Difference between revisions of "POC Conf. Call 7-31-12"

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In attendance:
 
In attendance:
  
−
POC members:
+
POC members: ''Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elser (OSU), Dennis Stevenson (NYBG), Pankaj Jaiswal (OSU)''
−
 
 
−
Absent:
 
  
 +
Absent:''Marie Alejandra Gandolfo (Cornell), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab), Barry Smith (University at Buffalo, NY)''
  
 
Collaborators: none
 
Collaborators: none
Line 14: Line 13:
  
 
Back to [[POC Meetings Minutes]]
 
Back to [[POC Meetings Minutes]]
 +
=News since last meeting July 3rd=
 +
* Release #18 is out [[July_2012_Release]]
 +
 +
Two significant new terms have been added to help categorize the problematic plant structures such as fruit and seed, and their parts.
 +
 +
* multi-tissue plant structure (PO:0025496) has been added as a direct sub-class of plant structure (PO:0009011) and is the new parent term for fruit (PO:0009001), seed (PO:0009010), and plant organ (PO:0009008).
 +
 +
* cardinal part of multi-tissue plant structure (PO:0025498)- This term includes cardinal parts of plant organs such as leaf lamina (PO:0020039) or receptacle (PO:0009064), as well as parts of other multi-tissue plant structures, such as fruit distal end (PO:0008001) or arilloid (PO:0019022).
 +
 +
A new term, collective plant structure (PO:0025497), was created to describe collections of plant structures and to serve as parent term to collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269). Note that collective plant organ structure (PO:0025007) was formerly named "collective plant structure" (the same name as the new upper-level term), but was renamed for clarity.
 +
 +
''We discussed the new terms and whether or not the names are appropriate or if they could be made less confusing.  We should review the names and definitions and make sure the child terms such as anther are in the appropriate class. BS suggested it might be helpful to ask Jose Mejino of the FMA to look at these.''
 +
 +
''PJ was concerned that users would be confused by seeing, for example, two structures that are siblings, but one is also part of the other. BS: People who want to use ontologies (domain experts) often are put off by the complex modeling of the ontology. One way to deal with this is to create simpler user vies (e.g., using Ontodog).''
 +
 +
* '''Please review the [[PO_Release_SOP_Page]]'''.  I revised and updated for the most recent release, but it is good to make sure we have not missed anything.
 +
 +
 +
* '''AJB paper is out!''' see link: [http://www.amjbot.org/content/early/2012/07/29/ajb.1200222.abstract Bio-ontologies]
 +
 +
''Need to post notices on PO home page and facebook and could send something out on po-announce as well.''
 +
 +
''Maybe look at PO web page to see if there is any change in visitors after publication of this paper or the Wood Ontology paper.''
 +
 +
* PAE paper is being revised-consolidated all the comments from everyone and updating to match the release. Will go out again to everyone this week.
 +
 +
 +
* PSDS invited paper- for Special Issue on "Functional Genomics and Systems Biology in the Post Genomics Era" that will be published in 2013 in Physiologia Plantarum.
 +
 +
''PJ: The PAE paper could also go into Phys. Plantarum instead, if it is too soon for this one.''
 +
 +
''RW would like everyone to send her ideas as to what they would like to see in it.''
 +
 +
''Do we know if this is the end of October or the beginning?''
 +
 +
''Either way, in order to get it done by October, we need to have a draft done by September. The question is whether or not the PSDS is ready to write about. The upper level structure has been extensivly revised, but we still have a lot of changes to make to more specific terms.''
 +
 +
''DS: Outlining what would go into paper would show what needs to be done.''
 +
 +
''PJ: New grape annotations. However, they are not in there yet.''
 +
 +
''BS: How having a development stage ontology could be useful to people's research. (Some of that is already published in the previous paper). Take what was said in the old paper and update it based on what has been learned about ontology building as well as on the on the data side.''
 +
 +
''What can new data sets accomplish. Not heavy on the actually current structure of the ontology, but a statement of what we are doing and the principles.''
 +
 +
''PJ: Highlight that there are no published reports or funding to compare development of different species (Is this true? It is true for examples like comparing berry of grape to other fruit say five days after pollenation). Highlight comparative aspects (yes!).''
 +
 +
=Plans for the next release=
 +
 +
Tentatively planned for [[October_2012_Release]]
 +
 +
Priorities for next release:
 +
 +
==Continue major revision of PSDS==
 +
Focus on the revisions on the stages that have the most annotations:
 +
 +
'''PO:0007033 : whole plant development stage'''
 +
 +
'''> PO:0028002 : sporophyte development stage'''
 +
 +
>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)
 +
 +
>>> PO:0007047 : 3 inflorescence detectable stage [29131]
 +
 +
>>>PO:0007016 : 4 flowering [28057]
 +
 +
>>>PO:0007042 : 5 fruit formation [31009]
 +
 +
>>>PO:0007010 : 6 ripening [37642]
 +
 +
 +
'''>> PO:0007134 : sporophyte vegetative stage [60370]:'''  (Some still have the numbers preceding them, others don't)
 +
 +
>>>PO:0007057 : 0 seed germination stage [29568]
 +
 +
>>>PO:0007112 : 1 main shoot growth stage [47411]
 +
 +
>>>PO:0007131 : seedling development stage [26673]
 +
 +
 +
 +
'''PO:0009012 : plant structure development stage:'''
 +
 +
> PO:0007615 : flower development stage [48067]
 +
 +
>PO:0001083 : inflorescence development stage [48067]
 +
 +
 +
'''PO:0025339 : plant organ development stage [46618]'''
 +
 +
>PO:0001050 : leaf development stage [45968]
 +
 +
>PO:0007520 : root development stage [25208]
 +
 +
 +
'''PO:0025338 : collective plant structure development stage [49645]'''
 +
 +
>PO:0007615 : flower development stage [48067]
 +
 +
''What about development of other anatomical entities? "Plant structure development stage" only covers structures, but we may want to talk about development of anatomical spaces of substances like cuticle.''
 +
 +
''BFO 2.0 addresses whether or not sites have histories the way material entities do.''
 +
 +
''We need to make sure, as we revise, that the PSDS terms correspond to the PAE terms (some upper level re-organization has already been done to align them).''
 +
 +
''Annotations of development stages:''
 +
 +
''PJ suggested that annotating directly to development stage should be required. We have mechanisms to move annotations back and forth between PAEs and PSDSs, based on ontology relations, but at this point, when people download annotation directly from the server (rather than via Amigo), they do not aggregate based on ontology relations.''
 +
 +
''Another issue is that the annotations only move to the generic term (e.g., an annotation to leaf may go to generic leaf development stage, but it would go to the more specific stage of development of the leaf.''
 +
 +
''Mysql queries also only give direct annotations.''
 +
 +
''Ultimately, we would like to have tools that suggest development stages, when annotator searches for a structure, or vice versa.''
 +
 +
==file naming and which variations of the file to create for each release==
 +
 +
see [[PO_Release_SOP_Page]]
 +
 +
''tabled for a future discussion''
 +
 +
==Complete outstanding user requests/SF tracker items==
 +
 +
See the list at: [[Items_for_future_meetings]]
 +
 +
''tabled for a future discussion''
 +
 +
==Update the Po webpages==
 +
- Which ones are top priority?
 +
 +
See: [[Plant_Ontology_Web_Site_Update:_Winter_2012]]
 +
 +
''tabled for a future discussion''
 +
 +
=Meeting reports=
 +
==[http://kr-med.org/icbofois2012/ ICBO 2012]==
 +
===Disease ontology===
 +
RW presented a paper on a plant disease extension of the Infectious Disease Ontology (IDOplant). The paper was well received, and there was a lot of discussion (after the talk) about how to model disease symptoms. The IDOplant manuscript defined "plant disase symptom", but did not include a term for it in the ontology. The Ontology for General Medical Science (OGMS) is planning to remove their term for symptom, for similar reasons -- a symptom can really be anything.
 +
 +
Symptoms should be modeled as dispositions. An infectious disease is a disposition, which is borne by some plant and has as a material basis some infectious disorder. As a result of having the infection, that plant also bears the disposition to undergo certain processes, which may lead to measurable/observable changes in the plant. For example, infection by a particular microbe results in the disposition to lose chlorophyll, which may lead to  yellow leaves. Of course, the mechanisms could be modeled in even more detail, for example, at the molecular level. As dispositions, symptoms or signs are mechanistically linked to a disease, but it is never stated that every instance of the disease course will display a particular symptom. This way of modeling diseases and symptoms requires that we think carefully about the processes involved in a disease course, which is what we will need if we want to use ontologies to learn something new about diseases.
 +
 +
===New tools for ontology editing===
 +
RW attended an OBI workshop while at IBCO. This included presentation of some of the tools being developed by Oliver He's lab. These may be of general interest to the PO curators.
 +
 +
*[http://www.ontobee.org/ Ontobee]: A web server aimed to facilitate ontology visualization, query, and development. This is already familiar to many people in the ontology community.
 +
*[http://ontofox.hegroup.org/ Ontofox]: An easy-to-use web-based tool for importing ontology terms using the MIREOT process.
 +
*[http://ontodog.hegroup.org/ Ontodog]: A web-based tool for generating community views of ontologies. Allows users to create subsets of an ontology with their own preferred term names. This could be very helpful for PO users who represent specific parts of the plant science community. ''RW: I haven't tried this one yet, so not sure how easy it is to use''.
 +
 +
==[http://austin2012.aspb.org/ ASPB 2012]==
 +
July 20 - 24, 2012 - Plant Biology 2012, Austin, TX
 +
 +
Link to meeting page: [http://austin2012.aspb.org/ ASPB2012]
 +
 +
Helped organize an [[Outreach booth- ASPB Plant Biology 2012]] along with Gramene, TAIR, BAR, iPlant, PMN, Kbase.  Many people came and talked with us about all the different projects and I got to talk to our collaborators a lot too. 
 +
 +
[http://my.aspb.org/default.asp?page=Meetings_PB12Wrkshps Plant Informatics Workshop] was held with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 9:00 PM.  About 53 people attended.
  
 
=Upcoming meetings and Presentations 2012:=
 
=Upcoming meetings and Presentations 2012:=
Line 20: Line 175:
 
Link to:  [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]
 
Link to:  [https://academy.nescent.org/wiki/Anatomy_ontologies Anatomy Ontology course]
  
−
from Paula Mabee: Opening are available the Anatomy Ontology course.
 
  
 
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]
 
Link to [https://academy.nescent.org/wiki/Ontologies_2012_course_materials Course materials]
Line 29: Line 183:
  
  
−
LM will be attending
+
LM is attending
 +
 
 
==Online Ontology Workshops at The University at Buffalo==
 
==Online Ontology Workshops at The University at Buffalo==
  
Line 64: Line 219:
 
The focus of the workshop will be on mostly development stages and traits for the crop plants
 
The focus of the workshop will be on mostly development stages and traits for the crop plants
  
−
=Next meeting scheduled for Tuesday, Aug 7th, 2012 at 10am PDT/1pm EDT=
+
=Next meeting scheduled for Tuesday, Aug 14th, 2012 at 10am PDT/1pm EDT=
−
See: [[POC_Conf._Call_8-7-12]]
+
See: [[POC_Conf._Call_8-14-12]]

Latest revision as of 18:33, 20 November 2013

POC meeting, Webex Conference Call; Date: Tuesday July 31st, 2012 10am PDT/1pm EDT

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Elser (OSU), Dennis Stevenson (NYBG), Pankaj Jaiswal (OSU)

Absent:Marie Alejandra Gandolfo (Cornell), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab), Barry Smith (University at Buffalo, NY)

Collaborators: none


Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_7-3-12?

Back to POC Meetings Minutes

News since last meeting July 3rd

Two significant new terms have been added to help categorize the problematic plant structures such as fruit and seed, and their parts.

  • multi-tissue plant structure (PO:0025496) has been added as a direct sub-class of plant structure (PO:0009011) and is the new parent term for fruit (PO:0009001), seed (PO:0009010), and plant organ (PO:0009008).
  • cardinal part of multi-tissue plant structure (PO:0025498)- This term includes cardinal parts of plant organs such as leaf lamina (PO:0020039) or receptacle (PO:0009064), as well as parts of other multi-tissue plant structures, such as fruit distal end (PO:0008001) or arilloid (PO:0019022).

A new term, collective plant structure (PO:0025497), was created to describe collections of plant structures and to serve as parent term to collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269). Note that collective plant organ structure (PO:0025007) was formerly named "collective plant structure" (the same name as the new upper-level term), but was renamed for clarity.

We discussed the new terms and whether or not the names are appropriate or if they could be made less confusing. We should review the names and definitions and make sure the child terms such as anther are in the appropriate class. BS suggested it might be helpful to ask Jose Mejino of the FMA to look at these.

PJ was concerned that users would be confused by seeing, for example, two structures that are siblings, but one is also part of the other. BS: People who want to use ontologies (domain experts) often are put off by the complex modeling of the ontology. One way to deal with this is to create simpler user vies (e.g., using Ontodog).

  • Please review the PO_Release_SOP_Page. I revised and updated for the most recent release, but it is good to make sure we have not missed anything.


Need to post notices on PO home page and facebook and could send something out on po-announce as well.

Maybe look at PO web page to see if there is any change in visitors after publication of this paper or the Wood Ontology paper.

  • PAE paper is being revised-consolidated all the comments from everyone and updating to match the release. Will go out again to everyone this week.


  • PSDS invited paper- for Special Issue on "Functional Genomics and Systems Biology in the Post Genomics Era" that will be published in 2013 in Physiologia Plantarum.

PJ: The PAE paper could also go into Phys. Plantarum instead, if it is too soon for this one.

RW would like everyone to send her ideas as to what they would like to see in it.

Do we know if this is the end of October or the beginning?

Either way, in order to get it done by October, we need to have a draft done by September. The question is whether or not the PSDS is ready to write about. The upper level structure has been extensivly revised, but we still have a lot of changes to make to more specific terms.

DS: Outlining what would go into paper would show what needs to be done.

PJ: New grape annotations. However, they are not in there yet.

BS: How having a development stage ontology could be useful to people's research. (Some of that is already published in the previous paper). Take what was said in the old paper and update it based on what has been learned about ontology building as well as on the on the data side.

What can new data sets accomplish. Not heavy on the actually current structure of the ontology, but a statement of what we are doing and the principles.

PJ: Highlight that there are no published reports or funding to compare development of different species (Is this true? It is true for examples like comparing berry of grape to other fruit say five days after pollenation). Highlight comparative aspects (yes!).

Plans for the next release

Tentatively planned for October_2012_Release

Priorities for next release:

Continue major revision of PSDS

Focus on the revisions on the stages that have the most annotations:

PO:0007033 : whole plant development stage

> PO:0028002 : sporophyte development stage

>> PO:0007130 : sporophyte reproductive stage [46604]: (Some still have the numbers preceding them, others don't)

>>> PO:0007047 : 3 inflorescence detectable stage [29131]

>>>PO:0007016 : 4 flowering [28057]

>>>PO:0007042 : 5 fruit formation [31009]

>>>PO:0007010 : 6 ripening [37642]


>> PO:0007134 : sporophyte vegetative stage [60370]: (Some still have the numbers preceding them, others don't)

>>>PO:0007057 : 0 seed germination stage [29568]

>>>PO:0007112 : 1 main shoot growth stage [47411]

>>>PO:0007131 : seedling development stage [26673]


PO:0009012 : plant structure development stage:

> PO:0007615 : flower development stage [48067]

>PO:0001083 : inflorescence development stage [48067]


PO:0025339 : plant organ development stage [46618]

>PO:0001050 : leaf development stage [45968]

>PO:0007520 : root development stage [25208]


PO:0025338 : collective plant structure development stage [49645]

>PO:0007615 : flower development stage [48067]

What about development of other anatomical entities? "Plant structure development stage" only covers structures, but we may want to talk about development of anatomical spaces of substances like cuticle.

BFO 2.0 addresses whether or not sites have histories the way material entities do.

We need to make sure, as we revise, that the PSDS terms correspond to the PAE terms (some upper level re-organization has already been done to align them).

Annotations of development stages:

PJ suggested that annotating directly to development stage should be required. We have mechanisms to move annotations back and forth between PAEs and PSDSs, based on ontology relations, but at this point, when people download annotation directly from the server (rather than via Amigo), they do not aggregate based on ontology relations.

Another issue is that the annotations only move to the generic term (e.g., an annotation to leaf may go to generic leaf development stage, but it would go to the more specific stage of development of the leaf.

Mysql queries also only give direct annotations.

Ultimately, we would like to have tools that suggest development stages, when annotator searches for a structure, or vice versa.

file naming and which variations of the file to create for each release

see PO_Release_SOP_Page

tabled for a future discussion

Complete outstanding user requests/SF tracker items

See the list at: Items_for_future_meetings

tabled for a future discussion

Update the Po webpages

- Which ones are top priority?

See: Plant_Ontology_Web_Site_Update:_Winter_2012

tabled for a future discussion

Meeting reports

ICBO 2012

Disease ontology

RW presented a paper on a plant disease extension of the Infectious Disease Ontology (IDOplant). The paper was well received, and there was a lot of discussion (after the talk) about how to model disease symptoms. The IDOplant manuscript defined "plant disase symptom", but did not include a term for it in the ontology. The Ontology for General Medical Science (OGMS) is planning to remove their term for symptom, for similar reasons -- a symptom can really be anything.

Symptoms should be modeled as dispositions. An infectious disease is a disposition, which is borne by some plant and has as a material basis some infectious disorder. As a result of having the infection, that plant also bears the disposition to undergo certain processes, which may lead to measurable/observable changes in the plant. For example, infection by a particular microbe results in the disposition to lose chlorophyll, which may lead to yellow leaves. Of course, the mechanisms could be modeled in even more detail, for example, at the molecular level. As dispositions, symptoms or signs are mechanistically linked to a disease, but it is never stated that every instance of the disease course will display a particular symptom. This way of modeling diseases and symptoms requires that we think carefully about the processes involved in a disease course, which is what we will need if we want to use ontologies to learn something new about diseases.

New tools for ontology editing

RW attended an OBI workshop while at IBCO. This included presentation of some of the tools being developed by Oliver He's lab. These may be of general interest to the PO curators.

  • Ontobee: A web server aimed to facilitate ontology visualization, query, and development. This is already familiar to many people in the ontology community.
  • Ontofox: An easy-to-use web-based tool for importing ontology terms using the MIREOT process.
  • Ontodog: A web-based tool for generating community views of ontologies. Allows users to create subsets of an ontology with their own preferred term names. This could be very helpful for PO users who represent specific parts of the plant science community. RW: I haven't tried this one yet, so not sure how easy it is to use.

ASPB 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Link to meeting page: ASPB2012

Helped organize an Outreach booth- ASPB Plant Biology 2012 along with Gramene, TAIR, BAR, iPlant, PMN, Kbase. Many people came and talked with us about all the different projects and I got to talk to our collaborators a lot too.

Plant Informatics Workshop was held with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 9:00 PM. About 53 people attended.

Upcoming meetings and Presentations 2012:

Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012

Link to: Anatomy Ontology course


Link to Course materials

This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).

Apply here: [1]


LM is attending

Online Ontology Workshops at The University at Buffalo

The University at Buffalo is pleased to announce two on-line tutorials in ontology:

1. Introduction to Protégé for absolute beginners:

Saturday and Sunday, August 11-12, 2012.

Faculty: Ron Rudnicki (CUBRC, Buffalo), Alan Ruttenberg (University at Buffalo), Barry Smith (University at Buffalo)

This course will provide an introduction to the Protégé 4.2 ontology editor. It will begin with a brief introduction to ontology building, and to the use and importance of ontologies. This will be followed by an introduction to the Web Ontology Language (OWL). The bulk of the course will consist of an interactive introduction to the use of Protégé in building an ontology. No background in the use of computer languages and programming is presupposed. All sessions will be highly interactive.


2. Basic Formal Ontology 2.0

Saturday and Sunday, August 18-19, 2012

Faculty: Alan Ruttenberg and Barry Smith (University at Buffalo)


Basic Formal Ontology is currently being used by over 100 ontology-based research projects in biomedical informatics and increasingly in other fields. The tutorial will provide an introduction to the content and use of BFO in ontology development. Participants will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the new version 2.0 of the BFO ontology, including new formalizations of BFO in first-order logic and in OWL.


Both tutorials are also open for face-to-face participation.


PO/TO Crop Annotation Workshop at OSU

For more information see the wiki page: Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012

Dates: Sept. 13-15th

The focus of the workshop will be on mostly development stages and traits for the crop plants

Next meeting scheduled for Tuesday, Aug 14th, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_8-14-12

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_7-31-12&oldid=25162"