Difference between revisions of "POC Conf. Call 12-28-10"
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''PJ: add reference to CO where they are being referred to, LC will check with Rosemary/Elizabeth about the changes that were discussed @ CO- using PO terms rather than CO?'' | ''PJ: add reference to CO where they are being referred to, LC will check with Rosemary/Elizabeth about the changes that were discussed @ CO- using PO terms rather than CO?'' | ||
| − | ''see [[GCP_Crop_Ontology]] | + | ''see ''[[http://pantheon.generationcp.org/index.php?option=com_content&task=view&id=20&Itemid=37 GCP_Crop_Ontology]] |
| − | ''GCP used numbers like: CO_125. | + | ''GCP used numbers like: CO_125:0000012. CO is already in use for Cell Ontology, so need to use numerical suffix to distinguish Crop Ontology from Cell Ontology. Different numerical suffixes refer to different crops. Will add xrefs to GCP terms for Musa as: CO_125:0000012.'' |
===Musa flower terms=== | ===Musa flower terms=== | ||
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is_a shoot system, part_of inflorescence | is_a shoot system, part_of inflorescence | ||
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| + | ''Species other than bananas can have a crown, so will make the term more general.'' | ||
''Revised term name and def'n:'' | ''Revised term name and def'n:'' | ||
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| − | '' | + | ''Male bud will be a synonym of inflorescence bud, with a reference to the crop ontology.'' |
===[https://sourceforge.net/tracker/?func=detail&aid=3147080&group_id=76834&atid=835555 Inflorescence and infructescence]=== | ===[https://sourceforge.net/tracker/?func=detail&aid=3147080&group_id=76834&atid=835555 Inflorescence and infructescence]=== | ||
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*'''bunch''': The descriptive term for all the fruits along the rachis. part_of CO_125.0000048 ! inflorescence. Syn: "infructescence" BROAD | *'''bunch''': The descriptive term for all the fruits along the rachis. part_of CO_125.0000048 ! inflorescence. Syn: "infructescence" BROAD | ||
| − | This could be a narrow synonym of infructescence (PO:0006342). | + | This could be a narrow synonym of infructescence (PO:0006342). Rachis in this definition refers the main axis of the infructescence. |
''synonym of infructescence, subset Musa'' | ''synonym of infructescence, subset Musa'' | ||
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''A Musa inflorescence is a raceme of cymes (not compound spike)'' | ''A Musa inflorescence is a raceme of cymes (not compound spike)'' | ||
| − | ''There was some debate about whether or not to name the sub-inflorescences that arise from the first order branches primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders. We don't actually have terms for different branching orders yet, but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes. We do have terms for inflorescence branch orders. For example, an inflorescence branch is "Any branch forming from | + | ''There was some debate about whether or not to name the sub-inflorescences that arise from the first order branches primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders. We don't actually have terms for different branching orders yet, but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes. We do have terms for inflorescence branch orders. For example, an inflorescence branch is "Any branch forming from the primary or the higher order inflorescence axis," while a second order inflorescence branch is "Any branch forming from a primary or first order inflorescence branch." Similar for third order inflorescence branch. We don't actually have terms for first order inflorescence branch or the primary axis, so I don't know if the first order branch refers to the main axis or a branch from this axis. These definitions are ambiguous, but since they have annotation attached to them, I cannot change them until I know what they mean.'' |
''I am creating new terms for secondary inflorescence and secondary infructescence. Can change names and definitions and add higher orders later if needed.'' | ''I am creating new terms for secondary inflorescence and secondary infructescence. Can change names and definitions and add higher orders later if needed.'' | ||
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''secondary infructescence: A reproductive shoot system that is part of an infructescence and has a second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit'' | ''secondary infructescence: A reproductive shoot system that is part of an infructescence and has a second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit'' | ||
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| + | ''need to add new terms for infructescence branches as well.'' | ||
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Probably should just annotate to whatever part of the flower it is that remains (petal, tepal, etc.) | Probably should just annotate to whatever part of the flower it is that remains (petal, tepal, etc.) | ||
| − | '' | + | ''Persistent phyllomes are common in persimmons, eggplant, tomatoes, peppers, tomatillos, etc. Need new terms that can have part_of relations to fruit rather than flowers.'' |
| − | ''sepal is part of the flower, add comment that it may persist in fruit'' | + | ''revised term names and proposed def'ns:'' |
| + | |||
| + | ''persistent sepal: A phyllome that develops from a sepal and remains attached to a fruit at maturity. Comment: May be alive or dead at maturity. Broad syn: flower relic.'' | ||
| + | |||
| + | ''persistent tepal: A phyllome that develops from a tepal and remains attached to a fruit at maturity. Comment: May be alive or dead at maturity. Broad syn: flower relic.'' | ||
| + | |||
| + | ''persistent stamen: A phyllome that develops from a stamen and remains attached to a fruit at maturity. Comment: May be alive or dead at maturity. Broad syn: flower relic.'' | ||
| + | |||
| + | |||
| + | ''sepal is part of the flower, add comment that it may persist in fruit.'' | ||
===Musa shoot terms=== | ===Musa shoot terms=== | ||
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''Note: 'sucker shoot' is a synonym of PO:0004544 : root-borne shoot system, '' | ''Note: 'sucker shoot' is a synonym of PO:0004544 : root-borne shoot system, '' | ||
| − | ''need both root-borne and shoot-borne suckers.'' | + | ''need both root-borne and shoot-borne suckers. Important point is that suckers come from buds (adventitious or axillary) at the older or basal of the plant'' |
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Could this be a collective phyllome structure (it is only composed of petioles, not phyllomes)? If not, we could make it a collective plant structure. If this structure is unique to Musa, we should call it "Musa pseudostem," but maybe it occurs in other taxa? | Could this be a collective phyllome structure (it is only composed of petioles, not phyllomes)? If not, we could make it a collective plant structure. If this structure is unique to Musa, we should call it "Musa pseudostem," but maybe it occurs in other taxa? | ||
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| + | ''Will add term pseudostem, is_a collective plant structure.'' | ||
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| − | ''add | + | ''Will add new terms for leaf sheath ab/adaxial epidermis. Pseudostem underlayers will be narrow synonym of leaf sheath abaxial epidermis..'' |
''Note: need to check with Rosemary/Elizabeth whether we should use 'banana' or 'Musa'? ''Musa'' is the Genus name.'' | ''Note: need to check with Rosemary/Elizabeth whether we should use 'banana' or 'Musa'? ''Musa'' is the Genus name.'' | ||
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''Accepted, approved by PJ, who was not on the call on 12-22'' | ''Accepted, approved by PJ, who was not on the call on 12-22'' | ||
| − | ''Also, | + | ''Also, checked that we have subset: Poaceae "Term used for grasses", we do'' |
===PO Next release=== | ===PO Next release=== | ||
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- complete changes discussed this week, put on Beta browser after Justin E returns from vacation (tomorrow?) | - complete changes discussed this week, put on Beta browser after Justin E returns from vacation (tomorrow?) | ||
| − | ''The next set of items should be slated for the | + | ''The next set of items should be slated for the next round of revisions, so we can deal with the annotations, documentation, TIPs paper and preparing for PAG. Also we need to do an 'internal' review before releasing it early in the New Year.'' |
- look for annotations that need to be moved: | - look for annotations that need to be moved: | ||
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| − | ''RW will focus on doing the changes to the PSO that have been discussed in the last 2 weeks. Will be done by Thursday, Dec 30th | + | ''RW will focus on doing the changes to the PSO that have been discussed in the last 2 weeks. Will be done by Thursday, Dec 30th, then it will be loaded on the beta browser'' |
===TIPS proposal=== | ===TIPS proposal=== | ||
Latest revision as of 22:37, 3 January 2011
POC meeting, Webex Conference Call; Date: Tuesday Dec 28th, 2010 10am (PST)
In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU).
Absent: Justin Elser (OSU), Alejandra Gandolfo; (Cornell University), Chris Mungall (Lawrence Berkeley National Lab)
Collaborators: none
Acceptance of the minutes from the POC Conf. Call 12-22-10?
There were no additions, deletions or changes to the minutes of the last meeting.
Musa requests still needing to be resolved:
Issues arising from new terms:
- petiole canal: The upper (adaxial) canal along the petiole. part_of CO_125.0000057 ! petiole
Added term 'adaxial petiole': A cardinal organ part that is the adaxial portion of petiole. Comment: Adaxial petiole may be concave or form a canal. Narrow synonym: petiole canal.
Also added abaxial petiole, with parallel definition.
Now that we have plant anatomical space, maybe we should add petiole canal as a space? See tracker for canal
All present last week agreed that canal should be a plant anatomical space, BS suggested we check FMA. They do not have canal per se, but classify canals as organ cavities (e.g., lumen of anal canal is part_of lumen of intestine, which is an organ cavity subdivision).
Proposed definition of canal: A plant anatomical space that is roughly linear or cylindrical in shape. Comment: May be enclosed within a plant structure or on the surface of a plant structure.
new proposed def'n of petiole canal: A canal that is part of a petiole. Comment: May occur on the surface or be internal.
Can make children abaxial petiole canal and adaxial petiole canal: a petiole canal on the ab/adaxial surface of a petiole.
Canal: Revised proposed def'n: A plant anatomical space that is either a groove on the surface or a tube in the interior of a plant structure. Comment: May be cylindrical (ref: PATO?) in shape, with a circular, D-shaped or other irregularly-shaped cross-section.
BS: need to address connectivity of plant parts, see Virtual Physiological Human (VPH) site
- Fused tepal: Added a new term to PO that is a cross-product of PO tepal and PATO fused (PATO:0000642).
This will cover the individual tepals that are fused, but they have requested the term Compound tepal: The outer perianth sheath of 5 fused tepals which has 3 major lobes and 2 minor ones.
Suggest we add new term fused collective tepal structure: A collective tepal structure which has as parts at least two fused tepals. Exact synonym: compound tepal, subset for Musa
accepted. Also add syntepalous perianth as exact synonym.
PJ: add reference to CO where they are being referred to, LC will check with Rosemary/Elizabeth about the changes that were discussed @ CO- using PO terms rather than CO?
see [GCP_Crop_Ontology]
GCP used numbers like: CO_125:0000012. CO is already in use for Cell Ontology, so need to use numerical suffix to distinguish Crop Ontology from Cell Ontology. Different numerical suffixes refer to different crops. Will add xrefs to GCP terms for Musa as: CO_125:0000012.
Musa flower terms
- crown: The raised ridge of tissue to which the pedicels are attached.
Is this part of an inflorescence, part of an inflorescence axis?
This refers to the inflorescence axes between individual flowers that do not elongate. It is a shoot system that is part of the inflorescence (which is also a shoot system).
Added the following term:
- Musa crown (PO:0025134): A shoot system that forms the basal part of an inflorescence in Musa species to which the pedicels are attached and in which the internodes do not elongate, giving the appearance of a ridge of raised tissue.
is_a shoot system, part_of inflorescence
Species other than bananas can have a crown, so will make the term more general.
Revised term name and def'n: inflorescence branch crown (PO:0025134): A shoot system that forms the basal part of an inflorescence to which the pedicels are attached and in which the internodes do not elongate, giving the appearance of a ridge of raised tissue.
- basal flower: First flowers emerging on the inflorescence with the potential to give rise to fruits. part_of CO_125.0000136 ! basal bud
Do we want to describe different flowers on the inflorescence? If so, we could add general term basal flower: a flower at the proximal end of on an inflorescence. Comment: in Musa, the basal flowers are the first to emerge and have the potential to give rise to fruits.
This generated a lot of discussion and suggestions of examples; for now 'basal flower' will be added as a synonym of flower, not part of basal bud but develops from basal bud. Need to bring in PATO to help describe the phenotypes and positioning.
RW and DWS will plan a time to work on the descriptions of various types of inforescences.
- male bud: The usually persistent bud when it is only composed of bracts with male flowers. is_a: CO_125.0000146 ! bud; is_a: CO_125.0000146 ! bud
Proposed definition: An inflorescence bud that develops into a male inflorescence.
If we go this route, we will need to add male, female and hermaphrodite reproductive bud, male, female and hermaphrodite inflorescence bud, male, female and hermaphrodite floral bud, and male, female and hermaphrodite inflorescence, plus the floral terms described above.
At the 11-5-10 POC meeting, we decided not to add separate terms for male and female flowers. Probably want to be consistent with bud.
Male bud will be a synonym of inflorescence bud, with a reference to the crop ontology.
Inflorescence and infructescence
The Musa fruit terms deal with infructescence parts. Before we define them, we need a solid definition of inflorescence and infructescence that follow the genus/differentia form.
Current definition of inflorescence: That part of the axial system of plants above the uppermost foliage leaf/pair of foliage leaves that bears flowers, is_a reproductive shoot system.
Proposed definition of inflorescence: a reproductive shoot system that has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and all of the flowers borne by those axes. Must have two or more flowers as parts.
Current definition of infructescence: The grouping or arrangement in which fruits are borne on a plant.
Proposed definition of infructescence: a reproductive shoot system that develops_from an inflorescence and has as parts all of the shoot axes distal to the most distal foliage leaf of a shoot axis and all of the fruits borne by those axes.
accepted
Musa fruit terms
- bunch: The descriptive term for all the fruits along the rachis. part_of CO_125.0000048 ! inflorescence. Syn: "infructescence" BROAD
This could be a narrow synonym of infructescence (PO:0006342). Rachis in this definition refers the main axis of the infructescence.
synonym of infructescence, subset Musa
- hand of fruits: All the fruits that develop in the axil of a single bract. part_of CO_125.0000014 ! bunch
A Musa inflorescence is a compound spike. A branch of the spike develops from the axil of a single bract. This branch branches again to form a subdivision of the spike (spikelet), which when mature produces a 'hand' of fruits. All of the subdivisions of the compound spike together, when mature, are a bunch of bananas. A hand is a subdivision of an infructescence that develops from a subdivision (spikelet) of an inflorescence (compound spike).
We already have the term inflorescence branch (PO:0009081), is_a branch, but this refers specifically to a shoot axis, not the entire branching part of an inflorescence. Suggest we add term infructescence branch (is_a branch, develops from inflorescence branch). We need terms to refer to the subdivisions (loosely called branches, but not branches in as PO defines them) of an inflorescence or infructescence.
Suggest two new terms:
inflorescence subdivision (maybe we can come up with a better name): A reproductive shoot system that is part of an inflorescence and has a parts an inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence
spikelet (PO:0009051) would be a child of this term.
infructescence subdivision: A reproductive shoot system that is part of an infructescence and has a parts an infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence
A Musa inflorescence is a raceme of cymes (not compound spike)
There was some debate about whether or not to name the sub-inflorescences that arise from the first order branches primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders. We don't actually have terms for different branching orders yet, but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes. We do have terms for inflorescence branch orders. For example, an inflorescence branch is "Any branch forming from the primary or the higher order inflorescence axis," while a second order inflorescence branch is "Any branch forming from a primary or first order inflorescence branch." Similar for third order inflorescence branch. We don't actually have terms for first order inflorescence branch or the primary axis, so I don't know if the first order branch refers to the main axis or a branch from this axis. These definitions are ambiguous, but since they have annotation attached to them, I cannot change them until I know what they mean.
I am creating new terms for secondary inflorescence and secondary infructescence. Can change names and definitions and add higher orders later if needed.
revised term names and proposed def'ns:
secondary inflorescence: A reproductive shoot system that is part of an inflorescence and has a parts a second order inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence, has_part inflorescence branch, flower
secondary infructescence: A reproductive shoot system that is part of an infructescence and has a second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit
need to add new terms for infructescence branches as well.
- flower relics: Remains of a female flower when it persists on the fruit. part_of CO_125.0000033 ! fruit
Probably should just annotate to whatever part of the flower it is that remains (petal, tepal, etc.)
Persistent phyllomes are common in persimmons, eggplant, tomatoes, peppers, tomatillos, etc. Need new terms that can have part_of relations to fruit rather than flowers.
revised term names and proposed def'ns:
persistent sepal: A phyllome that develops from a sepal and remains attached to a fruit at maturity. Comment: May be alive or dead at maturity. Broad syn: flower relic.
persistent tepal: A phyllome that develops from a tepal and remains attached to a fruit at maturity. Comment: May be alive or dead at maturity. Broad syn: flower relic.
persistent stamen: A phyllome that develops from a stamen and remains attached to a fruit at maturity. Comment: May be alive or dead at maturity. Broad syn: flower relic.
sepal is part of the flower, add comment that it may persist in fruit.
Musa shoot terms
- sucker: Lateral shoot that develops from the corm and usually emerges close to the parent plant. is_a: CO_125.0000001 ! plant part
This could be a synonym of axillary shoot system (PO:0006343): A shoot-borne shoot system that develops from an axillary vegetative bud.
Will probably need to be a broad synonym, because (I think) people also use the term sucker to refer to root-borne shoots. Alternatively, we could make the phrase "Musa sucker" a narrow synonym of axillary shoot system, and make "sucker" a synonym of root-borne shoot.
Note: 'sucker shoot' is a synonym of PO:0004544 : root-borne shoot system,
need both root-borne and shoot-borne suckers. Important point is that suckers come from buds (adventitious or axillary) at the older or basal of the plant
- pseudostem: 'False stem' of cylinders formed by the concentric leaf sheaths through which the peduncle later grows. is_a: CO_125.0000001 ! plant part
Could this be a collective phyllome structure (it is only composed of petioles, not phyllomes)? If not, we could make it a collective plant structure. If this structure is unique to Musa, we should call it "Musa pseudostem," but maybe it occurs in other taxa?
Will add term pseudostem, is_a collective plant structure.
- pseudostem underlayers: Abaxial side of the inner sheath which is not visible until the outermost sheath has been removed. part_of CO_125.0000046 ! pseudostem
This is the abaxial portion of a leaf sheath (PO:0020104). We could make a new term leaf sheath abaxial epidermis (sibling of petiole abaxial epidermis, is_a leaf epidermis), and add pseudostem underlayer as a narrow synonym.
Will add new terms for leaf sheath ab/adaxial epidermis. Pseudostem underlayers will be narrow synonym of leaf sheath abaxial epidermis..
Note: need to check with Rosemary/Elizabeth whether we should use 'banana' or 'Musa'? Musa is the Genus name.
Other Items:
'sensu' terms
from 12-22-10:
- There are a bunch of terms where the name has been changed from something (sensu Poaceae) to Poaceae something. This means we have a mix of sensu and non-sensu terms.
Should we go through and fix these for this release?
All present were in favor of this, BS: these have been removed by the GO, PO should do the same.
Accepted, approved by PJ, who was not on the call on 12-22
Also, checked that we have subset: Poaceae "Term used for grasses", we do
PO Next release
Timeline and Plan for Upcoming Release - complete changes discussed this week, put on Beta browser after Justin E returns from vacation (tomorrow?)
The next set of items should be slated for the next round of revisions, so we can deal with the annotations, documentation, TIPs paper and preparing for PAG. Also we need to do an 'internal' review before releasing it early in the New Year.
- look for annotations that need to be moved:
- List of changes: Summary_of_Changes_to_PO_Jan2011 (still under construction)
see also Jan 2011_Release_Page
RW will focus on doing the changes to the PSO that have been discussed in the last 2 weeks. Will be done by Thursday, Dec 30th, then it will be loaded on the beta browser
TIPS proposal
A abstract/proposal has been circulated.
LC will focus on doing the summarizing the suggested changes to the proposal, needs to incorporate some detail on what is new in the PO, and novel.
Also should add additional, more current refs. Will aim for Thursday, Dec 30th or Friday for submission
PJ: suggested a collaboration with Nick Provart of BAR on the analysis, but I am not sure if this was for the larger paper in 2011...
Dennis will send out something to the group...
