https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=Lgcowell 2026-06-05T11:02:21Z User contributions MediaWiki 1.35.9 https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=12734 2015-05-22T14:53:42Z

<p>Lgcowell: </p> <hr /> <div>== More Information about IDO ==<br /> <br /> http://bioportal.bioontology.org/ontologies/IDO<br /> <br /> == Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the 2007 Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. More recent files and information about the email list can be found via the link above.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].<br /> <br /> == Past Meetings ==<br /> <br /> '''2007'''<br /> <br /> '''[[IDO Kick-Off Meeting | Infectious Disease Ontology Kick-off Workshop and Public Meeting]]''', Cold Spring Harbor Laboratories, NY, September 19-21, 2007<br /> <br /> '''2008'''<br /> <br /> '''[http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_2008 Infectious Disease Ontology Meeting]''', Buffalo, NY, September 16 - 17, 2008<br /> <br /> '''2009'''<br /> <br /> '''[https://www.vbi.vt.edu/component/option,com_events/Itemid,81/task,view_detail/agid,385/year,2010/month,3/day,24/ Presentation by Lindsay Cowell in Virginia Bioinformatics Institute]'''<br /> <br /> == Medinfo 2010 Workshop ==<br /> There will be an IDO workshop at the [http://www.medinfo2010.org/ 13th World Congress on Medical and Health Informatics (Medinfo 2010)]. A separate wiki for this workshop can be found here: [[Infectious Disease Ontology Workshop - Medinfo 2010]]<br /> <br /> == IDO Workshop, December 8-9, 2010 ==<br /> <br /> Further details are [[http://www.bioontology.org/wiki/index.php/IDO_Workshop_2010 here]]<br /> Venue: to be determined</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=12733 2015-05-22T14:53:19Z

<p>Lgcowell: </p> <hr /> <div>== More Information about IDO ==<br /> <br /> The main IDO website is http://www.infectiousdiseaseontology.org.<br /> <br /> == Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the 2007 Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. More recent files and information about the email list can be found via the link above.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].<br /> <br /> == Past Meetings ==<br /> <br /> '''2007'''<br /> <br /> '''[[IDO Kick-Off Meeting | Infectious Disease Ontology Kick-off Workshop and Public Meeting]]''', Cold Spring Harbor Laboratories, NY, September 19-21, 2007<br /> <br /> '''2008'''<br /> <br /> '''[http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_2008 Infectious Disease Ontology Meeting]''', Buffalo, NY, September 16 - 17, 2008<br /> <br /> '''2009'''<br /> <br /> '''[https://www.vbi.vt.edu/component/option,com_events/Itemid,81/task,view_detail/agid,385/year,2010/month,3/day,24/ Presentation by Lindsay Cowell in Virginia Bioinformatics Institute]'''<br /> <br /> == Medinfo 2010 Workshop ==<br /> There will be an IDO workshop at the [http://www.medinfo2010.org/ 13th World Congress on Medical and Health Informatics (Medinfo 2010)]. A separate wiki for this workshop can be found here: [[Infectious Disease Ontology Workshop - Medinfo 2010]]<br /> <br /> == IDO Workshop, December 8-9, 2010 ==<br /> <br /> Further details are [[http://www.bioontology.org/wiki/index.php/IDO_Workshop_2010 here]]<br /> Venue: to be determined</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=12732 2015-05-22T14:52:20Z

<p>Lgcowell: </p> <hr /> <div>== Please Visit the Main IDO Website ==<br /> <br /> The main IDO website is http://www.infectiousdiseaseontology.org.<br /> <br /> == Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the 2007 Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. More recent files and information about the email list can be found via the link above.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> Most current version of the ontology can be found [http://infectiousdiseaseontology.org here].<br /> <br /> == Past Meetings ==<br /> <br /> '''2007'''<br /> <br /> '''[[IDO Kick-Off Meeting | Infectious Disease Ontology Kick-off Workshop and Public Meeting]]''', Cold Spring Harbor Laboratories, NY, September 19-21, 2007<br /> <br /> '''2008'''<br /> <br /> '''[http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_2008 Infectious Disease Ontology Meeting]''', Buffalo, NY, September 16 - 17, 2008<br /> <br /> '''2009'''<br /> <br /> '''[https://www.vbi.vt.edu/component/option,com_events/Itemid,81/task,view_detail/agid,385/year,2010/month,3/day,24/ Presentation by Lindsay Cowell in Virginia Bioinformatics Institute]'''<br /> <br /> == Medinfo 2010 Workshop ==<br /> There will be an IDO workshop at the [http://www.medinfo2010.org/ 13th World Congress on Medical and Health Informatics (Medinfo 2010)]. A separate wiki for this workshop can be found here: [[Infectious Disease Ontology Workshop - Medinfo 2010]]<br /> <br /> == IDO Workshop, December 8-9, 2010 ==<br /> <br /> Further details are [[http://www.bioontology.org/wiki/index.php/IDO_Workshop_2010 here]]<br /> Venue: to be determined</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10446 2010-12-05T18:38:58Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> <br /> This NCBO Workshop on the Infectious Disease Ontology is funded by the United States National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Its content is solely the responsibility of the organizers and presenters and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. Information on the National Centers for Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> **The tasks for which terminologies are needed<br /> **The terminologies currently being used <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> ==New Pre-Release Version of IDO==<br /> Following the workshop, we will release a new version of IDO. This version has only minor differences from the version released in May 2010 with respect to terms, definitions, and hierarchy. The primary difference is in the addition of OWL DL restrictions for many terms. This new version of IDO will be presented at the workshop and can be accessed via the following PURLs:<br /> *Full IDO http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl<br /> *Obsolete classes omitted http://purl.obolibrary.org/obo/ido/2010-12-02/ido-main.owl<br /> *Axioms omitted http://purl.obolibrary.org/obo/ido/2010-12-02/ido-base.owl<br /> *Asserted hierarchy only http://purl.obolibrary.org/obo/ido/2010-12-02/ido-asserted.owl<br /> *OBO version, no axioms http://purl.obolibrary.org/obo/ido/2010-12-02/ido.obo<br /> <br /> As always, comments, criticisms, and term requests are welcome. Please submit them on the issue tracker (http://code.google.com/p/infectious-disease-ontology/), email the discussion list (http://groups.google.com/group/ido-discuss), or email them directly to Lindsay Cowell (lindsay DOT cowell AT utsouthwestern DOT edu).<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00-9:00pm Welcome Reception (Sponsored by the University of Texas Southwestern Medical Center at Dallas; Cash Bar) <br /> :Private Room in BWI Hilton's Acqua Restaurant (1st floor, to the right of the front desk)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> '''PLEASE NOTE: Wireless Internet Access is available at no charge in the lobby area and in NCBO/IDO guest rooms.'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research (Session chair: Smith)<br /> ::Lindsay Cowell: Scope and Content of IDO<br /> ::Barry Smith: How use of IDO creates information integration across multiple domains <br /> <br /> *10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 continued (Session chair: Sobral)<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2: Additional large data and information repositories relevant for infectious disease research (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::Barry Smith<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> *3:00pm Session 3: General discussion of the Utility of IDO as a Controlled Vocabulary (Session chair: Smith)<br /> <br /> *4:00pm Refreshment Break <br /> <br /> *4:30pm Session 4: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (for interested participants; No-host/Dutch treat)<br /> :Private Room in BWI Hilton's Acqua Restaurant (1st floor, to the right of the front desk)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> '''PLEASE NOTE: Wireless Internet Access is available at no charge in the lobby area and in NCBO/IDO guest rooms.'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 1: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data<br /> ::Anna Maria Masci - CFAR - Centers for AIDS Research<br /> ::Mélanie Courtot - PCIRN - Public Health Agency of Canada / Canadian Institutes of Health Research Influenza Research Network<br /> ::Albert Goldfain - Linking Vital Signs Data to a ''Staphylococcus aureus'' IDO Disease Model <br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 2: IDO Extensions (Session chair: Ruttenberg)<br /> ::Yu Lin - Brucellosis Ontology<br /> ::Burke Squires - Flu-IDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> *3:00pm Session 3: Next Steps Lindsay Cowell<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport, and complimentary internet access in the lobby-area. <br /> <br /> * NCBO–IDO 2010 attendees will also receive complimentary internet access in their guest room.<br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Confirmed Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (University at Buffalo)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc. and Rensselaer Polytechnic Institute (RPI))<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Miguel H. Torres-Urquidy (CDC / OID / NCIRD)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10444 2010-12-04T20:01:39Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> <br /> This NCBO Workshop on the Infectious Disease Ontology is funded by the United States National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Its content is solely the responsibility of the organizers and presenters and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. Information on the National Centers for Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> **The tasks for which terminologies are needed<br /> **The terminologies currently being used <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> ==New Pre-Release Version of IDO==<br /> Following the workshop, we will release a new version of IDO. This version has only minor differences from the version released in May 2010 with respect to terms, definitions, and hierarchy. The primary difference is in the addition of OWL DL restrictions for many terms. This new version of IDO will be presented at the workshop and can be accessed via the following PURLs:<br /> *Full IDO http://purl.obolibrary.org/obo/ido/2010-12-02/ido.owl<br /> *Obsolete classes omitted http://purl.obolibrary.org/obo/ido/2010-12-02/ido-main.owl<br /> *Axioms omitted http://purl.obolibrary.org/obo/ido/2010-12-02/ido-base.owl<br /> *Asserted hierarchy only http://purl.obolibrary.org/obo/ido/2010-12-02/ido-asserted.owl<br /> <br /> As always, comments, criticisms, and term requests are welcome. Please submit them on the issue tracker (http://code.google.com/p/infectious-disease-ontology/), email the discussion list (http://groups.google.com/group/ido-discuss), or email them directly to Lindsay Cowell (lindsay DOT cowell AT utsouthwestern DOT edu).<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00-9:00pm Welcome Reception (Sponsored by the University of Texas Southwestern Medical Center at Dallas; Cash Bar) <br /> :Private Room in BWI Hilton's Acqua Restaurant (1st floor, to the right of the front desk)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> '''PLEASE NOTE: Wireless Internet Access is available at no charge in the lobby area and in NCBO/IDO guest rooms.'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research (Session chair: Smith)<br /> ::Lindsay Cowell: Scope and Content of IDO<br /> ::Barry Smith: How use of IDO creates information integration across multiple domains <br /> <br /> *10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 continued (Session chair: Sobral)<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2: Additional large data and information repositories relevant for infectious disease research (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::Barry Smith<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> *3:00pm Session 3: General discussion of the Utility of IDO as a Controlled Vocabulary (Session chair: Smith)<br /> <br /> *4:00pm Refreshment Break <br /> <br /> *4:30pm Session 4: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (for interested participants; No-host/Dutch treat)<br /> :Private Room in BWI Hilton's Acqua Restaurant (1st floor, to the right of the front desk)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> '''PLEASE NOTE: Wireless Internet Access is available at no charge in the lobby area and in NCBO/IDO guest rooms.'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 1: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data<br /> ::Anna Maria Masci - CFAR - Centers for AIDS Research<br /> ::Mélanie Courtot - PCIRN - Public Health Agency of Canada / Canadian Institutes of Health Research Influenza Research Network<br /> ::Albert Goldfain - Linking Vital Signs Data to a ''Staphylococcus aureus'' IDO Disease Model <br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 2: IDO Extensions (Session chair: Ruttenberg)<br /> ::Yu Lin - Brucellosis Ontology<br /> ::Burke Squires - Flu-IDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> *3:00pm Session 3: Next Steps Lindsay Cowell<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport, and complimentary internet access in the lobby-area. <br /> <br /> * NCBO–IDO 2010 attendees will also receive complimentary internet access in their guest room.<br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Confirmed Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc. and Rensselaer Polytechnic Institute (RPI))<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Miguel H. Torres-Urquidy (CDC / OID / NCIRD)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10431 2010-11-30T18:29:14Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> <br /> This NCBO Workshop on the Infectious Disease Ontology is funded by the United States National Institutes of Health through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Its content is solely the responsibility of the organizers and presenters and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. Information on the National Centers for Biomedical Computing can be found at http://nihroadmap.nih.gov/bioinformatics.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> **The tasks for which terminologies are needed<br /> **The terminologies currently being used <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00-9:00pm Welcome Reception (Sponsored by the University of Texas Southwestern Medical Center at Dallas; Cash Bar)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research (Session chair: Smith)<br /> ::Lindsay Cowell: Scope and Content of IDO<br /> ::Barry Smith: How use of IDO creates information integration across multiple domains <br /> <br /> *10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 continued (Session chair: Sobral)<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2: Additional large data and information repositories relevant for infectious disease research (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> *3:00pm Session 3: General discussion of the Utility of IDO as a Controlled Vocabulary (Session chair: Smith)<br /> <br /> *4:00pm Refreshment Break <br /> <br /> *4:30pm Session 4: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (for interested participants; No-host/Dutch treat)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 1: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data<br /> ::Anna Maria Masci - CFAR - Centers for AIDS Research<br /> ::Mélanie Courtot - PCIRN - Public Health Agency of Canada / Canadian Institutes of Health Research Influenza Research Network<br /> ::Albert Goldfain - Linking Vital Signs Data to a ''Staphylococcus aureus'' IDO Disease Model <br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 2: IDO Extensions (Session chair: Ruttenberg)<br /> ::Yu Lin - Brucellosis Ontology<br /> ::Burke Squires - Flu-IDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> *3:00pm Session 3: Next Steps Lindsay Cowell<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport, and complimentary internet access in the lobby-area. <br /> <br /> * NCBO–IDO 2010 attendees will also receive complimentary internet access in their guest room.<br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc. and Rensselaer Polytechnic Institute (RPI))<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Miguel H. Torres-Urquidy (CDC / OID/ NCIRD)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10373 2010-11-10T03:15:27Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> **The tasks for which terminologies are needed<br /> **The terminologies currently being using <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 continued (Session chair: Sobral)<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2: Additional large data and information repositories relevant for infectious disease research (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> *3:00pm Session 3: General discussion of the Utility of IDO as a Controlled Vocabulary (Session chair: Smith)<br /> <br /> *4:00pm Refreshment Break <br /> <br /> *4:30pm Session 4: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 1: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data<br /> ::Anna Maria Masci - CFAR - Centers for AIDS Research<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN - Public Health Agency of Canada / Canadian Institutes of Health Research Influenza Research Network<br /> ::Albert Goldfain - Host Genetic Susceptibility to ''Staphylococcus aureus''<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 2: IDO Extensions (Session chair: Ruttenberg)<br /> ::Yu Lin - Brucellosis Ontology<br /> ::Burke Squires - Flu-IDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> *3:00pm Session 3: Next Steps Lindsay Cowell<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10372 2010-11-10T03:13:34Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> **The tasks for which terminologies are needed<br /> **The terminologies currently being using <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 continued (Session chair: Sobral)<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2: Additional large data and information repositories relevant for infectious disease research (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> *3:00pm Session 3: General discussion of the Utility of IDO as a Controlled Vocabulary (Session chair: Smith)<br /> <br /> *4:00pm Refreshment Break <br /> <br /> *4:30pm Session 4: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 1: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - Host Genetic Susceptibility to ''Staphylococcus aureus''<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 2: IDO Extensions (Session chair: Ruttenberg)<br /> ::Yu Lin - Brucellosis Ontology<br /> ::Burke Squires - Flu-IDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> *3:00pm Session 3: Next Steps Lindsay Cowell<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10367 2010-11-09T23:24:51Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> **The tasks for which terminologies are needed<br /> **The terminologies currently being using <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 continued (Session chair: Sobral)<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2: Additional large data and information repositories relevant for infectious disease research (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> *3:00pm Session 3: General discussion of the Utility of IDO as a Controlled Vocabulary (Session chair: Smith)<br /> <br /> *4:00pm Refreshment Break <br /> <br /> *4:30pm Session 3: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Yu Lin - Brucellosis Ontology<br /> ::Burke Squires - Flu-IDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10366 2010-11-09T23:18:29Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> **The tasks for which terminologies are needed<br /> **The terminologies currently being using <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2: Additional large data and information repositories relevant for infectious disease research<br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> *3:00pm Session 3: The Utility of IDO as a Controlled Vocabulary (Session chair: Diehl)<br /> ::Alexander Diehl - Comprehensive Annotation System for Infectious Disease Data<br /> ::General discussion<br /> <br /> *4:00pm Refreshment Break <br /> <br /> *4:30pm Session 3: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Lindsay Cowell - SaIDO<br /> ::Burke Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Yu Lin - BO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10365 2010-11-09T23:15:09Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> **The tasks for which terminologies are needed<br /> **The terminologies currently being using <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *10:00am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 2: Other related data and information repositories<br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> ::Alexander Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *4:00pm Refreshment Break <br /> <br /> *4:30pm Session 3: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Lindsay Cowell - SaIDO<br /> ::Burke Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Yu Lin - BO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10364 2010-11-09T23:04:29Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> **The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> ::The tasks for which terminologies are needed<br /> ::The terminologies currently being using <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::Alexander Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Lindsay Cowell - SaIDO<br /> ::Burke Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Yu Lin - BO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10363 2010-11-09T23:03:47Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary, especially in advancing the work of the Bioinformatics Resource Centers, in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> *To address these goals, speakers are asked to address the following points<br /> ::The goals of their project<br /> :::biological questions for research projects<br /> :::content and functions for computational resource projects<br /> ::The tasks for which terminologies are needed<br /> ::The terminologies currently being using <br /> :::brief description of any terminologies developed specifically for the project<br /> :::description of the ways in which current terminologies are inadequate for the project’s needs<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Richard Scheuermann<br /> :::BRCs Overview<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> ::Richard Scheuermann<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentation<br /> <br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::Alexander Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Lindsay Cowell - SaIDO<br /> ::Burke Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Yu Lin - BO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10362 2010-11-09T22:57:13Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> Outline the terminology needs of each BRC, and the terminologies that are currently being used.<br /> ::Richard Scheuermann<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME - Program for Research on Immune Modeling and Experimentatoin<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal - Bioinformatics Resource Centers Portal<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::Alexander Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT - Detecting and Eliminating Bacteria using Information Technology<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Lindsay Cowell - SaIDO<br /> ::Burke Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Yu Lin - BO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10361 2010-11-09T22:51:10Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> Outline the terminology needs of each BRC, and the terminologies that are currently being used.<br /> ::Richard Scheuermann<br /> :::ViPR - Virus Pathogen Resource <br /> :::IRD - Influenza Research Database<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD<br /> :::PRIME<br /> ::Chris Stoeckert<br /> :::EuPathDB - Eukaryotic Pathogen Database Resource<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Bruno Sobral<br /> :::PATRIC - Pathosystems Resource Integration Center<br /> :::PathogenPortal<br /> ::Pantelis Topalis<br /> :::VectorBase - Invertebrate Vectors of Human Pathogens<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::Alexander Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Lindsay Cowell - SaIDO<br /> ::Burke Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Yu Lin - BO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10358 2010-11-09T18:37:30Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> Outline the terminology needs of each BRC, and the terminologies that are currently being used.<br /> ::Richard Scheuermann<br /> :::ViPR - Virus Pathogen Resource, <br /> :::IRD - Influenza Research Database<br /> :::ImmPort - Immunology Database and Analysis Portal<br /> ::TBD - PRIME<br /> ::Chris Stoeckert<br /> :::EuPathDB<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Bruno Sobral - PATRIC and PathogenPortal<br /> ::Pantelis Topalis - VectorDB<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::Alexander Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Lindsay Cowell - SaIDO<br /> ::Burke Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Yu Lin - BO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10357 2010-11-09T18:19:26Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Lindsay Cowell and Barry Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> Outline the terminology needs of each BRC, and the terminologies that are currently being used.<br /> ::Richard Scheuermann<br /> :::ViPR - Virus Pathogen Resource, IRD, and ImmPort<br /> ::TBD - PRIME<br /> ::Stoeckert - EuPathDB<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Bruno Sobral - PATRIC and PathogenPortal<br /> ::Pantelis Topalis - VectorDB<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::Alexander Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Saul Lozano-Fuentes - Dengue/vector control<br /> ::Daniel Schober - DeBugIT<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Anna Maria Masci - CFAR<br /> ::Stanley Schwartz - UB HIV project<br /> ::Mélanie Courtot - PCIRN<br /> ::Albert Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Lindsay Cowell - SaIDO<br /> ::Burke Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::Oliver He - VIOLIN - VO<br /> ::Yu Lin - BO<br /> ::Pankaj Jaswal - Plant IDO<br /> <br /> 3:30<br /> ::Lindsay Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Ashley Xia (NIH/NIAID)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10353 2010-11-08T05:24:33Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Cowell and Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> Outline the terminology needs of each BRC, and the terminologies that are currently being used.<br /> ::Scheuermann - ViPR, IRD, and ImmPort<br /> ::TBD - PRIME<br /> ::Stoeckert - EuPathDB<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Sobral - PATRIC and PathogenPortal<br /> ::Topalis - VectorDB<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Fuentes - Dengue/vector control<br /> ::Schober - DeBugIT<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3: Data Integration Use Cases (Session chair: Goldfain)<br /> ::Masci - CFAR<br /> ::Schwartz - UB HIV project<br /> ::Courtot - PCIRN<br /> ::Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 IDO Extensions (Session chair: Ruttenberg)<br /> ::Cowell - SaIDO<br /> ::Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm session 4 continued<br /> ::He - VIOLIN - VO<br /> ::Lin - BO<br /> ::Jaswal - Plant IDO<br /> <br /> ::Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Intending Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10352 2010-11-08T05:19:46Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Cowell and Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> Outline the terminology needs of each BRC, and the terminologies that are currently being used.<br /> ::Scheuermann - ViPR, IRD, and ImmPort<br /> ::TBD - PRIME<br /> ::Stoeckert - EuPathDB<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Sobral - PATRIC and PathogenPortal<br /> ::Topalis - VectorDB<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::Diehl - comprehensive annotation system for infectious disease data<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Fuentes - Dengue/vector control<br /> ::Schober - DeBugIT<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9: Data Integration Use Cases'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3 (Session chair: Goldfain)<br /> ::Masci - CFAR<br /> ::Schwartz - UB HIV project<br /> ::Courtot - PCIRN<br /> ::Goldfain - SABG<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 (Session chair: Ruttenberg)<br /> ::Cowell - SaIDO<br /> ::Squires - fluIDO<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 5 Extension ontologies (Session chair: Cowell)<br /> ::He - VIOLIN - VO<br /> ::Lin - BO<br /> ::Jaswal - Plant IDO<br /> ::Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Intending Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10351 2010-11-08T05:01:39Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Cowell and Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Scheuermann - ViPR, IRD, and ImmPort<br /> ::TBD - PRIME<br /> ::Stoeckert - EuPathDB<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Sobral - PATRIC and PathogenPortal<br /> ::Topalis - VectorDB<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Fuentes - Dengue/vector control<br /> ::Schober - DeBugIT<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9: Data Integration Use Cases'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3 (Session chair: Goldfain)<br /> ::Masci - CFAR<br /> ::Schwartz - UB HIV project<br /> ::Courtot - PCIRN<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 (Session chair: Ruttenberg)<br /> ::Goldfain - SABG<br /> ::Diehl - <br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 5 (Session chair: Cowell)<br /> ::He - VIOLIN<br /> <br /> ::Jaswal - Plant IDO<br /> ::Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Intending Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10350 2010-11-08T04:50:51Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Goals of the Meeting ==<br /> <br /> *The primary goal of this meeting is to explore the potential benefits of using the IDO Infectious Disease Ontology as a controlled vocabulary for promoting consistency in the ways infectious disease data are described. IDO provides both a vocabulary of terms and a set of precise definitions that have been thoroughly reviewed for biological accuracy and logical consistency. <br /> <br /> *We will explore the benefits of the IDO controlled vocabulary especially in advancing the work of the BRCs in areas such as:<br /> <br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> <br /> *The meeting will also address relations between IDO and other parallel initiatives, including [http://tsb.mssm.edu/primeportal/ PRIME], [http://www.debugit.eu/ DebugIT], and the various IDO extension ontologies.<br /> <br /> == Schedule ==<br /> <br /> '''Tuesday, December 7'''<br /> <br /> *7:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am Registration &amp; Continental Breakfast<br /> <br /> *9:00am Introduction: The current state of IDO and its role as a controlled vocabulary for infectious disease research - Cowell and Smith<br /> <br /> *9:30am Session 1: Bioinformatics Resource Centers (Session chair: Scheuermann)<br /> ::Scheuermann - ImmPort<br /> ::Squires - ViPR<br /> ::TBD - PRIME<br /> ::Stoeckert - EuPathDB<br /> <br /> *11:00am Refreshment Break <br /> <br /> *11:30am Session 1 (continued)<br /> ::Sobral - PATRIC and PathogenPortal<br /> ::Topalis - VectorDB<br /> <br /> *12:30pm Lunch Break<br /> <br /> *2:00pm Session 1 (continued)<br /> ::General discussion on the utility of IDO as Controlled Vocabulary<br /> <br /> *3:30pm Refreshment Break <br /> <br /> *4:00pm Session 2: Decision Support Use Cases (Session chair: Fuentes) <br /> ::Fuentes - Dengue/vector control<br /> ::Schober - DeBugIT<br /> <br /> *5:30pm End of Day 1<br /> <br /> *6:00pm Dinner (Dutch treat, venue to be announced)<br /> <br /> <br /> '''Day 2: Thursday, December 9: Data Integration Use Cases'''<br /> <br /> *8:30am Continental Breakfast<br /> <br /> *9:00am Session 3 (Session chair: Goldfain)<br /> ::Masci - CFAR<br /> ::Schwartz - UB HIV project<br /> <br /> *11:00am Refreshment Break<br /> <br /> *11:30am Session 4 (Session chair: Ruttenberg)<br /> ::Goldfain - SABG<br /> ::Courtot - PCIRN<br /> <br /> *12:15pm Lunch Break<br /> <br /> *1:45pm Session 5 (Session chair: Cowell)<br /> ::He - VIOLIN<br /> ::Jaswal - Plant IDO<br /> ::Cowell - Next Steps<br /> <br /> *4:00pm Close of NCBO/IDO 2010 Workshop<br /> <br /> <br /> '''Format'''<br /> <br /> Presentations will be short introductions to group discussion. All sessions will emphasize group discussion over presentation.<br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name:''' NCBO – IDO 2010''' / Group Code: '''NCBO'''. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation '''no later than November 15, 2010'''. <br /> <br /> Driving directions for local participants can be found here [http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do]<br /> <br /> == Intending Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=IDO_Workshop_2010&diff=10330 2010-11-03T21:59:16Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held on December 8-9, 2010. Venue: Baltimore Airport Hilton. This meeting is being organized as part of the series of Dissemination Workshops organized under the auspices of the National Center for <br /> Biomedical Ontology ([http://bioontology.org NCBO]). <br /> <br /> The Infectious Disease Ontology (IDO) is a general terminology, taxonomy, and logical representation of entities relevant to all <br /> infectious diseases. IDO is already being applied through disease-specific IDO extensions to the study of seven diseases, <br /> including diseases of bacterial, viral, and eukaryotic origin.<br /> <br /> Recently, the IDO has been adopted by the virus and bacterial Bioinformatics Resource Centers (BRCs) established by the NIAID to <br /> serve integration of a broad array of -omics, epidemiological and clinical data. <br /> <br /> For more information about IDO and its sub-domain extensions especially in the areas of HIV, influenza, Malaria, and Staphylococcus aureus bacteremia. See http://www.infectiousdiseaseontology.org.<br /> <br /> == Provisional Goals ==<br /> <br /> *Review of the IDO core and of existing IDO extensions<br /> *IDO and the BRCs<br /> *Presentation of applications of IDO in areas such as:<br /> ::clinical data integration<br /> ::text and data mining<br /> ::genetic susceptibility to infectious disease<br /> ::disease surveillance<br /> ::plant infectious disease<br /> *Planning for the introduction of new IDO extensions<br /> *Relations between IDO and other initiatives (including DebugIT)<br /> *Relations between IDO and other ontologies<br /> <br /> == Schedule ==<br /> <br /> '''Day 0: Tuesday, December 7'''<br /> <br /> *7:00pm - Dinner<br /> <br /> '''Day 1: Wednesday, December 8'''<br /> <br /> *8:30am - Continental Breakfast<br /> <br /> *9:00am - Session 1<br /> Bioinformatics Resource Centers; Session chair - Scheuermann<br /> ::Scheuermann – VIPR<br /> ::Stoeckert – EuPathDB<br /> <br /> *11:00am - Refreshment Break<br /> <br /> *11:30am - Session 1 continued<br /> ::Sobral – PATRIC and PathogenPortal<br /> ::Topalis - VectorDB<br /> <br /> *12:30pm - Lunch<br /> <br /> *1:30pm - Session 2<br /> Decision Support Use Cases; Session chair - Fuentes <br /> ::Fuentes – Dengue/vector control<br /> ::Schober – DeBugIT<br /> <br /> *3:30pm - Refreshment Break<br /> <br /> *4:00pm - Session 2 continued<br /> <br /> *6:00pm - Dinner<br /> <br /> '''Day 2: Wednesday, December 9'''<br /> <br /> *8:30am - Continental Breakfast<br /> <br /> *9:00am - Session 3<br /> Data Integration Use Cases; Session chair - Ruttenberg<br /> ::Masci – CFAR<br /> ::Schwartz – UB HIV project<br /> <br /> *11:00am - Refreshment Break<br /> <br /> *11:30am - Session 3 continued<br /> ::Goldfain – SABG<br /> ::Courtot – PCIRN<br /> <br /> *12:15pm - Lunch<br /> <br /> *1:45pm - Session 3 continued<br /> ::He - VIOLIN<br /> ::Jaswal – Plant IDO<br /> <br /> *4:00pm - Close<br /> <br /> '''Format'''<br /> <br /> One person will be designated as moderator for each session. All sessions will emphasize group discussion over presentation. <br /> <br /> == Venue ==<br /> <br /> A block of guest rooms at a discounted rate has been arranged for those NCBO/IDO 2010 attendees requiring lodging at:<br /> <br /> [http://www.hiltonbaltimorebwi.com Hilton Baltimore BWI Airport]<br /> 1739 West Nursery Road<br /> Linthicum Heights, MD 21090<br /> <br /> To make reservations by phone call 1-800-HILTONS (or the hotel 443-577-2411) and be sure to mention that you are part of Group Name: NCBO – IDO 2010 / Group Code: NCBO. <br /> <br /> To access our online reservation link, click [http://www.hilton.com/en/hi/groups/personalized/BWIAPHF-NCBO-20101207/index.jhtml?WT.mc_id=POG]<br /> <br /> * NCBO–IDO 2010 attendees will receive complimentary internet access in their guest room.<br /> <br /> * The Hilton Baltimore BWI Airport offers complimentary shuttle service from/to BWI airport. <br /> <br /> * To take advantage of the special rate and free internet access in your guest room, you must secure your room reservation no later than November 15, 2010. <br /> <br /> Driving directions for local participants can be found [ <br /> http://www1.hilton.com/en_US/hi/hotel/BWIAPHF-Hilton-Baltimore-BWI-Airport-Maryland/directions.do here].<br /> <br /> == Intending Participants ==<br /> <br /> Mauricio B. Almeida (Universidade Federal de Minas Gerais, Brazil)<br /> <br /> Sivaram Arabandi (Case Western Reserve University)<br /> <br /> Mathias Brochhausen (Institute for Formal Ontology and Medical Information Science, Saarland University)<br /> <br /> Mélanie Courtot (British Columbia Cancer Research Center, Vancouver)<br /> <br /> Lindsay Cowell (University of Texas Southwestern Medical Center, Dallas)<br /> <br /> Alexander Diehl (Gene Ontology / The Jackson Laboratory)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Albert Goldfain (University at Buffalo)<br /> <br /> Yongqun &quot;Oliver&quot; He (University of Michigan Medical Center)<br /> <br /> Pankaj Jaiswal (Plant Ontology / Oregon State University) <br /> <br /> Jessica Kissinger (Center for Tropical &amp; Emerging Global Diseases / University of Georgia)<br /> <br /> Yu Lin (University of Michigan Medical Center)<br /> <br /> Joanne Luciano (Predictive Medicine, Inc.)<br /> <br /> Supriya Mahajan (University at Buffalo)<br /> <br /> Chunhong Mao (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Jessica Reynolds (University at Buffalo)<br /> <br /> Alan Ruttenberg (Science Commons / University at Buffalo)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Daniel Schober (Universität Freiburg, Germany)<br /> <br /> Stanley D. Schwartz (University at Buffalo)<br /> <br /> Maulik Shukla (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> Bruno Sobral (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Burke Squires (University of Texas Southwestern Medical Center at Dallas)<br /> <br /> Christian Stoeckert (Penn Center for Bioinformatics / University of Pennsylvania)<br /> <br /> Dan Sullivan (PATRIC, Virginia Bioinformatics Institute)<br /> <br /> Pantelis Topalis (VectorBase / IMBB-FORTH, Crete)<br /> <br /> Patricia Whetzel (NCBO, Stanford)<br /> <br /> Allen Xiang (University of Michigan Medical Center)<br /> <br /> Jie Zheng (Penn Center for Bioinformatics / University of Pennsylvania)</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology_Workshop_-_Medinfo_2010&diff=10115 2010-08-23T11:47:19Z

<p>Lgcowell: removed flu talks; updated Cowell's affiliation</p> <hr /> <div>== Medinfo 2010 Workshop ==<br /> There will be an [http://www.infectiousdiseaseontology.org/Home.html IDO] workshop at the [http://www.medinfo2010.org/ 13th World Congress on Medical and Health Informatics (Medinfo 2010)] in Cape Town, South Africa on September 11, 2010 (17:00-18:30). A detailed program for Medinfo can be found [http://www.medinfo2010.org/docs/detailed_programme.pdf here].<br /> <br /> Infectious diseases inflict a disproportionate burden on developing countries. A lack of adequate treatment and prevention resources has resulted in a higher prevalence of infectious disease among the world's poorest people. This underscores the need for approaches to informatics support which leverage limited resources as effectively and efficiently as possible. Increasingly, response to infectious disease requires the use of information from multiple, constantly changing data sources. Currently, such information is collected using discipline-specific methodologies and is stored in heterogeneous databases, electronic health records, paper charts, and clinical and public health data repositories. Infectious disease data thus often remains only locally accessible, and because it<br /> is expressed in incompatible formats it does not allow for broad spectrum computational processing, querying, inference, or verification. Data silos hinder translational and comparative research. Aggregating data through use of a common data format and a common terminology (i.e., an ontology) allows a variety of secondary uses of data such as: rapid determination of pathogen type in infections or disease outbreaks, treatment decision support based on genetic characteristics of host and pathogen (e.g., drug resistance), and research to improve understanding of disease pathogenesis leading to development of new types of treatments. The Infectious Disease Ontology (IDO) addresses the problem of data silos by providing a consistent terminology, taxonomy, and logical representation of entities relevant to all infectious diseases. IDO is already being applied to the study of seven diseases, including diseases of bacterial, viral, and eukaryotic origin. The objectives of this workshop are to introduce IDO and the methodology for creating disease-specific IDO extensions, to present applications of the ontologies to the study of<br /> Malaria, HIV, and Influenza, and to open up the IDO enterprise to a wider audience of medical informaticians.<br /> <br /> ==Workshop Description==<br /> The workshop will consist of five presentations addressing the scope, design, evolution, and practical utility of IDO. Specifically, the first two will describe the principles of IDO and of the ontologies derived from it, and provide also a description of existing database efforts in the infectious disease domain. The remaining presentations will describe disease-specific ontologies developed from IDO and their application to specific data integration and processing tasks, including the planning of disease control measures, the integration of data from<br /> studies in humans and studies in model organisms, the study of co-infection, disease surveillance, and the study of viral evolution.<br /> <br /> ==Presenters==<br /> * [http://ontology.buffalo.edu/smith/ Barry Smith] (University at Buffalo)<br /> * [http://org.buffalo.edu/goldfain/index.html Albert Goldfain] (Blue Highway LLC)<br /> * [http://biostat.duke.edu/modules/dukefaculty/viewDetails.php?d=cowel001&amp;t=1 Lindsay G. Cowell] (University of Texas Southwestern Medical Center)<br /> * [http://www.anobase.org/~louis/ Christos Louis] (IMBB-FORTH and University of Crete)<br /> <br /> ==Talk Abstracts==<br /> <br /> === Infectious Disease Ontology: The Very Idea. ''Speaker: Barry Smith'' ===<br /> When computers are used in the storage and processing of data about infectious diseases and their causes, incidence, and treatment, there are obvious advantages to the use of a common controlled vocabulary or ‘ontology’. By making data comparable even when it derives from different sources, the ontology not only aids information-driven research directed towards elucidation of the disease mechanisms involved and the development of novel therapeutics, it also enhances our ability to use legacy disease data in rapid analysis of data pertaining to novel pathogens or mutations. This talk will describe the IDO strategy for creating a common ontology resource that can support these ends, and outline the work of the IDO Consortium, which is attempting to realize this strategy in a variety of disease domains by means of a general purpose core containing disease-neutral terms (such as ‘host’, ‘pathogen’, ‘virulence’) together with a number of extension vocabularies created by communities of researchers managing data pertaining to specific human, animal and plant infectious diseases, as well as by vaccine researchers. One advantage of this strategy is that, as each new group of infectious disease researchers confronts the need for a controlled vocabulary to represent the phenomena in its specific domain, it has a ready-made set of terms to begin this process in the application of which it can draw on the lessons learned by others while at the same time ensuring interoperability of their own data with the data collected in other disease domains.<br /> <br /> === Introduction to the IDO Core. ''Speaker: Albert Goldfain'' ===<br /> <br /> Despite the recent surge of interest in biomedical ontology, there was until recently little ontology coverage of the infectious disease domain, resulting in both an urgent need for ontology development in this field and the opportunity for a coordinated, community-wide development effort producing broad interoperability across the disease-specific specialties and across the clinical care, public health, and biomedical research domains. To provide the foundation for such an effort, we have developed a general infectious disease ontology (IDO Core) designed to serve as a central ontology (hub) from which disease-specific extensions (spokes) can be built through a process of specialization. The IDO core was designed i) to provide ontology coverage of terms generally relevant to infectious disease research, ii) to ensure interoperability between the IDO extensions, and iii) to achieve these ends on the basis of a W3C standard logical formalism intended to ensure extensibility of the ontologies while preserving their utility for computational applications. Each extension can be developed and maintained by domain experts, allowing for rapid progress towards the needed set of ontologies, ensuring biological accuracy of the extensions, and increasing the likelihood of broad adoption by the infectious disease research community. IDO Core thus provides an invaluable ontology resource for infectious disease researchers, allowing cross-domain data integration and supporting the computation-intensive data processing and analysis tasks becoming the basis of biomedical research.<br /> <br /> IDO Core is intended to represent information along three dimensions:<br /> <br /> * biological scale (gene, cell, organ, organism, and population)<br /> * discipline (clinical, immunological, microbiological, epidemiological)<br /> * host, pathogen, and vector organisms (e.g., human, rat, pig, maize, HIV, influenza, mosquito). <br /> <br /> IDO Core makes distinctions between infections, infectious diseases, infectious disease courses, the diagnosis of infectious disease, and the signs and symptoms of infectious diseases. The conflation of any of these entities can lead to incoherent reasoning, inconsistent models of specific diseases, and even medical errors in electronic health records.<br /> <br /> As a case-study in the use of IDO across diseases, we will describe the IDO Core representation of protective resistance. The resistance of pathogens to certain drugs is a central obstacle to the treatment and management of infectious disease. More generally, resistance can be used to describe phenomena such as the immunity of an individual to specific diseases and the resistance of disorders to specific treatments.<br /> <br /> === Malaria Ontology (IDOMAL) ''Speaker: Christos Louis'' ===<br /> <br /> Hundreds of millions of cases of vector-borne diseases occur annually, the vast majority of which affect populations in tropical regions of the world. Malaria, the most prominent among them, causes more than one million deaths each year, mostly among small children in these areas. For a number of reasons, including the development of resistance against both drugs and insecticides, the numbers of cases, and of deaths, has not decreased substantially, in spite of the progress achieved in medical sciences in recent decades. There is there-fore a need for new tools that will help alleviate this problem. These will include IT tools such as decision support systems (DSS), which, especially in the cases of emerging epidemics, will use data collections to help local authorities plan their disease control measures. This module will describe our work on the IDOMAL malaria ontology, an IDO extension ontology that is designed to advance work in this broad area and will be used to drive both databases and the DSSs that rely on them. IDOMAL will contain terms from all four corners of the malaria domain, which is to say: the biology of vectors and of disease, epidemiology, and clinical features. We have already recruited the participation of expert collaborators in order to ensure the broadest and most accurate coverage of the disease. Our plans for the future include the expansion of IDOMAL to cover other vector-borne diseases.<br /> <br /> === HIV Ontology (IDOHIV) ''Speaker: Lindsay G. Cowell'' ===<br /> <br /> In 2007, 33 million people were living with Human Immunodeficiency Virus (HIV), including 2 million children. Annually, there are approximately 2 million deaths as a result of HIV, with the leading cause of death being co-infection with Myco-bacterium tuberculosis (Mtb), a problem that is increasing with the appearance of new, highly virulent, drug-resistant strains of Mtb. A number of factors suggest that real progress towards alleviating the global HIV burden will require development of the terminological and logical infrastructure for broad data interoperability, and in particular for data interoperability across multiple disease domains. These include the central role of secondary infections in the HIV disease course, the importance of model infections to the study of HIV pathogenesis and vaccine efficacy, and the increasing need to synchronize the collection of data from patients enrolled in observational studies and clinical trials being carried out throughout the world. IDO is designed to provide the basis for the needed common terminological and logical architecture. This talk will describe the HIV Ontology (IDOHIV) developed as an IDO extension and will sketch the application of IDOHIV to i) the integration of results from Simian Immunodeficiency Virus (SIV) and HIV studies, ii) the study of HIV co-infection with Mtb and Hepatitis C Virus (HCV), and iii) the creation of an interactive, comprehensive database for the Duke Center for Aids Research (CFAR).<br /> <br /> ==Intended Audience==<br /> The workshop does not assume any prior knowledge of ontologies or the infectious disease domain, and is aimed at a broad audience, including:<br /> * medical informaticians<br /> * biologists<br /> * health care providers<br /> * epidemiologists and public health workers<br /> * bioinformatics researchers<br /> * biomedical researchers<br /> * computer scientists<br /> <br /> ==Goals==<br /> * To demonstrate the advantages of a common approach for annotating infectious disease data<br /> * To show how the IDO terminology can be used as a teaching tool.<br /> * To showcase the multidisciplinary nature of IDO.<br /> * To enable interested attendees to begin using IDO for annotating their own datasets.<br /> * To enable interested attendees to begin creating their own [http://www.infectiousdiseaseontology.org/IDO_Extensions.html IDO extensions].</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=8398 2009-02-01T14:28:49Z

<p>Lgcowell: </p> <hr /> <div>== Please Visit the Main IDO Website ==<br /> <br /> The main IDO website is http://www.infectiousdiseaseontology.org.<br /> <br /> == Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Meeting in Buffalo (September 16 - 17, 2008)==<br /> <br /> Details available [http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_2008 here].<br /> <br /> == Past Meetings ==<br /> <br /> '''Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007)'''<br /> <br /> The Infectious Disease Ontology Workshop and Meeting (see link below under &quot;Past Meetings&quot;) were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the [http://www.bwfund.org Burroughs Wellcome Fund].<br /> <br /> Training Workshop: September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> Public Meeting: September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> ''Report''<br /> <br /> *http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Infectious_Disease_Ontology_Meeting_Report.doc<br /> <br /> ''Slides''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> September 21, 2007<br /> *Topics in Infectious Disease Research<br /> **Stefan Kaufmann: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Kaufmann_Infectious_Disease_Ontology_Meeting.ppt Global Threats Need Global Research Efforts: The Example of Tuberculosis]<br /> **Ronald Veazey: Utility of Nonhuman Primates for Examining Transmission and Pathogenesis of HIV Infection<br /> *Ontologies and their Application to Infectious Disease<br /> **Steve Gordon: Surgical Endocarditis: Bringing Ontology into the Operating Room<br /> **Michael Ashburner: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt Ontologies for Biomedicine: The GO Experience]<br /> **Lynn Schriml: The GEMINA Information Resource<br /> *Ontology and the Future of Infectious Disease Research (Panel Session)<br /> **Cowell: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> **Scheuermann: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> **Stein: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Stein_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> ''Software Downloads''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> '''Workshop on the Ontology of Diseases, November 6-7, 2006'''<br /> <br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is for [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]<br /> * [http://www.biotec.tu-dresden.de/sealife Sealife]<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * Streaming video introduction to ontology by Barry Smith: http://ontology.buffalo.edu/smith/Ontology_Course.html<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology_2008&diff=7205 2008-06-03T02:29:37Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> A two-day IDO workshop for invited participants will be held in Buffalo, New York on September 16-17, 2008.<br /> <br /> 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:<br /> <br /> *Training of a core set of infectious disease researchers in ontology-development methods, facilitating their participation in ontology development;<br /> <br /> *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;<br /> <br /> *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);<br /> <br /> *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.<br /> <br /> == IDO 2008 Goals ==<br /> <br /> 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:<br /> <br /> *i) to provide training for new consortium members,<br /> <br /> *ii) to formualte and test a development methodology that can be adopted on a broad scale by experts in a wide variety of infectious disease sub-domains<br /> <br /> *iii) to critically evaluate the ontology development test cases initiated at IDO 2007 to improve both the ontologies themselves and the methodology used for their development,<br /> <br /> *iv) to identify key application test cases, such as ontology-based natural language processing, to be developed over the coming year,<br /> <br /> *v) to expand representation of sub-domains still lacking development effort, and<br /> <br /> *vi) to involve representatives from key information sources and institutions that could be important contributors and users of the IDO set of ontologies.<br /> <br /> <br /> == IDO 2008 Schedule ==<br /> <br /> '''Day 1: Tuesday September 16'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am Introduction to Biomedical Ontology (Barry Smith)<br /> <br /> *10:00 am to 11:00 am Introduction to the Infectious Disease Ontology (Lindsay Cowell)<br /> <br /> *11:00 am to 11:30 am Refreshment Break<br /> <br /> *11:30 am to 12:30 pm The Infectious Disease Portion of the Immune Epitope Database Ontology and its Relationship to IDO (Bjoern Peters)<br /> <br /> *12:30 pm to 1:30 pm Lunch<br /> <br /> *1:30 pm to 2:30 pm The Vaccine Ontology (Yongqun He)<br /> <br /> *2:30 pm to 3:30 pm The Staphylococcus aureus Ontology (Vance Fowler)<br /> <br /> *3:30 pm to 4:00 pm Refreshment Break<br /> <br /> *4:00 pm to 5:00 pm The Infective Endocarditis Ontology and SemanticDB (Sivaram Arabandi)<br /> <br /> *5:30 pm to 7:30 pm Dinner<br /> <br /> *7:30 pm to 9:00 pm Ontologies in the Future of Infectious Disease Research: A Discussion Introduced and Moderated by Christos Louis<br /> <br /> '''Day 2: Wednesday September 17'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am The Vector-borne Disease Ontology (Christos Louis)<br /> <br /> *10:00 am to 11:00 am The Dengue Fever Ontology (Saul Lozano-Fuentes)<br /> <br /> *11:00 am to 11:30 am Refreshment Break<br /> <br /> *11:30 am to 12:30 pm The Influenza Ontology (Richard Scheuermann)<br /> <br /> *12:30 pm to 2:00 pm Working Lunch: Refining IDO and Its Extensions to Better Support Interoperability (Barry Smith)<br /> <br /> *2:00 pm to 3:00 pm Current and Future Applications of the IDO Methodology (Alan Ruttenberg)<br /> <br /> *3:00 pm to 3:30 pm Refreshment Break<br /> <br /> *3:30 pm to 4:00 pm Goals for the Coming Year (Lindsay Cowell)<br /> <br /> '''Format'''<br /> <br /> 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.<br /> <br /> == IDO 2008 Venue ==<br /> <br /> The venue for our meeting will be the [http://www.ramadahotelamherst.com/ramada-hotel.html Ramada Inn and Conference Center] in Amherst, NY.<br /> <br /> == Confirmed Participants ==<br /> <br /> Sivaram Arabandi (Cleveland Clinic)<br /> <br /> Robert Arp (NCBO / University at Buffalo)<br /> <br /> Lindsay Cowell (Duke University Medical Center)<br /> <br /> Alex Diehl (Gene Ontology/ The Jackson Laboratory)<br /> <br /> Vance Fowler (Duke University Medical Center)<br /> <br /> Steve Gill (University at Buffalo)<br /> <br /> Louis Goldberg (University at Buffalo)<br /> <br /> Yongqun He (University of Michigan)<br /> <br /> Alan J. Lesse (University at Buffalo)<br /> <br /> Kitsos Louis (FORTH, Crete)<br /> <br /> Saul Lozano-Fuentes (Colorado State University)<br /> <br /> Joanne Luciano (Mitre Corp.)<br /> <br /> Anna Maria Masci (Duke University Medical Center)<br /> <br /> Chris Mungall (Gene Ontology/ Lawrence Berkeley National Laboratory)<br /> <br /> Darren Natale (Protein Ontology / Georgetown University)<br /> <br /> Chimezie Ogbuji (Cleveland Clinic)<br /> <br /> Bjoern Peters (University of California at San Diego)<br /> <br /> Alan Ruttenberg (Science Commons)<br /> <br /> Richard Scheuermann (University of Texas Southwestern Medical Center)<br /> <br /> Lynn Schriml (University of Maryland)<br /> <br /> Brahm Segal (Roswell Park Cancer Institute, Buffalo)<br /> <br /> Barry Smith (NCBO / University at Buffalo)<br /> <br /> == Progress Since the IDO 2007 ==<br /> 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:<br /> ::Tuberculosis (Carol Dukes-Hamilton, Duke University Medical Center)<br /> ::Staphylococcus aureus bacteremia (Vance Fowler, Duke University Medical Center)<br /> ::Infective endocarditis (Sivaram Arabandi, Cleveland Clinic Foundation)<br /> ::Malaria and other vector-borne diseases (Christos Louis, Institute for Molecular Biology and Biochemistry – FORTH)<br /> ::Dengue fever (Saul Lozano-Fuentes, Colorado State)<br /> ::Influenza (Stuart Sealfon, Mount Sinai School of Medicine; Richard Scheuermann, University of Texas, Southwestern Medical Center)<br /> <br /> 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.<br /> <br /> 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. <br /> <br /> 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. <br /> <br /> In collaboration with Dr. Vance Fowler at Duke University Medical Center, Drs. Cowell and Smith have developed a '''draft ontology of Staphylococcus aureus bacteremia'''.<br /> <br /> 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'''.<br /> <br /> 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.<br /> <br /> 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<br /> 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.<br /> <br /> 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<br /> 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<br /> ontology of terms has been created with a cross reference of terms to existing OBO Foundry ontologies.<br /> <br /> 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<br /> BHB portal.<br /> <br /> For more information about IDO and its sub-domain extensions, see http://www.infectiousdiseaseontology.org.</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology_2008&diff=7169 2008-05-27T14:26:46Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> 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:<br /> <br /> *Training of a core set of infectious disease researchers in ontology-development methods, facilitating their participation in ontology development;<br /> <br /> *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;<br /> <br /> *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);<br /> <br /> *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.<br /> <br /> == IDO 2008 Goals ==<br /> <br /> 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:<br /> <br /> *i) to provide training for new consortium members,<br /> <br /> *ii) to formualte and test a development methodology that can be adopted on a broad scale by experts in a wide variety of infectious disease sub-domains<br /> <br /> *iii) to critically evaluate the ontology development test cases initiated at IDO 2007 to improve both the ontologies themselves and the methodology used for their development,<br /> <br /> *iv) to identify key application test cases, such as ontology-based natural language processing, to be developed over the coming year,<br /> <br /> *v) to expand representation of sub-domains still lacking development effort, and<br /> <br /> *vi) to involve representatives from key information sources and institutions that could be important contributors and users of the IDO set of ontologies.<br /> <br /> <br /> == IDO 2008 Schedule ==<br /> <br /> '''Day 1: Tuesday September 16'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am Introduction to Biomedical Ontology (Barry Smith)<br /> <br /> *10:00 am to 11:00 am Introduction to the Infectious Disease Ontology (Lindsay Cowell)<br /> <br /> *11:00 am to 11:30 am Refershment Break<br /> <br /> *11:30 am to 12:30 pm The Infectious Disease Portion of the Immune Epitope Database Ontology and its Relationship to IDO (Bjoern Peters)<br /> <br /> *12:30 pm to 1:30 pm Lunch<br /> <br /> *1:30 pm to 2:30 pm The Vaccine Ontology (Yongqun He)<br /> <br /> *2:30 pm to 3:30 pm The Staphylococcus aureus Ontology (Vance Fowler)<br /> <br /> *3:30 pm to 4:00 pm Refreshment Break<br /> <br /> *4:00 pm to 5:00 pm The Infective Endocarditis Ontology and SemanticDB (Sivaram Arabandi)<br /> <br /> *5:30 pm to 7:30 pm Dinner<br /> <br /> *7:30 pm to 9:00 pm Ontologies in the Future of Infectious Disease Research: A Discussion Introduced and Moderated by Christos Louis<br /> <br /> '''Day 2: Wednesday September 17'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am The Vector-borne Disease Ontology (Christos Louis)<br /> <br /> *10:00 am to 11:00 am The Dengue Fever Ontology (Saul Lozano-Fuentes)<br /> <br /> *11:00 am to 11:30 am Refreshment Break<br /> <br /> *11:30 am to 12:30 pm The Influenza Ontology (Richard Scheuermann)<br /> <br /> *12:30 pm to 2:00 pm Working Lunch: Refining IDO and Its Extensions to Better Support Interoperability (Barry Smith)<br /> <br /> *2:00 pm to 3:00 pm Current and Future Applications of the IDO Methodology (Alan Ruttenberg)<br /> <br /> *3:00 pm to 3:30 pm Refreshment Break<br /> <br /> *3:30 pm to 4:00 pm Goals for the Coming Year (Lindsay Cowell)<br /> <br /> '''Format'''<br /> <br /> 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.<br /> <br /> == Confirmed Participants ==<br /> <br /> Sivaram Arabandi<br /> <br /> Lindsay Cowell<br /> <br /> Alex Diehl<br /> <br /> Vance Fowler<br /> <br /> Steve Gill<br /> <br /> Yongqun He<br /> <br /> Joanne Luciano<br /> <br /> Kitsos Louis<br /> <br /> Saul Lozano-Fuentes<br /> <br /> Anna Maria Masci<br /> <br /> Chris Mungal<br /> <br /> Darren Natale<br /> <br /> Chimezie Ogbuji<br /> <br /> Bjoern Peters<br /> <br /> Alan Ruttenberg<br /> <br /> Richard Scheuermann<br /> <br /> Lynn Schriml<br /> <br /> Barry Smith<br /> <br /> == Progress Since the IDO 2007 ==<br /> 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:<br /> ::Tuberculosis (Carol Dukes-Hamilton, Duke University Medical Center)<br /> ::Staphylococcus aureus bacteremia (Vance Fowler, Duke University Medical Center)<br /> ::Infective endocarditis (Sivaram Arabandi, Cleveland Clinic Foundation)<br /> ::Malaria and other vector-borne diseases (Christos Louis, Institute for Molecular Biology and Biochemistry – FORTH)<br /> ::Dengue fever (Saul Lozano-Fuentes, Colorado State)<br /> ::Influenza (Stuart Sealfon, Mount Sinai School of Medicine; Richard Scheuermann, University of Texas, Southwestern Medical Center)<br /> <br /> 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.<br /> <br /> IDO is supplemented also by a '''[http://www.violinet.org/wiki/index.php/Vaccine_Ontology Vaccine Ontology]''' which is being developed by Yonggun He (University of Michigan) in collaboration with Lindsay Cowell and Barry Smith. <br /> <br /> 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. <br /> <br /> In collaboration with Dr. Vance Fowler at Duke University Medical Center, Drs. Cowell and Smith have developed a '''draft ontology of Staphylococcus aureus bacteremia'''.<br /> <br /> 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'''.<br /> <br /> 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.<br /> <br /> 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<br /> 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.<br /> <br /> 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<br /> 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<br /> ontology of terms has been created with a cross reference of terms to existing OBO Foundry ontologies.<br /> <br /> 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<br /> BHB portal.<br /> <br /> For more information about IDO and its sub-domain extensions, see http://www.infectiousdiseaseontology.org.</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology_2008&diff=7168 2008-05-27T00:54:43Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> 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:<br /> <br /> *Training of a core set of infectious disease researchers in ontology-development methods, facilitating their participation in ontology development;<br /> <br /> *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;<br /> <br /> *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);<br /> <br /> *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.<br /> <br /> == IDO 2008 Goals ==<br /> <br /> 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:<br /> <br /> *i) to provide training for new consortium members,<br /> <br /> *ii) to formualte and test a development methodology that can be adopted on a broad scale by experts in a wide variety of infectious disease sub-domains<br /> <br /> *iii) to critically evaluate the ontology development test cases initiated at IDO 2007 to improve both the ontologies themselves and the methodology used for their development,<br /> <br /> *iv) to identify key application test cases, such as ontology-based natural language processing, to be developed over the coming year,<br /> <br /> *v) to expand representation of sub-domains still lacking development effort, and<br /> <br /> *vi) to involve representatives from key information sources and institutions that could be important contributors and users of the IDO set of ontologies.<br /> <br /> <br /> == IDO 2008 Schedule ==<br /> <br /> '''Day 1: Tuesday September 16'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am Introduction to Biomedical Ontology<br /> <br /> *10:00 am to 11:00 am Introduction to the Infectious Disease Ontology<br /> <br /> *11:00 am to 11:30 am Refershment Break<br /> <br /> *11:30 am to 12:30 pm The Vaccine Ontology<br /> <br /> *12:30 pm to 1:30 pm Lunch<br /> <br /> *1:30 pm to 2:30 pm The Tuberculosis Ontology<br /> <br /> *2:30 pm to 3:30 pm The Staphylococcus aureus Ontology<br /> <br /> *3:30 pm to 4:00 pm Refreshment Break<br /> <br /> *4:00 pm to 5:00 pm The Infective Endocarditis Ontology<br /> <br /> *5:30 pm to 7:30 pm Dinner<br /> <br /> *7:30 pm to 9:00 pm Ontologies in the Future of Infectious Disease Research: A Discussion Introduced and Moderated by Christos Louis<br /> <br /> '''Day 2: Wednesday September 17'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am The Vector-borne Disease Ontology<br /> <br /> *10:00 am to 11:00 am The Dengue Fever Ontology<br /> <br /> *11:00 am to 11:30 am Refreshment Break<br /> <br /> *11:30 am to 12:30 pm The Influenza Ontology<br /> <br /> *12:30 pm to 1:30 pm Lunch<br /> <br /> *1:30 pm to 2:30 pm Current and Future Applications of the IDO Methodology<br /> <br /> *2:30 pm to 3:00 pm Refreshment Break<br /> <br /> *3:00 pm to 4:00 pm Goals for the Coming Year<br /> <br /> '''Format'''<br /> <br /> 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.<br /> <br /> == Confirmed Participants ==<br /> <br /> Sivaram Arabandi<br /> <br /> Lindsay Cowell<br /> <br /> Alex Diehl<br /> <br /> Vance Fowler<br /> <br /> Steve Gill<br /> <br /> Yongqun He<br /> <br /> Joanne Luciano<br /> <br /> Kitsos Louis<br /> <br /> Saul Lozano-Fuentes<br /> <br /> Anna Maria Masci<br /> <br /> Chris Mungal<br /> <br /> Darren Natale<br /> <br /> Chimezie Ogbuji<br /> <br /> Bjoern Peters<br /> <br /> Alan Ruttenberg<br /> <br /> Richard Scheuermann<br /> <br /> Lynn Schriml<br /> <br /> Barry Smith<br /> <br /> == Progress Since the IDO 2007 ==<br /> 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:<br /> ::Tuberculosis (Carol Dukes-Hamilton, Duke University Medical Center)<br /> ::Staphylococcus aureus bacteremia (Vance Fowler, Duke University Medical Center)<br /> ::Infective endocarditis (Sivaram Arabandi, Cleveland Clinic Foundation)<br /> ::Malaria and other vector-borne diseases (Christos Louis, Institute for Molecular Biology and Biochemistry – FORTH)<br /> ::Dengue fever (Saul Lozano-Fuentes, Colorado State)<br /> ::Influenza (Stuart Sealfon, Mount Sinai School of Medicine; Richard Scheuermann, University of Texas, Southwestern Medical Center)<br /> <br /> 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.<br /> <br /> IDO is supplemented also by a '''[http://www.violinet.org/wiki/index.php/Vaccine_Ontology Vaccine Ontology]''' which is being developed by Yonggun He (University of Michigan) in collaboration with Lindsay Cowell and Barry Smith. <br /> <br /> 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. <br /> <br /> In collaboration with Dr. Vance Fowler at Duke University Medical Center, Drs. Cowell and Smith have developed a '''draft ontology of Staphylococcus aureus bacteremia'''.<br /> <br /> 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'''.<br /> <br /> 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.<br /> <br /> 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<br /> 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.<br /> <br /> 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<br /> 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<br /> ontology of terms has been created with a cross reference of terms to existing OBO Foundry ontologies.<br /> <br /> 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<br /> BHB portal.<br /> <br /> For more information about IDO and its sub-domain extensions, see http://www.infectiousdiseaseontology.org.</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology_2008&diff=7167 2008-05-27T00:54:10Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> 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:<br /> <br /> *Training of a core set of infectious disease researchers in ontology-development methods, facilitating their participation in ontology development;<br /> <br /> *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;<br /> <br /> *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);<br /> <br /> *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.<br /> <br /> == IDO 2008 Goals ==<br /> <br /> 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:<br /> <br /> *i) to provide training for new consortium members,<br /> <br /> *ii) to formualte and test a development methodology that can be adopted on a broad scale by experts in a wide variety of infectious disease sub-domains<br /> <br /> *iii) to critically evaluate the ontology development test cases initiated at IDO 2007 to improve both the ontologies themselves and the methodology used for their development,<br /> <br /> *iv) to identify key application test cases, such as ontology-based natural language processing, to be developed over the coming year,<br /> <br /> *v) to expand representation of sub-domains still lacking development effort, and<br /> <br /> *vi) to involve representatives from key information sources and institutions that could be important contributors and users of the IDO set of ontologies.<br /> <br /> <br /> == IDO 2008 Schedule ==<br /> <br /> '''Day 1: Tuesday September 16'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am Introduction to Biomedical Ontology<br /> <br /> *10:00 am to 11:00 am Introduction to the Infectious Disease Ontology<br /> <br /> *11:00 am to 11:30 am Refershment Break<br /> <br /> *11:30 am to 12:30 pm The Vaccine Ontology<br /> <br /> *12:30 pm to 1:30 pm Lunch<br /> <br /> *1:30 pm to 2:30 pm The Tuberculosis Ontology<br /> <br /> *2:30 pm to 3:30 pm The Staphylococcus aureus Ontology<br /> <br /> *3:30 pm to 4:00 pm Refreshment Break<br /> <br /> *4:00 pm to 5:00 pm The Infective Endocarditis Ontology<br /> <br /> *5:30 pm to 7:30 pm Dinner<br /> <br /> *7:30 pm to 9:00 pm Ontologies in the Future of Infectious Disease Research: A Discussion Introduced and Moderated by Christos Louis<br /> <br /> '''Day 2: Wednesday September 17'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am The Vector-borne Disease Ontology<br /> <br /> *10:00 am to 11:00 am The Dengue Fever Ontology<br /> <br /> *11:00 am to 11:30 am Refreshment Break<br /> <br /> *11:30 am to 12:30 pm The Influenza Ontology<br /> <br /> *12:30 pm to 1:30 pm Lunch<br /> <br /> *1:30 pm to 2:30 pm Current and Future Applications of the IDO Methodology<br /> <br /> *2:30 pm to 3:00 pm Refreshment Break<br /> <br /> *3:00 pm to 4:00 pm Goals for the Coming Year<br /> <br /> '''Format'''<br /> <br /> 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.<br /> <br /> == Confirmed Participants ==<br /> <br /> Sivaram Arabandi<br /> <br /> Lindsay Cowell<br /> <br /> Alex Diehl<br /> <br /> Vance Fowler<br /> <br /> Yongqun He<br /> <br /> Joanne Luciano<br /> <br /> Kitsos Louis<br /> <br /> Saul Lozano-Fuentes<br /> <br /> Anna Maria Masci<br /> <br /> Chris Mungal<br /> <br /> Darren Natale<br /> <br /> Chimezie Ogbuji<br /> <br /> Bjoern Peters<br /> <br /> Alan Ruttenberg<br /> <br /> Richard Scheuermann<br /> <br /> Lynn Schriml<br /> <br /> Barry Smith<br /> <br /> == Progress Since the IDO 2007 ==<br /> 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:<br /> ::Tuberculosis (Carol Dukes-Hamilton, Duke University Medical Center)<br /> ::Staphylococcus aureus bacteremia (Vance Fowler, Duke University Medical Center)<br /> ::Infective endocarditis (Sivaram Arabandi, Cleveland Clinic Foundation)<br /> ::Malaria and other vector-borne diseases (Christos Louis, Institute for Molecular Biology and Biochemistry – FORTH)<br /> ::Dengue fever (Saul Lozano-Fuentes, Colorado State)<br /> ::Influenza (Stuart Sealfon, Mount Sinai School of Medicine; Richard Scheuermann, University of Texas, Southwestern Medical Center)<br /> <br /> 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.<br /> <br /> IDO is supplemented also by a '''[http://www.violinet.org/wiki/index.php/Vaccine_Ontology Vaccine Ontology]''' which is being developed by Yonggun He (University of Michigan) in collaboration with Lindsay Cowell and Barry Smith. <br /> <br /> 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. <br /> <br /> In collaboration with Dr. Vance Fowler at Duke University Medical Center, Drs. Cowell and Smith have developed a '''draft ontology of Staphylococcus aureus bacteremia'''.<br /> <br /> 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'''.<br /> <br /> 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.<br /> <br /> 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<br /> 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.<br /> <br /> 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<br /> 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<br /> ontology of terms has been created with a cross reference of terms to existing OBO Foundry ontologies.<br /> <br /> 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<br /> BHB portal.<br /> <br /> For more information about IDO and its sub-domain extensions, see http://www.infectiousdiseaseontology.org.</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology_2008&diff=7166 2008-05-27T00:52:43Z

<p>Lgcowell: </p> <hr /> <div>== Background ==<br /> <br /> 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:<br /> <br /> *Training of a core set of infectious disease researchers in ontology-development methods, facilitating their participation in ontology development;<br /> <br /> *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;<br /> <br /> *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);<br /> <br /> *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.<br /> <br /> == IDO 2008 Goals ==<br /> <br /> 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:<br /> <br /> *i) to provide training for new consortium members,<br /> <br /> *ii) to formualte and test a development methodology that can be adopted on a broad scale by experts in a wide variety of infectious disease sub-domains<br /> <br /> *iii) to critically evaluate the ontology development test cases initiated at IDO 2007 to improve both the ontologies themselves and the methodology used for their development,<br /> <br /> *iv) to identify key application test cases, such as ontology-based natural language processing, to be developed over the coming year,<br /> <br /> *v) to expand representation of sub-domains still lacking development effort, and<br /> <br /> *vi) to involve representatives from key information sources and institutions that could be important contributors and users of the IDO set of ontologies.<br /> <br /> <br /> == IDO 2008 Schedule ==<br /> <br /> '''Day 1: Tuesday September 16'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am Introduction to Biomedical Ontology<br /> <br /> *10:00 am to 11:00 am Introduction to the Infectious Disease Ontology<br /> <br /> *11:00 am to 11:30 am Refershment Break<br /> <br /> *11:30 am to 12:30 pm The Vaccine Ontology<br /> <br /> *12:30 pm to 1:30 pm Lunch<br /> <br /> *1:30 pm to 2:30 pm The Tuberculosis Ontology<br /> <br /> *2:30 pm to 3:30 pm The Staphylococcus aureus Ontology<br /> <br /> *3:30 pm to 4:00 pm Refreshment Break<br /> <br /> *4:00 pm to 5:00 pm The Infective Endocarditis Ontology<br /> <br /> *5:30 pm to 7:30 pm Dinner<br /> <br /> *7:30 pm to 9:00 pm Ontologies in the Future of Infectious Disease Research: A Discussion Introduced and Moderated by Christos Louis<br /> <br /> '''Day 2: Wednesday September 17'''<br /> <br /> *8:30 am to 9:00 am Continental Breakfast<br /> <br /> *9:00 am to 10:00 am The Vector-borne Disease Ontology<br /> <br /> *10:00 am to 11:00 am The Dengue Fever Ontology<br /> <br /> *11:00 am to 11:30 am Refreshment Break<br /> <br /> *11:30 am to 12:30 pm The Influenza Ontology<br /> <br /> *12:30 pm to 1:30 pm Lunch<br /> <br /> *1:30 pm to 2:30 pm Current and Future Applications of the IDO Methodology<br /> <br /> *2:30 pm to 3:00 pm Refreshment Break<br /> <br /> *3:00 pm to 4:00 pm Goals for the Coming Year<br /> <br /> '''Format'''<br /> <br /> 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.<br /> <br /> == Confirmed Participants ==<br /> <br /> Sivaram Arabandi<br /> Lindsay Cowell<br /> Alex Diehl<br /> Vance Fowler<br /> Yongqun He<br /> Joanne Luciano<br /> Kitsos Louis<br /> Saul Lozano-Fuentes<br /> Anna Maria Masci<br /> Chris Mungal<br /> Darren Natale<br /> Chimezie Ogbuji<br /> Bjoern Peters<br /> Alan Ruttenberg<br /> Richard Scheuermann<br /> Lynn Schriml<br /> Barry Smith<br /> <br /> == Progress Since the IDO 2007 Workshop ==<br /> 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:<br /> ::Tuberculosis (Carol Dukes-Hamilton, Duke University Medical Center)<br /> ::Staphylococcus aureus bacteremia (Vance Fowler, Duke University Medical Center)<br /> ::Infective endocarditis (Sivaram Arabandi, Cleveland Clinic Foundation)<br /> ::Malaria and other vector-borne diseases (Christos Louis, Institute for Molecular Biology and Biochemistry – FORTH)<br /> ::Dengue fever (Saul Lozano-Fuentes, Colorado State)<br /> ::Influenza (Stuart Sealfon, Mount Sinai School of Medicine; Richard Scheuermann, University of Texas, Southwestern Medical Center)<br /> <br /> 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.<br /> <br /> IDO is supplemented also by a '''[http://www.violinet.org/wiki/index.php/Vaccine_Ontology Vaccine Ontology]''' which is being developed by Yonggun He (University of Michigan) in collaboration with Lindsay Cowell and Barry Smith. <br /> <br /> 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. <br /> <br /> In collaboration with Dr. Vance Fowler at Duke University Medical Center, Drs. Cowell and Smith have developed a '''draft ontology of Staphylococcus aureus bacteremia'''.<br /> <br /> 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'''.<br /> <br /> 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.<br /> <br /> 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<br /> 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.<br /> <br /> 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<br /> 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<br /> ontology of terms has been created with a cross reference of terms to existing OBO Foundry ontologies.<br /> <br /> 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<br /> BHB portal.<br /> <br /> For more information about IDO and its sub-domain extensions, see http://www.infectiousdiseaseontology.org.</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6307 2007-11-10T17:31:20Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop and Meeting (see link below under &quot;Past Meetings&quot;) were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the [http://www.bwfund.org Burroughs Wellcome Fund].<br /> <br /> '''Report'''<br /> <br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Infectious_Disease_Ontology_Meeting_Report.doc<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> <br /> September 21, 2007<br /> *Topics in Infectious Disease Research<br /> **Stefan Kaufmann: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Kaufmann_Infectious_Disease_Ontology_Meeting.ppt Global Threats Need Global Research Efforts: The Example of Tuberculosis]<br /> **Ronald Veazey: Utility of Nonhuman Primates for Examining Transmission and Pathogenesis of HIV Infection<br /> *Ontologies and their Application to Infectious Disease<br /> **Steve Gordon: Surgical Endocarditis: Bringing Ontology into the Operating Room<br /> **Michael Ashburner: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt Ontologies for Biomedicine: The GO Experience]<br /> **Lynn Schriml: The GEMINA Information Resource<br /> *Ontology and the Future of Infectious Disease Research (Panel Session)<br /> **Cowell: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> **Scheuermann: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> **Stein: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Stein_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is for [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6263 2007-11-01T20:20:18Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop and Meeting (see link below under &quot;Past Meetings&quot;) were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the [http://www.bwfund.org Burroughs Wellcome Fund].<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> <br /> September 21, 2007<br /> *Topics in Infectious Disease Research<br /> **Stefan Kaufmann: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Kaufmann_Infectious_Disease_Ontology_Meeting.ppt Global Threats Need Global Research Efforts: The Example of Tuberculosis]<br /> **Ronald Veazey: Utility of Nonhuman Primates for Examining Transmission and Pathogenesis of HIV Infection<br /> *Ontologies and their Application to Infectious Disease<br /> **Steve Gordon: Surgical Endocarditis: Bringing Ontology into the Operating Room<br /> **Michael Ashburner: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt Ontologies for Biomedicine: The GO Experience]<br /> **Lynn Schriml: The GEMINA Information Resource<br /> *Ontology and the Future of Infectious Disease Research (Panel Session)<br /> **Cowell: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> **Scheuermann: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> **Stein: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Stein_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is for [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6254 2007-11-01T16:08:34Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop and Meeting (see link below under &quot;Past Meetings&quot;) were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the [http://www.bwfund.org Burroughs Wellcome Fund].<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> <br /> September 21, 2007<br /> *Topics in Infectious Disease Research<br /> **Stefan Kaufmann: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Kaufmann_Infectious_Disease_Ontology_Meeting.ppl Global Threats Need Global Research Efforts: The Example of Tuberculosis]<br /> **Ronald Veazey: Utility of Nonhuman Primates for Examining Transmission and Pathogenesis of HIV Infection<br /> *Ontologies and their Application to Infectious Disease<br /> **Steve Gordon: Surgical Endocarditis: Bringing Ontology into the Operating Room<br /> **Michael Ashburner: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt Ontologies for Biomedicine: The GO Experience]<br /> **Lynn Schriml: The GEMINA Information Resource<br /> *Ontology and the Future of Infectious Disease Research (Panel Session)<br /> **Cowell: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> **Scheuermann: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> **Stein: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Stein_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is for [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6253 2007-11-01T15:23:18Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop and Meeting (see link below under &quot;Past Meetings&quot;) were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the [http://www.bwfund.org Burroughs Wellcome Fund].<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> <br /> September 21, 2007<br /> *Topics in Infectious Disease Research<br /> **Stefan Kaufmann: Global Threats Need Global Research Efforts: The Example of Tuberculosis<br /> **Ronald Veazey: Utility of Nonhuman Primates for Examining Transmission and Pathogenesis of HIV Infection<br /> *Ontologies and their Application to Infectious Disease<br /> **Steve Gordon: Surgical Endocarditis: Bringing Ontology into the Operating Room<br /> **Michael Ashburner: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt Ontologies for Biomedicine: The GO Experience]<br /> **Lynn Schriml: The GEMINA Information Resource<br /> *Ontology and the Future of Infectious Disease Research (Panel Session)<br /> **Cowell: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> **Scheuermann: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> **Stein: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Stein_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is for [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6252 2007-11-01T14:24:53Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop and Meeting (see link below under &quot;Past Meetings&quot;) were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the [http://www.bwfund.org Burroughs Wellcome Fund].<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> <br /> September 21, 2007<br /> *Topics in Infectious Disease Research<br /> **Stefan Kaufmann: Global Threats Need Global Research Efforts: The Example of Tuberculosis<br /> **Ronald Veazey: Utility of Nonhuman Primates for Examining Transmission and Pathogenesis of HIV Infection<br /> *Ontologies and their Application to Infectious Disease<br /> **Steve Gordon: Surgical Endocarditis: Bringing Ontology into the Operating Room<br /> **Michael Ashburner: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt Ontologies for Biomedicine: The GO Experience]<br /> **Lynn Schriml: The GEMINA Information Resource<br /> *Ontology and the Future of Infectious Disease Research (Panel Session)<br /> **Cowell: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> **Scheuermann: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is for [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6251 2007-11-01T14:21:17Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop and Meeting (see link below under &quot;Past Meetings&quot;) were intended to serve as both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The workshop and meeting were supported by the [http://www.bwfund.org Burroughs Wellcome Fund].<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> September 21, 2007<br /> *Topics in Infectious Disease Research<br /> **Stefan Kaufmann<br /> **Ronald Veazey<br /> *Ontologies and their Application to Infectious Disease<br /> **Steve Gordon<br /> **Michael Ashburner: [http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Ashburner_Infectious_Disease_Ontology_Meeting.ppt Ontologies for Biomedicine: The GO Experience]<br /> **Lynn Schriml<br /> *Ontology and the Future of Infectious Disease Research (Panel Session)<br /> **Cowell: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> **Scheuermann: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is for [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6119 2007-10-09T11:54:48Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_10.08.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop (see link below under &quot;Past Meetings&quot;) was intended to be both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO).<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> September 21, 2007<br /> *Panel Session (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> *Panel Session (Scheuermann): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. Links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is for [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6085 2007-09-28T11:44:50Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop (see link below under &quot;Past Meetings&quot;) was intended to be both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO).<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> September 21, 2007<br /> *Panel Session (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> *Panel Session (Scheuermann): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Scheuermann_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6075 2007-09-23T16:46:03Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop (see link below under &quot;Past Meetings&quot;) was intended to be both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO).<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> '''Meeting Slides'''<br /> September 21, 2007<br /> *Panel Session (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> '''Recommended Background Reading'''<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> '''Software Downloads'''<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6074 2007-09-23T16:45:03Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop (see link below under &quot;Past Meetings&quot;) was intended to be both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO).<br /> <br /> '''Workshop Slides'''<br /> <br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> &quot;&quot;Meeting Slides&quot;&quot;<br /> September 21, 2007<br /> *Panel Session (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> &quot;&quot;Recommended Background Reading&quot;&quot;<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> &quot;&quot;Software Downloads&quot;&quot;<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6073 2007-09-23T16:44:30Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop (see link below under &quot;Past Meetings&quot;) was intended to be both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO).<br /> <br /> ''''Workshop Slides''''<br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> &quot;&quot;Meeting Slides&quot;&quot;<br /> September 21, 2007<br /> *Panel Session (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> &quot;&quot;Recommended Background Reading&quot;&quot;<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> &quot;&quot;Software Downloads&quot;&quot;<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6072 2007-09-23T16:42:25Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop (see link below under &quot;Past Meetings&quot;) was intended to be both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO).<br /> <br /> &quot;&quot;Workshop Slides&quot;&quot;<br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> &quot;&quot;Meeting Slides&quot;&quot;<br /> September 21, 2007<br /> *Panel Session (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Cowell_Infectious_Disease_Ontology_Panel.ppt<br /> <br /> &quot;&quot;Recommended Background Reading&quot;&quot;<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> &quot;&quot;Software Downloads&quot;&quot;<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]<br /> * [http://www.phidias.us/phinfo Integrated pathogen-host interaction data in PHIDIAS]<br /> * [http://www.violinet.org VIOLIN: University of Michigan Vaccine Database]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6067 2007-09-22T00:46:58Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings of an Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop (see link below under &quot;Past Meetings&quot;) was intended to be both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO).<br /> <br /> Workshop Slides<br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> Meeting Slides<br /> <br /> Recommended Background Reading<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> Software Downloads<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6066 2007-09-22T00:45:10Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Bare Beginnings and Infectious Disease Ontology ==<br /> <br /> At the recent Infectious Disease Ontology Workshop (see below), we began preliminary work on a draft infectious disease ontology. OBO edit and Protege OWL versions of the ontology are available for download. Please send comments and suggestions to ido@duke.edu.<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Infectious Disease Ontology Kick-off Workshop (September 19 - 20, 2007) and Meeting (September 21, 2007) ==<br /> <br /> The Infectious Disease Ontology Workshop (see link below under &quot;Past Meetings&quot;) was intended to be both a training workshop for participants and a forum through which to establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO).<br /> <br /> == Workshop Slides ==<br /> September 19, 2007<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> == Meeting Slides ==<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Software Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Past Meetings ==<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Talk:Infectious_Disease_Ontology&diff=6065 2007-09-21T20:13:59Z

<p>Lgcowell: </p> <hr /> <div>I just had a look at the ontology and I was a bit surprised that there is no sub-BFO Hierarchy. Fly, Insect and Organism are siblings which strikes me as odd. Is there a reason for this? (Mathias Brochhausen, IFOMIS)<br /> <br /> '''Hi Mathias - agreed, fly, insect and organism should not be siblings. These terms should probably not even be in IDO as they are (i think) in other ontologies. What do others think?'''<br /> <br /> By the way is there a chance of getting a owl file (with definitions) in order to work directly on it? Mathias<br /> <br /> '''Owl file should be there now, along with an OBO Edit file. Dates in filenames indicate which is the most recent. In the near term, we will work in OBO Edit and use the converter to update the OWL file. When we begin asserting relations other than is_a and part_of, we will probably migrate to OWL. We will keep the group informed.'''<br /> <br /> How do you define &quot;pain&quot;. Depending on the definition I would not agree that pain is an object. Mathias<br /> <br /> '''Good question. We had lots of interesting discussion about pain. Is pain the perception or the signals that the brain receives and perceives as pain? What do you think?<br /> '''<br /> I am not sure whether being epidemic and being pandemic qualifies as a criterion differntiating two universals. I'd think this is either two FiatProcessParts (since the thresholds are defied by humans, if I remember that right, or maybe a property or a quality.....What do you think? Mathias<br /> <br /> '''hmmm. i think i need to go reread parts of the BFO manual ...<br /> '''<br /> <br /> '''ps i bolded my responses so they would stand out but feel free to unbold them and bold yours so the new comments standout.'''</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6064 2007-09-21T19:25:20Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email list. Anyone can subscribe, and anyone can email the list. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. To email the list, write to ido@duke.edu.<br /> <br /> == Infectious Disease Ontology Kick-off Meeting ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here in pdf: [[Image:IDO Draft.pdf]]. OBO edit and Protege OWL versions of the ontology are also available:<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6063 2007-09-21T19:24:20Z

<p>Lgcowell: </p> <hr /> <div>== New Email List ==<br /> <br /> Please subscribe to the Infectious Disease Ontology email. Anyone can subscribe and anyone can send messages. We plan to use the email list to discuss the addition of new terms and proposed changes to the current ontology. To subscribe, visit https://lists.duke.edu/sympa/. The email the list, write to ido@duke.edu.<br /> <br /> == Infectious Disease Ontology Kick-off Meeting ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here in pdf: [[Image:IDO Draft.pdf]]. OBO edit and Protege OWL versions of the ontology are also available:<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6062 2007-09-21T14:29:42Z

<p>Lgcowell: </p> <hr /> <div>== News ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here in pdf: [[Image:IDO Draft.pdf]]. OBO edit and Protege OWL versions of the ontology are also available:<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.21.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6061 2007-09-21T14:28:34Z

<p>Lgcowell: </p> <hr /> <div>== News ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here in pdf: [[Image:IDO Draft.pdf]]. OBO edit and Protege OWL versions of the ontology are also available:<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.20.07.obo<br /> <br /> Accessible data to test the ontology, existing ontologies of related interest can be found here: [[Toolbox]]<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2 (Cowell): http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> * Afternoon and Evening Sessions (Smith): http://ontology.buffalo.edu/bio/IDO/<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6046 2007-09-20T13:08:06Z

<p>Lgcowell: </p> <hr /> <div>== News ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here in pdf: [[Image:IDO Draft.pdf]]. OBO edit and Protege OWL versions of the ontology are also available:<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.owl<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO.9.19.07.pprj<br /> * http://www.duke.edu/~lgcowell/IDO_Workshop_Files/IDO_9.19.07.obo<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For corrections on Relation Ontology, especially the derives_from relation, see http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Lgcowell https://www.bioontology.org//mediawiki/index.php?title=Infectious_Disease_Ontology&diff=6043 2007-09-19T19:03:43Z

<p>Lgcowell: </p> <hr /> <div>== News ==<br /> <br /> The upcoming Infectious Disease Ontology Workshop (see link below under &quot;Meetings&quot;) is intended to be both a training workshop for participants and a forum through which we can establish a community for development, maintenance, and use of the Infectious Disease Ontology (IDO). The current agenda for the workshop can be viewed [http://meetings.cshl.edu/courses/Workshop%20Curriculum.html here].<br /> <br /> In preparation for the workshop, we have prepared a draft infectious disease ontology and hope that workshop attendees will take time to comment on the ontology in advance of the workshop using the discussion page of this wiki. The ontology can be viewed here: [[Image:IDO Draft.pdf]]<br /> <br /> == Workshop Slides ==<br /> * Morning Session 1: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_the_Human_Immune_System.ppt<br /> * Morning Session 2: http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Introduction_to_Microbial_Pathogenesis.ppt<br /> <br /> == Recommended Background Reading ==<br /> * For a comprehensive introduction to ontology in general and the Basic Formal Ontology specifically, see http://www.ifomis.uni-saarland.de/projects/bfo/manual/<br /> * For an explanation of the necessity of logic-based relations for automatic reasoning over ontologies, see [[Image:Relations_in_anatomical_ontologies_sa.pdf‎]]<br /> * For an introduction to the Relations Ontology and a description of the formulation of logic-based relations for OBO foundry ontologies, see [[Image:Relations_in_Biomedical_Ontologies.pdf‎]]<br /> * For a description of the Foundational Model of Anatomy and the basic principles of ontology development, see http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.pdf<br /> * For a description of the representation of immunological processes in the Gene Ontology Biological Process Ontology, see http://bioinformatics.oxfordjournals.org/cgi/reprint/23/7/913<br /> * For a discussion of common errors in OWL, see http://www.co-ode.org/resources/papers/CommonErrorsInOWL.pdf<br /> * For an introduction to microbial pathogenisis, see http://www.duke.edu/~lgcowell/IDO_Workshop_Files/Pathogenicity_of_Micro-Organisms.pdf<br /> <br /> == Downloads ==<br /> * Download the OBO-Edit ontology editor: http://oboedit.org/<br /> * Download the Protege OWL ontology editor: http://protege.stanford.edu/download/download.html <br /> * Protege OWL contains a very useful tutorial, you can access it by opening Protege OWL and looking under &quot;Help&quot;<br /> * Download Pellet (a reasoner for OWL): http://pellet.owldl.com/<br /> * The Protege developers have created a short, helpful guide to installing Pellet and making sure that Pellet is running in conjunction with Protege OWL: http://protege.stanford.edu/shortcourse/protege/200703/prepare.html <br /> <br /> == Meetings ==<br /> <br /> September 19-20, 2007<br /> * [http://meetings.cshl.edu/courses/c-ontol07.shtml Training Workshop on Infectious Disease Ontology]<br /> <br /> September 21, 2007<br /> * [http://meetings.cshl.edu/courses/m-ontol07.html Infectious Disease: A Challenge for Biomedical Informatics]<br /> <br /> == Past Meetings ==<br /> <br /> November 6-7, 2006<br /> * [http://bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Diseases Workshop on Ontology of Diseases]. See especially the links to presentations at this meeting:<br /> ** Kent Spackman: SNOMED CT [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/spackman.ppt Slides]<br /> ** Barry Smith: What a Disease Ontology is For [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Smith.WMA Audio]<br /> **Neil Williams: The Ontology of Powers, Dispositions and Tendencies [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Williams.ppt Slides]<br /> ** Louis J. Goldberg: Networks and the Ontology of Disease [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Goldberg.WMA Audio]<br /> ** Werner Ceusters: The Ontology of Diagnosis: [http://www.org.buffalo.edu/RTU/papers/WhatIsaDiagnosis.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Ceusters.WMA Audio]<br /> ** Chris Mungall: DO and the OBO Foundry [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/mungall.ppt Slides] [http://ontology.buffalo.edu/medo/DiseaseOntology/2006/Mungall.WMA Audio]<br /> <br /> == Links ==<br /> <br /> * [http://obofoundry.org The OBO Foundry]<br /> * [http://diseaseontology.sourceforge.net/ The Disease Ontology]<br /> <br /> * [ftp://ftp.tigr.org/pub/data/gemina/gemina_disease_02-21-07.obo.gz TIGR's Gemina Project Infectious Disease Ontology]<br /> * [ftp://ftp.tigr.org/pub/data/gemina/ TIGR's Gemina Project Infectious Disease Ontology Data]<br /> * [http://gemina.tigr.org Gemina Query Tool]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/kr89.pdf Mereotopology of Phagocytosis and Exocytosis]<br /> * [http://www.comp.leeds.ac.uk/qsr/pub/AAAI92.ps Qualitative Simulation of Phagocytosis]</div>

Lgcowell