Difference between revisions of "CL:Main Page"
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=CL - OBO Cell Ontology= | =CL - OBO Cell Ontology= | ||
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| + | 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= | =Resources= | ||
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==Ontology== | ==Ontology== | ||
| − | + | http://obofoundry.org/obo/CL | |
===Applications=== | ===Applications=== | ||
[[CL:Aligning species-specific anatomy ontologies with CL]] | [[CL:Aligning species-specific anatomy ontologies with CL]] | ||
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| + | [[Media:CLalign.biocuratorposter.final.ppt|CL_alignment_Biocurator07_poster]] | ||
==Request tracker== | ==Request tracker== | ||
| − | + | - [http://sourceforge.net/tracker/?group_id=76834&atid=925065 CL tracker] | |
| − | + | You can also submit requests to the list. | |
==Mail Lists== | ==Mail Lists== | ||
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GO is pre-coordinating biological process terms that refer to cell types using CL IDs | GO is pre-coordinating biological process terms that refer to cell types using CL IDs | ||
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| + | ==Cell ontology restructuring efforts== | ||
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| + | The cell ontology is being restructured with the general goals of improving definitions, moving towards single inheritance and is_a completeness, and making the CL more interoperable with the GO and CARO. These discussions are occurring via chat, the histories of which will be posted here. Please email the OBO cell list if you would like to participate. | ||
| + | |||
| + | [[Media:cell_ontology_evaluation.doc|cell ontology evaluation.doc]] | ||
| + | |||
| + | [[Media:cellchat.2.12.07.doc|cellchat.2.12.07.doc]] | ||
| + | |||
| + | [[Media:cellchat.2.23.07.doc|cellchat.2.23.07.doc]] | ||
| + | |||
| + | [[Media:cellchat.2.27.07.doc|cellchat.2.27.07.doc]] | ||
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| + | [[Media:cellchat.3.15.07.doc|cellchat.3.15.07.doc]] | ||
| + | |||
| + | [[Media:cellchat.6.1.07.doc|cellchat.6.1.07.doc]] | ||
| + | |||
| + | [[Media:cellchat.8-9-2007.doc|cellchat.8-9-2007]] | ||
| + | |||
| + | [[Media:cell_chat_8-24-2007.doc|cell_chat_8-24-2007]] | ||
| + | |||
| + | An initial rough draft can be found below in OBO format with the proposed new branch at the same level as 'cell'. Current tasks include moving cells over to the 'by structure' branch to test for compatibility and potential problems. | ||
| + | |||
| + | [[Media:CLRevised.obo|CL Revised.obo]] | ||
| + | |||
| + | Notes and action items from the cell ontology breakout session at the 2nd International Biocuration Meeting 2007. | ||
| + | [[Media:Cell_ontology_reorganization_working_group_notes.doc|Cell_ontology_reorganization_working_group_notes.doc]] | ||
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| + | |||
| + | ===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. | ||
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| + | == A list of useful differentia for defining cell-type terms== | ||
| + | |||
| + | has_part: <GO:cellular_compomnent> | ||
| + | |||
| + | has_function_from_process: <GO:biological_process> | ||
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| + | 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>) | ||
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
Applications
CL:Aligning species-specific anatomy ontologies with CL
CL_alignment_Biocurator07_poster
Request tracker
You can also submit requests to the list.
Mail Lists
- OBO Cell
The following list may also be of interest
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.
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.
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>)