Difference between revisions of "POC Conf. Call 11-6-12"
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Asilomar, CA | Asilomar, CA | ||
| − | LC attended and has been working with LM to compile EQ | + | LC attended and has been working with LM to compile EQ statements. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago. |
The project (headed by EH) be combining the mutants with similar E and Q and looking at the genes and if they are orthologs. | The project (headed by EH) be combining the mutants with similar E and Q and looking at the genes and if they are orthologs. | ||
| Line 37: | Line 37: | ||
PJ: were there missing Po entities? Recommend using the dev version. Document of recommendations | PJ: were there missing Po entities? Recommend using the dev version. Document of recommendations | ||
| − | e.g. tomato flesh | + | e.g. tomato flesh- center core and material around seeds- variation in placentation |
| − | PJ: All phenotype annotation to anatomical entity needs an annotation to the stage, whether you think you need it or not | + | ''PJ: All phenotype annotation to anatomical entity needs an annotation to the stage, whether you think you need it or not. It is critical. In the GAF column 16 can be used for this. Should use the more generic stage if it is not known'' |
| − | In the GAF column 16 can be used for this. Should use the more generic stage if it is not known | ||
| − | + | ''BS: problem exists since we have PO growth stages and the PO structures that are in those growth stages. If you are annotating growth stage-specific qualities, the primary entity should be the growth stage and then generate automatically another annotation with the gs in column 16. Then we will generate a another annotation where the PO structure is the primary entity. To do this you will need to generate 2 annotations'' | |
| + | |||
| + | PJ: This is how I am doing this for the rice annotations. Translating it automatically could be difficult if 1 structure is associated with >1 stage. | ||
| + | |||
| + | Should look at some examples, do not want to lose the stage info. It it is in col 16, we can recreate the GS info. Does not necessarily need to be repeated. PJ is testing with rice gene expression data. | ||
| + | |||
| + | ''Note that the EQ statements are not being put into the GAF format at this time. We are following the format defined by the database creators- George G and Anika from EBI. '' | ||
| + | |||
| + | ''PJ recommends that the EQs statements should include the growth stage, even it is not dependent on the gs. Try with a mandatory aspect and then it could be relaxed.'' | ||
| + | |||
| + | Whole plant vs plant structure development; could use more than one leaf development | ||
=PO "Aspect" vs. "Ontology Branch"= | =PO "Aspect" vs. "Ontology Branch"= | ||
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=Plans for Upcoming Release #19= | =Plans for Upcoming Release #19= | ||
| − | Timeline for Release: Goal is | + | Timeline for Release: Goal is Mid-December 2012 |
[[Release_19]] | [[Release_19]] | ||
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What are the priorities for inclusion in the Release? | What are the priorities for inclusion in the Release? | ||
| − | -fruit development stages | + | - fruit development stages |
| − | -grape | + | - New datasets: grape, cotton, rice |
| + | |||
| + | LC: will send MAG a list of the new terms that we need translation. | ||
| + | |||
| + | PJ will be out last week of Nov, till Dec 2nd. | ||
=Stage terms continued from last meeting:= | =Stage terms continued from last meeting:= | ||
| Line 73: | Line 86: | ||
At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages. | At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages. | ||
| − | ''What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of | + | ''What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of their existing annotations and move them to fruit development stage and its new subtypes as necessary.'' |
====FF.00 fruit size up to 10% stage (PO:0007032)==== | ====FF.00 fruit size up to 10% stage (PO:0007032)==== | ||
'''proposed new name and definition:''' | '''proposed new name and definition:''' | ||
| − | '''whole plant fruit formation stage up to 10%:''' A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) | + | '''whole plant fruit formation stage up to 10%:''' A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001) has reached 10% of ''expected'' final size. |
| − | comment: This terms is best used for | + | ''Can be the first fruit of the plant's life or of a fruiting cycle (e.g. for plants that fruit more than once). Can leave out the 2nd whole plant (PO:0000003) in the def'n.'' |
| + | |||
| + | |||
| + | comment: This terms is best used for plants with more or less synchronous fruit development and can only be used if the ''expected'' final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size up to 10% stage (PO:0025504). | ||
| + | |||
| + | ''can only be used if the normal size of the fruit is known. healthy plants, must have a knowledge of the expected final size.'' | ||
| + | |||
| + | ''what is a normal size? Could depend on the environment e.g. fruits in OR vs CA'' | ||
====FF.01 fruit size 10 to 30% stage (PO:0007009)==== | ====FF.01 fruit size 10 to 30% stage (PO:0007009)==== | ||
| Line 87: | Line 107: | ||
'''whole plant fruit formation stage 10 to 30%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size. | '''whole plant fruit formation stage 10 to 30%:''' A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size. | ||
| − | comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505). | + | comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505). |
====FF.02 fruit size 30 to 50% stage (PO:0007029)==== | ====FF.02 fruit size 30 to 50% stage (PO:0007029)==== | ||
| Line 112: | Line 132: | ||
related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79 | related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79 | ||
| − | + | Add new synonyms for grapes: | |
''Add related synonym: BBCH principle growth stage 77; Berries beginning to touch'' | ''Add related synonym: BBCH principle growth stage 77; Berries beginning to touch'' | ||
| Line 122: | Line 142: | ||
''Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)'' | ''Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)'' | ||
| − | = | + | =Sub-classes of whole plant fruit ripening stage (PO:0007010)= |
The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point. | The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point. | ||
| − | + | ''Tabled for a future meeting, as they have not been worked on yet- moved to [[Items_for_future_meetings]] page. | |
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=Upcoming meetings and Presentations 2012-2013:= | =Upcoming meetings and Presentations 2012-2013:= | ||
| Line 213: | Line 175: | ||
==PRO-PO-GO meeting, May 2013== | ==PRO-PO-GO meeting, May 2013== | ||
| + | Please see this page for more information: [[PRO-PO-GO_Meeting]] | ||
Location: Buffalo, NY | Location: Buffalo, NY | ||
Latest revision as of 19:16, 13 November 2012
POC meeting, Webex Conference Call; Date: Tuesday Nov 6th, 2012 10am PT/1pm ET
In attendance:
POC members: Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU)
Absent: Ramona Walls (NYBG), Chris Mungall (LBLL)
Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=69722257&rKey=09fcebd51b0b1458
Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=69722257&rKey=3ee6b9a8ef9afcfe
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_10-16-12? No additions, deletions, or changes.
Back to POC Meetings Minutes
Update on Manuscripts in progress:
Plant and Cell Physiology has accepted the Plant Anatomy paper. Revisions are underway.
LC will address all the issues brought up and will circulate to the rest of the group by the end week and then we can get it sent back in by the end of next week.
Meeting Report
Phenotype RCN meeting, Oct 26-29th 2012
Asilomar, CA
LC attended and has been working with LM to compile EQ statements. These are going to be compiled with similar statements from maize, Arabidopsis, Soybean, SGN- tomato, and Medicago.
The project (headed by EH) be combining the mutants with similar E and Q and looking at the genes and if they are orthologs.
Our role: Representing the PO and compiling the descriptions of ~100 rice mutants
PJ: were there missing Po entities? Recommend using the dev version. Document of recommendations
e.g. tomato flesh- center core and material around seeds- variation in placentation
PJ: All phenotype annotation to anatomical entity needs an annotation to the stage, whether you think you need it or not. It is critical. In the GAF column 16 can be used for this. Should use the more generic stage if it is not known
BS: problem exists since we have PO growth stages and the PO structures that are in those growth stages. If you are annotating growth stage-specific qualities, the primary entity should be the growth stage and then generate automatically another annotation with the gs in column 16. Then we will generate a another annotation where the PO structure is the primary entity. To do this you will need to generate 2 annotations
PJ: This is how I am doing this for the rice annotations. Translating it automatically could be difficult if 1 structure is associated with >1 stage.
Should look at some examples, do not want to lose the stage info. It it is in col 16, we can recreate the GS info. Does not necessarily need to be repeated. PJ is testing with rice gene expression data.
Note that the EQ statements are not being put into the GAF format at this time. We are following the format defined by the database creators- George G and Anika from EBI.
PJ recommends that the EQs statements should include the growth stage, even it is not dependent on the gs. Try with a mandatory aspect and then it could be relaxed.
Whole plant vs plant structure development; could use more than one leaf development
PO "Aspect" vs. "Ontology Branch"
Discussion from POC_Conf._Call_10-16-12- BS was concerned about the heading "Aspect" on the PO term pages, because it has a very specific meaning in library science. We should change it to say "Ontology branch".
Updated to "Ontology Branch" on po-dev on the term pages and "Filter tree view" in browser.
Decided to use just "branch"; Can be updated on dev, live and beta sites. This is also consistent with the way it is used in the PAE manuscript.
The use of "Aspect" is widely adopted throughout our system. In June 2012, RW went through a number of the webpages and changed the references to "ontology" to "Aspect", so those pages will have to be updated as well. In addition, column 9 on the association file is "Aspect. Not sure is this is an issue. Go still uses 'Ontology' on their browser"
We will make a note on the website that it is still aspect on the association files.
Plans for Upcoming Release #19
Timeline for Release: Goal is Mid-December 2012
What are the priorities for inclusion in the Release?
- fruit development stages
- New datasets: grape, cotton, rice
LC: will send MAG a list of the new terms that we need translation.
PJ will be out last week of Nov, till Dec 2nd.
Stage terms continued from last meeting:
whole plant fruit formation stage (PO:0007042)
See SF tracker for FF.00 fruit size 10% and sibling terms
At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages.
What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of their existing annotations and move them to fruit development stage and its new subtypes as necessary.
FF.00 fruit size up to 10% stage (PO:0007032)
proposed new name and definition:
whole plant fruit formation stage up to 10%: A whole plant fruit formation stage (PO:0007042) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) enters a fruit initiation stage (PO:0025503) and ends when the average size of fruits (PO:0009001) has reached 10% of expected final size.
Can be the first fruit of the plant's life or of a fruiting cycle (e.g. for plants that fruit more than once). Can leave out the 2nd whole plant (PO:0000003) in the def'n.
comment: This terms is best used for plants with more or less synchronous fruit development and can only be used if the expected final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size up to 10% stage (PO:0025504).
can only be used if the normal size of the fruit is known. healthy plants, must have a knowledge of the expected final size.
what is a normal size? Could depend on the environment e.g. fruits in OR vs CA
FF.01 fruit size 10 to 30% stage (PO:0007009)
proposed new name and definition:
whole plant fruit formation stage 10 to 30%: A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size.
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 10 to 30% stage (PO:0025505).
FF.02 fruit size 30 to 50% stage (PO:0007029)
proposed new name and definition:
whole plant fruit formation stage 30 to 50%: A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 30% to 50% of its final size.
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 30 to 50% stage (PO:0025506).
FF.03 fruit size 50 to 70% stage (PO:0007007)
proposed new name and definition:
whole plant fruit formation stage 50 to 70%: A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 50% to 70% of its final size.
comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 50 to 70% stage (PO:0025507).
FF.04 fruit size 70% to final size stage (PO:0007027)
proposed new name and definition:
whole plant fruit formation stage 70% to final size: A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 70% of its final size to its final size.
comment: Succeeded by a whole plant fruit ripening stage (PO:0007010). This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage is to be used for the development stage of a whole plant (PO:0000003). For an individual fruit, use fruit size 70% to final size stage (PO:0025508).
related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79
Add new synonyms for grapes:
Add related synonym: BBCH principle growth stage 77; Berries beginning to touch
Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)
Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)
Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)
Sub-classes of whole plant fruit ripening stage (PO:0007010)
The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point.
Tabled for a future meeting, as they have not been worked on yet- moved to Items_for_future_meetings page.
Upcoming meetings and Presentations 2012-2013:
PAG 2013, San Diego, CA; January 12th - 16th, 2013
- Date and Time: Saturday, January 12, 2013: 08:00 AM - 10:10 AM, Royal Palm Salon 5-6
We will be running a workshop focusing on:
Applications of Ontologies for Plant and Animal Genomics
Speakers so far: Eva, Reinhard Simon and Elizabeth Arnaud, Chris, PJ present the Ref Plant Ontology Vision
- Need to submit the abstracts for the speakers by November 9, 2012.
Deadline for abstracts for computer demos and posters and workshops is Nov 9th
JP will be presenting a SIA computer demo.
Biocuration 2013 conference, Cambridge, 7-10th April 2013
submission deadline for papers and abstracts for posters is 30th November. Papers will be published by DATABASE.
possible venue for cROP white paper?
website and registration are now open: Biocuration 2013
PRO-PO-GO meeting, May 2013
Please see this page for more information: PRO-PO-GO_Meeting
Location: Buffalo, NY
Tentative Dates: May 8-9th or May 15-16th, 2013.
Goals:
- To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
- To identify potentially fruitful applications which such enhanced coordination might bring
- To enhance the Protein Ontology treatment of plant-related proteins
- To address coordination issues between the GO and PO, for example as concerns treatment of development stages
- To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]
Tentative participant list:
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)
BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO
MONOCOTS V Meeting at NYBG
5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)
The New York Botanical Garden & Fordham University
