&srchid=27153661400790133689&srchindex=1&srchtotal=387&trk=vsrp_people_res_name&trkInfo=VSRPsearchId%3A27153661400790133689%2CVSRPtargetId%3A106844090%2CVSRPcmpt%3Aprimary William Hogan]: Biobanking and Digital Pathology: How to Make Ontologies that Work Together'''

:'''[http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters]: Referent Tracking: How to Use Ontologies to Deal with Instance Data'''

:12:00 Lunch

 Afternoon 

:13:00 Hackathon: Building an Ontology for Digital Pathology'''

16:00 Close

== Sponsors ==

*[http://wings.buffalo.edu/smbs/biomedicalinformatics/ Department of Biomedical Informatics], University at Buffalo

*[http://www.smbs.buffalo.edu/path/index.htm Department of Pathology and Anatomy], School of Medicine and Biomedical Sciences, University at Buffalo

*[https://www.ctsacentral.org/committee/ikfc-clinical-and-translational-science-affinity-group-ctso-ag Clinical and Translational Science Ontology Affinity Group].

*[http://bioontologies.org National Center for Biomedical Ontology (NCBO)]
:This meeting forms part of a series of [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki ontology workshops] sponsored by the NCBO. A [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images precursor event] in this series, devoted to the ontology of images, was held in 2006.

== Background ==

::[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910932/ Histopathological Image Analysis]
::[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293096/ Cell Image Ontologies]; see also [http://sbd.nist.gov/image/cell_image.html here].
::[http://www.ncbi.nlm.nih.gov/pubmed/23589184 Qualitative Imaging Biomarker Ontology]
::[http://www.openmicroscopy.org/ The Open Microscopy Environment] (OME)
::[[Gamuts | The Radiology Gamuts Ontology]]
::[http://www.aperio.com/healthcare/eslide Aperio ePathology]
::[http://obi-ontology.org/page/Main_Page Ontology for Biomedical Investigations] (OBI)

== Organizing Committee ==

:Barry Smith (Buffalo)
:William Hogan (Arkansas)
:John Tomaszewski (Buffalo)

== Participants ==

Travis Allen (Buffalo)

Sivaram Arabandi (Houston)

Ulysses J. Balis (Ann Arbor)

Carol Bean (NCBO / Stanford)

Michael Becich (Pittsburgh)

Andrew H. Beck (Harvard)

Tanja Bekhuis (Pittsburgh)

Mathias Brochhausen (Arkansas)

Wiam Bshara (Buffalo)

Michael Calhoun (Sinq Systems)

Alexander Cox (Buffalo)

Ilya Goldberg (Open Microscopy Initiative / NIH National Institute on Aging)

Werner Ceusters (Buffalo)

Paolo Ciccarese (Harvard)

Chris Crowner (Buffalo)

Alexander Diehl (Buffalo)

Michael Dwyer (Buffalo)

Peter Elkin (Buffalo)

Carmelo Gaudioso (Buffalo)

Nancy Gertrudiz (@CARES, Mexico City)

Bernard Gibaud ([http://www.ltsi.univ-rennes1.fr/?q=en/node/269 LTSI], Rennes)

Allan S. Goldberg (Touro University, California)

Metin Gurcan (Ohio)

William Hogan (Arkansas)

Mark Jensen (Buffalo)

Charles E. Kahn (Milwaukee)

Warren A. Kibbe (National Cancer Institute)

Venkat N. Krovi (Buffalo)

Anant Madabhushi (Case)

Tatiana Malyuta (CUNY)

Anna Maria Masci (Duke)

Kevin Mitchell (Pittsburgh)

Heiner Oberkampf (Siemens, Munich)

James A. Overton ([http://Knocean.com Knocean], Toronto)

Patrick Ray (Buffalo)

Michael Riben, MD (MD Anderson Cancer Center, Houston)

Daniel Rubin (Stanford)

Alan Ruttenberg (Buffalo)

András Sablauer (Memphis)

Ferdinand Schweser (Buffalo)

Barry Smith (Buffalo)

Jose Luis Tapia (Buffalo)

John Tomaszewski (Buffalo)

Eugene Tseytlin (Pittsburgh)

Amber Worral (Buffalo)

ImmPort Home

2013-09-12T06:39:41Z

Alan Ruttenberg:

A starting point for ImmPort related pages

== Background ==

* [https://immport.niaid.nih.gov ImmPort: Immunology Database and Analysis Portal]
* [http://medicine.buffalo.edu/news_and_events/news.host.html/content/shared/smbs/news/2013/04/immunology-ontologies-2446.detail.html Press release annoucing UB involvment]
* [http://projectreporter.nih.gov/project_info_description.cfm?aid=8557840&icde=17642037 NIH Reporter page: Bioinformatics Integration Support Contract (BISC) For Immune-Mediated Diseases]
* [[Immunology_Ontologies]]

== Meetings ==

* [[First ImmPort Ontology Group Web Conference]]
* [[4th Immport Ontology Group Web Conference]]
* [[ImmPort_Ontology_Conference]] Dates: September 4-5, 2013
* [[ImmPort|ImmPort: A Guide for Submitters]] Date: October 9-10, 2013

== Documents and Specifications ==

[[ClassificationByMarkerSpec|Draft protocol for classifying and recording cell type/populations from CYTOF experiments]]

== Ontologies ==

* [http://obofoundry.org/wiki/index.php/CL_ImmPort_Collaboration CL ImmPort Collaboration], [http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell Cell Ontology description page]]
* [https://www.dropbox.com/s/64c5kghuo5406jd/AntibodyRegistry.xlsx Antibody Registry]
* [http://pir.georgetown.edu/pro/ Protein Ontology]
* [http://obi-ontology.org/ Ontology for Biomedical Investigations]
* [http://code.google.com/p/reagent-ontology/ Reagent Ontology]
* [http://code.google.com/p/information-artifact-ontology Information Artifact Ontology] (draft spreadsheet)

ImmPort Home

2013-09-12T06:38:33Z

Alan Ruttenberg:

A starting point for ImmPort related pages

== Background ==

* [https://immport.niaid.nih.gov ImmPort: Immunology Database and Analysis Portal]
* [http://medicine.buffalo.edu/news_and_events/news.host.html/content/shared/smbs/news/2013/04/immunology-ontologies-2446.detail.html Press release annoucing UB involvment]
* [http://projectreporter.nih.gov/project_info_description.cfm?aid=8557840&icde=17642037 NIH Reporter page: Bioinformatics Integration Support Contract (BISC) For Immune-Mediated Diseases]

== Meetings ==

* [[First ImmPort Ontology Group Web Conference]]
* [[4th Immport Ontology Group Web Conference]]
* [[ImmPort_Ontology_Conference]] Dates: September 4-5, 2013
* [[ImmPort|ImmPort: A Guide for Submitters]] Date: October 9-10, 2013

== Documents and Specifications ==

[[ClassificationByMarkerSpec|Draft protocol for classifying and recording cell type/populations from CYTOF experiments]]

== Ontologies ==

* [http://obofoundry.org/wiki/index.php/CL_ImmPort_Collaboration CL ImmPort Collaboration], [http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell Cell Ontology description page]]
* [https://www.dropbox.com/s/64c5kghuo5406jd/AntibodyRegistry.xlsx Antibody Registry]
* [http://pir.georgetown.edu/pro/ Protein Ontology]
* [http://obi-ontology.org/ Ontology for Biomedical Investigations]
* [http://code.google.com/p/reagent-ontology/ Reagent Ontology]
* [http://code.google.com/p/information-artifact-ontology Information Artifact Ontology] (draft spreadsheet)
* [[Immunology_Ontologies]]

ImmPort Home

2013-09-12T06:30:45Z

Alan Ruttenberg:

A starting point for ImmPort related pages

== Meetings ==

* [[First ImmPort Ontology Group Web Conference]]
* [[4th Immport Ontology Group Web Conference]]
* [[ImmPort_Ontology_Conference]] Dates: September 4-5, 2013
* [[ImmPort|ImmPort: A Guide for Submitters]] Date: October 9-10, 2013

== Specifications ==

[[ClassificationByMarkerSpec|Draft protocol for classifying and recording cell type/populations from CYTOF experiments]]

== Ontologies ==

* [http://obofoundry.org/wiki/index.php/CL_ImmPort_Collaboration CL ImmPort Collaboration], [http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell Cell Ontology description page]]
* [https://www.dropbox.com/s/64c5kghuo5406jd/AntibodyRegistry.xlsx Antibody Registry]
* [http://pir.georgetown.edu/pro/ Protein Ontology]
* [http://obi-ontology.org/ Ontology for Biomedical Investigations]
* [http://code.google.com/p/reagent-ontology/ Reagent Ontology]
* [http://code.google.com/p/information-artifact-ontology Information Artifact Ontology] (draft spreadsheet)

ImmPort Home

2013-09-12T06:28:55Z

Alan Ruttenberg: Created page with 'A starting point for ImmPort related pages == Meetings == * First ImmPort Ontology Group Web Conference * 4th_Immport_Ontology_Group_Web_Conference * [[ImmPort_Ontology...'

A starting point for ImmPort related pages

== Meetings ==

* [[First ImmPort Ontology Group Web Conference]]
* [[4th_Immport_Ontology_Group_Web_Conference]]
* [[ImmPort_Ontology_Conference]] Dates: September 4-5, 2013
* [[ImmPort: A Guide for Submitters]] Date: October 9-10, 2013

== Specifications ==

[[ClassificationByMarkerSpec|Draft protocol for classifying and recording cell type/populations from CYTOF experiments]]

== Ontologies ==

* [http://obofoundry.org/wiki/index.php/CL_ImmPort_Collaboration CL ImmPort Collaboration], [http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell Cell Ontology description page]]
* [https://www.dropbox.com/s/64c5kghuo5406jd/AntibodyRegistry.xlsx Antibody Registry]
* [http://pir.georgetown.edu/pro/ Protein Ontology]
* [http://obi-ontology.org/ Ontology for Biomedical Investigations]
* [http://code.google.com/p/reagent-ontology/ Reagent Ontology]
* [http://code.google.com/p/information-artifact-ontology Information Artifact Ontology] (draft spreadsheet)

ClassificationByMarkerSpec

2013-09-12T06:18:11Z

Alan Ruttenberg: Created page with '== Goal == Write a protocol for recording of CYTOF experimental results and a method for determining cell type based on recorded markers. == Status == This is an early draft. ...'

== Goal ==

Write a protocol for recording of CYTOF experimental results and a method for determining cell type based on recorded markers.

== Status ==

This is an early draft. In particular since writing this I have come to the conclusion that we should be using more information in the determination of cell type, and that information necessary to do the determination should reside in both the Cell Ontology and the Ontology for Biomedical Investigations. See [http://ncor.buffalo.edu/2013/Immunology/Ruttenberg.pdf Motivation for ontological representation of cell type identiﬁcation assays for ﬂow cytometry and CyTOF] presented at the [[ImmPort_Ontology_Conference]]

== Draft ==
<nowiki>
Protocol for classifying and recording cell type/populations from CYTOF experiments
Alan Ruttenberg

Assumptions:
===========

1. Clustering/gating of CYTOF results will be done by the submitter. If
this assumption is incorrect we should describe the clustering in a
separate protocol (protocol-clustering)

2. Targeted proteins will be clearly identified. Where an antibody is
used as surrogate, and if the submitter wishes to use the antibody to
identify the protein, the antibody must be identified by an Immport
antibody registry identifier. If the antibody is not yet present in
the Immport antibody registry, it needs to be submitted and
curated according to (protocol-antibody)

3. Information specifying a protein target will generally be in most
cases unambiguous. However it may be determined to be ambiguous, for
example, in a case where we have a protein specified as CD8 (or an
antibody whose target is so specified), and whose specification is
thus ambiguous as to whether CD8a or CD8b is targeted, or in the case
that where protein has isoforms and the isoform is not specified. In
such cases the submitter should be queried as to whether this was
intended. The submitter can either fix the ambiguity, explain how we
should handle it in the analysis (e.g. perform analysis for each
possibility, ignore differences in isoforms), or remove the protein
target from the submission.

How to read this document
=========================

(type:xx) informally indicates a data type, which may be referred in
different parts of this protocol. The data types will be formalized in
subsequent revision.

For each data type, elements are enumerated by a common letter and ascending number
p1.
p2.
...
g1.
...

Inputs:
======

CYTOF results data for which cell type needs to be determined or
validated. Note that not all CYTOF experiments are of this nature - of
the experiments reported at http://www.cytobank.org/nolanlab/reports/,
for example, one characterized phases of the cell cycle using known
markers for cell types probed, one validated a surrogate CYTOF-based
marker for cell death. Such experiments are outside the scope of this
protocol.

Input data should consist of sets of proteins that were probed in the
experiment and which are grouped together as representative of a cell
type or state, analogous to gating information for flow cytometry
experiments.

--

type: cytof-experiment-protein-set

The first part of the input should be a complete listing of the
proteins used in the experiement

s1. Name or identifier of this protein set

--

type: cytof-experiment-protein-readout

For each of the proteins probed in the name set s1 the following
information should be provided:

p1. Name and/or identifiers of the target protein. Where more than one
identifier or more than one name is known to the investigator as a
common way to identify the protein, please include these.

p2. If a modified form of the protein is targeted (e.g. phosphorylated
at a specific site) then include a description of the targeted
form. If the protein is known not to be modified in certain ways, then
make this knowledge explicit (e.g. report 'not phosphorylated at
S235')

p3. If the readout is of an antibody to the protein, then the clone
name, manufacturer (if commercial) or other source (if not), and
catalog number (if manufacturer) or other identifier.

p4. If the readout is of some other marker, information that specifies
that marker.

p5. If the researcher expects that the marker may be ambiguous -
e.g. targets more than one isoform, or different gene products, please
include this information.

p6. A local synonym(handle) for the protein, for the purposes of easily
referring to it elsewhere during the protocol.

p7. In the case that a PRO identifier for the protein is known or has
been obtained through Immport resources, it can be substituted for p1
and p2.

p8. In the case that the antibody or marker has been registered and
curated into an Immport resource, it's Immport-chosen identifier can
be used in place of p1-p7. However, inclusion of redundant information
can serve as a quality check and so the submitter is encouraged to
include all fields if feasible.

--

type: cytof-cluster-protein-markers

Each set of proteins that are grouped together as representative of a
cell type or state, should have

g1. a name for the group

g2. The name of the complete set of proteins probed as named in s1

g3. Whether or not proteins in s1 but not listed as members of this cluster
should be considered as not having detectable levels ('assume-absent')
or whether only the listed proteins should be considered part of the
group ('assumed-complete').

--

type: cytof-cluster-protein-marker-level

The following information for each protein in a
cytof-cluster-protein-markers should be provided.

ml1. The chosen local synonym/handle for the protein (p6), or PRO identifer (p7)

ml2. Whether the targeted protein was present or the amount was below
detectable levels. ('present'/'+' or 'absent'/'-')

ml3. If the targeted protein is present and quantitated then the
quantity of the protein and associated unit (give unit name), unless
the measurement is relative to an arbitrary standard. (enter as
'experiment unit')

ml4. If available, a qualitative assessment of the level of the
protein, one of:

'high' (synonym: 'bright')
'low' (synonym: 'dim')

Question: Do we need "mid", as in "CD38mid"

If the submitter does not want to use qualitative level in the query, instead write
'ignore'

If the submitter wants the qualitative assesment computed write
'computed' (Question: do we want to allow this?)

Notes:

If protein levels are quantitated in ml3, and ml4 is 'compute', then we
need to design (protocol-assign-qualitative-marker-level)

If ml4 is 'ignore' then only 'absent'/'present' information will be used

--

Validation
==========

Ensure required combinations of fields are present in input

Ensure that any antibodies specified in place of proteins are
registered in Immport antibody registry

Ensure that if any cytof-cluster-protein-marker-level ml4 is
'computed', then all cytof-cluster-protein-marker-level ml3 must be
quantitated

Ensure that all cytof-cluster-protein-marker-level ml3 units are either
'experiement unit' or all are units that are convertible with one
another.

Ensure that for any cytof-protein-marker-level that where ml2 is
absent, ml3 and ml4 are empty

Question: Are there more validations (Alan guesses yes)

If any validation fails, return the submission to investigator with
report.

== TODO: Provide an example of valid input.==

Processing each protein target in cytof-experiment-protein-set
==============================================================

1. For proteins specified using an antibody in the Immport antibody
registry, retrieve the associated PRO ID.

2. For proteins that are not specified by a PRO ID, first
a. Attempt to look up the PRO entry given the information, or if that fails
b. Submit a term request for the protein to Alex Diehl for submission to the PRO team

3. If the the result of 2 is that the pro term is ambiguous, contact
the submitter for instructions on how to handle the ambiguity.

4. When all proteins have PRO IDs we can proceed to the processing of
the cytof-cluster-protein-markers

Processing of each cytof-cluster-protein-markers
================================================

type: cl-triple-store

Required: A triple store providing SPARQL query answering over the
fully reasoner CL.

sqa1: The SPARQL endpoint for the triple store

Assumes: All protein targets have PRO IDs

1. If any ml4 is 'compute' use protocol-assign-qualitative-marker-level to assign qualitative levels

2. Construct a class query based on all the cytof-cluster-protein-marker-level in the cytof-cluster-protein-markers. This query will be a conjunction of terms. Below we list the
forms the terms using OWL2 functional syntax (http://www.w3.org/TR/owl2-syntax/)

The relations we will use are:

<lacks_part> <http://purl.obolibrary.org/obo/cl#lacks_part>
<has_high_plasma_membrane_amount> <http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount>
<has_low_plasma_membrane_amount> <http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount>
<has_plasma_membrane_part> <http://purl.obolibrary.org/obo/RO_0002104>

(note: some of these relations have legacy URLs - check/fix)

If mp2 is 'absent' or '-'
then the clause is ObjectSomeValuesFrom(<lacks_part> <PRO_ID>)

If mp2 is 'present' or '+' and p4 is 'ignore'
then the clause is ObjectSomeValuesFrom(<has_plasma_membrane_part> <PRO_ID>)

If mp2 is 'present' and p4 is 'high' or 'bright'
then the clause is ObjectSomeValuesFrom(<has_high_plasma_membrane_amount> <PRO_ID>)

If mp2 is 'present' and p4 is 'low' or 'dim'
then the clause is ObjectSomeValuesFrom(<has_low_plasma_membrane_amount> <PRO_ID>)

If mp3 is 'assume-absent' then for each protein identified in
cytof-experiment-protein-set that is not identified in a
cytof-experiment-protein-readout (ap), add the clause

add the clause ObjectSomeValuesFrom(<lacks_part> <PRO_ID of ap>)

join the terms above using ObjectIntersectionOf

The class (ObjectIntersectionOf <cell> <E1>) defines a class of cells
(C1) with the markers as specified.

2. Using the expression for C1 above we will construct 2 SPARQL queries.

- A query Q1 for the most specific of the more general class types - this will yield the immediate superclasses of C1

- A query Q2 for the most general of the more specific class types - this will yield the immediate subclasses of C1

To construct Q1, Q2, first render the expression for C1 as RDF triples
<R>. This can be accomplished with a call to the OWLAPI, or equivalent
(see below, LSW2 code)

Retrieve the node that is the class defined by the expression. (S)

For the subclasses query, construct the sparql query

SELECT ?subclasses where { ?subclasses rdfs:subClassOf S . <R> }

For the superclasses query, construct the SPARQL query

SELECT ?superclasses where { S rdfs:subClassOf ?superclasses . <R> }

Here is an example of this transformation using LSW2.

(sparql-stringify ;; render a sparql query from sexp
`(:select
(?subclasses) ;; The variable for which we want solutions
()
,@(let ((p1 !<http://purl.obolibrary.org/obo/PR_P01730>) ;; CD4 human
(p2 !<http://purl.obolibrary.org/obo/PR_000025405>) ;; CD8a human
(has-high !<http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount>)
(cell !<http://purl.obolibrary.org/obo/CL_0000000>)) ;; Cell
(let ((translated
(butlast
(t-collect
`(ontology (object-intersection-of
,cell
(object-some-values-from ,has-high ,p1)
(object-some-values-from ,has-high ,p2)))))))
(let ((class-defined (first (first translated)))) ;; The blank node representing the defined class
`((?subclasses ,!rdfs:subClassOf ,class-defined) ;; The additional triple
,@translated)))))) ;; The rest of the RDF triples

PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?subclasses
WHERE {
?subclasses rdfs:subClassOf _:b2 .
_:b2 owl:intersectionOf _:b3 .
_:b3 rdf:rest _:b4 .
_:b4 rdf:rest _:b6 .
_:b6 rdf:rest rdf:nil .
_:b6 rdf:first _:b7 .
_:b7 owl:someValuesFrom obo:PR_000025405 .
_:b7 owl:onProperty <http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount> .
_:b7 rdf:type owl:Restriction .
_:b4 rdf:first _:b5 .
_:b5 owl:someValuesFrom obo:PR_P01730 .
_:b5 owl:onProperty <http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount> .
_:b5 rdf:type owl:Restriction .
_:b3 rdf:first obo:CL_0000000 .
_:b2 rdf:type owl:Class . }

== TO BE DONE: Add clauses to get just the immediate subs and supers ==

Construct a report:

For each cytof-cluster-protein-markers give it's name, g1
Show the logical definition of the class defined for the query of this cluster (C1)
List the immediate superclasses, each of their URI, their logical definitions, and their textual definitions.
List the same for the immediate subclasses

We can predict a number of cases, but at this point in development we
should present this report to the submitter for review and comment.

Some cases we can imagine:

Result: The immediate superclasses and subclasses yield a single class.
Interpretation: Direct hit - the population measured is precisely C1

Result: The superclass expression(s) only differ from C1 by including
clauses that reflect absences of protein.
Interpretation: Here a judgement may need to be made as to whether the
absences reflect knowledge missing at the time the CL term was
curated, or whether they might define a distinct population.

Result: The subclass expression(s) only differ from C1 by the presence
of clauses that reflect properties or capabilities not measured in
this experiment.
Interpretation: Here a judgement may need to be made as to whether the
the extra conditions in the subclass expressions are also true of
the cell defined by the cluster, or whether they might be a distinct
population.

Result: The subclasses and superclasses look odd/incorrect.
Interpretation: The cluster might represent a population including different cell types.

================================================================

Our next step is review of several experiements and scrutiny of the
generated reports to gain experience with the protocol, with the aim
of removing or shortening the review step as much as possible.
</nowiki>

4th Immport Ontology Group Web Conference

2013-06-24T04:00:09Z

Alan Ruttenberg:

'''Draft Schedule'''

4:00pm (EST) Discussion of CyTOF / PRO / CL workflow

== CyTOF –CL workflow ==

Alan Ruttenberg - https://bisc2012.atlassian.net/browse/OD-48

Protocol for classifying and recording cell type/populations from CYTOF experiments (will be posted before Monday AM)
* Review proposed inputs
** Is information gathered adequate
** Is offering choices for input useful
* Splitting out into separate workflows:
** Registering/curating an antibody
** Assigning qualitative marker levels
** Clustering/gating
* Understanding the SPARQL query
* The review step
* Reminder of the general issue of cell type versus state
* Caveats/Open issues
* Identifying a data set for validating the workflow. -
** is Bendall et al., 332 (6030): 687-696 a good source? Review.
** Arranging time with someone on Nolan team to prepare this set

== Protein Ontology ==
* How to use the PRO (Alex Diehl)
* Curating protein complexes

== Adding markers to CL classes so that they can be computed on (instead of having them as comments) ==
Alex Diehl, Alan Ruttenberg

* https://bisc2012.atlassian.net/browse/ID-205
** Difference between initial spreadsheets and Dougall's
** Asserting surface marker appear on every instance of annotated-to cell type
** Asserting capability of secreting cytokine on every instance of annotated-to cell type
** Ignoring other types (e.g. transcription factors) for now
* https://bisc2012.atlassian.net/browse/OD-28
** Discussion of where different types of information goes.
*** Distinguish CL from resource to support Immport experimental work (which includes CL) ?
*** Antibodies used to detect cell type in different experimental paradigms
*** Extrinsic experimental properties such as side-scatter

== Immport Antibody Registry ==
Alex Diehl

* What is planned/should be recorded
* How to host work in progress (triple store?)
* Do we need indications of status of curation?
* What to expect when
* Process for Identifying new antibodies to be included in registry

6:00pm (EST) Close

Note that the originally planned discussion of [[HIPC Standards and Ontologies]] has been postponed, due to urgency of this workflow issue.

2013 BFO Meeting

2013-05-01T02:30:01Z

Alan Ruttenberg: /* Participants */

'''Venue''': [http://www.ramada.com/hotels/new-york/amherst/ramada-amherst-conference-center/hotel-overview Ramada Inn], Amherst, NY 14051

'''Date''': May 13-14, 2013.

This meeting is co-located with the [http://wiki.plantontology.org/index.php/PRO-PO-GO_Meeting PRO-PO-GO] meeting, to be held on May 15-16, 2013.

== '''Goal''' ==

The goal of the meeting is to assess the current state of the BFO 2.0 Specification and to consider proposals regarding BFO 2.0 OWL. As the OWL working group formally decided not to meet at this time, work on BFO 2.0 OWL will contribute to subsequent meetings of this group, but decisions that require vote will not be taken.

== Draft Schedule ==

Monday, May 13, 2013

11:30 Registration and Lunch

12:30 The BFO 2.0 Specification

:1. Brief introduction (Barry Smith)
:2. Role of [http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx BFO 2.0 Specification] in relation to BFO 2.0 FOL, CLIF and OWL
:3. Report on semi-automatic conversion of BFO from v1.1 to v2.0 (Zheng)
:4. Reports from current users of BFO 2.0
::CHEBI's experience with BFO 2.0 (Hastings)
::Experiences with BFO 2.0 in developing the Neurological Disease Ontology (Cox, Diehl, Jensen)

14:30 Break

:5. Issues with the Specification, especially as concerns

:*Need for a shorter and more user-friendly version
:*Process profiles
:*Granularity
:*Exists-at-t'
:*Rigid vs. non-rigid types
:*BFO and range of IAO:aboutness
:See also list [http://code.google.com/p/bfo/issues/list here]

18:00 Dinner

Tuesday, May 14, 2013

9:00 [http://ontology.buffalo.edu/bfo/FOL BFO 2.0 FOL] (Dipert)

10:30 Break

11:00 BFO 2.0 OWL

:Issues with the BFO 2.0 OWL version

:including the treatment of time and relations in BFO 2.0 OWL

12:30 Lunch

13:00 Issues with the BFO 2.0 OWL version (continued)

14:30 Break

15:00 Spatial Relations

:BFO and anatomy
::location
::fiat boundary
::holes

16:30 Plans to create a paper on BFO

18:00 Dinner

== Background Reading ==

The current draft version of the BFO 2.0 Specification is available [http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx here].

For further information please write to [mailto:phismith@buffalo.edu Barry Smith] or see [http://www.ifomis.uni-saarland.de/bfo/ here].

For introductory reading see: Pierre Grenon and Barry Smith: "[http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf SNAP and SPAN: Towards Dynamic Spatial Ontology]", ''Spatial Cognition and Computation'', 4 (2004), 69-103.

For introductory reading on relations see: Barry Smith, Werner Ceusters, et al., “[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]”, ''Genome Biology'' (2005), 6 (5), R46.

For discussion of core BFO issues see: Barry Smith and Werner Ceusters, “[http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]”, ''Applied Ontology'', 5 (2010), 139–188.

The paper [http://ontology.buffalo.edu/smith/articles/Classifying_Processes.pdf here] contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, ''Ratio'', in press.

And the paper [http://ontology.buffalo.edu/smith/articles/Material_Entities.pdf here] contains material on the proposed BFO 2.0 classification of objects: “On Classifying Material Entities in Basic Formal Ontology”, in Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting, Tokyo: Keio University Press, 2012, 1-13.

== Participants ==

Judith Blake (Jackson Lab)

Matthias Brochhausen (Arkansas)

Werner Ceusters (Buffalo)

Alexander Cox (Buffalo)

Alex Diehl (Buffalo)

Randall Dipert (Buffalo)

Bill Duncan (Buffalo)

Janna Hastings (EBI / Geneva)

William Hogan (Arkansas)

Leonard Jacuzzo (Buffalo)

Mark Jensen (Buffalo)

Tatiana Malyuta (CUNY)

Darren Natale (Georgetown)

Fabian Neuhaus (NIST)

James Overton (Toronto)

Alan Ruttenberg (Buffalo)

Stefan Schulz (Medical University of Graz)

Selja Seppälä (Buffalo)

Barry Smith (Buffalo)

Jie Zheng (Penn)

User:Alan Ruttenberg

2013-04-26T14:46:30Z

Alan Ruttenberg:

Please see my [http://alan.ruttenbergs.com home page]

User:Alan Ruttenberg

2013-04-26T14:46:00Z

Alan Ruttenberg: Created page with '#REDIRECT http://alan.ruttenbergs.com'

#REDIRECT http://alan.ruttenbergs.com

NCOR Wiki:Copyrights

2013-04-26T14:42:36Z

Alan Ruttenberg: Replaced content with 'There are currently no exceptions to the default license terms: Attribution-Noncommercial-Share Alike 3.0 Unported'

There are currently no exceptions to the default license terms: Attribution-Noncommercial-Share Alike 3.0 Unported

2013 BFO Meeting

2013-04-14T19:38:31Z

Alan Ruttenberg: /* Goal */

'''Venue''': [http://www.ramada.com/hotels/new-york/amherst/ramada-amherst-conference-center/hotel-overview Ramada Inn], Amherst, NY 14051

'''Date''': May 13-14, 2013.

This meeting is co-located with the [http://wiki.plantontology.org/index.php/PRO-PO-GO_Meeting PRO-PO-GO] meeting, to be held on May 15-16, 2013.

== '''Goal''' ==

The goal of the meeting is to finalize the BFO 2.0 specification and to address issues with BFO 2.0 OWL. As the OWL working group formally decided not to meet at this time, work on BFO OWL will contribute to subsequent meetings of that group, but decisions that require vote will not be taken.

== Draft Schedule ==

Monday, May 13, 2013

12:00 Lunch

12:30 The BFO 2.0 Specification

:1. Brief introduction (Barry Smith)
:2. Role of BFO 2.0 Specification in relation to BFO 2.0 FOL, CLIF and OWL
:3. Reports from current users of BFO 2.0

14:30 Break

:4. Issues with the Specification, especially as concerns

:*Process profiles
:*BFO and IAO
:*Rigid vs. non-rigid types

18:00 Dinner

Tuesday, May 14, 2013

9:00 [http://ontology.buffalo.edu/bfo/FOL BFO 2.0 FOL]

10:30 Break

11:00 BFO 2.0 OWL

:Issues with the BFO 2.0 OWL version

:including

::the treatment of time and relations in BFO 2.0 OWL.

12:30 Lunch

13:00 Issues with the BFO 2.0 OWL version (continued)

14:30 Break

15:00 Issues with the BFO 2.0 OWL version (continued)

:spatial relations, BFO and anatomy
::location
::fiat boundary
::holes

16:30 Release strategy and plans to create a paper on BFO

== Background Reading ==

The current draft version of the BFO 2.0 Specification is available [http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx here].

For further information please write to [mailto:phismith@buffalo.edu Barry Smith] or see [http://www.ifomis.uni-saarland.de/bfo/ here].

For introductory reading see: Pierre Grenon and Barry Smith: "[http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf SNAP and SPAN: Towards Dynamic Spatial Ontology]", ''Spatial Cognition and Computation'', 4 (2004), 69-103.

For introductory reading on relations see: Barry Smith, Werner Ceusters, et al., “[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]”, ''Genome Biology'' (2005), 6 (5), R46.

For discussion of core BFO issues see: Barry Smith and Werner Ceusters, “[http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]”, ''Applied Ontology'', 5 (2010), 139–188.

The paper [http://ontology.buffalo.edu/smith/articles/Classifying_Processes.pdf here] contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, ''Ratio'', in press.

And the paper [http://ontology.buffalo.edu/smith/articles/Material_Entities.pdf here] contains material on the proposed BFO 2.0 classification of objects: “On Classifying Material Entities in Basic Formal Ontology”, in Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting, Tokyo: Keio University Press, 2012, 1-13.

== Participants ==

Judith Blake (Jackson Lab)

Matthias Brochhausen (Arkansas)

Werner Ceusters (Buffalo)

Alexander Cox (Buffalo)

Randall Dipert (Buffalo)

Janna Hastings (EBI / Geneva)

William Hogan (Arkansas)

Leonard Jacuzzo (Buffalo)

Mark Jensen (Buffalo)

Tatiana Malyuta (CUNY)

Darren Natale (Georgetown)

Fabian Neuhaus (NIST)

Alan Ruttenberg (Buffalo)

Stefan Schulz (Medical University of Graz)

Selja Seppälä (Buffalo)

Barry Smith (Buffalo)

Basic Formal Ontology 2.0

2012-08-24T04:49:49Z

Alan Ruttenberg: /* DESCRIPTION */

'''DATE''': Saturday and Sunday, August 18-19, 2012.

----

== IMPORTANT NOTE FOR INTENDING PARTICIPANTS ==

'''If you intend to participate in this tutorial and have not received an email with instructions please write to phismith@buffalo.edu immediately'''
----

'''VENUE for FACE-TO-FACE PARTICIPATION''': 141 [http://www.buffalo.edu/buildings/building?id=PARK Park Hall], University at Buffalo [http://www.buffalo.edu/home/visiting-ub/north-campus-directions.html North Campus], Amherst, NY.

Suggested hotels: [http://www.expedia.ca/Amherst-Buffalo-Hotels.0-n6056530-0.Travel-Guide-Filter-Hotels]

'''ONLINE PARTICIPATION''': Instructions will for Webex participation will be sent by e-mail. The Webex sessions will be recorded and the recordings will be linked from this page.

'''FACULTY''': Alan Ruttenberg and Barry Smith (University at Buffalo)

== DESCRIPTION ==

Basic Formal Ontology is currently being used by over 100 ontology-based research projects in biomedical informatics and increasingly in other fields. The course will provide an introduction to the content and use of BFO in ontology development. Attendees will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the ontology and acquire basic knowledge of the new formalizations of BFO in first-order logic (FOL) and in OWL.

The current version of the draft Specification and User Guide for BFO 2.0 is available [http://purl.obolibrary.org/obo/bfo/Reference here].

The current version of the BFO 2.0 OWL file is available [http://purl.obolibrary.org/obo/bfo.owl here]. Please read the [http://purl.obolibrary.org/obo/bfo/2012-07-20/ReleaseNotes release notes]

These links, and also further information concerning the BFO 2.0 release can be found at the BFO page here: http://code.google.com/p/bfo/

== SCHEDULE ==

*[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Smith slides]
*[http://bfo.googlecode.com/svn/trunk/docs/BFO2-Tutorial-Implementation-Buffalo-2012-08-18-Ruttenberg.pdf Ruttenberg slides]

'''Saturday, August 18'''

[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21314907&rKey=e35d4e26d0ca7af3 Video]

*9:00 '''The main principles underlying Basic Formal Ontology'''
::What BFO is used for
:::BFO is an upper-level ontology
:::Ontological realism: an evidence-based strategy for ontology development
:::Starting point for downward population
:::Annotation of scientific and administrative data
:::Part storehouse of lessons learned, part QWERTY keyboard
:::Basis for common training
:::Works best under the hood
::Brief history of BFO
:::Pre-History
::::Aristotle's Ontological Square
:::Edmund Husserl
:::Truthmakers
:::The Naive Physics Manifesto
:::Mereotopology
:::The Gene Ontology and the Foundational Model of Anatomy

::BFO's competitors
:::DOLCE
:::SUMO
:::CYC
:::What BFO, DOLCE, SUMO, CYC have in common
:::Arguments in favor of using BFO
::Important users of BFO
:::OBO Foundry
:::NIF Standard
:::OBI
:::IDO Consortium
:::Plant Ontology
:::Universal Core Semantic Layer
::How BFO is constructed and maintained
:::Conservative evolution
:::Simplicity (two levels; no qualities of qualities)
:::Strict formality (no overlap with domain ontologies)
:::Asserted monohierarchy and inferred polyhierarchy
:::Truthmaker
:::Non-multiplicative (the statue is the portion of clay during the time when the latter has a certain role)
:::Perspectivalism
:::No reductionism, no phenomenalism
:::No 'context'
:::No meanings, fictions, non-existents
::::The Semiotic Triangle
:::No 'possible worlds'
:::No abstracta
:::How to deal with thoughts, beliefs, information artifacts

*10:30 Break

*11:00 '''Overview of BFO 1.0'''
:::Instances and universals
:::Continuants and occurrents
:::Dependent entities and independent entities
::::PATO qualities
:::Different kinds of relations
::::Symmetry, asymmetry and inverses
::::The all-some rule
::::What to do with probabilistic and other some-some relations?
:::Realizables
::::Roles
::::Dispositions and the treatment of modality
::::Functions
::Added in BFO 1.1
:::Generically and specifically dependent continuants, concretizations, and relations of dependence
:::Information entities

*12:30 Lunch

*13:30 '''Introduction to OWL and to the Semantic Web''' (Alan Ruttenberg)

*15:00 Break

*15:30 '''Formalization of Basic Formal Ontology''' (Alan Ruttenberg)
:::Relations between the BFO Specification and BFO FOL, BFO CLIF, BFO OWL
:::BFO in First Order Logic
:::BFO in OWL
:::Applications of BFO in OWL
:::How to migrate from BFO 1.0 to BFO 2.0
:::The BFO 2.0 OWL temporalization strategy

*16:00 '''New Features of BFO 2.0'''
::The BFO 2.0 Specification and Its Status
:::Relation to FOL and OWL realizations
:::Definitions and elucidations
:::New treatment of Relations
::::Incorporation of top-level relations into BFO 2.0
::::Focus primarily on instance-instance relations
::::Added relation of concretization
:::::::A musical work and its performance
:::Sites and regions
:::Representation of boundaries
::::Frames of reference; space, time and spacetime
:::SpaceR, TimeR and Spacetime
:::Material and immaterial entities
:::Three subtypes of material entity: objects, object aggregates, and fiat object parts
:::Continuant fiat boundaries
::::Coordinate systems and frames of reference
:::Object aggregates and the member_of relation, with an application to groups and organizations
::::Cognitive selection in the realm of continuants
:::Granularity on the side of continuants
::::Modeling and simulation
:::Map-based partitions of reality and the fiat entities they create
::::Map layers
::::Cadaster
::::Environments and ecology
::::Habitats, niches
:::Partitions of occurrent reality
::::Partition sequences
::::Partitions and plans (two sorts of direction of fit)

*17:00 Close of Day 1

'''Sunday, August 19'''

[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21315352&rKey=27ba15b47f3454cc Video]

*9:00 '''Process Profiles, Rates, and Process Measurement Data'''
:::Mutual dependence of qualities: The case of color
:::How quality instances change over time
:::Rigid and non-rigid universals
:::Universals and continuous change
::Complete and partial processses
:::Lives and other histories
:::A top is spinning and simultaneously warming up
::Process profiles as targets of process measurements
:::The Wiggers diagram
::::Cognitive selection
:::Quality process profiles
::::What did your temperature do since last night?
:::Rate process profiles
::::Relation to object aggregates
:::Other quantitative process profiles
:::Process profiles and time-series graphs

*10:30 Break

*11:00 '''Qualitative process profiles, granularity and the partitioning of reality'''
:::Map-based partitions of occurrent reality and the fiat entities they create
::::Weather
:::Granularity on the side of occurrents
::::Journalism, history
::::Napoleon's March to Moscow
:::Many map-based fiat entities existed trillions of years before the technology of maps
:::Music
::::Focusing on the cello part when you listen to a string quartet
:::Dance
:::Planning
:::Chess
:::Football
:::Experiments and experimental protocols
:::Language
::::Speech acts
:::Zeno Vendler
::::Accomplishments: processes which have an endpoint and are incremental or gradual (paint a picture, build a house)
::::Achievements: occur instantaneously (recognize, notice)
::::Basic Actions

:*12:00 Lunch

:*13:00 '''BFO Applied to Disease''' [http://ncor.buffalo.edu/2012/BFO-Disease-Tutorial-August2012.pptx Slides]
:::Creating a domain ontology by extending BFO
:::An overview of the Ontology for General Medical Science
:::Disease courses are process profiles
:::Occurrent symptoms are process profiles

:*14:30 Break

:*15:00 '''Concluding Discussion'''

:*17:00 Close

== PARTICIPATION ==

Participants should have some background in ontology (including either philosophical or applied ontology). No specific knowledge of BFO is presupposed. This tutorial allows both face-to-face and on-line participation. Participation may be for credit (with an official university transcript), or the tutorial may be audited (with a certificate of completion if needed). The course will take place on the weekend of August 18-19, 2012, with follow-up meetings as necessary for those taking the course for credit.

Log-on/dial-in instructions for on-line participation will be provided by email to registered participants prior to the meeting.

'''FOR CREDIT'''

Participation in this tutorial will yield 1 credit hour; up to 3 further credit hours can be received through completion of a project under the guidance of an assigned faculty member. Projects must be completed before November 30, 2012.

::Registration details for students taking this course for credit are available:
:::[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI&regnum=12518 here], for face-to-face participation;
:::[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI&regnum=12708 here], for on-line participation.

::External (non-UB) participants who wish to take this course for credit, either on-line or through face-to-face participation, should use the links above and follow the procedures outlined [http://registrar.buffalo.edu/registration/procedures/index.php here] under 'Non-matriculated student'. External students will be able to apply credits from participation in this tutorial to the UB [http://philosophy.buffalo.edu/graduate/areas_of_study/ma_ontology/ Masters] and [http://philosophy.buffalo.edu/graduate/areas_of_study/phd_ontology/ PhD] Programs in Ontology, and also to the planned on-line UB Advanced Graduate Certificate Program in Ontology which is currently being established. Further details can be obtained from [mailto:phismith@buffalo.edu Barry Smith].

'''AUDITING'''

Auditing, both on-line and face-to-face, is free to registered participants. All those wishing to audit this tutorial should fill in the registration form provided [http://ncor.buffalo.edu/Tutorial_Registation_Form.pdf here] as soon as possible. A certificate of participation will be supplied on request, but auditing the course does not count for credit.

==FACULTY==

'''[http://ontology.buffalo.edu/smith Barry Smith]''' is a prominent contributor to both theoretical and applied research in ontology. He is the author of some 500 publications, and his research has been funded by the National Institutes of Health, the US, Swiss and Austrian National Science Foundations, the US Department of Defense, the Volkswagen Foundation, and the European Union. In 2010 he was awarded the first Paolo Bozzi Prize in Ontology by the University of Turin. Smith is one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, and a PI on the Protein Ontology and Infectious Disease Ontology projects. He has organized over 100 ontology conferences, workshops and tutorials.

'''[http://alan.ruttenbergs.com Alan Ruttenberg]''' was a Principal Scientist at Creative Commons for 5 years and is now the Director of the University at Buffalo Clinical and Translational Data Exchange. His project, the Neurocommons, prototypes the use of Semantic Web technology for integrating and querying biomedical knowledge, working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a former chair of the OWL Working Group.

==FURTHER INFORMATION==
Background information concerning BFO is available [http://www.ifomis.uni-saarland.de/bfo/ here].

For introductory reading see: Pierre Grenon and Barry Smith: "[http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf SNAP and SPAN: Towards Dynamic Spatial Ontology]", ''Spatial Cognition and Computation'', 4 (2004), 69-103.

For introductory reading on relations see: Barry Smith, Werner Ceusters, et al., “[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]”, ''Genome Biology'' (2005), 6 (5), R46.

For (optional) philosophical discussion of core BFO issues see: Barry Smith and Werner Ceusters, “[http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]”, ''Applied Ontology'', 5 (2010), 139–188.

The paper [http://ontology.buffalo.edu/smith/articles/Classifying_Processes.pdf here] contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, ''Ratio'', in press.

And the paper [http://ontology.buffalo.edu/smith/articles/Material_Entities.pdf here] contains material on the proposed BFO 2.0 classification of objects: “On Classifying Material Entities in Basic Formal Ontology”, in Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting, Tokyo: Keio University Press, 2012, 1-13.

The current draft version of the BFO 2.0 Specification is available [http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx here].

For further information please write to [mailto:phismith@buffalo.edu Barry Smith].

Basic Formal Ontology 2.0

2012-08-24T04:44:50Z

Alan Ruttenberg:

'''DATE''': Saturday and Sunday, August 18-19, 2012.

----

== IMPORTANT NOTE FOR INTENDING PARTICIPANTS ==

'''If you intend to participate in this tutorial and have not received an email with instructions please write to phismith@buffalo.edu immediately'''
----

'''VENUE for FACE-TO-FACE PARTICIPATION''': 141 [http://www.buffalo.edu/buildings/building?id=PARK Park Hall], University at Buffalo [http://www.buffalo.edu/home/visiting-ub/north-campus-directions.html North Campus], Amherst, NY.

Suggested hotels: [http://www.expedia.ca/Amherst-Buffalo-Hotels.0-n6056530-0.Travel-Guide-Filter-Hotels]

'''ONLINE PARTICIPATION''': Instructions will for Webex participation will be sent by e-mail. The Webex sessions will be recorded and the recordings will be linked from this page.

'''FACULTY''': Alan Ruttenberg and Barry Smith (University at Buffalo)

== DESCRIPTION ==

Basic Formal Ontology is currently being used by over 100 ontology-based research projects in biomedical informatics and increasingly in other fields. The course will provide an introduction to the content and use of BFO in ontology development. Attendees will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the ontology and acquire basic knowledge of the new formalizations of BFO in first-order logic (FOL) and in OWL.

The current version of the draft Specification and User Guide for BFO 2.0 is available [http://purl.obolibrary.org/obo/bfo/Reference here].

The current version of the BFO 2.0 OWL file is available [http://purl.obolibrary.org/obo/bfo.owl here].

These links, and also further information concerning the BFO 2.0 release can be found at the BFO page here: http://code.google.com/p/bfo/

== SCHEDULE ==

*[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Smith slides]
*[http://bfo.googlecode.com/svn/trunk/docs/BFO2-Tutorial-Implementation-Buffalo-2012-08-18-Ruttenberg.pdf Ruttenberg slides]

'''Saturday, August 18'''

[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21314907&rKey=e35d4e26d0ca7af3 Video]

*9:00 '''The main principles underlying Basic Formal Ontology'''
::What BFO is used for
:::BFO is an upper-level ontology
:::Ontological realism: an evidence-based strategy for ontology development
:::Starting point for downward population
:::Annotation of scientific and administrative data
:::Part storehouse of lessons learned, part QWERTY keyboard
:::Basis for common training
:::Works best under the hood
::Brief history of BFO
:::Pre-History
::::Aristotle's Ontological Square
:::Edmund Husserl
:::Truthmakers
:::The Naive Physics Manifesto
:::Mereotopology
:::The Gene Ontology and the Foundational Model of Anatomy

::BFO's competitors
:::DOLCE
:::SUMO
:::CYC
:::What BFO, DOLCE, SUMO, CYC have in common
:::Arguments in favor of using BFO
::Important users of BFO
:::OBO Foundry
:::NIF Standard
:::OBI
:::IDO Consortium
:::Plant Ontology
:::Universal Core Semantic Layer
::How BFO is constructed and maintained
:::Conservative evolution
:::Simplicity (two levels; no qualities of qualities)
:::Strict formality (no overlap with domain ontologies)
:::Asserted monohierarchy and inferred polyhierarchy
:::Truthmaker
:::Non-multiplicative (the statue is the portion of clay during the time when the latter has a certain role)
:::Perspectivalism
:::No reductionism, no phenomenalism
:::No 'context'
:::No meanings, fictions, non-existents
::::The Semiotic Triangle
:::No 'possible worlds'
:::No abstracta
:::How to deal with thoughts, beliefs, information artifacts

*10:30 Break

*11:00 '''Overview of BFO 1.0'''
:::Instances and universals
:::Continuants and occurrents
:::Dependent entities and independent entities
::::PATO qualities
:::Different kinds of relations
::::Symmetry, asymmetry and inverses
::::The all-some rule
::::What to do with probabilistic and other some-some relations?
:::Realizables
::::Roles
::::Dispositions and the treatment of modality
::::Functions
::Added in BFO 1.1
:::Generically and specifically dependent continuants, concretizations, and relations of dependence
:::Information entities

*12:30 Lunch

*13:30 '''Introduction to OWL and to the Semantic Web''' (Alan Ruttenberg)

*15:00 Break

*15:30 '''Formalization of Basic Formal Ontology''' (Alan Ruttenberg)
:::Relations between the BFO Specification and BFO FOL, BFO CLIF, BFO OWL
:::BFO in First Order Logic
:::BFO in OWL
:::Applications of BFO in OWL
:::How to migrate from BFO 1.0 to BFO 2.0
:::The BFO 2.0 OWL temporalization strategy

*16:00 '''New Features of BFO 2.0'''
::The BFO 2.0 Specification and Its Status
:::Relation to FOL and OWL realizations
:::Definitions and elucidations
:::New treatment of Relations
::::Incorporation of top-level relations into BFO 2.0
::::Focus primarily on instance-instance relations
::::Added relation of concretization
:::::::A musical work and its performance
:::Sites and regions
:::Representation of boundaries
::::Frames of reference; space, time and spacetime
:::SpaceR, TimeR and Spacetime
:::Material and immaterial entities
:::Three subtypes of material entity: objects, object aggregates, and fiat object parts
:::Continuant fiat boundaries
::::Coordinate systems and frames of reference
:::Object aggregates and the member_of relation, with an application to groups and organizations
::::Cognitive selection in the realm of continuants
:::Granularity on the side of continuants
::::Modeling and simulation
:::Map-based partitions of reality and the fiat entities they create
::::Map layers
::::Cadaster
::::Environments and ecology
::::Habitats, niches
:::Partitions of occurrent reality
::::Partition sequences
::::Partitions and plans (two sorts of direction of fit)

*17:00 Close of Day 1

'''Sunday, August 19'''

[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21315352&rKey=27ba15b47f3454cc Video]

*9:00 '''Process Profiles, Rates, and Process Measurement Data'''
:::Mutual dependence of qualities: The case of color
:::How quality instances change over time
:::Rigid and non-rigid universals
:::Universals and continuous change
::Complete and partial processses
:::Lives and other histories
:::A top is spinning and simultaneously warming up
::Process profiles as targets of process measurements
:::The Wiggers diagram
::::Cognitive selection
:::Quality process profiles
::::What did your temperature do since last night?
:::Rate process profiles
::::Relation to object aggregates
:::Other quantitative process profiles
:::Process profiles and time-series graphs

*10:30 Break

*11:00 '''Qualitative process profiles, granularity and the partitioning of reality'''
:::Map-based partitions of occurrent reality and the fiat entities they create
::::Weather
:::Granularity on the side of occurrents
::::Journalism, history
::::Napoleon's March to Moscow
:::Many map-based fiat entities existed trillions of years before the technology of maps
:::Music
::::Focusing on the cello part when you listen to a string quartet
:::Dance
:::Planning
:::Chess
:::Football
:::Experiments and experimental protocols
:::Language
::::Speech acts
:::Zeno Vendler
::::Accomplishments: processes which have an endpoint and are incremental or gradual (paint a picture, build a house)
::::Achievements: occur instantaneously (recognize, notice)
::::Basic Actions

:*12:00 Lunch

:*13:00 '''BFO Applied to Disease''' [http://ncor.buffalo.edu/2012/BFO-Disease-Tutorial-August2012.pptx Slides]
:::Creating a domain ontology by extending BFO
:::An overview of the Ontology for General Medical Science
:::Disease courses are process profiles
:::Occurrent symptoms are process profiles

:*14:30 Break

:*15:00 '''Concluding Discussion'''

:*17:00 Close

== PARTICIPATION ==

Participants should have some background in ontology (including either philosophical or applied ontology). No specific knowledge of BFO is presupposed. This tutorial allows both face-to-face and on-line participation. Participation may be for credit (with an official university transcript), or the tutorial may be audited (with a certificate of completion if needed). The course will take place on the weekend of August 18-19, 2012, with follow-up meetings as necessary for those taking the course for credit.

Log-on/dial-in instructions for on-line participation will be provided by email to registered participants prior to the meeting.

'''FOR CREDIT'''

Participation in this tutorial will yield 1 credit hour; up to 3 further credit hours can be received through completion of a project under the guidance of an assigned faculty member. Projects must be completed before November 30, 2012.

::Registration details for students taking this course for credit are available:
:::[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI&regnum=12518 here], for face-to-face participation;
:::[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI&regnum=12708 here], for on-line participation.

::External (non-UB) participants who wish to take this course for credit, either on-line or through face-to-face participation, should use the links above and follow the procedures outlined [http://registrar.buffalo.edu/registration/procedures/index.php here] under 'Non-matriculated student'. External students will be able to apply credits from participation in this tutorial to the UB [http://philosophy.buffalo.edu/graduate/areas_of_study/ma_ontology/ Masters] and [http://philosophy.buffalo.edu/graduate/areas_of_study/phd_ontology/ PhD] Programs in Ontology, and also to the planned on-line UB Advanced Graduate Certificate Program in Ontology which is currently being established. Further details can be obtained from [mailto:phismith@buffalo.edu Barry Smith].

'''AUDITING'''

Auditing, both on-line and face-to-face, is free to registered participants. All those wishing to audit this tutorial should fill in the registration form provided [http://ncor.buffalo.edu/Tutorial_Registation_Form.pdf here] as soon as possible. A certificate of participation will be supplied on request, but auditing the course does not count for credit.

==FACULTY==

'''[http://ontology.buffalo.edu/smith Barry Smith]''' is a prominent contributor to both theoretical and applied research in ontology. He is the author of some 500 publications, and his research has been funded by the National Institutes of Health, the US, Swiss and Austrian National Science Foundations, the US Department of Defense, the Volkswagen Foundation, and the European Union. In 2010 he was awarded the first Paolo Bozzi Prize in Ontology by the University of Turin. Smith is one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, and a PI on the Protein Ontology and Infectious Disease Ontology projects. He has organized over 100 ontology conferences, workshops and tutorials.

'''[http://alan.ruttenbergs.com Alan Ruttenberg]''' was a Principal Scientist at Creative Commons for 5 years and is now the Director of the University at Buffalo Clinical and Translational Data Exchange. His project, the Neurocommons, prototypes the use of Semantic Web technology for integrating and querying biomedical knowledge, working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a former chair of the OWL Working Group.

==FURTHER INFORMATION==
Background information concerning BFO is available [http://www.ifomis.uni-saarland.de/bfo/ here].

For introductory reading see: Pierre Grenon and Barry Smith: "[http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf SNAP and SPAN: Towards Dynamic Spatial Ontology]", ''Spatial Cognition and Computation'', 4 (2004), 69-103.

For introductory reading on relations see: Barry Smith, Werner Ceusters, et al., “[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]”, ''Genome Biology'' (2005), 6 (5), R46.

For (optional) philosophical discussion of core BFO issues see: Barry Smith and Werner Ceusters, “[http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]”, ''Applied Ontology'', 5 (2010), 139–188.

The paper [http://ontology.buffalo.edu/smith/articles/Classifying_Processes.pdf here] contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, ''Ratio'', in press.

And the paper [http://ontology.buffalo.edu/smith/articles/Material_Entities.pdf here] contains material on the proposed BFO 2.0 classification of objects: “On Classifying Material Entities in Basic Formal Ontology”, in Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting, Tokyo: Keio University Press, 2012, 1-13.

The current draft version of the BFO 2.0 Specification is available [http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx here].

For further information please write to [mailto:phismith@buffalo.edu Barry Smith].

Main Page

2010-11-08T16:16:39Z

Alan Ruttenberg: Protected "Main Page" ([edit=autoconfirmed] (indefinite) [move=autoconfirmed] (indefinite))

The goal of the National Center for Ontological Research is to advance ontological investigation within the United States. NCOR serves as a vehicle to coordinate, to enhance, to publicize, and to seek funding for ontological research activities. It lays a special focus on ontology training and on the establishment of tools and measures for quality assurance of ontologies.

NCOR provides ontology services to the US Army and to the US Joint Forces Command.

'''[http://ncorwiki.buffalo.edu/index.php/Newsevents Events]'''

Main Page

2010-11-08T16:16:14Z

Alan Ruttenberg: revert from vandalism

An Introduction to Ontology Building

2010-10-29T07:03:53Z

Alan Ruttenberg: Protected "An Introduction to Ontology Building" ([edit=autoconfirmed] (indefinite) [move=autoconfirmed] (indefinite))

The [http://www.buffalo.edu University at Buffalo], the [http://ncor.us National Center for Ontological Research] and the [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki National Center for Biomedical Ontology] are sponsoring a one-day training event on ontology building, which is to take place in Buffalo, NY on Saturday, October 23.

This event is being organized as part of the graduate course PHI 548, taught by Barry Smith and Mathias Brochhausen. External participants are welcome. See registration details below.

----
'''Schedule'''

:8:30 Registration and Coffee
:9:00 Barry Smith: An Introduction to Ontology Building '''[http://ontology.buffalo.edu/10/HowToBuildAnOntology_Oct2010.ppt SLIDES]'''
:10:30 Coffee
:10:45 Alan Ruttenberg: An Introduction to OWL, the Web Ontology Language [http://ashby.csail.mit.edu/presentations/An%20Introduction%20To%20OWL%2010-2010.pdf SLIDES]
:12:15 Lunch
:1:00 Mathias Brochhausen: An Introduction to the Protege Ontology Editor '''[http://ontology.buffalo.edu/10/protege61.pdf SLIDES]'''
:3:00 Coffee
:3:15 Mathias Brochhausen: A Practical Exercise in Ontology Building
:4:00 Mathias Brochhausen, Alan Ruttenberg, Barry Smith: Question and Answer Session
:6:00 Dinner

The primary audience for this event consists of persons with an interest in ontology but who have '''no background in the use of the computer languages and software tools employed in ontology construction, editing and use'''. All sessions will be highly interactive.

----
'''Registration'''

Advance registration fee, received on or before October 20, is $150. Late registration fee, received on or before October 23, is $200. The registration fee includes lunch and refreshments during coffee breaks.

A '''registration form''' is available [http://ontology.buffalo.edu/10/RegistrationForm.pdf here]. To obtain further information please write to [mailto:ncor@buffalo.edu ↑].

----
'''Venue'''

The venue is: [http://www.buffalo.edu/search/search.cgi?source=www+Home&query=NSC&x=0&y=0 Natural Science Complex], Lecture Room 210 on the North Campus of the University at Buffalo.

'''University map''': [http://www.buffalo.edu/buildings/maps/NorthCampus.pdf ↑].

The Natural Sciences Complex is building number 23. Please park in the Cooke A or B or Hochstetter A or B lots to the South of the building.

'''Directions''': [http://www.buffalo.edu/community/visitor_directions_north.html ↑].

Google map: [http://maps.google.com/maps?f=q&hl=en&geocode=&time=&date=&ttype=&q=Flint+Entrance+%26+Maple+Rd,+Buffalo,+NY+14226&sll=37.0625,-95.677068&sspn=31.564064,58.710937&ie=UTF8&ll=42.991873,-78.79225&spn=0.00711,0.014334&z=16&iwloc=addr&om=1 ↑]

Information concerning local hotels [http://ncor.buffalo.edu/areahotels.pdf ↑].

----
'''Faculty'''

'''[http://www.ifomis.org/wiki/Mathias_Brochhausen Mathias Brochhausen]''' is Senior Research Scientist at the Institute for
Formal Ontology and Medical Information Science in Saarbruecken, Germany.

'''[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg]''' is Director of the Clinical and Translational Data
Exchange at the University at Buffalo and a leader in the W3C OWL community.

'''[http://ontology.buffalo.edu/smith Barry Smith]''' is Director of the National Center for Ontological Research and a Principal Scientist of the National Center for Biomedical Ontology.

An Introduction to Ontology Building

2010-10-29T07:03:33Z

Alan Ruttenberg: revert spam

Ontology Class 2009

2010-10-27T17:27:57Z

Alan Ruttenberg: Protected "Ontology Class 2009": Excessive vandalism ([edit=autoconfirmed] (indefinite) [move=autoconfirmed] (indefinite))

Ontology Class 2009

2010-10-27T17:27:31Z

Alan Ruttenberg: revert

Ontology Class 2009

2010-10-27T17:26:27Z

Alan Ruttenberg: Reverted edits by Alan Ruttenberg (Talk) to last version by 188.92.76.92

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Ontology Class 2009

2010-10-27T17:25:53Z

Alan Ruttenberg: Reverted edits by 188.92.76.92 (Talk) to last version by 188.92.76.153

The [http://ncor.us National Center for Ontological Research], [http://bioontology.org National Center for Biomedical Ontology] and the University at Buffalo [http://www.philosophy.buffalo.edu/ Department of Philosophy] are sponsoring a two-day ontology training event to be held in Buffalo, NY on October 10-11, 2009. The course will be made up of lectures given by Barry Smith accompanied by highly interactive discussions. It is designed to be of interest to both philosophers and those with a background in computer and information science. No prior knowledge of ontology is presupposed.

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