NCBO Wiki - User contributions [en]

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-06-12T15:27:43Z

Adiehl: /* Day 2: Tuesday, June 12, 2012 */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue: [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]'''

'''Goals'''

The goals of this meeting are: To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

'''THIS MEETING IS NOW FULL. NO FURTHER REGISTRATIONS ACCEPTED.'''

----
'''
== Day 1: Monday, June 11, 2012 ==
'''

08:30 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:15 Barry Smith (University at Buffalo) and Cathy Wu (University of Delaware) [http://ontology.buffalo.edu/12/immunology_ontology/smith.pptx slides]
::Bio-Ontologies for Immunology Research: An Introduction
:::Brief survey of the goals of the meeting.

09:30 Alexander Diehl (University at Buffalo) [http://ontology.buffalo.edu/12/immunology_ontology/Dieh_GO_IP.pptx slides]
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:00 Cliburn Chan (Duke University) [http://ontology.buffalo.edu/12/immunology_ontology/Chan_Networks.pptx slides]
::Ontology for Cellular Immune Networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

10:30 Break

11:00 Anna Maria Masci (Duke University) [http://ontology.buffalo.edu/12/immunology_ontology/Masci%20AM.pdf slides]
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

11:30 Peter d'Eustacho (New York University) [http://ontology.buffalo.edu/12/immunology_ontology/dEustachio.pptx slides]
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:00 '''Lunchtime talk'''
Atul Butte (Stanford)
::Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

14:00 Lindsay Cowell (University of Texas Southwestern Medical Center) [http://ontology.buffalo.edu/12/immunology_ontology/Cowell.pdf slides]
::An Introduction to the Infectious Disease Ontology
:::The IDO-Core; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

14:30 Albert Goldfain (Blue Highway) http://ontology.buffalo.edu/12/immunology_ontology/Goldfain_IDO-Staph.pptx slides]
::Staph Aureus (Sa) IDO

15:00 Break

15:30 Christos (Kitsos) Louis (IMBB-FORTH, Crete) [http://ontology.buffalo.edu/12/immunology_ontology/Kitsos_IDOMAL.ppt slides]
::IDO Mal (Malaria Ontology)
:::We will outline the Malaria Ontology, including three new sub-domains dealing with:
::::a) drug resistance
::::b) remedies and traditional medicinal plants
::::c) vector-mediated transmission.
:::We will also describe our conversion from the OBO to the OWL format.

16:00 Yu Lin (University of Michigan)
::IDO Bru (Brucellosis Ontology)
:::IDO Bru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

16:30 Oliver He (University of Michigan) [http://ontology.buffalo.edu/12/immunology_ontology/He_VO.pptx slides]
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----
'''

== Day 2: Tuesday, June 12, 2012 ==
'''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

:Background Reading
::[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013777/?tool=pubmed The Protein Ontology: a structured representation of protein forms and complexes]
::[http://www.biomedcentral.com/1471-2105/12/6 Logical Development of the Cell Ontology]
::Cytometry-Ontology Framework ([http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf Draft])

08:30 Breakfast

'''9:00-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''

9:00 Cathy Wu (University of Delaware): Introduction to the Protein Ontology

9:30 Alexander Diehl (Buffalo)
::Hematopoietic Cell Types in the Cell Ontology
:::The Cell Ontology includes over 350 terms that represent hematopoietic cell types. I will provide an overview of these terms and our strategy for representing key properties of cell types through logical definitions, with examples from Leukemia and Multiple Myeloma

10:00 Discussion of the PRO Driving Biomedical Project
Moderator: Alexander Diehl (Buffalo)
:Presentation of key issues:
::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

10:45 Break

11:15 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

11:45 Dave Parrish ([http://www.labanswer.com/ LabAnswer])
::Storing and Retrieving Flow Cytometry Data
:::The Flow Cytometry Laboratory at Roswell Park Cancer Institute has recently deployed an internally developed application managing the operational workflow of the laboratory. We will describe the use of the relational database in capturing assay results and ultimately associating with a final interpretation. Although early in the process the goal is to support the use of the Cell and Protein Ontologies in panel design and interpretation classification.

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal
:::Cytobank is a platform to manage, share and analyze flow cytometry data over the web. I will describe the challenges addressed in working with large numbers of samples as well as incorporating novel visualizations and algorithms (e.g. SPADE) for high dimensional data (e.g. 40+ parameter mass cytometry experiments). Central to much of this work is interfaces to promote and incorporate annotations into the analysis workflow. I will also highlight some recent work in Cytobank to incorporate ontologies via NCBO's BioPortal

14:30 Melanie Courtot (Ryan Brinkman's group, Vancouver)
::1. Overview of the representation of flow cytometry assays in [http://purl.obolibrary.org/obo/obi OBI]
::2. Connecting results from automated FCM analysis systems with the Cell Ontology

15:00 Break

15:30 General Discussion of Ontologies and Flow Cytometry (Moderator: Alan Ruttenberg, Buffalo)

16:30 End

----
'''

== Day 3: Wednesday, June 13, 2012 ==
'''

8:30 Breakfast

'''9:00-noon: Immunology Ontologies (Continued)'''

9:00 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards an Auto-Immune Disease Ontology
::I will discuss the construction of an auto-immune disease ontology through use of the Ontology of General Medical Sciences as a general framework for ontology development.

'''The Role of Ontologies in Clinical Medicine'''

12:00: Lunch

1:00pm :Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

1:30 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

2:00 Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

2:30 Refreshment Break

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants ==

:Alex Benns (Frontier Science, Amherst, NY)
:Anthony Bloom (Frontier Science, Amherst, NY)
:Kenneth Braun (Frontier Science, Amherst, NY)
:Ryan Brinkman (University of British Columbia, Vancouver)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Alexander Cox (University at Buffalo)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:William Duncan (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-06-05T16:05:33Z

Adiehl: /* Day 2: Tuesday, June 12, 2012 */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue: [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]'''

'''Goals'''

The goals of this meeting are: To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

'''THIS MEETING IS NOW FULL. NO FURTHER REGISTRATIONS ACCEPTED.'''

----
'''
== Day 1: Monday, June 11, 2012 ==
'''

08:30 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:15 Barry Smith (University at Buffalo) and Cathy Wu (University of Delaware)
::Bio-Ontologies for Immunology Research: An Introduction
:::Brief survey of the goals of the meeting.

09:30 Alexander Diehl (University at Buffalo)
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:00 Cliburn Chan (Duke University)
::Ontology for Cellular Immune Networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

10:30 Break

11:00 Anna Maria Masci (Duke University)
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

11:30 Peter d'Eustacho (New York University)
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:00 '''Lunchtime talk'''
Atul Butte (Stanford)
::Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

13:30 Alexander C. Yu (University at Buffalo)
::The Allergy Ontology

14:00 Lindsay Cowell (University of Texas Southwestern Medical Center)
::An Introduction to the Infectious Disease Ontology
:::The IDO-Core; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

14:30 Albert Goldfain (Blue Highway)
::Staph Aureus (Sa) IDO

15:00 Break

15:30 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::IDO Mal (Malaria Ontology)
:::We will outline the Malaria Ontology, including three new sub-domains dealing with:
::::a) drug resistance
::::b) remedies and traditional medicinal plants
::::c) vector-mediated transmission.
:::We will also describe our conversion from the OBO to the OWL format.

16:00 Yu Lin (University of Michigan)
::IDO Bru (Brucellosis Ontology)
:::IDO Bru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

16:30 Oliver He (University of Michigan)
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----
'''

== Day 2: Tuesday, June 12, 2012 ==
'''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

:Background Reading
::[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013777/?tool=pubmed The Protein Ontology: a structured representation of protein forms and complexes]
::[http://www.biomedcentral.com/1471-2105/12/6 Logical Development of the Cell Ontology]
::Cytometry-Ontology Framework ([http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf Draft])

08:30 Breakfast

'''9:00-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''

9:00 Cathy Wu (University of Delaware): Introduction to the Protein Ontology

9:30 Alexander Diehl (Buffalo)
::Hematopoietic Cell Types in the Cell Ontology
:::The Cell Ontology includes over 350 terms that represent hematopoietic cell types. I will provide an overview of these terms and our strategy for representing key properties of cell types through logical definitions, with examples from Leukemia and Multiple Myeloma

10:00 Discussion of the PRO Driving Biomedical Project
Moderator: Lindsay Cowell (University of Texas Southwestern Medical Center)
:Presentation of key issues:
::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

10:45 Break

11:15 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

11:45 Dave Parrish ([http://www.labanswer.com/ LabAnswer])
::Storing and Retrieving Flow Cytometry Data
:::The Flow Cytometry Laboratory at Roswell Park Cancer Institute has recently deployed an internally developed application managing the operational workflow of the laboratory. We will describe the use of the relational database in capturing assay results and ultimately associating with a final interpretation. Although early in the process the goal is to support the use of the Cell and Protein Ontologies in panel design and interpretation classification.

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal
:::Cytobank is a platform to manage, share and analyze flow cytometry data over the web. I will describe the challenges addressed in working with large numbers of samples as well as incorporating novel visualizations and algorithms (e.g. SPADE) for high dimensional data (e.g. 40+ parameter mass cytometry experiments). Central to much of this work is interfaces to promote and incorporate annotations into the analysis workflow. I will also highlight some recent work in Cytobank to incorporate ontologies via NCBO's BioPortal

14:30 Melanie Courtot (Ryan Brinkman's group, Vancouver)
::1. Overview of the representation of flow cytometry assays in [http://purl.obolibrary.org/obo/obi OBI]
::2. Connecting results from automated FCM analysis systems with the Cell Ontology

15:00 Break

15:30 Discussion
::Integration of Ontologies into flow cytometry Assay representation and data analysis.
::Outlining of collaborative efforts.

16:30 End

----
'''

== Day 3: Wednesday, June 13, 2012 ==
'''

8:30 Breakfast

'''9:00-noon: Immunology Ontologies (Continued)'''

9:00 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards an Auto-Immune Disease Ontology
::I will discuss the construction of an auto-immune disease ontology through use of the Ontology of General Medical Sciences as a general framework for ontology development.

'''The Role of Ontologies in Clinical Medicine'''

12:00: Lunch

1:00pm :Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

1:30 Alan Ruttenberg (Buffalo)
::The Protein Ontology and the Treatment of Protein Isoforms, Mutations, and Aggregates of Relevance to Alzheimer's Disease

2:00 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

2:30 Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants ==

:Alex Benns (Frontier Science, Amherst, NY)
:Anthony Bloom (Frontier Science, Amherst, NY)
:Kenneth Braun (Frontier Science, Amherst, NY)
:Ryan Brinkman (University of British Columbia, Vancouver)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Alexander Cox (University at Buffalo)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:William Duncan (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-06-05T16:05:14Z

Adiehl: /* Day 2: Tuesday, June 12, 2012 */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue: [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]'''

'''Goals'''

The goals of this meeting are: To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

'''THIS MEETING IS NOW FULL. NO FURTHER REGISTRATIONS ACCEPTED.'''

----
'''
== Day 1: Monday, June 11, 2012 ==
'''

08:30 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:15 Barry Smith (University at Buffalo) and Cathy Wu (University of Delaware)
::Bio-Ontologies for Immunology Research: An Introduction
:::Brief survey of the goals of the meeting.

09:30 Alexander Diehl (University at Buffalo)
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:00 Cliburn Chan (Duke University)
::Ontology for Cellular Immune Networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

10:30 Break

11:00 Anna Maria Masci (Duke University)
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

11:30 Peter d'Eustacho (New York University)
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:00 '''Lunchtime talk'''
Atul Butte (Stanford)
::Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

13:30 Alexander C. Yu (University at Buffalo)
::The Allergy Ontology

14:00 Lindsay Cowell (University of Texas Southwestern Medical Center)
::An Introduction to the Infectious Disease Ontology
:::The IDO-Core; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

14:30 Albert Goldfain (Blue Highway)
::Staph Aureus (Sa) IDO

15:00 Break

15:30 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::IDO Mal (Malaria Ontology)
:::We will outline the Malaria Ontology, including three new sub-domains dealing with:
::::a) drug resistance
::::b) remedies and traditional medicinal plants
::::c) vector-mediated transmission.
:::We will also describe our conversion from the OBO to the OWL format.

16:00 Yu Lin (University of Michigan)
::IDO Bru (Brucellosis Ontology)
:::IDO Bru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

16:30 Oliver He (University of Michigan)
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----
'''

== Day 2: Tuesday, June 12, 2012 ==
'''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

:Background Reading
::[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013777/?tool=pubmed The Protein Ontology: a structured representation of protein forms and complexes]
::[http://www.biomedcentral.com/1471-2105/12/6 Logical Development of the Cell Ontology]
::Cytometry-Ontology Framework ([http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf Draft])

08:30 Breakfast

'''9:00-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''

9:00 Cathy Wu (University of Delaware): Introduction to the Protein Ontology

9:30 Alexander Diehl (Buffalo)
::Hematopoietic Cell Types in the Cell Ontology
:::The Cell Ontology includes over 350 terms that represent hematopoietic cell types. I will provide an overview of these terms and our strategy for representing key properties of cell types through logical definitions, with examples from Leukemia and Multiple Myeloma

10:00 Discussion of the PRO Driving Biomedical Project
Moderator: Lindsay Cowell (University of Texas Southwestern Medical Center)
:Presentation of key issues:
::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

10:45 Break

11:15 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

11:45 Dave Parrish ([http://www.labanswer.com/ LabAnswer])
::Storing and Retrieving Flow Cytometry Data
:::The Flow Cytometry Laboratory at Roswell Park Cancer Institute has recently deployed an internally developed application managing the operational workflow of the laboratory. We will describe the use of the relational database in capturing assay results and ultimately associating with a final interpretation. Although early in the process the goal is to support the use of the Cell and Protein Ontologies in panel design and interpretation classification.

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal
:::Cytobank is a platform to manage, share and analyze flow cytometry data over the web. I will describe the challenges addressed in working with large numbers of samples as well as incorporating novel visualizations and algorithms (e.g. SPADE) for high dimensional data (e.g. 40+ parameter mass cytometry experiments). Central to much of this work is interfaces to promote and incorporate annotations into the analysis workflow. I will also highlight some recent work in Cytobank to incorporate ontologies via NCBO's BioPortal

14:30 Melanie Courtot (Ryan Brinkman's group, Vancouver)
::1. Overview of the representation of flow cytometry assays in [http://purl.obolibrary.org/obo/obi OBI]
::2. Connecting results from automated FCM analysis systems with the Cell Ontology

15:00 Break

15:30 Discussion
::Integration of 0ntologies into flow cytometry Assay representation and data analysis.
::Outlining of collaborative efforts.

16:30 End

----
'''

== Day 3: Wednesday, June 13, 2012 ==
'''

8:30 Breakfast

'''9:00-noon: Immunology Ontologies (Continued)'''

9:00 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards an Auto-Immune Disease Ontology
::I will discuss the construction of an auto-immune disease ontology through use of the Ontology of General Medical Sciences as a general framework for ontology development.

'''The Role of Ontologies in Clinical Medicine'''

12:00: Lunch

1:00pm :Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

1:30 Alan Ruttenberg (Buffalo)
::The Protein Ontology and the Treatment of Protein Isoforms, Mutations, and Aggregates of Relevance to Alzheimer's Disease

2:00 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

2:30 Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants ==

:Alex Benns (Frontier Science, Amherst, NY)
:Anthony Bloom (Frontier Science, Amherst, NY)
:Kenneth Braun (Frontier Science, Amherst, NY)
:Ryan Brinkman (University of British Columbia, Vancouver)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Alexander Cox (University at Buffalo)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:William Duncan (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-06-05T16:01:57Z

Adiehl: /* Day 2: Tuesday, June 12, 2012 */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue: [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]'''

'''Goals'''

The goals of this meeting are: To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

'''THIS MEETING IS NOW FULL. NO FURTHER REGISTRATIONS ACCEPTED.'''

----
'''
== Day 1: Monday, June 11, 2012 ==
'''

08:30 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:15 Barry Smith (University at Buffalo) and Cathy Wu (University of Delaware)
::Bio-Ontologies for Immunology Research: An Introduction
:::Brief survey of the goals of the meeting.

09:30 Alexander Diehl (University at Buffalo)
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:00 Cliburn Chan (Duke University)
::Ontology for Cellular Immune Networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

10:30 Break

11:00 Anna Maria Masci (Duke University)
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

11:30 Peter d'Eustacho (New York University)
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:00 '''Lunchtime talk'''
Atul Butte (Stanford)
::Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

13:30 Alexander C. Yu (University at Buffalo)
::The Allergy Ontology

14:00 Lindsay Cowell (University of Texas Southwestern Medical Center)
::An Introduction to the Infectious Disease Ontology
:::The IDO-Core; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

14:30 Albert Goldfain (Blue Highway)
::Staph Aureus (Sa) IDO

15:00 Break

15:30 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::IDO Mal (Malaria Ontology)
:::We will outline the Malaria Ontology, including three new sub-domains dealing with:
::::a) drug resistance
::::b) remedies and traditional medicinal plants
::::c) vector-mediated transmission.
:::We will also describe our conversion from the OBO to the OWL format.

16:00 Yu Lin (University of Michigan)
::IDO Bru (Brucellosis Ontology)
:::IDO Bru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

16:30 Oliver He (University of Michigan)
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----
'''

== Day 2: Tuesday, June 12, 2012 ==
'''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

:Background Reading
::[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013777/?tool=pubmed The Protein Ontology: a structured representation of protein forms and complexes]
::[http://www.biomedcentral.com/1471-2105/12/6 Logical Development of the Cell Ontology]
::Cytometry-Ontology Framework ([http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf Draft])

08:30 Breakfast

'''9:00-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''

9:00 Cathy Wu (University of Delaware): Introduction to the Protein Ontology

9:30 Alexander Diehl (Buffalo)
::Hematopoietic Cell Types in the Cell Ontology
:::The Cell Ontology includes over 350 terms that represent hematopoietic cell types. I will provide an overview of these terms and our strategy for representing key properties of cell types through logical definitions, with examples from Leukemia and Multiple Myeloma

10:00 Discussion of the PRO Driving Biomedical Project
Moderator: Lindsay Cowell (University of Texas Southwestern Medical Center)
:Presentation of key issues:
::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

10:45 Break

11:15 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

11:45 Dave Parrish ([http://www.labanswer.com/ LabAnswer])
::Storing and Retrieving Flow Cytometry Data
:::The Flow Cytometry Laboratory at Roswell Park Cancer Institute has recently deployed an internally developed application managing the operational workflow of the laboratory. We will describe the use of the relational database in capturing assay results and ultimately associating with a final interpretation. Although early in the process the goal is to support the use of the Cell and Protein Ontologies in panel design and interpretation classification.

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal
:::Cytobank is a platform to manage, share and analyze flow cytometry data over the web. I will describe the challenges addressed in working with large numbers of samples as well as incorporating novel visualizations and algorithms (e.g. SPADE) for high dimensional data (e.g. 40+ parameter mass cytometry experiments). Central to much of this work is interfaces to promote and incorporate annotations into the analysis workflow. I will also highlight some recent work in Cytobank to incorporate ontologies via NCBO's BioPortal

14:30 Melanie Courtot (Ryan Brinkman's group, Vancouver)
::1. Overview of the representation of flow cytometry assays in [http://purl.obolibrary.org/obo/obi OBI]
::2. Connecting results from automated FCM analysis systems with the Cell Ontology

15:00 Break

15:30

16:00

----
'''

== Day 3: Wednesday, June 13, 2012 ==
'''

8:30 Breakfast

'''9:00-noon: Immunology Ontologies (Continued)'''

9:00 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards an Auto-Immune Disease Ontology
::I will discuss the construction of an auto-immune disease ontology through use of the Ontology of General Medical Sciences as a general framework for ontology development.

'''The Role of Ontologies in Clinical Medicine'''

12:00: Lunch

1:00pm :Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

1:30 Alan Ruttenberg (Buffalo)
::The Protein Ontology and the Treatment of Protein Isoforms, Mutations, and Aggregates of Relevance to Alzheimer's Disease

2:00 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

2:30 Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants ==

:Alex Benns (Frontier Science, Amherst, NY)
:Anthony Bloom (Frontier Science, Amherst, NY)
:Kenneth Braun (Frontier Science, Amherst, NY)
:Ryan Brinkman (University of British Columbia, Vancouver)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Alexander Cox (University at Buffalo)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:William Duncan (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Carmelo Gaudioso (Roswell Park Cancer Institute, Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-21T18:53:50Z

Adiehl: /* Draft Schedule */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue:
:Days 1 and 2, [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]
:Day 3: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

'''Goals'''

Provisional goals of the meeting are:

To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

This meeting is free for registered participants. Space is limited and those interested in participating should contact [mailto:phismith@buffalo.edu Barry Smith] as soon as possible.

----

'''
== Draft Schedule ==
'''

''Day 1: Monday, June 11, 2012''

09:00 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:30 Cathy Wu (University of Delaware) and Barry Smith (University at Buffalo)
'''Bio-Ontologies for Immunology Research: An Introduction
:::We will survey the goals of the meeting, and describe the relations between a number of interdependent ontologies being developed in the domain of immunology.

10:00 Alexander Diehl (University at Buffalo)
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:30 Break

11:00 Cliburn Chan (Duke University)
::Ontology for cellular immune networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

11:30 Anna Maria Masci (Duke University)
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

12:00 Peter d'Eustacho (New York University)
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:30 Lunch
'''Lunchtime talk'''
:Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

14:00 Alexander C. Yu (University at Buffalo)
::The Allergy Ontology

14:30 Lindsay Cowell (University of Texas Southwestern Medical Center)
::An Introduction to the Infectious Disease Ontology
:::Update on IDO-Core; simplified definitions; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

15:00 Break

15:30 Albert Goldfain (Blue Highway)
::Staph Aureus (Sa) IDO

16:00 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::IDO Mal (Malaria Ontology)

16:30 Yu Lin (University of Michigan)
::IDOBru (Brucellosis Ontology)
:::IDOBru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

17:00 Oliver He (University of Michigan)
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----

''Day 2: Tuesday, June 12, 2012''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

08:30 Breakfast

'''9:00-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''

Alexander Diehl (Buffalo) and Lindsay Cowell (University of Texas Southwestern Medical Center)
:Presentation of key issues:
::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

Presentations during the morning session will include:
Cathy Wu (Delaware), Darren Natale (Georgetown) and Alexander Diehl (Buffalo)
::The Protein Ontology

Alexander Diehl (Buffalo)
::Hematopoietic Cell Types in the Cell Ontology
:::The Cell Ontology includes over 350 terms that represent hematopoietic cell types. I will provide an overview of these terms and our strategy for representing key properties of cell types through logical definitions.

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal

14:30 Alexander Diehl (Buffalo)
::An Ontological Treatment of Flow Cytometry Typing Panels for Leukemia and Multiple Myeloma.

15:00 Break

15:30 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

16:00 Ryan Brinkman (Vancouver)
::1. Overview of the representation of flow cytometry assays in OBI
::2. Overview of [http://www.bioconductor.org/packages/release/bioc/html/flowMeans.html flowMeans] and [http://flowcap.flowsite.org/ flowCAP]
::3. Connecting results from automated FCM analysis systems with the Cell Ontology

----

''Day 3: Wednesday, June 13, 2012:9:00am-6:00pm''

'''The Role of Ontologies in Clinical Medicine'''

Note change of venue to: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

9:00 Breakfast

Further discussion of Immunology Ontology including:

9:30 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards an Auto-Immune Disease Ontology
::I will discuss the construction of an auto-immune disease ontology through use of the Ontology of General Medical Sciences as a general framework for ontology development.

'''noon-3pm SESSION OPEN TO THE PUBLIC: Practical Applications of Ontologies in Clinical Research''' (includes lunch)

:Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

:Alan Ruttenberg (Buffalo)
::The Protein Ontology and the treatment of protein isoforms, mutations, and aggregates of relevance to Alzheimer's Disease

:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

:Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants will include ==
'''

:Ryan Brinkman (University of British Columbia)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-21T18:42:15Z

Adiehl: /* Draft Schedule */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue:
:Days 1 and 2, [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]
:Day 3: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

'''Goals'''

Provisional goals of the meeting are:

To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

This meeting is free for registered participants. Space is limited and those interested in participating should contact [mailto:phismith@buffalo.edu Barry Smith] as soon as possible.

----

'''
== Draft Schedule ==
'''

''Day 1: Monday, June 11, 2012''

09:00 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:30 Cathy Wu (University of Delaware) and Barry Smith (University at Buffalo)
'''Bio-Ontologies for Immunology Research: An Introduction
:::We will survey the goals of the meeting, and describe the relations between a number of interdependent ontologies being developed in the domain of immunology.

10:00 Alexander Diehl (University at Buffalo)
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:30 Break

11:00 Cliburn Chan (Duke University)
::Ontology for cellular immune networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

11:30 Anna Maria Masci (Duke University)
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

12:00 Peter d'Eustacho (New York University)
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:30 Lunch
'''Lunchtime talk'''
:Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

14:00 Alexander C. Yu (University at Buffalo)
::The Allergy Ontology

14:30 Lindsay Cowell (University of Texas Southwestern Medical Center)
::An Introduction to the Infectious Disease Ontology
:::Update on IDO-Core; simplified definitions; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

15:00 Break

15:30 Albert Goldfain (Blue Highway)
::Staph Aureus (Sa) IDO

16:00 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::IDO Mal (Malaria Ontology)

16:30 Yu Lin (University of Michigan)
::IDOBru (Brucellosis Ontology)
:::IDOBru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

17:00 Oliver He (University of Michigan)
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----

''Day 2: Tuesday, June 12, 2012''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

08:30 Breakfast

'''9:00-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''

Alexander Diehl (Buffalo) and Lindsay Cowell (University of Texas Southwestern Medical Center)
:Presentation of key issues:
::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

Presentations during the morning session will include:
Cathy Wu (Delaware), Darren Natale (Georgetown) and Alexander Diehl (Buffalo)
::The Protein Ontology and Cell Type Definitions

Alexander Diehl (Buffalo)
::Hematopoietic Cell Types in the Cell Ontology
:::The Cell Ontology includes over 350 terms that represent hematopoietic cell types. I will provide an overview of these terms and our strategy for representing key properties of cell types through logical definitions.

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal

14:30 Alexander Diehl (Buffalo)
::An Ontological Treatment of Protein Marker Expression on Multiple Myeloma Subtypes
::Overview of Euroflow Leukemia Typing Panels
:::Recent work on the ontological representation of typing panels will be presented.

15:00 Break

15:30 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

16:00 Ryan Brinkman (Vancouver)
::1. Overview of the representation of flow cytometry assays in OBI
::2. Overview of [http://www.bioconductor.org/packages/release/bioc/html/flowMeans.html flowMeans] and [http://flowcap.flowsite.org/ flowCAP]
::3. Connecting results from automated FCM analysis systems with the Cell Ontology

----

''Day 3: Wednesday, June 13, 2012:9:00am-6:00pm''

'''The Role of Ontologies in Clinical Medicine'''

Note change of venue to: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

9:00 Breakfast

Further discussion of Immunology Ontology including:

9:30 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards an Auto-Immune Disease Ontology
::I will discuss the construction of an auto-immune disease ontology through use of the Ontology of General Medical Sciences as a general framework for ontology development.

'''noon-3pm SESSION OPEN TO THE PUBLIC: Practical Applications of Ontologies in Clinical Research''' (includes lunch)

:Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

:Alan Ruttenberg (Buffalo)
::The Protein Ontology and the treatment of protein isoforms, mutations, and aggregates of relevance to Alzheimer's Disease

:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

:Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants will include ==
'''

:Ryan Brinkman (University of British Columbia)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-21T18:41:39Z

Adiehl: /* Draft Schedule */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue:
:Days 1 and 2, [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]
:Day 3: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

'''Goals'''

Provisional goals of the meeting are:

To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

This meeting is free for registered participants. Space is limited and those interested in participating should contact [mailto:phismith@buffalo.edu Barry Smith] as soon as possible.

----

'''
== Draft Schedule ==
'''

''Day 1: Monday, June 11, 2012''

09:00 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:30 Cathy Wu (University of Delaware) and Barry Smith (University at Buffalo)
'''Bio-Ontologies for Immunology Research: An Introduction
:::We will survey the goals of the meeting, and describe the relations between a number of interdependent ontologies being developed in the domain of immunology.

10:00 Alexander Diehl (University at Buffalo)
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:30 Break

11:00 Cliburn Chan (Duke University)
::Ontology for cellular immune networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

11:30 Anna Maria Masci (Duke University)
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

12:00 Peter d'Eustacho (New York University)
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:30 Lunch
'''Lunchtime talk'''
:Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

14:00 Alexander C. Yu (University at Buffalo)
::The Allergy Ontology

14:30 Lindsay Cowell (University of Texas Southwestern Medical Center)
::An Introduction to the Infectious Disease Ontology
:::Update on IDO-Core; simplified definitions; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

15:00 Break

15:30 Albert Goldfain (Blue Highway)
::Staph Aureus (Sa) IDO

16:00 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::IDO Mal (Malaria Ontology)

16:30 Yu Lin (University of Michigan)
::IDOBru (Brucellosis Ontology)
:::IDOBru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

17:00 Oliver He (University of Michigan)
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----

''Day 2: Tuesday, June 12, 2012''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

08:30 Breakfast

'''9:00-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''
Alexander Diehl (Buffalo) and Lindsay Cowell (University of Texas Southwestern Medical Center)
:Presentation of key issues:
::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

Presentations during the morning session will include:
Cathy Wu (Delaware), Darren Natale (Georgetown) and Alexander Diehl (Buffalo)
::The Protein Ontology and Cell Type Definitions

Alexander Diehl (Buffalo)
::Hematopoietic Cell Types in the Cell Ontology
:::The Cell Ontology includes over 350 terms that represent hematopoietic cell types. I will provide an overview of these terms and our strategy for representing key properties of cell types through logical definitions.

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal

14:30 Alexander Diehl (Buffalo)
::An Ontological Treatment of Protein Marker Expression on Multiple Myeloma Subtypes
::Overview of Euroflow Leukemia Typing Panels
:::Recent work on the ontological representation of typing panels will be presented.

15:00 Break

15:30 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

16:00 Ryan Brinkman (Vancouver)
::1. Overview of the representation of flow cytometry assays in OBI
::2. Overview of [http://www.bioconductor.org/packages/release/bioc/html/flowMeans.html flowMeans] and [http://flowcap.flowsite.org/ flowCAP]
::3. Connecting results from automated FCM analysis systems with the Cell Ontology

----

''Day 3: Wednesday, June 13, 2012:9:00am-6:00pm''

'''The Role of Ontologies in Clinical Medicine'''

Note change of venue to: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

9:00 Breakfast

Further discussion of Immunology Ontology including:

9:30 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards an Auto-Immune Disease Ontology
::I will discuss the construction of an auto-immune disease ontology through use of the Ontology of General Medical Sciences as a general framework for ontology development.

'''noon-3pm SESSION OPEN TO THE PUBLIC: Practical Applications of Ontologies in Clinical Research''' (includes lunch)

:Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

:Alan Ruttenberg (Buffalo)
::The Protein Ontology and the treatment of protein isoforms, mutations, and aggregates of relevance to Alzheimer's Disease

:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

:Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants will include ==
'''

:Ryan Brinkman (University of British Columbia)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-21T18:35:32Z

Adiehl: /* Draft Schedule */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue:
:Days 1 and 2, [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]
:Day 3: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

'''Goals'''

Provisional goals of the meeting are:

To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

This meeting is free for registered participants. Space is limited and those interested in participating should contact [mailto:phismith@buffalo.edu Barry Smith] as soon as possible.

----

'''
== Draft Schedule ==
'''

''Day 1: Monday, June 11, 2012''

09:00 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:30 Cathy Wu (University of Delaware) and Barry Smith (University at Buffalo)
'''Bio-Ontologies for Immunology Research: An Introduction
:::We will survey the goals of the meeting, and describe the relations between a number of interdependent ontologies being developed in the domain of immunology.

10:00 Alexander Diehl (University at Buffalo)
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:30 Break

11:00 Cliburn Chan (Duke University)
::Ontology for cellular immune networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

11:30 Anna Maria Masci (Duke University)
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

12:00 Peter d'Eustacho (New York University)
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:30 Lunch
'''Lunchtime talk'''
:Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

14:00 Alexander C. Yu (University at Buffalo)
::The Allergy Ontology

14:30 Lindsay Cowell (University of Texas Southwestern Medical Center)
::An Introduction to the Infectious Disease Ontology
:::Update on IDO-Core; simplified definitions; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

15:00 Break

15:30 Albert Goldfain (Blue Highway)
::Staph Aureus (Sa) IDO

16:00 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::IDO Mal (Malaria Ontology)

16:30 Yu Lin (University of Michigan)
::IDOBru (Brucellosis Ontology)
:::IDOBru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

17:00 Oliver He (University of Michigan)
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----

''Day 2: Tuesday, June 12, 2012''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

08:30 Breakfast

09:00 Alexander Diehl (Buffalo) and Lindsay Cowell (University of Texas Southwestern Medical Center)
'''9am-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''

::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

Presentations during the morning session will include:
Cathy Wu (Delaware), Darren Natale (Georgetown) and Alexander Diehl (Buffalo)
::The Protein Ontology and Cell Type Definitions

Alexander Diehl (Buffalo)
::Overview of Hematopoietic Cell Types in the Cell Ontology
:::The Cell Ontology includes over 350 terms that represent hematopoietic cell types. I will provide an overview of these terms and our strategy for representing key properties of cell types through logical definitions.

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal

14:30 Alexander Diehl (Buffalo)
::An Ontological Treatment of Protein Marker Expression on Multiple Myeloma Subtypes
::Overview of Euroflow Leukemia Typing Panels
:::Recent work on the ontological representation of typing panels will be presented.

15:00 Break

15:30 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

16:00 Ryan Brinkman (Vancouver)
::1. Overview of the representation of flow cytometry assays in OBI
::2. Overview of [http://www.bioconductor.org/packages/release/bioc/html/flowMeans.html flowMeans] and [http://flowcap.flowsite.org/ flowCAP]
::3. Connecting results from automated FCM analysis systems with the Cell Ontology

----

''Day 3: Wednesday, June 13, 2012:9:00am-6:00pm''

'''The Role of Ontologies in Clinical Medicine'''

Note change of venue to: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

9:00 Breakfast

Further discussion of Immunology Ontology including:

9:30 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards an Auto-Immune Disease Ontology
::I will discuss the construction of an auto-immune disease ontology through use of the Ontology of General Medical Sciences as a general framework for ontology development.

'''noon-3pm SESSION OPEN TO THE PUBLIC: Practical Applications of Ontologies in Clinical Research''' (includes lunch)

:Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

:Alan Ruttenberg (Buffalo)
::The Protein Ontology and the treatment of protein isoforms, mutations, and aggregates of relevance to Alzheimer's Disease

:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

:Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants will include ==
'''

:Ryan Brinkman (University of British Columbia)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-21T18:14:27Z

Adiehl: /* Draft Schedule */

The National Center for Biomedical Ontology [http://bioontology.org (NCBO)] in collaboration with the Protein Ontology [http://pir.georgetown.edu/pro/ (PRO)] and the Infectious Disease Ontology [http://infectiousdiseaseontology.org/page/Main_Page (IDO)] will host a three-day dissemination workshop in Buffalo, NY on June 11-13, 2012.
:Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
:Day 2 will be focused on flow cytometry, including the question of the Cell and Protein Ontologies and of the role of surface protein expression in cell type classification.
:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.

'''Venue:
:Days 1 and 2, [http://www.universityinn.com/ Ramada Inn, UB North Campus, Buffalo]
:Day 3: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

'''Goals'''

Provisional goals of the meeting are:

To identify and coordinate activities on-going in immunology ontology and related fields, with special attention to the use of ontologies to support clinical data analysis in flow cytometry and related fields.

'''Registration'''

This meeting is free for registered participants. Space is limited and those interested in participating should contact [mailto:phismith@buffalo.edu Barry Smith] as soon as possible.

----

'''
== Draft Schedule ==
'''

''Day 1: Monday, June 11, 2012''

09:00 Registration and Breakfast

'''An Overview of Ontologies to Support Research in Immunology and Infectious Disease'''

'''Morning: The Gene Ontology, Reactome, The Immunology Ontology, The Immune Epitope Ontology and the Allergy Ontology'''

09:30 Cathy Wu (University of Delaware) and Barry Smith (University at Buffalo)
'''Bio-Ontologies for Immunology Research: An Introduction
:::We will survey the goals of the meeting, and describe the relations between a number of interdependent ontologies being developed in the domain of immunology.

10:00 Alexander Diehl (University at Buffalo)
::The Gene Ontology and Immune System Processes
:::The Gene Ontology contains a wealth of terms covering immune system processes for the annotation of proteins involved in the functioning of the immune system. I will provide a overview of these terms and their use in GO annotation.

10:30 Break

11:00 Cliburn Chan (Duke University)
::Ontology for cellular immune networks
:::Will describe initial work on an ontology of cellular immune networks that is designed to capture the qualitative cytokine expression patterns and cellular phenotypes associated with specific immune activation networks (e.g. Th1 network). We will outline use of the ontology for immune assay integration and statistical enrichment analysis.

11:30 Anna Maria Masci (Duke University)
::The Immunology Ontology (with special focus on the liver)
:::An emerging scenario is uncovering immune response as a sophisticated biological process, which requires an intensive cross-talk between immunocytes, parenchymal and stromal cell types. These timely and anatomically restricted interactions regulate the outcome of immune response to damage induced by stress and pathogens. Due to its complexity and patho-physiological relevance, the liver represents an interesting prototype of context-dependent immune response. We will introduce the Liver Immunology Ontology (LIO), which has as primary goal the representation of the immune response induced in the context of the liver.

12:00 Peter d'Eustacho (New York University)
::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
:::The innate immune responses mediated by Toll-like receptors (TLR) provide a first line of defense against microbial pathogens in many vertebrates. In Reactome we have integrated annotations of human TLR molecular functions with those of 6800 other human proteins involved in diverse biological processes to generate a resource suitable for data mining, pathway analysis, and other systems biology approaches. These annotations allow human TLR proteins, the complexes they form, and the functions they mediate to be classified and related to those of structurally similar TLR proteins from chicken, mouse, and other species.

12:30 Lunch
'''Lunchtime talk'''
:Atul Butte (Stanford): Discovery of a novel inflammatory receptor and related drug for type 2 diabetes from integration of publicly-available microarray data

14:00 Alexander C. Yu (University at Buffalo)
::The Allergy Ontology

14:30 Lindsay Cowell (University of Texas Southwestern Medical Center)
::An Introduction to the Infectious Disease Ontology
:::Update on IDO-Core; simplified definitions; new approach to MIREOTing; new terms/definitions/relations; a template for creating an IDO Extension

15:00 Break

15:30 Albert Goldfain (Blue Highway)
::Staph Aureus (Sa) IDO

16:00 Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::IDO Mal (Malaria Ontology)

16:30 Yu Lin (University of Michigan)
::IDOBru (Brucellosis Ontology)
:::IDOBru is an extension ontology of IDO. We will focus on those aspects of Brucellosis represented in IDOBru as outlined in [http://www.jbiomedsem.com/content/2/1/9]. We will also discuss IDOBru's policy on use of IDs, and its treatment of Brucella-host interaction.

17:00 Oliver He (University of Michigan)
::Contributions of the Vaccine Ontology (VO) to Immunology Research and Public Health
:::Vaccinology is applied immunology. VO is a community-based biomedical ontology in the domain of vaccine and vaccination. We will introduce the top level of VO, and sketch applications of VO in elucidating fundamental protective immune mechanisms and improving public health.

----

''Day 2: Tuesday, June 12, 2012''

'''Ontologies and Flow Cytometry Informatics'''

:'''Background''' Increasingly, flow cytometry is being employed in clinical laboratories for the diagnosis, prognosis and monitoring of disease. The advent of highly multidimensional flow cytometry and automated gating algorithms for the analysis of flow cytometry data, coupled with the rise of personalized medicine, are poised to expand greatly the need for a reliable, structured framework for the representation of the types of cells present in human blood and tissues. We are currently enhancing the representation of hematopoietic and other cell types in the Cell Ontology (CL) to allow for the logical definition of cell types based on cellular attributes, and in doing so we rely on relations to terms of the Protein Ontology (PRO) as a key component of these definitions. The goal of today's session is explore how the use of clinical flow cytometry data can serve as a driver of ontology development in both the PRO and the CL by assessing current standard clinical assays and recent approaches based on automated gating of multidimensional flow cytometry.

:Examples of questions to be addressed include:
::Which protein isoforms and post-translationally modified forms identified by flow cytometry typing reagents need to be represented in the PRO to enable cell types defined in their terms to be represented in the CL?
::How can use of the PRO and CL ontologies will promote standardization in interpretation and integration of clinical flow cytometry data?

08:30 Breakfast

09:00 Alexander Diehl (Buffalo) and Lindsay Cowell (University of Texas Southwestern Medical Center)
'''9am-noon: Introduction to the Protein Ontology Flow Cytometry Driving Biological Project'''

:::Assessing representation requirements for Flow Cytometry in PRO, CL, IEDB, OBI, ImmPort, and Immune System Modeling.
::Development of a data store to collect extended cell type-protein relationships.
::Defining a tool wish-list for CL-linked flow cytometry analysis and CL-assisted marker selection for cell type analysis.

Presentations during the morning session will include:
Cathy Wu (Delaware), Darren Natale (Georgetown) and Alexander Diehl (Buffalo)
::The Protein Ontology and Cell Type Definitions

Alexander Diehl (Buffalo)
::Overview of Hematopoietic Cell Types in the Cell Ontology

12:30 Lunch

'''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology. Flow cytometry typing of normal and malignant cell types'''

13:30 Cliburn Chan (Duke)
::Automated flow cytometry analysis in HIV studies
:::Will describe recent work on automated cell subset identification and alignment across multiple HIV-related data sets with statistical mixture models. What do we need in order to be able to use ontologies for automated annotation and labeling of cell subsets?

14:00 Nikesh Kotecha (Cytobank)
::Incorporating annotations into the analysis workflow - examples using Cytobank and NCBO's BioPortal

14:30 Alexander Diehl (Buffalo)
::An Ontological Treatment of Protein Marker Expression on Multiple Myeloma Subtypes
::Overview of Euroflow Leukemia Typing Panels

15:00 Break

15:30 Oliver He (University of Michigan)
::How Flow Cytometry can be used in Vaccine Research
:::To better understand fundamental protective immune mechanisms, flow cytometry has frequently been used to measure vaccine-induced innate immunity, and antigen-specific T-cell and B-cell responses. Biomedical ontologies (e.g., VO, OBI, and PRO) play important roles in data representation, integration, and automated reasoning in vaccine-related flow cytometry research.

16:00 Ryan Brinkman (Vancouver)
::1. Overview of the representation of flow cytometry assays in OBI
::2. Overview of [http://www.bioconductor.org/packages/release/bioc/html/flowMeans.html flowMeans] and [http://flowcap.flowsite.org/ flowCAP]
::3. Connecting results from automated FCM analysis systems with the Cell Ontology

----

''Day 3: Wednesday, June 13, 2012:9:00am-6:00pm''

'''The Role of Ontologies in Clinical Medicine'''

Note change of venue to: [http://www.hwi.buffalo.edu/about_hwi/visitor/maps_directions.html, Hauptmann-Woodward Institute, Buffalo]

9:00 Breakfast

Further discussion of Immunology Ontology including:

9:30 Bjoern Peters (La Jolla Institute for Allergy and Immunology)
::Representation of immunology experiments using OBI
::Representing epitope mapping experiments for the Immune Epitope Database (IEDB)
:::The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meaning to describe all aspects of how biomedical investigations are conducted. OBI builds on the Gene Ontology (GO) and related efforts that provide a formal and interoperable representation of biomedical knowledge. OBI adds the ability to describe how this knowledge was derived. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. The presentation will describe the state of OBI and several applications that are using it. Specific focus will be on epitope mapping and characterization experiments captured in the Immune Epitope Database (IEDB) which heavily utilizes OBI. The presentation will also point out gaps in coverage of immunological terms that are currently in OBI but poorly defined and outside the scope of OBI, and which deserve a better home.

10:30 Break

11:00 Alexander Diehl (Buffalo)
:Towards Auto-Immune Disease Ontology

'''noon-3pm SESSION OPEN TO THE PUBLIC: Practical Applications of Ontologies in Clinical Research''' (includes lunch)

:Albert Goldfain (Blue Highway / Syracuse)
::Creating Personalized Infectious Disease Ontologies

:Alan Ruttenberg (Buffalo)
::The Protein Ontology and the treatment of protein isoforms, mutations, and aggregates of relevance to Alzheimer's Disease

:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
::Ontologies and Vector-Borne Diseases

:Werner Ceusters (Buffalo)
::Assessment instruments and biomedical reality: examples in the pain domain

'''3pm-6pm: Working Session on the Ontology for General Medical Science (OGMS)'''

:Moderator: Albert Goldfain (Blue Highway / Syracuse)
:Topics to be treated will include:
::Current status of OGMS and the OGMS Reference
::Linking diseases to their underlying disorders using basis relations
::Defining 'relapse' and 'remission' processes.
::Updates on the Vital Sign Ontology
::Recipes for OGMS-conformant extension ontologies
:''Close: 6:00pm''
----
'''Relevant ontology efforts'''

:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
:CL Cell ontology immune branches (e.g. for dendritic cells)
:PRO Protein Ontology
:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
:IEO Immune Epitope Ontology (Bjoern Peters)
:MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
:OGMS Ontology for General Medical Science (Albert Goldfain)
:IDO Infectious Disease Ontology (Lindsay Cowell)
:Vaccine Ontology (Oliver He)
:AO Allergy Ontology (Alex C. Yu)
:ND Neurological Disease Ontology (Alexander Diehl)
----
'''

== Participants will include ==
'''

:Ryan Brinkman (University of British Columbia)
:Atul Butte (Stanford University)
:James S. Cavenaugh (University of Rochester Medical Center)
:Werner Ceusters (University at Buffalo)
:Cliburn Chan (Duke University)
:Quan Chen (NIH/NIAID)
:Melanie Courtot (BCCRC, Vancouver)
:Lindsay Cowell (University of Texas Southwestern Medical Center)
:Oliver Crespo (BD Biosciences, San Jose, CA)
:Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
:Peter d'Eustachio (New York University)
:Alexander Diehl (University at Buffalo)
:Chester Fox (University at Buffalo)
:Lee Ann Garrett-Sinha (University at Buffalo)
:Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
:Oliver He (University of Michigan)
:Leonard Jacuzzo (University at Buffalo)
:Mark Jensen (University at Buffalo)
:Christos (Kitsos) Louis (IMBB-FORTH, Crete)
:Nikesh Kotecha (Cytobank)
:Yu Lin (University of Michigan)
:Wei Luo (University at Buffalo)
:Supriya Mahajan (University at Buffalo)
:Anna Maria Masci (Duke University)
:Darren Natale (Georgetown University)
:Dave Parrish (Digital Infuzion)
:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
:Mark Ressler (University at Buffalo)
:Jessica L. Reynolds (University at Buffalo)
:Alan Ruttenberg (University at Buffalo)
:Stanley A. Schwartz (University at Buffalo)
:Prontip Saelee (University at Buffalo)
:Veronica Shamovsky (NYU School of Medicine)
:Barry Smith (University at Buffalo)
:Cathy Wu (University of Delaware, Georgetown University)
:Alex C. Yu (University at Buffalo)

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-14T14:35:30Z

Adiehl:

Alzforum / Protein Ontology Kick-Off Meeting

2011-09-27T16:18:57Z

Adiehl: /* Intending Participants */

The Alzforum / Protein Ontology collaboration is a driving biological project of the NIGMS-funded [http://pir.georgetown.edu/pro/ Protein Ontology] initiative.

==Goals of the meeting==

The goal of this meeting is to initiate a project to create a protein information resource that will address the needs of Alzheimer's Disease (AD) researchers in a maximally effective way. The focus of the meeting will be directed primarily towards identifying these needs through discussion with specialists in different aspects of AD research. The intended long-term outcome will take the form of elaborations and extensions of the Protein Ontology (PRO), of new applications of the ontology to annotation of AD research results, and of new PRO-based applications to support AD research.

==Date and Venue==

October 4-5, 2011, [http://www.hotelbuffaloamherst.com/ Hotel Indigo], Buffalo, NY

==Topics to be addressed==

'''Protein Variants'''

How can we most effectively represent information pertaining to the variants associated with AD and to the relations between them; for example, what level of specificity of descriptions of variants would best address the requirements of AD researchers? In the case of APP, for example, what are the genetic variants of relevance to APP? How should the Protein Ontology deal with such variants in order to assist researchers?

'''Aggregates of proteins / Protein complexes'''

What are the different kinds of aggregates and complexes relevant to AD, how do AD researchers treat them?

We envisage two case studies in the course of the meeting, both of which will be designed to serve as guidance for Protein Ontology developers in the initial phases of the project:

1. Protein case study: Perform a detailed review of one class of proteins important to AD research, chosen to be part of the research agenda of at least one of the AD scientists, to bring all participants up to the same level of understanding about what is known. Issues to be addressed will include:
:: importance of recording non-protein constituents
:: multimerism
:: relations to disease hypotheses
:: kinds of evidence
:: research plan
:: protein knowledge queries that would aid the AD researchers
:: protein knowledge queries that would help others retrieve AD research results

2. Protein complex case study: In addition to the issues addressed above as these arise for protein complexes, this case study will address in addition: criteria for being a complex - what amount of stability is necessary, component stoichiometry and structure, modifications/changes to complexes and associated functional changes.

==Schedule==

'''Monday, October 3'''

7:00pm Dinner [for available participants / Location to be Announced]

'''Tuesday, October 4'''

8:30am Continental Breakfast

9:30am

*Alan Ruttenberg: Introduction to the project; introduction of project personnel
*Dominic Walsh: Introduction to the Alzheimer's Disease research
*Barry Smith: Introduction to ontology for scientists
*Cathy Wu: Introduction to PRO

10:30am Refreshment Break

11:00am

*Darren Natale: Short tutorial on the Protein Ontology and associated web tools (including feedback)
*NNN: Review of proteomics information tools and resources used by AD researchers, unmet needs

12:30pm Lunch

1:30pm
*AD-relevant variants, complexes, aggregates

3:00pm Refreshment Break

3:30
*Session TBD

6:00pm Dinner [Location to be Announced]

'''Wednesday, October 5'''

8:30am Continental Breakfast

9:00am Case Studies

10:30am Refreshment Break

12:30pm Lunch

1:30pm Case Studies

2:30pm Project planning

3:30pm Main meeting ends / Refreshment Break

Technical session for selected participants during rest of day.

6:00pm Dinner [for available participants / Location to be Announced]

==Intending Participants==
*Cecilia Arighi (PRO / University of Delaware)
*Paolo Ciccarese (Massachusetts General Hospital / Harvard Medical School, Boston)
*Kelly Anne Dakin (Alzforum, Boston)
*Paresh Dandona (University at Buffalo)
*Timothy Danford (Novartis, Boston)
*Peter D'Eustachio (Reactome / NYU School of Medicine, New York)
*Alexander Diehl (CL, GO / University at Buffalo)
*Fahim Imam (NIF / University of California at San Diego)
*Darren Natale (PRO / Georgetown University Medical Center, Washington DC)
*Caryn-Amy Rose (Alzforum, Boston)
*Alan Ruttenberg (University at Buffalo)
*Barry Smith (University at Buffalo)
*Kinga Szigati (University at Buffalo)
*Dominic M. Walsh (Brigham & Women's Hospital, Harvard Institutes of Medicine, Boston)
*Michael Wolfe (Brigham & Women's Hospital, Center for Neurologic Diseases, Boston)
*Cathy Wu (PRO / University of Delaware)
*Elizabeth Wu (Alzforum, Boston)

May 2008 Is a Orphans in the Cell Ontology

2009-10-09T18:16:51Z

Adiehl:

(Note that this page is hosted at www.bioontology.org/wiki)

[http://obofoundry.org/wiki/index.php/CL:Main_Page Return to CL:Main Page]

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node cell. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please look at the list below and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.

Please note that some of these cells do have a direct is_a parent but lack an is_a path to the root because their parent or grandparent has no is_a parent itself. In such cases correcting the parentage of a higher level cell type may correct the parentage of many lower level cell types as well.

ID Name Suggested Is_a Parent
CL:0000462 adepithelial cell
CL:0000336 adrenal medulla cell
CL:0000127 astrocyte
CL:0000644 Bergmann glial cell
CL:0000569 cardiac mesenchymal cell
CL:0000141 cementocyte
CL:0000348 choroidal cell
CL:0000392 crystal cell
CL:0000345 dental papilla cell
CL:0000715 embryonic crystal cell
CL:0000736 embryonic gland hemocyte
CL:0000734 embryonic gland plasmatocyte
CL:0000683 ependymoglial cell
CL:0000082 epithelial cell of lung
CL:0000083 epithelial cell of pancreas
CL:0000135 fibrocyte
CL:0000125 glial cell
CL:0000243 glial cell (sensu Vertebrata)
CL:0000292 guard cell
CL:0000262 guard mother cell
CL:0000143 guidepost cell
CL:0000346 hair papilla cell
CL:0000387 hemocyte (sensu Nematoda and Protostomia)
CL:0000142 hyalocyte
CL:0000854 interneuromast cell
CL:0000396 lamellocyte
CL:0000716 lymph gland crystal cell
CL:0000735 lymph gland hemocyte
CL:0000733 lymph gland plasmatocyte
CL:0000126 macroglial cell
CL:0000401 macrophage (sensu Diptera)
CL:0000242 Merkel cell
CL:0000650 mesangial cell
CL:0000335 mesenchyme condensation cell
CL:0000636 Muller cell
CL:0000680 muscle precursor cell
CL:0000133 neurectodermal cell
CL:0000710 neuroepithelial cell
CL:0000095 neuron associated cell
CL:0000130 neuron associated cell (sensu Nematoda and Protostomia)
CL:0000123 neuron associated cell (sensu Vertebrata)
CL:0000029 neuron neural crest derived
CL:0000128 oligodendrocyte
CL:0000570 parafollicular cell
CL:0000516 perineuronal satellite cell
CL:0000645 pituicyte
CL:0000394 plasmatocyte
CL:0000391 podocyte (sensu Diptera)
CL:0000398 polygonal cell
CL:0000395 procrystal cell
CL:0000347 scleral cell
CL:0000297 socket cell
CL:0000499 stromal cell
CL:0000114 surface ectodermal cell
CL:0000643 tanycyte
CL:0000307 tracheal epithelial cell
CL:0000282 trichome

Thanks for your help!

NIAID Cell Ontology Workshop May 2008

2009-10-09T18:13:26Z

Adiehl:

(Note that this page is hosted at www.bioontology.org/wiki)

[http://obofoundry.org/wiki/index.php/CL:Main_Page Return to CL:Main Page]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==
(note the '.obo' files below all have a bogus '.doc' extension added to allow them to be loaded in to the wiki) 

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, last revised 8-20-08) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revisions.obo.doc|Macrophage_ontology_revisions.obo]] 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Anna Maria Masci) 
[[Media:Revised_Dendritic_Cells.pdf|Revised Dendritic Cells.pdf]] 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Penny Morel) 
[[Media:NK cell and further T cell revision.ppt|NK cell and further T cell revision.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, same file as above, last revised 8-20-08) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

CL:Main Page

2009-10-09T18:08:56Z

Adiehl: /* CL - OBO Cell Ontology */

=CL - OBO Cell Ontology=

The official Cell Ontology wiki is now hosted at [http://obofoundry.org/wiki/index.php/CL:Main_Page http://obofoundry.org/wiki/index.php/CL:Main_Page], although certain links on that wiki refer back to older content here.

=Resources=

==Ontology==

http://obofoundry.org/obo/CL

===Applications===

[[CL:Aligning species-specific anatomy ontologies with CL]]

[[Media:CLalign.biocuratorposter.final.ppt|CL_alignment_Biocurator07_poster]]

==Request tracker==

- [http://sourceforge.net/tracker/?group_id=76834&atid=925065 CL tracker]

You can also submit requests to the list.

==Mail Lists==

- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct OBO CrossProduct]

GO is pre-coordinating biological process terms that refer to cell types using CL IDs

==Cell ontology restructuring efforts==

The cell ontology is being restructured with the general goals of improving definitions, moving towards single inheritance and is_a completeness, and making the CL more interoperable with the GO and CARO. These discussions are occurring via chat, the histories of which will be posted here. Please email the OBO cell list if you would like to participate.

[[Media:cell_ontology_evaluation.doc|cell ontology evaluation.doc]]

[[Media:cellchat.2.12.07.doc|cellchat.2.12.07.doc]]

[[Media:cellchat.2.23.07.doc|cellchat.2.23.07.doc]]

[[Media:cellchat.2.27.07.doc|cellchat.2.27.07.doc]]

[[Media:cellchat.3.15.07.doc|cellchat.3.15.07.doc]]

[[Media:cellchat.6.1.07.doc|cellchat.6.1.07.doc]]

[[Media:cellchat.8-9-2007.doc|cellchat.8-9-2007]]

[[Media:cell_chat_8-24-2007.doc|cell_chat_8-24-2007]]

An initial rough draft can be found below in OBO format with the proposed new branch at the same level as 'cell'. Current tasks include moving cells over to the 'by structure' branch to test for compatibility and potential problems.

[[Media:CLRevised.obo|CL Revised.obo]]

Notes and action items from the cell ontology breakout session at the 2nd International Biocuration Meeting 2007.
[[Media:Cell_ontology_reorganization_working_group_notes.doc|Cell_ontology_reorganization_working_group_notes.doc]]

===NIAID Cell Ontology Workshop, May 13-14, 2008===

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

More information on the workshop can be found [[NIAID Cell Ontology Workshop May 2008|here]].

===Is_a Completeness for the current Cell Ontology===

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node '''cell'''. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please check out the page for [[May 2008 Is_a Orphans in the Cell Ontology]] and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.

== A list of useful differentia for defining cell-type terms==

has_part: <GO:cellular_compomnent>

has_function_from_process: <GO:biological_process>

has_quality: <PATO:quality/monadic quality of continuant>

develops_into: <CL:cell>

has_part: <CHEBI:chebi_ontology>

has_part: (<CHEBI:chebi_ontology>^part_of <GO:cellular_component>)

CL:Main Page

2009-10-09T18:08:17Z

Adiehl: /* CL - OBO Cell Ontology */

=CL - OBO Cell Ontology=

The official Cell Ontology wiki is now hosted at [http://obofoundry.org/wiki/index.php/CL:Main_Page], although certain links on that wiki refer back to older content here.

=Resources=

==Ontology==

http://obofoundry.org/obo/CL

===Applications===

[[CL:Aligning species-specific anatomy ontologies with CL]]

[[Media:CLalign.biocuratorposter.final.ppt|CL_alignment_Biocurator07_poster]]

==Request tracker==

- [http://sourceforge.net/tracker/?group_id=76834&atid=925065 CL tracker]

You can also submit requests to the list.

==Mail Lists==

- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct OBO CrossProduct]

GO is pre-coordinating biological process terms that refer to cell types using CL IDs

==Cell ontology restructuring efforts==

The cell ontology is being restructured with the general goals of improving definitions, moving towards single inheritance and is_a completeness, and making the CL more interoperable with the GO and CARO. These discussions are occurring via chat, the histories of which will be posted here. Please email the OBO cell list if you would like to participate.

[[Media:cell_ontology_evaluation.doc|cell ontology evaluation.doc]]

[[Media:cellchat.2.12.07.doc|cellchat.2.12.07.doc]]

[[Media:cellchat.2.23.07.doc|cellchat.2.23.07.doc]]

[[Media:cellchat.2.27.07.doc|cellchat.2.27.07.doc]]

[[Media:cellchat.3.15.07.doc|cellchat.3.15.07.doc]]

[[Media:cellchat.6.1.07.doc|cellchat.6.1.07.doc]]

[[Media:cellchat.8-9-2007.doc|cellchat.8-9-2007]]

[[Media:cell_chat_8-24-2007.doc|cell_chat_8-24-2007]]

An initial rough draft can be found below in OBO format with the proposed new branch at the same level as 'cell'. Current tasks include moving cells over to the 'by structure' branch to test for compatibility and potential problems.

[[Media:CLRevised.obo|CL Revised.obo]]

Notes and action items from the cell ontology breakout session at the 2nd International Biocuration Meeting 2007.
[[Media:Cell_ontology_reorganization_working_group_notes.doc|Cell_ontology_reorganization_working_group_notes.doc]]

===NIAID Cell Ontology Workshop, May 13-14, 2008===

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

More information on the workshop can be found [[NIAID Cell Ontology Workshop May 2008|here]].

===Is_a Completeness for the current Cell Ontology===

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node '''cell'''. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please check out the page for [[May 2008 Is_a Orphans in the Cell Ontology]] and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.

== A list of useful differentia for defining cell-type terms==

has_part: <GO:cellular_compomnent>

has_function_from_process: <GO:biological_process>

has_quality: <PATO:quality/monadic quality of continuant>

develops_into: <CL:cell>

has_part: <CHEBI:chebi_ontology>

has_part: (<CHEBI:chebi_ontology>^part_of <GO:cellular_component>)

Infectious Disease Ontology 2008

2008-09-17T13:53:30Z

Adiehl: /* Participants */

== Background ==

A two-day IDO workshop for invited participants will be held in Buffalo, New York on September 16-17, 2008. This workshop is being organized with the generous support of the Burroughs Wellcome Fund.

The background to this meeting is an Infectious Disease Ontology workshop ([http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology IDO 2007]), which was organized in Cold Spring Harbor Laboratories in 2007. The workshop had four primary outcomes:

*Training of a core set of infectious disease researchers in ontology-development methods, facilitating their participation in ontology development;

*Development of a core Infectious Disease Ontology (IDO) which is designed to serve as a consensus-based controlled vocabulary resource for annotation of data representing all entities relevant to infectious diseases generally;

*Establishment of a method for creating, on the basis of IDO, a set of ontologies that can be developed in a distributed fashion yet together cover the entire infectious disease domain (the set consists of the above-described core IDO ontology plus sub-domain-specific extensions of the core, such as IDO-tuberculosis, IDO-malaria);

*Formation of an Infectious Disease Ontology Consortium (IDOC) whose members have agreed to contribute towards continued development of the core IDO and to develop seven different sub-domain-specific ontologies.

== IDO 2008 Goals ==

To capitalize on these outcomes and to sustain the momentum gained from the 2007 workshop, we have scheduled a second Infectious Disease Ontology workshop, to be held in Buffalo, NY on September 16-17, 2008. The goals of this meeting are:

1. to critically evaluate the IDO core ontology for biological and ontological correctness

2. to critically evaluate the ontology development test cases initiated at IDO 2007 for biological and ontological correctness

3. to identify specific research questions that the ontologies should help to provide answers to in domains such as:
*analysis of high-throughput data (data mining)
*analysis of literature (text-mining)
*clinical decision support
*case-control studies
*disease surveillance
*genetic susceptibility of infectious disease
*design of prevention and treatment strategies

== IDO 2008 Schedule ==

'''Day 1: Tuesday, September 16'''

*8:30am - Continental Breakfast

*9:00am - ''Introduction to the Workshop'' [http://ontology.buffalo.edu/08/IDO/COWELL.ppt slides] (Lindsay Cowell)

*9:15am - ''Introduction to Biomedical Ontology'' [http://ontology.buffalo.edu/08/IDO/SMITH.ppt slides] (Barry Smith)

*10:00am - ''Introduction to the Infectious Disease Ontology'' [http://ontology.buffalo.edu/08/IDO/Cowell%20IDO.ppt slides] (Lindsay Cowell)

*11:00am - Refreshment Break

*11:30am - ''The Infectious Disease Portion of the Immune Epitope Database Ontology and its Relationship to IDO'' [http://ontology.buffalo.edu/08/IDO/PETERS.ppt slides] (Bjoern Peters)

*12:30pm - Lunch

*1:30pm - ''The Vaccine Ontology'' [http://ontology.buffalo.edu/08/IDO/HE.ppt slides] (Yongqun He)

*2:30pm - ''The Staphylococcus Aureus Ontology'' (Vance Fowler)

*3:30pm - Refreshment Break

*4:00pm - ''The Infective Endocarditis Ontology and SemanticDB'' [http://ontology.buffalo.edu/08/IDO/ARABANDI.pdf slides] (Sivaram Arabandi)

*5:30pm - Dinner

*7:30pm - ''Ontologies in the Future of Infectious Disease Research: A Discussion'' (Introduced and Moderated by Christos Louis)

'''Day 2: Wednesday, September 17'''

*8:30am - Continental Breakfast

*9:00am - ''The Vector-Borne Disease Ontology'' (Christos Louis)

*10:00am - ''The Dengue Fever Ontology'' (Saul Lozano-Fuentes)

*11:00am - Refreshment Break

*11:15am - ''The Influenza Ontology'' (Burke Squires)

*12:15pm - Working Lunch: ''Refining IDO and Its Extensions to Better Support Interoperability'' (Barry Smith)

*1:45pm - ''Current and Future Applications of the IDO Methodology'' (Alan Ruttenberg)

*2:45pm - Refreshment Break

*3:00pm - ''Goals for the Coming Year'' (Lindsay Cowell)

*4:00pm - Close

'''Format'''

One person will designated as moderator for each session. All sessions will emphasize group discussion over presentation. Moderators of the ontology evaluation sessions will be responsible for beginning the session with a brief presentation of the ontology and will be prepared to navigate and display the ontology throughout the discussion. Moderators for the remaining sessions will be responsible for jumpstarting discussion with a brief outline of discussion points.

== IDO 2008 Venue ==

The venue for our meeting will be the [http://www.ramadahotelamherst.com/ramada-hotel.html Ramada Inn and Conference Center] in Amherst, NY.

== Participants ==

Sivaram Arabandi (Cleveland Clinic)

Robert Arp (NCBO / University at Buffalo)

Tiffani Bright (Columbia University)

Marlize Coleman (Colorado State University)

Lindsay Cowell (Duke University Medical Center)

Alexander Diehl (Gene Ontology / The Jackson Laboratory)

Vance Fowler (Duke University Medical Center)

Steve Gill (University at Buffalo)

Louis Goldberg (University at Buffalo)

Yongqun "Oliver" He (University of Michigan Medical Center)

Yentram Huyen (Lockheed Martin, OTIS/NIAID/NIH Contractor)

Carla Kuiken (Los Alamos National Laboratory)

Alan J. Lesse (University at Buffalo)

Christos (Kitsos) Louis (IMBB-FORTH, Crete)

Saul Lozano-Fuentes (Colorado State University)

Joanne Luciano (The MITRE Corp.)

Anna Maria Masci (Duke University Medical Center)

Simon Milton (University of Melbourne)

Chris Mungall (Gene Ontology / Lawrence Berkeley National Laboratory)

Darren Natale (Protein Ontology / Georgetown University)

Bjoern Peters (La Jolla Institute for Allergy & Immunology)

Alan Ruttenberg (Science Commons)

Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)

Lynn Schriml (University of Maryland)

Barry Smith (NCBO / University at Buffalo)

Burke Squires (University of Texas Southwestern Medical Center at Dallas)

Christian Stoeckert (Penn Center for Bioinformatics / Univ of PA)

Tod Strugnell (Sanofi Pasteur)

Pantelis Topalis (IMBB-FORTH, Crete)

== Progress Since the IDO 2007 ==
Progress has been made in the development of IDO and seven sub-domain-specific extensions of IDO. The sub-domain-specific extensions ontologies for the following diseases:
::Tuberculosis (Carol Dukes-Hamilton, Duke University Medical Center)
::Staphylococcus aureus bacteremia (Vance Fowler, Duke University Medical Center)
::Infective endocarditis (Sivaram Arabandi, Cleveland Clinic Foundation)
::Malaria and other vector-borne diseases (Christos Louis, Institute for Molecular Biology and Biochemistry – FORTH)
::Dengue fever (Saul Lozano-Fuentes, Colorado State)
::Influenza (Stuart Sealfon, Mount Sinai School of Medicine; Richard Scheuermann, University of Texas, Southwestern Medical Center)

Development of IDO has continued along two fronts, expansion of content driven by development of the subdomain-specific ontologies and refinement of the approach to representing infectious disease-relevant entities ontologically.

IDO is supplemented also by a '''[http://www.violinet.org/wiki/index.php/Vaccine_Ontology Vaccine Ontology]''' which is being developed by Yongqun He (University of Michigan) in collaboration with Lindsay Cowell and Barry Smith.

In collaboration with Dr. Carol Dukes-Hamilton at Duke University Medical Center, Drs. Cowell and Smith have begun developing a '''draft ontology of tuberculosis''' and a method for defining ISO 11179 data elements using logical constructs based on terms derived from ontologies. Dr. Dukes-Hamilton’s research group has defined eighty tuberculosis data elements and curated these into the National Cancer Institute’s metadata repository, caDSR. Definition of these data elements using ontology terms provides not only a formal method for data element definition, significantly improving the resulting definitions, but also interoperability between data elements (along with the data associated therewith) and the vast amount of biomedical data and information annotated with terms from the same or an interoperable set of ontologies.

In collaboration with Dr. Vance Fowler at Duke University Medical Center, Drs. Cowell and Smith have developed a '''draft ontology of Staphylococcus aureus bacteremia'''.

Dr. Sivaram Arabandi of the Cleveland Clinic Foundation is part of a large team developing SemanticDB technology, a semantic datastore with query functionality, having primary focus on Cardiology and Cardiothoracic Surgery. A portion of this work involves developing an IDO extension '''ontology for infective endocarditis'''.

Dr. Christos Louis’ research group at the Institute of Molecular Biology and Biochemistry (IMBB), one of the seven institutes of the Foundation for Research and Technology – Hellas (FORTH), based in Crete, is developing an '''IDO extension for malaria and other vector-borne diseases'''. The group is working in parallel to develop an '''ontology of the physiological processes of disease vectors''' that play a direct or indirect role in disease transmission. These ontology development efforts are being pursued within the context of VectorBase (http://www.vectorbase.org), an NIAID Bioinformatics Resource Center for invertebrate vectors of human pathogens, and embracing efforts to construct decision support systems for vector-borne diseases.

A collaborative group of researchers including Joanne Luciano (MITRE), Burke Squires (University of Texas, Southwestern Medical Center) and Lynn Schriml (University of Maryland, School of Medicine), have utilized the Ontology of Biomedical Investigations (OBI) components of
materials/objects, qualities and processes to develop an '''influenza ontology''' and to map influenza virus sequence and surveillance terms to their respective materials and qualities.

The Influenza Ontology describes by category the Investigator, Event, Location, Strain Specimen, Amplified Strain Specimen, Virion RNA, Treatment, and Host. The groups from BHB, IGS and MITRE have consolidated influenza sequence and surveillance terms from resources
such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS), and the Gemina and Influenza Virus Genome Projects. The list of data fields that describe influenza virus isolates and surveillance data has been created by consolidating data fields from data contributors and separate CEIRS participants. The initial
ontology of terms has been created with a cross reference of terms to existing OBO Foundry ontologies.

The CEIRS projects consist of two research areas: influenza virus surveillance and basic influenza virus sequence and genetic reassortment. Working in collaboration with Dr. Richard Scheuermann, University of Texas, Southwestern Medical Center, the immediate goal is to apply the Influenza Virus Ontology to data collected as part of the CEIRS projects in an effort to enable influenza researchers to more easily elucidate the causes of influenza virulence and pathogenesis. Once completed, a database schema based upon the OBI will serve as the repository for influenza sequence and surveillance data through the
BHB portal.

For more information about IDO and its sub-domain extensions, see http://www.infectiousdiseaseontology.org.

NIAID Cell Ontology Workshop May 2008

2008-08-21T20:06:47Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==
(note the '.obo' files below all have a bogus '.doc' extension added to allow them to be loaded in to the wiki) 

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, last revised 8-20-08) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revisions.obo.doc|Macrophage_ontology_revisions.obo]] 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Anna Maria Masci) 
[[Media:Revised_Dendritic_Cells.pdf|Revised Dendritic Cells.pdf]] 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Penny Morel) 
[[Media:NK cell and further T cell revision.ppt|NK cell and further T cell revision.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, same file as above, last revised 8-20-08) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

File:NK cell and further T cell revision.ppt

2008-08-21T20:05:30Z

Adiehl: Slides showing revisions to the NK cell ontology and further revisions to the T cell ontology.

Slides showing revisions to the NK cell ontology and further revisions to the T cell ontology.

NIAID Cell Ontology Workshop May 2008

2008-08-21T15:51:03Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==
(note the '.obo' files below all have a bogus '.doc' extension added to allow them to be loaded in to the wiki) 

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, last revised 8-20-08) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revisions.obo.doc|Macrophage_ontology_revisions.obo]] 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Anna Maria Masci) 
[[Media:Revised_Dendritic_Cells.pdf|Revised Dendritic Cells.pdf]] 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, same file as above, last revised 8-20-08) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-08-21T15:49:18Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==
(note the '.obo' files below all have a bogus '.doc' extension added to allow them to be loaded in to the wiki) 

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, last revised 8-20-08) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revisions.obo.doc|Macrophage_ontology_revisions.obo]] 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Anna Maria Masci) 
[[Media:Revised_Dendritic_Cells.pdf|Revised Dendritic Cells.pdf]] 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, same file as above, last revised 8-20-08) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-08-21T15:48:37Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==
(note the '.obo' files below all have a bogus '.doc' extension added to allow them to be loaded in to the wiki) 

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, last revised 8-20-08) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revisions.obo.doc|Macrophage_ontology_revisions.obo]] 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Anna Maria Masci) 
[[Media:Revised_Dendritic_Cells.pdf|Revised Dendritic Cells.pdf]] 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, same file as above, last revised 8-20-08) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-08-21T15:45:08Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, last revised 8-20-08) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revisions.obo.doc|Macrophage_ontology_revisions.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Anna Maria Masci) 
[[Media:Revised_Dendritic_Cells.pdf|Revised Dendritic Cells.pdf]] 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (T cell and NK revisions, same file as above, last revised 8-20-08) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

File:Revised Dendritic Cells.pdf

2008-08-21T15:39:14Z

Adiehl: Graph of revised dendritic cells as prepared by Lindsay Cowell and Anna Maria Masci.

Graph of revised dendritic cells as prepared by Lindsay Cowell and Anna Maria Masci.

File:Conventional Dendritic Cells.pdf

2008-08-21T15:35:05Z

Adiehl:

Revised dendritic cells, both conventional and plasmacytoid DCs.

File:Conventional Dendritic Cells.pdf

2008-08-21T15:28:40Z

Adiehl: Revised conventional dendritic cells

Revised conventional dendritic cells

NIAID Cell Ontology Workshop May 2008

2008-07-28T20:49:38Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-24-08) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revisions.obo.doc|Macrophage_ontology_revisions.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-28T20:49:19Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-24-08) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revisions.obo.doc|Macrophage_ontology_revisions.obo]](added a bogus .doc extension to get this to load into the wiki) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-28T20:48:33Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-24-08) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 
[[Media:Macrophage_ontology_revision.pdf|Macrophage_ontology_revision.pdf]] 
[[Media:Macrophage_ontology_revision.obo.doc|Macrophage_ontology_revision.obo]](added a bogus .doc extension to get this to load into the wiki) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

File:Macrophage ontology revision.pdf

2008-07-28T20:46:45Z

Adiehl: A graphical view of the revised macrophages in the Cell Ontology.

A graphical view of the revised macrophages in the Cell Ontology.

File:Macrophage ontology revisions.obo.doc

2008-07-28T20:45:17Z

Adiehl: The macrophage revisions as incorporated in the current Cell Ontology.

The macrophage revisions as incorporated in the current Cell Ontology.

NIAID Cell Ontology Workshop May 2008

2008-07-28T20:41:43Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-24-08) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: Thursday, August 21, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

'''B Cells: Thursday, August 21, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-28T20:40:51Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-24-08) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''Macrophages: Friday, August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

'''B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-28T20:40:21Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-24-08) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''Macrophages: Friday,: August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

'''B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-24T17:22:45Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-24-08) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

'''Macrophages: Date to be determined. Tentative date: August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-24T05:00:10Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-23-08) 
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

'''Macrophages: Date to be determined. Tentative date: August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-24T04:59:54Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
(revised versions of the following files uploaded 7-23-08)
[[Media:T_cell_ontology_revisions.ppt|T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

'''Macrophages: Date to be determined. Tentative date: August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-21T20:51:21Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

'''T Cells: July 24, 3:30 PM-4:30 PM ET''' (Discussion leader: Penny Morel) 
[[Media:T_cell_ontology_revisions.ppt]] 
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki) 

'''B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET''' (Discussion leader: Martin Zand) 

'''Macrophages: Date to be determined. Tentative date: August 1st., 2:00 PM-3:00 PM ET''' (Discussion leaders: Anastasia Nijnik and Elizabeth Gold) 

'''Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET''' (Discussion leaders: Lindsay Cowell and Bali Pulendran) 

'''NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET''' (Discussion leader: Alex Diehl and Penny Morel) 

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-21T20:48:11Z

Adiehl: /* Cell Ontology Workshop Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

T Cells: July 24, 3:30 PM-4:30 PM ET (Discussion leader: Penny Morel)
[[Media:T_cell_ontology_revisions.ppt]]
[[Media:T_cell_ontology.obo.doc|T_cell_ontology.obo]] (added a bogus .doc extension to get this to load into the wiki)

B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET (Discussion leader: Martin Zand)

Macrophages: Date to be determined. Tentative date: August 1st., 2:00 PM-3:00 PM ET (Discussion leaders: Anastasia Nijnik and Elizabeth Gold)

Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET (Discussion leaders: Lindsay Cowell and Bali Pulendran)

NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET (Discussion leader: Alex Diehl and Penny Morel)

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

File:T cell ontology.obo.doc

2008-07-21T20:46:19Z

Adiehl: A revised version of the Cell Ontology file incorporating changes to the representation of T cells.

A revised version of the Cell Ontology file incorporating changes to the representation of T cells.

File:T cell ontology revisions.ppt

2008-07-21T20:41:19Z

Adiehl: This file shows the new T cell terms and the revised structure of the Cell Ontology in the area of T cells.

This file shows the new T cell terms and the revised structure of the Cell Ontology in the area of T cells.

NIAID Cell Ontology Workshop May 2008

2008-07-21T20:39:11Z

Adiehl: /* Cell Ontology Follow Up Conference Calls, July-August 2008 */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Workshop Follow Up Conference Calls, July-August 2008==

T Cells: July 24, 3:30 PM-4:30 PM ET (Discussion leader: Penny Morel)

B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET (Discussion leader: Martin Zand)

Macrophages: Date to be determined. Tentative date: August 1st., 2:00 PM-3:00 PM ET (Discussion leaders: Anastasia Nijnik and Elizabeth Gold)

Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET (Discussion leaders: Lindsay Cowell and Bali Pulendran)

NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET (Discussion leader: Alex Diehl and Penny Morel)

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

NIAID Cell Ontology Workshop May 2008

2008-07-21T20:38:48Z

Adiehl: /* Slide Presentations from Meeting */

[[CL:Main Page|Return to CL:Main Page]]

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

[[NIAID Cell Ontology Workshop Agenda|Workshop Agenda]]

[[NIAID_Cell_Ontology_Workshop_Summary|Summary of Workshop Proceedings]]

==Graphical Views of Hematopoietic Cells in the Cell Ontology (May 2008)==

<gallery>
Image:T cells.jpg|T Cells
Image:B cells.jpg|B Cells
Image:Natural Killer Cells.jpg|Natural Killer Cells
Image:DendriticCells.jpg|Dendritic Cells
Image:Macrophages-osteoclasts.jpg|Macrophages and Osteoclasts
Image:Granulocytes and Mast_Cells.jpg|Granulocytes and Mast Cells
Image:Erythrocytes and Platelets.jpg|Erythrocytes and Platelets
</gallery>

==Slide Presentations from Meeting==

[[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|A_Diehl_Cell_Ontology_Workshop_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|C_Mungall_OBO_Introduvtion]]

[[Media:A_Diehl_Meeting_Goals.ppt|A_Diehl_Meeting_Goals]]

[[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|R_Scheuermann_Cell_Ontology_Intro]]

[[Media:A_Diehl_T_cell_Introduction.ppt|A_Diehl_T_cell_Introduction]]

[[Media:P_Morel_Tcellworkshop.ppt|P_Morel T cells]]

[[Media:B_Cell_introduction_A_Diehl.ppt|A_Diehl_B_Cell_Introduction]]

[[Media:Cell-NIAID-OBO-Mungall.ppt|OBO Foundry, Chris Mungall]]

==Cell Ontology Follow Up Conference Calls, July-August 2008==

T Cells: July 24, 3:30 PM-4:30 PM ET (Discussion leader: Penny Morel)

B Cells: August 21, Thursday, 4:30 PM - 5:30 PM ET (Discussion leader: Martin Zand)

Macrophages: Date to be determined. Tentative date: August 1st., 2:00 PM-3:00 PM ET (Discussion leaders: Anastasia Nijnik and Elizabeth Gold)

Dendritic Cells: Tuesday, August 19, 3:00 PM-4:00 PM ET (Discussion leaders: Lindsay Cowell and Bali Pulendran)

NK Cells: August 21, Thursday, 3:00 PM-4:00 PM ET (Discussion leader: Alex Diehl and Penny Morel)

==Important Links==

[http://www.obofoundry.org/ OBO Foundry Ontologies]

[http://tsb.mssm.edu/NIAID/index.php/CellType_Ontology Cell Type Ontology page on the Modeling Immunity for Biodefense WIki] (requires approval)

[http://obo.cvs.sourceforge.net/obo/obo/ontology/anatomy/cell_type/cdo.obo?view=log Leukocyte Surface Marker Ontology] (cdo.obo, created by Martin Zand)

[http://www.geneontology.org/ GO Consortium Home Page]

[[Media:ImmuneProt.xls|Immune Protein List (excel)]]

An Excel spreadsheet of current immune and hematopoietic cell types in the Cell Ontology can be found [[Media:Hematopoietic_Cell_List.xls|here]]. This spreadsheet has columns for additional descriptive information for the existing immune cell types that participants are invited to fill in as they like: proper is_a parent, morphology, surface markers, transcription factors, location, role or process, and lineage. This information will be used in constructing formal definitions for these cell types.

CL:Main Page

2008-05-30T17:00:27Z

Adiehl: /* Is_a Completeness for the current Cell Ontology */

=CL - OBO Cell Ontology=

=Resources=

==Ontology==

Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net

===Applications===

[[CL:Aligning species-specific anatomy ontologies with CL]]

[[Media:CLalign.biocuratorposter.final.ppt|CL_alignment_Biocurator07_poster]]

==Request tracker==

- [http://sourceforge.net/tracker/?group_id=76834&atid=925065 CL tracker]

You can also submit requests to the list.

==Mail Lists==

- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct OBO CrossProduct]

GO is pre-coordinating biological process terms that refer to cell types using CL IDs

==Cell ontology restructuring efforts==

The cell ontology is being restructured with the general goals of improving definitions, moving towards single inheritance and is_a completeness, and making the CL more interoperable with the GO and CARO. These discussions are occurring via chat, the histories of which will be posted here. Please email the OBO cell list if you would like to participate.

[[Media:cell_ontology_evaluation.doc|cell ontology evaluation.doc]]

[[Media:cellchat.2.12.07.doc|cellchat.2.12.07.doc]]

[[Media:cellchat.2.23.07.doc|cellchat.2.23.07.doc]]

[[Media:cellchat.2.27.07.doc|cellchat.2.27.07.doc]]

[[Media:cellchat.3.15.07.doc|cellchat.3.15.07.doc]]

[[Media:cellchat.6.1.07.doc|cellchat.6.1.07.doc]]

[[Media:cellchat.8-9-2007.doc|cellchat.8-9-2007]]

[[Media:cell_chat_8-24-2007.doc|cell_chat_8-24-2007]]

An initial rough draft can be found below in OBO format with the proposed new branch at the same level as 'cell'. Current tasks include moving cells over to the 'by structure' branch to test for compatibility and potential problems.

[[Media:CLRevised.obo|CL Revised.obo]]

Notes and action items from the cell ontology breakout session at the 2nd International Biocuration Meeting 2007.
[[Media:Cell_ontology_reorganization_working_group_notes.doc|Cell_ontology_reorganization_working_group_notes.doc]]

===NIAID Cell Ontology Workshop, May 13-14, 2008===

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

More information on the workshop can be found [[NIAID Cell Ontology Workshop May 2008|here]].

===Is_a Completeness for the current Cell Ontology===

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node '''cell'''. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please check out the page for [[May 2008 Is_a Orphans in the Cell Ontology]] and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.

== A list of useful differentia for defining cell-type terms==

has_part: <GO:cellular_compomnent>

has_function_from_process: <GO:biological_process>

has_quality: <PATO:quality/monadic quality of continuant>

develops_into: <CL:cell>

has_part: <CHEBI:chebi_ontology>

has_part: (<CHEBI:chebi_ontology>^part_of <GO:cellular_component>)

May 2008 Is a Orphans in the Cell Ontology

2008-05-30T16:57:05Z

Adiehl:

[[CL:Main Page|Return to CL:Main Page]]

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node cell. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please look at the list below and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.

Please note that some of these cells do have a direct is_a parent but lack an is_a path to the root because their parent or grandparent has no is_a parent itself. In such cases correcting the parentage of a higher level cell type may correct the parentage of many lower level cell types as well.

ID Name Suggested Is_a Parent
CL:0000462 adepithelial cell
CL:0000336 adrenal medulla cell
CL:0000127 astrocyte
CL:0000644 Bergmann glial cell
CL:0000569 cardiac mesenchymal cell
CL:0000141 cementocyte
CL:0000348 choroidal cell
CL:0000392 crystal cell
CL:0000345 dental papilla cell
CL:0000715 embryonic crystal cell
CL:0000736 embryonic gland hemocyte
CL:0000734 embryonic gland plasmatocyte
CL:0000683 ependymoglial cell
CL:0000082 epithelial cell of lung
CL:0000083 epithelial cell of pancreas
CL:0000135 fibrocyte
CL:0000125 glial cell
CL:0000243 glial cell (sensu Vertebrata)
CL:0000292 guard cell
CL:0000262 guard mother cell
CL:0000143 guidepost cell
CL:0000346 hair papilla cell
CL:0000387 hemocyte (sensu Nematoda and Protostomia)
CL:0000142 hyalocyte
CL:0000854 interneuromast cell
CL:0000396 lamellocyte
CL:0000716 lymph gland crystal cell
CL:0000735 lymph gland hemocyte
CL:0000733 lymph gland plasmatocyte
CL:0000126 macroglial cell
CL:0000401 macrophage (sensu Diptera)
CL:0000242 Merkel cell
CL:0000650 mesangial cell
CL:0000335 mesenchyme condensation cell
CL:0000636 Muller cell
CL:0000680 muscle precursor cell
CL:0000133 neurectodermal cell
CL:0000710 neuroepithelial cell
CL:0000095 neuron associated cell
CL:0000130 neuron associated cell (sensu Nematoda and Protostomia)
CL:0000123 neuron associated cell (sensu Vertebrata)
CL:0000029 neuron neural crest derived
CL:0000128 oligodendrocyte
CL:0000570 parafollicular cell
CL:0000516 perineuronal satellite cell
CL:0000645 pituicyte
CL:0000394 plasmatocyte
CL:0000391 podocyte (sensu Diptera)
CL:0000398 polygonal cell
CL:0000395 procrystal cell
CL:0000347 scleral cell
CL:0000297 socket cell
CL:0000499 stromal cell
CL:0000114 surface ectodermal cell
CL:0000643 tanycyte
CL:0000307 tracheal epithelial cell
CL:0000282 trichome

Thanks for your help!

May 2008 Is a Orphans in the Cell Ontology

2008-05-30T16:56:22Z

Adiehl:

[[CL:Main Page|Return to CL:Main Page]

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node cell. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please look at the list below and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.

Please note that some of these cells do have a direct is_a parent but lack an is_a path to the root because their parent or grandparent has no is_a parent itself. In such cases correcting the parentage of a higher level cell type may correct the parentage of many lower level cell types as well.

ID Name Suggested Is_a Parent
CL:0000462 adepithelial cell
CL:0000336 adrenal medulla cell
CL:0000127 astrocyte
CL:0000644 Bergmann glial cell
CL:0000569 cardiac mesenchymal cell
CL:0000141 cementocyte
CL:0000348 choroidal cell
CL:0000392 crystal cell
CL:0000345 dental papilla cell
CL:0000715 embryonic crystal cell
CL:0000736 embryonic gland hemocyte
CL:0000734 embryonic gland plasmatocyte
CL:0000683 ependymoglial cell
CL:0000082 epithelial cell of lung
CL:0000083 epithelial cell of pancreas
CL:0000135 fibrocyte
CL:0000125 glial cell
CL:0000243 glial cell (sensu Vertebrata)
CL:0000292 guard cell
CL:0000262 guard mother cell
CL:0000143 guidepost cell
CL:0000346 hair papilla cell
CL:0000387 hemocyte (sensu Nematoda and Protostomia)
CL:0000142 hyalocyte
CL:0000854 interneuromast cell
CL:0000396 lamellocyte
CL:0000716 lymph gland crystal cell
CL:0000735 lymph gland hemocyte
CL:0000733 lymph gland plasmatocyte
CL:0000126 macroglial cell
CL:0000401 macrophage (sensu Diptera)
CL:0000242 Merkel cell
CL:0000650 mesangial cell
CL:0000335 mesenchyme condensation cell
CL:0000636 Muller cell
CL:0000680 muscle precursor cell
CL:0000133 neurectodermal cell
CL:0000710 neuroepithelial cell
CL:0000095 neuron associated cell
CL:0000130 neuron associated cell (sensu Nematoda and Protostomia)
CL:0000123 neuron associated cell (sensu Vertebrata)
CL:0000029 neuron neural crest derived
CL:0000128 oligodendrocyte
CL:0000570 parafollicular cell
CL:0000516 perineuronal satellite cell
CL:0000645 pituicyte
CL:0000394 plasmatocyte
CL:0000391 podocyte (sensu Diptera)
CL:0000398 polygonal cell
CL:0000395 procrystal cell
CL:0000347 scleral cell
CL:0000297 socket cell
CL:0000499 stromal cell
CL:0000114 surface ectodermal cell
CL:0000643 tanycyte
CL:0000307 tracheal epithelial cell
CL:0000282 trichome

Thanks for your help!

May 2008 Is a Orphans in the Cell Ontology

2008-05-30T16:56:02Z

Adiehl:

May 2008 Is a Orphans in the Cell Ontology

2008-05-30T16:48:28Z

Adiehl: New page: [[CL:Main Page|Return to CL:Main Page] As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node cell. We would like to provide this is_a path in short ord...

[[CL:Main Page|Return to CL:Main Page]

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node cell. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please look at the list below and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.

ID Name Suggested Is_a Parent
CL:0000462 adepithelial cell
CL:0000336 adrenal medulla cell
CL:0000127 astrocyte
CL:0000644 Bergmann glial cell
CL:0000569 cardiac mesenchymal cell
CL:0000141 cementocyte
CL:0000348 choroidal cell
CL:0000392 crystal cell
CL:0000345 dental papilla cell
CL:0000715 embryonic crystal cell
CL:0000736 embryonic gland hemocyte
CL:0000734 embryonic gland plasmatocyte
CL:0000683 ependymoglial cell
CL:0000082 epithelial cell of lung
CL:0000083 epithelial cell of pancreas
CL:0000135 fibrocyte
CL:0000125 glial cell
CL:0000243 glial cell (sensu Vertebrata)
CL:0000292 guard cell
CL:0000262 guard mother cell
CL:0000143 guidepost cell
CL:0000346 hair papilla cell
CL:0000387 hemocyte (sensu Nematoda and Protostomia)
CL:0000142 hyalocyte
CL:0000854 interneuromast cell
CL:0000396 lamellocyte
CL:0000716 lymph gland crystal cell
CL:0000735 lymph gland hemocyte
CL:0000733 lymph gland plasmatocyte
CL:0000126 macroglial cell
CL:0000401 macrophage (sensu Diptera)
CL:0000242 Merkel cell
CL:0000650 mesangial cell
CL:0000335 mesenchyme condensation cell
CL:0000636 Muller cell
CL:0000680 muscle precursor cell
CL:0000133 neurectodermal cell
CL:0000710 neuroepithelial cell
CL:0000095 neuron associated cell
CL:0000130 neuron associated cell (sensu Nematoda and Protostomia)
CL:0000123 neuron associated cell (sensu Vertebrata)
CL:0000029 neuron neural crest derived
CL:0000128 oligodendrocyte
CL:0000570 parafollicular cell
CL:0000516 perineuronal satellite cell
CL:0000645 pituicyte
CL:0000394 plasmatocyte
CL:0000391 podocyte (sensu Diptera)
CL:0000398 polygonal cell
CL:0000395 procrystal cell
CL:0000347 scleral cell
CL:0000297 socket cell
CL:0000499 stromal cell
CL:0000114 surface ectodermal cell
CL:0000643 tanycyte
CL:0000307 tracheal epithelial cell
CL:0000282 trichome

Thanks for your help!

CL:Main Page

2008-05-30T16:43:08Z

Adiehl:

=CL - OBO Cell Ontology=

=Resources=

==Ontology==

Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net

===Applications===

[[CL:Aligning species-specific anatomy ontologies with CL]]

[[Media:CLalign.biocuratorposter.final.ppt|CL_alignment_Biocurator07_poster]]

==Request tracker==

- [http://sourceforge.net/tracker/?group_id=76834&atid=925065 CL tracker]

You can also submit requests to the list.

==Mail Lists==

- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct OBO CrossProduct]

GO is pre-coordinating biological process terms that refer to cell types using CL IDs

==Cell ontology restructuring efforts==

The cell ontology is being restructured with the general goals of improving definitions, moving towards single inheritance and is_a completeness, and making the CL more interoperable with the GO and CARO. These discussions are occurring via chat, the histories of which will be posted here. Please email the OBO cell list if you would like to participate.

[[Media:cell_ontology_evaluation.doc|cell ontology evaluation.doc]]

[[Media:cellchat.2.12.07.doc|cellchat.2.12.07.doc]]

[[Media:cellchat.2.23.07.doc|cellchat.2.23.07.doc]]

[[Media:cellchat.2.27.07.doc|cellchat.2.27.07.doc]]

[[Media:cellchat.3.15.07.doc|cellchat.3.15.07.doc]]

[[Media:cellchat.6.1.07.doc|cellchat.6.1.07.doc]]

[[Media:cellchat.8-9-2007.doc|cellchat.8-9-2007]]

[[Media:cell_chat_8-24-2007.doc|cell_chat_8-24-2007]]

An initial rough draft can be found below in OBO format with the proposed new branch at the same level as 'cell'. Current tasks include moving cells over to the 'by structure' branch to test for compatibility and potential problems.

[[Media:CLRevised.obo|CL Revised.obo]]

Notes and action items from the cell ontology breakout session at the 2nd International Biocuration Meeting 2007.
[[Media:Cell_ontology_reorganization_working_group_notes.doc|Cell_ontology_reorganization_working_group_notes.doc]]

===NIAID Cell Ontology Workshop, May 13-14, 2008===

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

More information on the workshop can be found [[NIAID Cell Ontology Workshop May 2008|here]].

===Is_a Completeness for the current Cell Ontology===

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node '''cell'''. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please check out the page for [[May 2008 Is_a Orphans in the Cell Ontology]] and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node at that time.

== A list of useful differentia for defining cell-type terms==

has_part: <GO:cellular_compomnent>

has_function_from_process: <GO:biological_process>

has_quality: <PATO:quality/monadic quality of continuant>

develops_into: <CL:cell>

has_part: <CHEBI:chebi_ontology>

has_part: (<CHEBI:chebi_ontology>^part_of <GO:cellular_component>)

NIAID Cell Ontology Workshop Agenda

2008-05-22T23:38:20Z

Adiehl: /* '''Agenda''' */

[[NIAID Cell Ontology Workshop May 2008|Return to main workshop page]]

<big>'''NIAID-sponsored Workshop: Immune Cell Representation in the Cell Ontology'''</big> 
May 13 -14, 2008 
Bethesda North Marriott Hotel & Conference Center, Salon H 
5701 Marinelli Road 
Bethesda, Maryland 20852 USA 

''Note that the Agenda below reflects the timeline of the meeting as it actually occured ; the original Agenda is [[Media:NIAID_CL_Workshop_May_2008_Agenda.doc‎|here]].''

== '''Agenda''' ==

'''''May 13: Adaptive Immune Cell Representation'''''

8:00 - 9:00am Registration/Coffee

9:00 - 9:10 Welcome, NIAID staff

9:10 - 9:20 Brief introduction to the CL and its development, Dr. Alexander Diehl, The Jackson Laboratory ([[Media:A_Diehl_Cell_Ontology_Workshop_Introduction.ppt|slides]])

9:20 - 10:10 Ontologies and the OBO foundry vision of interrelated ontologies, Dr. Chris Mungall, Berkeley Bioinformatics and Ontologies Project ([[Media:Cell-NIAID-OBO-Mungall.ppt|slides]])

10:10 - 10:20 Presentation of Meeting Goals, Dr. Alexander Diehl ([[Media:A_Diehl_Meeting_Goals.ppt|slides]])

10:20 - 10:40 Presentation of additional introductory material, Dr. Richard Scheuermann, UT Southwestern Medical Center ([[Media:R_Scheuermann_Cell_Ontology_Intro.ppt|slides]])

10:40 - 11:00 BREAK

11:00 - 11:10 T cell representation in CL, Dr. Alexander Diehl ([[Media:A_Diehl_T_cell_Introduction.ppt|slides]], [http://www.bioontology.org/wiki/images/f/f7/T_cells.jpg graphical view])

11:10 - 11:30 T cell ontology extension, Dr. Penny Morel, University of Pittsburgh ([[Media:P_Morel_Tcellworkshop.ppt|slides]])

11:30 - 12:30 Discussion/Consensus on T cell representation

12:30 - 1:45 – LUNCH

1:45 - 1:55 B cell representation in CL, Dr. Alexander Diehl ([[Media:B_Cell_introduction_A_Diehl.ppt|slides]], [http://www.bioontology.org/wiki/images/9/97/B_cells.jpg graphical view])

1:55 - 2:30 B cell ontology extension, Dr. Martin Zand, University of Rochester Medical Center

2:30 - 3:20 Discussion/Consensus on B cell representation

3:20 - 3:40 BREAK

3:40 - 4:15 Discussion/Consensus on B cell representation

4:15 pm ADJOURN

'''''May 14: Innate Immune Cell Representation'''''

8:00 - 8:45 am Registration/Coffee

8:45 - 9:15 Discussion of proposed T cell changes illustrated in OBO-Edit based on previous day's discussion, led by Dr. Alexander Diehl

9:15 - 9:25 Dendritic cell representation in CL, Dr. Alexander Diehl ([http://www.bioontology.org/wiki/images/3/3b/DendriticCells.jpg graphical view])

9:25 - 10:00 Improvements in dendritic cell representation in CL, Dr. Lindsay G. Cowell, Duke University

10:00 - 10:55 Discussion/Consensus on dendritic cell representation

10:55 - 11:15 BREAK

11:15 - 12:15 Discussion/Consensus on dendritic cell representation

12:15 - 1:30 – LUNCH

1:30 - 2:10 Discussion about relationship types need for CL 2.0, led by Dr. Chris Mungall

2:10 - 2:20 Macrophage representation in CL, Dr. Alexander Diehl ([http://www.bioontology.org/wiki/images/c/ce/Macrophages-osteoclasts.jpg graphical view])

2:20 - 3:15 Discussion/Consensus on macrophage representation

3:15 - 3:25 BREAK

3:25 - 4:00 Meeting wrap up and setting of Action Items

4:00pm ADJOURN

NIAID Cell Ontology Workshop May 2008

2008-05-22T23:37:05Z

Adiehl: /* Slide Presentations from Meeting */