Hinxton meeting March 2008 - Revision history

Helenp at 13:52, 2 April 2008

2008-04-02T13:52:42Z

Helenp: /* Action Items */

2008-03-31T12:44:49Z

Action Items

Helenp at 12:27, 31 March 2008

2008-03-31T12:27:29Z

Helenp at 11:07, 31 March 2008

2008-03-31T11:07:02Z

Helenp: /* Action Items */

2008-03-31T11:03:06Z

Action Items

Helenp at 10:58, 31 March 2008

2008-03-31T10:58:43Z

Helenp: /* Discussion */

2008-03-31T10:42:53Z

Discussion

Helenp: /* Discussion */

2008-03-31T10:33:09Z

Discussion

Helenp at 10:31, 31 March 2008

2008-03-31T10:31:50Z

Helenp at 10:27, 31 March 2008

2008-03-31T10:27:13Z

@@ Line 87: / Line 87: @@
   * DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
   * communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes
 <b>AI:David(?) will communicate these suggestions CARO improvements to the CARO team</b>

@@ Line 56: / Line 56: @@
 E.g. delamination
-AI:Johnathan, David, Thorsten
+<b>AI:Johnathan, David, Thorsten</b>
 * 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. In consulatation with phenoscape and others, David has developed a system for representing homology groups using relations based on the "homologous_to" relation defined by phenoscape.
-AI:David will generate an OBO file containing his modelling strategy
+<b>AI:David will generate an OBO file containing his modelling strategy for representing homology groups</b>
-AI: David and Thorsten will work together to produce a single system based
+<b>AI: David and Thorsten will work together to produce a single system based
-on their approaches.  This will include consulations with phenoscape to
+on their respective modelling approaches.  This will include consultations with phenoscape to
-ensure the new approach is compatible with theirs.
+ensure the new approach is compatible with theirs.</b>
 * 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology
@@ Line 72: / Line 72: @@
 * 4. FMA update model.
-AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.
+<b>AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.</b>
 * 5. CARO improvements
@@ Line 87: / Line 87: @@
   * DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
   * communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes
 * 6. Funding
@@ Line 92: / Line 94: @@
 There are two possible sources of funding identified
   * an unsolicited R01
-  * EC funding. This will be conditional on use, rather than solely development of an ontology.
+  * EC funding. This will be conditional on use and implementation, rather than solely development of an ontology.
   * Datasets that could be integrated include Zebrafish, Gene Expression in situ/array based, VPH
-AI: Helen and Bernard will look into EC funding sources (ICAT)
+<b>AI: Helen and Bernard will look into EC funding sources (ICAT)
-AI: Suzi will look into submitting an R01 to develop the MCRA and do some work on CARO to support this.
+AI: Suzi will look into submitting an R01 to develop the MCRA
 * 7. MMIA ways forward
@@ Line 102: / Line 104: @@
 MMIA is a useful string matching tool, no ontological claims are made for it.
-AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multi-species anatomy ontology MCRA. See 3.
+<b>AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multi-species anatomy ontology MCRA. See 3. </b>
 * 8. Annotation/curator tools
@@ Line 112: / Line 114: @@
 Use of ontologies in developing a visualization methodology/standard e.g. using a schematic body plan to present gene expression and maps to pathways was also discussed. Bernard in particular is interested in this. Stuart Aitken (Edinburgh) has a new grant to develop 2.5D visualization tools. Suzi is interested in generic visualizations that also work for environments.
-AI:BdB to contact Stuart Aitken and Richard Baldock about visualization tools.
+<b>AI:BdB to contact Stuart Aitken and Richard Baldock about visualization tools.</b>
 === Shared Materials ===

@@ Line 20: / Line 20: @@
 * David Osumi-Sutherland
 * Helen Parkinson
@@ Line 56: / Line 58: @@
 AI:Johnathan, David, Thorsten
-* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. David suggested that the FMA relations be condensed and used.
+* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. In consulatation with phenoscape and others, David has developed a system for representing homology groups using relations based on the "homologous_to" relation defined by phenoscape.
 AI:David will generate an OBO file containing his modelling strategy
 * 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology

@@ Line 100: / Line 100: @@
 * 8. Annotation/curator tools
-Much of the discussion covered the needs of those using anatomy ontologies rather than those building them.
+Much of the discussion covered the needs of those using anatomy ontologies rather than those building them. Suggestion that an annotation tool could use some 'lite' version of the MCRA and users could navigate to mapped species specific ontologies if these were needed.
 * 9. Visualization
@@ Line 107: / Line 107: @@
 AI:BdB to contact Stuart Aitken and Richard Baldock about visualization tools.
 === Shared Materials ===

@@ Line 96: / Line 96: @@
 MMIA is a useful string matching tool, no ontological claims are made for it.
-AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multispecies anatomy ontology MCRA. See 3.
+AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multi-species anatomy ontology MCRA. See 3.
 * 8. Annotation/curator tools
 Much of the discussion covered the needs of those using anatomy ontologies rather than those building them.
 === Shared Materials ===

@@ Line 35: / Line 35: @@
 These include:
-  * queries for gene expression (array and in situ) across shared anatomical structures and developmental time
+  * queries for gene expression (array and in situ) across gross shared anatomical structures in eg. human/mouse/rat and zebrafish/Drosophila developmental time
   * need for pathway mapping and inference across species
   * need for annotation source that's multispecies for use in submission tools
@@ Line 41: / Line 41: @@
 *  CARO state of the art and experiences extending CARO  (David, Thorsten)
 *  Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)
 === Action Items ===

@@ Line 31: / Line 31: @@
 The presentations focussed on:
-*  the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard)
+*  the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard).
 *  CARO state of the art and experiences extending CARO  (David, Thorsten)
@@ Line 68: / Line 74: @@
   * DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
   * communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes
-−
 === Shared Materials ===