NCBO Wiki - Recent changes [en]

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-15T19:07:46Z

Draft Schedule:

BioPortal Mappings Service

2012-05-15T16:47:48Z

Get a list of mappings between two ontologies:

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-14T16:35:01Z

Participants will include:

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-14T14:35:30Z

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-11T13:57:23Z

Draft Schedule:

Using NCBO Technology In Your Project

2012-05-11T04:59:44Z

Main Page

2012-05-10T18:54:41Z

Technical Documentation:

Immunology Ontologies and Their Applications in Processing Clinical Data

2012-05-10T15:28:35Z

@@ Line 72: / Line 72: @@
 :Yu Lin (University of Michigan)
-::IDO Bru (Brucellosis Ontology)
+::IDOBru (Brucellosis Ontology)
 ----
@@ Line 102: / Line 109: @@
 ::Representation of cells used in experiments such as: PBMCs, splenocytes, adherent cells
 ::Discussion of the ontological treatment of typing panels.
 '''Afternoon: Automated gating of Flow Cytometry results and linking to the Cell Ontology'''

@@ Line 23: / Line 23: @@
 * '''Description''': Get a single mapping for the given mapping id.
 * '''Signature''': ./mappings?mappingid={mapping_id}&apikey={YourAPIKey}
-* '''Example''': http://rest.bioontology.org/bioportal/mappings/?mappingid=http%3A%2F%2Fpurl.bioontology.org%2Fmapping%2Ffb009110-004c-012e-74a1-005056bd0010&apikey=YourAPIKey
+* '''Example''': http://rest.bioontology.org/bioportal/mappings/?mappingid=http://purl.bioontology.org/mapping/loom/b17eed0d00ed3299eb07e0fbca3db67c&apikey=YourAPIKey
 == Get a list of mappings filtered by parameters ==
@@ Line 55: / Line 55: @@
 * '''Description''': Get a set of mappings for the given term id.
 * '''Signature''': ./virtual/mappings/ontologies/{ontology id}?apikey={YourAPIKey}
-* '''Example''': http://rest.bioontology.org/bioportal/virtual/mappings/ontologies/1009?pagesize=10&pagenum=1&apikey=YourAPIKey
+* '''Example''': http://rest.bioontology.org/bioportal/virtual/mappings/ontologies/1019?pagesize=10&pagenum=1&apikey=YourAPIKey
 * '''Optional Parameters''': See above.
 ** '''issource'''={true} - limit results to mappings where the concept id is the source.
@@ Line 63: / Line 63: @@
 * '''Description''': Get a set of mappings between two ontology ids.
 * '''Signature''': ./virtual/mappings/ontologies?apikey={YourAPIKey}
-* '''Example''': http://rest.bioontology.org/bioportal/virtual/mappings/ontologies?sourceontology=1009&targetontology=1032&pagesize=10&pagenum=1&apikey=YourAPIKey
+* '''Example''': http://rest.bioontology.org/bioportal/virtual/mappings/ontologies?sourceontology=1019&targetontology=1063&pagesize=10&pagenum=1&apikey=YourAPIKey
 * '''Required Parameters'''
 ** '''sourceontology'''={source ontology id}

@@ Line 2: / Line 2: @@
 :Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
 :Day 2 will be focused on flow cytometry.
-:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.\
+:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.
 '''Venue:
@@ Line 126: / Line 126: @@
 '''<u>The Role of Ontologies in Clinical Medicine</u>'''
-'''9am-noon: Next Steps in Protein Ontology Flow Cytometry Driving Biological Project'''
+'''9am-noon: The Protein Ontology Flow Cytometry Driving Biological Project'''
 :Alexander Diehl (Buffalo) and Lindsay Cowell (UT Southwestern), Discussion Leaders
@@ Line 177: / Line 177: @@
 :Ryan Brinkman (University of British Columbia)
 :Atul Butte (Stanford University)
 :Werner Ceusters (University at Buffalo)
 :Cliburn Chan (Duke University)

@@ Line 128: / Line 128: @@
 '''9am-noon: Next Steps in Protein Ontology Flow Cytometry Driving Biological Project'''
-:TBD
+:Alexander Diehl (Buffalo) and Lindsay Cowell (UT Southwestern), Discussion Leaders
 '''noon-3pm SESSION OPEN TO THE PUBLIC: Practical Applications of Ontologies in Clinical Research''' (includes lunch)
@@ Line 155: / Line 158: @@
 '''Relevant ontology efforts'''
-:GO-IP Gene Ontology -- Immunological Process (Alex Diehl)
+:GO-IP Gene Ontology -- Immunological Process (Alexander Diehl)
 :CL Cell ontology immune branches (e.g. for dendritic cells)
 :PRO Protein Ontology
-:IO Immunology Ontology (Lindsay Cowell and Alex Diehl)
+:IO Immunology Ontology (Lindsay Cowell and Alexander Diehl)
 :IEO Immune Epitope Ontology (Bjoern Peters)
 :MHC Major Histocompatibility Complex Ontology (Bjoern Peters)
@@ Line 165: / Line 168: @@
 :Vaccine Ontology (Oliver He)
 :AO Allergy Ontology (Alex C. Yu)
-:ND Neurological Disease Ontology (Alex Diehl)
+:ND Neurological Disease Ontology (Alexander Diehl)
 ----
 '''
@@ Line 181: / Line 184: @@
 :Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
 :Peter d'Eustachio (New York University)
-:Alex Diehl (University at Buffalo)
+:Alexander Diehl (University at Buffalo)
 :Chester Fox (University at Buffalo)
 :Lee Ann Garrett-Sinha (University at Buffalo)

@@ Line 41: / Line 41: @@
 :Peter d'Eustacho (New York University)
 ::Innate Immunity: Signaling via Toll-Like Receptors in Reactome
 :Bjoern Peters (La Jolla Institute for Allergy and Immunology)
@@ Line 166: / Line 168: @@
 ----
 '''
 == Participants will include ==
 '''

← Older revision		Revision as of 04:59, 11 May 2012
Line 1:		Line 1:
−	There are several ways in which you can use the NCBO technology on your own Web site or in your application.	+	There are several ways in which you can use the NCBO technology on your own Web site or in your application. For more ideas visit the [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Sample Code Cookbook]

	== [[NCBO_REST_services\|'''Ontology Web Services''']] ==		== [[NCBO_REST_services\|'''Ontology Web Services''']] ==

@@ Line 26: / Line 26: @@
 === Software ===
-*[http://bioportal.bioontology.org BioPortal:Main_Page] - Main page for accessing BioPortal
+*[http://bioportal.bioontology.org NCBO BioPortal] - Home page for BioPortal Web site
-*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
+* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries
-*[[BioPortal Help]] - Help text for BioPortal Web site
 *[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
 *[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
 === User Support Documentation ===
-* [http://www.bioontology.org/wiki/index.php/BioPortal_Help Help] - General BioPortal help documentation.
+*[[BioPortal Help]] - General BioPortal help documentation.
-* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages
+* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project
-* [[NCBO REST services]] - Documentation on how to use BioPortal functionality as Web services
-* [[View_Extraction]] - Documentation on how to extract subtree views from ontologies
+=== Technical Documentation ===
-* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings] - Documentation & information about accessing term mapping data
+* [[NCBO REST Web services]] - Listing of all NCBO web services with usage documentation
-* [[Ontology Notes]] - Documentation & information about posting and accessing comments and new term proposals submitted on ontologies
+* [http://www.bioontology.org/wiki/index.php/View_Extraction Ontology Subset Extraction Web service] - Documentation on how to extract subtree views from ontologies
 * [[Annotator Web service]] - Documentation & information about the NCBO Annotator
 * [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index
 * [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services
 * ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)
-=== Ontology Development Area ===
+=== Ontology Development Projects ===
-Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki
+Below are links for ontology development projects that NCBO is involved in.
 *[[BRO:Main_Page]] - Biomedical Resource Ontology
 *[[TMO:]] - Translational Medicine Ontology
@@ Line 57: / Line 61: @@
 *[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders
 *[[OCI:Main_Page]] - Ontology of Clinical Investigation
 === Research projects and Prototypes ===
@@ Line 63: / Line 66: @@
 *[[Path to Root]] - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)
 *[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)
 *[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)
 *[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)
 *[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms. (Rong Xu)
 *[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow. (Tejaswi Tenneti)

@@ Line 2: / Line 2: @@
 :Day 1 will provide a survey of current ontology-based research in immunology and infectious disease with a view to future coordination among ontology developers and users in this field.
 :Day 2 will be focused on flow cytometry.
-:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.
+:Day 3 will include a session devoted to the use of ontologies to assist clinicians working with infectious disease data, followed by a session on the Ontology for General Medical Science.\
 '''Goals'''
@@ Line 161: / Line 165: @@
 :ND Neurological Disease Ontology (Alex Diehl)
 ----
-'''Participants will include'''
+'''
-:Ryan Brinkman (University of British Columbia, June 11-12)
+:Ryan Brinkman (University of British Columbia)
 :Atul Butte (Stanford University)
 :Werner Ceusters (University at Buffalo)
-:Cliburn Chan (Duke University, June 11-12)
+:Cliburn Chan (Duke University)
 :Quan Chen (NIH/NIAID)
 :Lindsay Cowell (University of Texas Southwestern Medical Center)
 :Paresh Dandona (Diabetes and Endocrinology Center of Western New York / University at Buffalo)
@@ Line 173: / Line 180: @@
 :Alex Diehl (University at Buffalo)
 :Chester Fox (University at Buffalo)
 :Albert Goldfain (University at Buffalo, Syracuse University and Blue Highway, Inc.)
 :Oliver He (University of Michigan)
 :Leonard Jacuzzo (University at Buffalo)
 :Christos (Kitsos) Louis (IMBB-FORTH, Crete)
 :Nikesh Kotecha (Cytobank)
 :Yu Lin (University of Michigan)
 :Anna Maria Masci (Duke University)
 :Darren Natale (Georgetown University)
 :Dave Parrish (Digital Infuzion)
-:Bjoern Peters, (La Jolla Institute for Allergy and Immunology)
+:Bjoern Peters (La Jolla Institute for Allergy and Immunology)
 :Alan Ruttenberg (University at Buffalo)
 :Stanley A. Schwartz (University at Buffalo)
 :Veronica Shamovsky (NYU School of Medicine)
 :Barry Smith (University at Buffalo)
 :Cathy Wu (University of Delaware, Georgetown University)
 :Alex C. Yu (University at Buffalo)