POC-TraitNet meeting 05-28-2010, NYBG - Revision history

Rwalls at 22:47, 28 May 2010

2010-05-28T22:47:42Z

Rwalls at 22:47, 28 May 2010

2010-05-28T22:47:11Z

Rwalls at 21:25, 28 May 2010

2010-05-28T21:25:59Z

Rwalls at 20:31, 28 May 2010

2010-05-28T20:31:07Z

Rwalls: moved POC-Traitnet meeting 05-28-2010, NYBG to POC-TraitNet meeting 05-28-2010, NYBG: forgot to capitalize N

2010-05-28T20:29:22Z

moved POC-Traitnet meeting 05-28-2010, NYBG to POC-TraitNet meeting 05-28-2010, NYBG: forgot to capitalize N

Rwalls at 20:24, 28 May 2010

2010-05-28T20:24:29Z

Rwalls at 20:23, 28 May 2010

2010-05-28T20:23:51Z

Rwalls: Created page with 'Present: Ramona Walls (POC, New York Botanical Garden), Dan Bunker (Traitnet, New Jersey Institute of Technology), Farshid Ahrestani (TraitNet, Columbia University and NJIT) One…'

2010-05-28T19:56:59Z

Created page with 'Present: Ramona Walls (POC, New York Botanical Garden), Dan Bunker (Traitnet, New Jersey Institute of Technology), Farshid Ahrestani (TraitNet, Columbia University and NJIT) One…'

New page

Present: Ramona Walls (POC, New York Botanical Garden), Dan Bunker (Traitnet, New Jersey Institute of Technology), Farshid Ahrestani (TraitNet, Columbia University and NJIT)

One of their goals is to develop a sematic web application that would allow users to access ecological datasets. To do this they are developing a "functional trait ontology." Although the ultimate goal is to include all organisms, they are currently focusing on plants, because there are far more plant trait databases. Plant plant functional traits includes plant entities (the physical parts of the plant = plant structures) and plant characteristics (direct or derived measurements made by ecologists/biologists of plant entities).

They are well aware of the PO and TO, but decided to develope their own ontologies for several reasons. For plant characteristics, they found that many of the terms were too specific to the organism or specific experimental procedures, and they needed many new characteristics that were appropriate for ecologists. All of the terms in their plant entity ontology come from the PO plant structure. They have run into many of the same problems we dealt with for upper level structures (like where to classify terms or how to define upper level terms), and would be quite happy to use the solutions that we are working out. They do not need the level of detail that the PO has, since ecologists generally study a limited set of structures, and they would probably want to use a subset of PO terms. They are less concerned with is_a relationships than part_of relationships.

They would like to evaluate a newer version of the PO to see if the structure will work for them. If so, they will probably just adopt the PO, rather than have their own ontology.

Ramona gave them Pankaj and Laurel's names, and they said they would like to get in touch with Pankaj later, after returning from an NCEAS working group.

← Older revision		Revision as of 22:47, 28 May 2010
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	TraitNet would like to evaluate a newer version of the PO to see if the structure will work for them, and if so, they will probably just adopt the PO, rather than create their own ontology. Perhaps PO can complete one branch of the ontology from top level to leaf terms, so they can get a better idea of the structure. TraitNet could also provide a list of terms they anticipate needing, and PO could show them how the new PO structure would work for those terms.		TraitNet would like to evaluate a newer version of the PO to see if the structure will work for them, and if so, they will probably just adopt the PO, rather than create their own ontology. Perhaps PO can complete one branch of the ontology from top level to leaf terms, so they can get a better idea of the structure. TraitNet could also provide a list of terms they anticipate needing, and PO could show them how the new PO structure would work for those terms.

−	Farshid or Dan will contact Pankaj or Laurel after returning from an NCEAS working group on their semantic web application.	+	PO and TraitNet will stay in contact, and Farshid or Dan will contact Pankaj or Laurel after returning from an NCEAS working group on their semantic web application.

@@ Line 9: / Line 9: @@
 One of TraitNet's goals is to develop a sematic web application that would allow users to access ecological datasets on the web. To do this they are developing a "functional trait ontology." This is currently focusing on plants, because there are far more plant trait databases. Plant functional traits includes plant entities (the physical parts of the plant = plant structures in PO) and plant characteristics (direct or derived measurements of plant entities made by ecologists/biologists).
-They are aware of the PO and TO, but decided to develope their own ontologies for several reasons. For plant characteristics, they found that many of the terms in TO were too specific to crop organism or to specific experimental procedures, and they needed many new characteristics that would be appropriate for ecologists. The PO (plant structure) had the terms they need for their plant entity ontology, but at when they began working on their ontology, PO's structure was not suitable for their needs. After consulting with several ecologists/plant experts, they began working on their own ontology, using terms from PO. There are more interested in part_of relationships that is_a relationships. They have run into many of the same problems the PO has been dealing with, like where to classify terms or how to define upper level terms.
+They are aware of the PO and TO, but decided to develope their own ontologies for several reasons. For plant characteristics, they found that many of the terms in TO were too specific to crop organism or to specific experimental procedures, and they needed many new characteristics that would be appropriate for ecologists. The TraitNet plant characteristics ontology development is being headed by [http://www.cefe.cnrs.fr/ecopar/Eric_Garnier.htm Eric Garnier] at CNRS in France.
-Ramona gave them some background on the PO (how it originally united several individual species ontologies from model organisms and is currently being revised to include all plants, who were the people involved, our participation in the OBO Foundry), showed them how to access annotations, talked about how scientists might use the PO (primary uses being the the genetics/genomics field), showed them the current test ontology on the [http://dev.plantontology.org dev browser] and explained how to access the PO on [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/ SVN]. She also explained that the anatomy_test file is under active development and is constantly changing.
+The PO (plant structure) had the terms they need for their plant entity ontology, but at when they began working on their ontology, PO's structure was not suitable for their needs. After consulting with several ecologists/plant experts, they began working on their own ontology, using terms from PO. They are more interested in part_of relationships than is_a relationships. They have run into many of the same problems the PO has been dealing with, like where to classify terms or how to define upper level terms.
-There was a discussion of whether TraitNet should use the PO outright (once a new release is published) or use terms from the PO, but with their own structure. It was agreed that it would add power to both TraitNet and PO if the ontology was shared, since then users would have access to both genetic and ecological annotations. If they use PO terms with their own structure, they will probably need to create alternate IDs, to avoid issues with incorrect parentage. Since ecologists generally study a limited set of plant structures, and they would probably only need to use a subset of PO terms, and might consider making a PO-Slim (see [http://www.geneontology.org/GO.slims.shtml GO slims]) for TraitNet.
+Ramona gave them some background on the PO (how it originally united several individual species ontologies from model organisms and is currently being revised to include all plants; who were the people involved; our participation in the OBO Foundry), showed them how to access annotations, talked about how scientists might use the PO (primary uses being the the genetics/genomics field), showed them the current test ontology on the [http://dev.plantontology.org dev browser] and explained how to access the PO on [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/ SVN]. She also explained that the anatomy_test file is under active development and is constantly changing.
-They would like to evaluate a newer version of the PO to see if the structure will work for them. If so, they will probably just adopt the PO, rather than have their own ontology.
+Farshid or Dan will contact Pankaj or Laurel after returning from an NCEAS working group on their semantic web application.

@@ Line 7: / Line 7: @@
 '''Discussion Summary'''
-One of TraitNet's goals is to develop a sematic web application that would allow users to access ecological datasets that are on the web. To do this they are developing a "functional trait ontology." This is currently focusing on plants, because there are far more plant trait databases. Plant plant functional traits includes plant entities (the physical parts of the plant = plant structures in PO) and plant characteristics (direct or derived measurements of plant entities made by ecologists/biologists).
+One of TraitNet's goals is to develop a sematic web application that would allow users to access ecological datasets on the web. To do this they are developing a "functional trait ontology." This is currently focusing on plants, because there are far more plant trait databases. Plant functional traits includes plant entities (the physical parts of the plant = plant structures in PO) and plant characteristics (direct or derived measurements of plant entities made by ecologists/biologists).
-They are aware of the PO and TO, but decided to develope their own ontologies for several reasons. For plant characteristics, they found that many of the terms in TO were too specific to crop organism or to specific experimental procedures, and they needed many new characteristics that would be appropriate for ecologists. The PO (plant structure) had the terms they need for their plant entity ontology, but at when they began working on their ontology, its structure was not suitable for their needs. After consulting with several ecologists/plant experts, they began working on their own ontology, using many of the terms from PO. There are more interested in part_of relationships that is_a relationships. They have run into many of the same problems the PO has been dealing with, like where to classify terms or how to define upper level terms.
+They are aware of the PO and TO, but decided to develope their own ontologies for several reasons. For plant characteristics, they found that many of the terms in TO were too specific to crop organism or to specific experimental procedures, and they needed many new characteristics that would be appropriate for ecologists. The PO (plant structure) had the terms they need for their plant entity ontology, but at when they began working on their ontology, PO's structure was not suitable for their needs. After consulting with several ecologists/plant experts, they began working on their own ontology, using terms from PO. There are more interested in part_of relationships that is_a relationships. They have run into many of the same problems the PO has been dealing with, like where to classify terms or how to define upper level terms.

@@ Line 5: / Line 5: @@
 Present: Ramona Walls (POC, New York Botanical Garden), Dan Bunker (Traitnet, New Jersey Institute of Technology), Farshid Ahrestani (TraitNet, Columbia University and NJIT)
-Discussion Summary
+'''Discussion Summary'''
-One of TraitNet's mail goals is to develop a sematic web application that would allow users to access ecological datasets that are on the web. To do this they are developing a "functional trait ontology." This is currently focusing on plants, because there are far more plant trait databases. Plant plant functional traits includes plant entities (the physical parts of the plant = plant structures in PO) and plant characteristics (direct or derived measurements of plant entities made by ecologists/biologists).
+One of TraitNet's goals is to develop a sematic web application that would allow users to access ecological datasets that are on the web. To do this they are developing a "functional trait ontology." This is currently focusing on plants, because there are far more plant trait databases. Plant plant functional traits includes plant entities (the physical parts of the plant = plant structures in PO) and plant characteristics (direct or derived measurements of plant entities made by ecologists/biologists).
 They are aware of the PO and TO, but decided to develope their own ontologies for several reasons. For plant characteristics, they found that many of the terms in TO were too specific to crop organism or to specific experimental procedures, and they needed many new characteristics that would be appropriate for ecologists. The PO (plant structure) had the terms they need for their plant entity ontology, but at when they began working on their ontology, its structure was not suitable for their needs. After consulting with several ecologists/plant experts, they began working on their own ontology, using many of the terms from PO. There are more interested in part_of relationships that is_a relationships. They have run into many of the same problems the PO has been dealing with, like where to classify terms or how to define upper level terms.
 Ramona gave them some background on the PO (how it originally united several individual species ontologies from model organisms, and is currently being revised to include all plants), showed them how to access annotations and talked about how scientists might use the PO, and showed them the current test ontology on the [http://dev.plantontology.org dev browser] and how to access the PO on [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/ SVN]. She also explained that the anatomy_test file is under active development and is constantly changing.

@@ Line 1: / Line 1: @@
 POC-TraitNet Meeting 05-28-2010, 9:00 am, EDT New York Botanical Garden
 Present: Ramona Walls (POC, New York Botanical Garden), Dan Bunker (Traitnet, New Jersey Institute of Technology), Farshid Ahrestani (TraitNet, Columbia University and NJIT)
@@ Line 12: / Line 14: @@
 Ramona gave them some background on the PO (how it originally united several individual species ontologies from model organisms, and is currently being revised to include all plants), showed them how to access annotations and talked about how scientists might use the PO, and showed them the current test ontology on the [http://dev.plantontology.org dev browser] and how to access the PO on [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/ SVN]. She also explained that the anatomy_test file is under active development and is constantly changing.
-There was a discussion of whether or not TraitNet should use the PO as it is (once a new release is published) or use terms from the PO, but with their own structure. It was agreed that it would add power to both TraitNet and PO if the ontology was shared, since then users would have access to both genetic and ecological annotations. Since ecologists generally study a limited set of plant structures, and they would probably only need to use a subset of PO terms, and might consider making a PO-Slim (see [http://www.geneontology.org/GO.slims.shtml GO slims] for TraitNet.
+There was a discussion of whether or not TraitNet should use the PO as it is (once a new release is published) or use terms from the PO, but with their own structure. It was agreed that it would add power to both TraitNet and PO if the ontology was shared, since then users would have access to both genetic and ecological annotations. Since ecologists generally study a limited set of plant structures, and they would probably only need to use a subset of PO terms, and might consider making a PO-Slim (see [http://www.geneontology.org/GO.slims.shtml GO slims]) for TraitNet.

← Older revision	Revision as of 20:29, 28 May 2010
(No difference)