Latest revision as of 10:08, 9 October 2009

CL - OBO Cell Ontology

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

Resources

Ontology

http://obofoundry.org/obo/CL

Applications

CL:Aligning species-specific anatomy ontologies with CL

CL_alignment_Biocurator07_poster

Request tracker

- CL tracker

You can also submit requests to the list.

Mail Lists

- OBO Cell

The following list may also be of interest

- OBO CrossProduct

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

Cell ontology restructuring efforts

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

cell ontology evaluation.doc

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

CL Revised.obo

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

NIAID Cell Ontology Workshop, May 13-14, 2008

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

More information on the workshop can be found here.

Is_a Completeness for the current Cell Ontology

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

A list of useful differentia for defining cell-type terms

has_part: <GO:cellular_compomnent>

has_function_from_process: <GO:biological_process>

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

develops_into: <CL:cell>

has_part: <CHEBI:chebi_ontology>

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

@@ Line 1: / Line 1: @@
 =CL - OBO Cell Ontology=
+The official Cell Ontology wiki is now hosted at [http://obofoundry.org/wiki/index.php/CL:Main_Page http://obofoundry.org/wiki/index.php/CL:Main_Page], although certain links on that wiki refer back to older content here.
 =Resources=
@@ Line 5: / Line 7: @@
 ==Ontology==
-Will soon be available from [[NCBO BioPortal]]. For now you should just obtain it from http://obo.sourceforge.net
+http://obofoundry.org/obo/CL
 ===Applications===
@@ Line 11: / Line 13: @@
 [[CL:Aligning species-specific anatomy ontologies with CL]]
-[[Media:CL alignment Biocurator07 poster]]
+[[Media:CLalign.biocuratorposter.final.ppt|CL_alignment_Biocurator07_poster]]
 ==Request tracker==
@@ Line 32: / Line 34: @@
 The cell ontology is being restructured with the general goals of improving definitions, moving towards single inheritance and is_a completeness, and making the CL more interoperable with the GO and CARO. These discussions are occurring via chat, the histories of which will be posted here. Please email the OBO cell list if you would like to participate.
 [[Media:cell_ontology_evaluation.doc|cell ontology evaluation.doc]]
@@ Line 53: / Line 54: @@
 [[Media:CLRevised.obo|CL Revised.obo]]
 Notes and action items from the cell ontology breakout session at the 2nd International Biocuration Meeting 2007.
 [[Media:Cell_ontology_reorganization_working_group_notes.doc|Cell_ontology_reorganization_working_group_notes.doc]]
+===NIAID Cell Ontology Workshop, May 13-14, 2008===
+The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology.  The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.
+More information on the workshop can be found [[NIAID Cell Ontology Workshop May 2008|here]].
+===Is_a Completeness for the current Cell Ontology===
+As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node '''cell'''.  We would like to provide this is_a path in short order.  The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root.  We are taking suggestions about what is_a parents to use.  Please check out the page for [[May 2008 Is_a Orphans in the Cell Ontology]] and make some suggestions.  All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.
+== A list of useful differentia for defining cell-type terms==
+has_part: <GO:cellular_compomnent>
+has_function_from_process: <GO:biological_process>
+has_quality: <PATO:quality/monadic quality of continuant>
+develops_into: <CL:cell>
+has_part: <CHEBI:chebi_ontology>
+has_part: (<CHEBI:chebi_ontology>^part_of <GO:cellular_component>)

Difference between revisions of "CL:Main Page"