Difference between revisions of "POC Conf. Call 9-20-11"

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'''POC meeting, Webex Conference Call; Date: Tuesday Sept 20th, 2011 10am (PDT)'''
 
'''POC meeting, Webex Conference Call; Date: Tuesday Sept 20th, 2011 10am (PDT)'''
  
In attendance:  
+
In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),Justin Preece (OSU), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University),  Barry Smith (University at Buffalo, NY).
  
POC members:   
+
POC members:  Chris Mungall (Lawrence Berkeley National Lab), Justin Elsner (OSU)
 
 
Absent:
 
  
 +
Absent: ''no additions, deletions, or changes''
  
 
Collaborators: none
 
Collaborators: none
  
 +
Acceptance of the minutes from the [[POC Meeting at NYBG; Sept 10th-11th, 2011]]? ''no additions, deletions, or changes''
  
Acceptance of the minutes from the [[POC_Conf._Call_8-30-11]]?
 
  
 +
=Summary of Discussions at NYBG; Sept 10th-11th, 2011=
 +
*Main topics of discussion was the revision of the PGDSO and the upcoming release.
 +
*We made some significant steps on the PGDSO- see complete details: here [[Saturday_Sept_10th,_2011]]
 +
*The revision of the PGDSO will be the focus of the next major release later this fall.
  
=Tech issues=
+
==Upcoming Release==
these have been posted on the [[POC_Technical_Issues_Page]]
+
'''Major changes for this release are:'''
==OWL version stamp==
 
Request from Gavin Kennedy:
 
 
 
"Would it be possible to add an owl:versionInfo attribute to the OWL Plant Ontology so that we can track the changes in versions. This could be the version number or a date stamp, etc."
 
  
==filter translation==
+
'''1. Inclusion of Spanish synonyms.'''
from Mary Schaeffer at MaizeGDB
 
  
comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there.
+
They seem to be working fine, except that we still should have the descriptor "(Spanish:)" preceding them. ''9-21-11: this has been fixed''
  
For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.
+
Not clear if this is a problem with just the dev browser.
  
=Edits to complete before release: PAO=
+
''For the release, we will highlight this new feature as we are the first ontology to offer spanish (and possibly Japanese) translations. Will send out the announcements in Spanish as well.''
Includes user requests open on Source Forge: PAO
 
==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]==
 
===[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]===
 
  
At an earlier meeting, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.  
+
'''2. [[Eliminating_Zea/Poaceae_terms_from_PO]]'''
  
====Background:====
+
This is more or less complete. PGDSO may change as we go forward, but we can use as is for now.
  
Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:  
+
'''3. New annotation files:'''
  
"The seedling usually displays 1 even-pinnate leaf, 1 bipinnate leaf, and several transition forms. Pinnate leaves and transition forms possess an apical pointlet like that of the phyllode."
+
We are working on getting the new set of '''MaizeGDB annotations''' in.
  
 +
Addition of new annotations for '''grape''' (LC working on) and [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry]
  
The main reference people cite for phyllodes is: '''D.R. Kaplan 1980''', Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.
+
What is the status of the '''Physcomitrella''' annotations?  ''PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids''
  
Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."
 
  
 +
''We will move ahead with the release with the maizeGDB anatomy annotations (in SVN already), may need some minor fixing''
  
'''Some more contemporary uses of the term phyllode:'''
+
''There is increasing interest in the OBOEdit community to be able to include non-standard characters.  JP will bring it up ont he next AmiGO development meeting''
  
'''Gardner et al. 2005''' (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):
 
  
"A phyllode usually consists of a pulvinus and photosynthetic region, although it can be sessile, decurrent with the stem, or reduced to scales. The photosynthetic region is highly variable and ranges from vertically flattened, through terete, quadrangular and triquetrous to horizontally flattened. Phyllodes usually possess at least one extra-floral nectary on the adaxial nerve, and sometimes up to five. Boughton (1981, 1985) observed three types of extra-floral nectaries. She also investigated the indumentum and found almost all species have two kinds of trichomes, one glandular and one non-glandular (Boughton 1989). According to Arber (1918), '''the chief anatomical feature by which phyllodes differ from true leaf laminae is the occurrence of two opposing series of vascular bundles'''."
 
  
and later in the paper:
+
'''4. Other changes'''
  
"Previous approaches, such as basic anatomy and inferences from the sequence of heteroblastic leaf development in acacias, have led researchers to state that the phyllode is homologous with the petiole of a bipinnate leaf (e.g. Mann 1894; Goebel 1905; Troll 1939), or with the petiole and rachis (e.g. Bentham 1875; Reinke 1897), and make comparisons with the monocotyledonous leaf. Investigating the developmental morphology of phyllodes, Kaplan (1980) proposed a new model: that the phyllode is actually the positional homologue of the lamina of a bipinnate leaf. In essence, this suggests that the phyllode is directly comparable to a simple leaf. Kaplan’s theory does not, however, address the issue of the opposing vascular bundles found in phyllodes.
+
*Japanese synonyms?
  
"The pattern of branching observed in the vascular bundles of A. verniciflua phyllodes suggests that the abaxial marginal nerve is homologous to the mid-rib in a simple leaf. This implies that laminar expansion occurs on both sides of the ‘mid-rib’, but vertically, and fused together. The emergence of the adaxial marginal nerve as two separate bundles, originating on opposing sides that eventually fuse rather than directly from the vascular ring found in the pulvinus, supports our interpretation and has been observed (together with other patterns) in several other Acacia species (von Wartburg 1991)."
+
''Will have Japanese synonyms in obo file, but JE will strip them out before the file gets loaded on AmiGO.''
  
 +
''Japanese synonyms are not currently in the editors' file. Should be added.  What is the status on this?''
  
'''Leroy and Heuret 2007''' (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by '''a type of foliar organ''' called a phyllode."  and "...the different transitional forms range from pinnate leaves to phyllodes..." 
 
  
'''See fig. 1 in this paper.''' They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.
+
'''5. For more details see: [[Summary_of_Changes_to_PO_September_2011]]'''
  
 +
==Target dates:==
 +
We discussed having a release in September, 2011
  
'''Yang et al. 2008''' (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.
+
*Finish all edits: By Monday 9/26/2011 ''Or weds 9/28/11, after our meeting next week''
  
 +
*Update annotation files and test on beta browser: ''Grape annotation file is almost done, will ask JE to load on beta to test.''
  
'''Forster and Bonser 2009''', Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."
+
*Other tasks?
  
 +
*Final release:  First week of Oct, by Friday, October 7th.
  
RW did not find any contemporary papers that said that a phyllode is a petiole.
+
''Note:  Need to make sure all the Ontology QCs are run first, loading the annotations will be a big job''
  
Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.
+
=Tech issues:=
 +
these have been posted on the [[POC_Technical_Issues_Page]]
  
'''Unifacial leaf''' as synonym? No- not exactly the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311). 
+
==Adding Dbx Refs==
 +
===for MaizeGDB===
 +
See notes from the [[Follow_up_meeting_re:_Association_files_for_the_Kaeppler_data_set_Sept_15,_2011]]
  
====Proposed terms and definitions:====
+
We can use one database abbreviation to access all MaizeGDB pages. It uses their url for anything with a MaizeGDB id, but also works for gene model names.
  
vascular leaf
+
'''File format''' (modified from http://www.geneontology.org/cgi-bin/xrefs.cgi - changed object to include gene model name)''':'''
  
>unifacial leaf
+
abbreviation: MaizeGDB
  
>>terete leaf (round in cross section)
+
database: Maize Genetics and Genomics Database
  
>>ensiform leaf (flat in cross section)
+
object: MaizeGDB Object ID Number or Gene Model Name
  
>>>phyllode
+
example_id: MaizeGDB:881225
  
 +
generic_url: http://www.maizegdb.org/
  
'''unifacial leaf''': A vascular leaf that has increased activity of either the adaxial or abaxial meristem early in development, leading to absence of the opposite surface on the leaf. (ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)
+
url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id]
  
Comment: A unifacial leaf may be round in cross-section (terete) or it may be laminar (ensiform), in which case lamina development is in a median plane  (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Unifacial leaves may be bifacial at the leaf base. Many unifacial leaves develop by reduced (or absent) activity of the marginal meristems and increased activity of the adaxial meristem early in development, leading to mature leaves with only an adaxial surface (e.g., Acacia, most monocots?). However, some develop by increased activity of the abaxial meristem early in development, leading to mature leaves with only an abaxial surface.
+
url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225
  
  
 +
Mary will update all of the xrefs in MaizeGDB's old association files to use this abbreviation when she does her next update. Until then, we should keep the other MaizeGDB abbreviation in the dbxref file, so the links will still work.
  
'''RW: need to check and add references for all of these'''
+
Existing MaizeGDB stanzas are incorrectly formatted. We cannot add the new stanza to http://plantontology.org/docs/dbxref/PO_DBXref.txt without removing at least one of the old ones. Not sure what repurcussions this will have.
  
'''terete leaf''': A unifacial leaf that is round in cross section throughout all of part of the length of the leaf. (ref.: xxx)
+
===Gramene===
 +
Two of the Gramene dbxrefs in PO_DBXref.txt are not working:
 +
 +
GR: http://www.gramene.org/perl/protein_search?acc=P93436
  
Comment: The surface of a terete leaf corresponds to either the adaxial or abaxial surface of a normal leaf.
+
GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198
 +
 +
Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.
  
 +
===Others===
 +
We are also working on adding new annotation files for '''''Physcomitrella''''', '''grape''' and '''strawberry'''.  We will need to add DBXrefs for these sources as well.
  
'''ensiform leaf''': A unifacial leaf that is flat in cross section due to a lamina that develops in a median plane  (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout all of part of the length of the leaf.(ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)
+
===dbxref file===
 +
Does PO's version of AmiGO read from http://plantontology.org/docs/dbxref/PO_DBXref.txt? This file seems very out of date and appears to have incorrect formatting in a number of places.
  
Comment: Common in many monocots and some dicots. Both surfaces of an ensiform leaf correspond to only one of either the adaxial or abaxial surface of a normal leaf. In some leaves, the petiole may twist, giving the appearance that the lamina is ensiform, but it is not.
 
  
  
'''RW: Maybe phyllode should just be a narrow synonym of ensiform leaf?'''
+
''PJ will work with the JE/JP to get the Dbxrefs working.''
  
'''phyllode:''' An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in develop.
+
''PJ: The local file is not used.  The major library of Dbxrefs is coming from GO, as part of AmiGO.  For JP: when you are working with CM on the new AmiGO, need to make '''sure''' that the local installations, can amend the library of cross refs from GO with the ones from the local databse.
  
Comment: Common in legumes of the genus Acacia. Similar development occurs in other ensiform leaves in some monocots, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:xxxxxxx, phyllode-type transition leaf). Phyllodes are generally xeromorphic.
+
''RW: The problem we are having is that even if we request new DBxrefs to be added to the GO file, they are not showing up in our browser. It appears that our version of AmiGO has a built-in set of refs and it is not reading the current GO file.  Go is using an updated version of AmiGO, we are using a customized version of the older version. Suggestion is to have the new AmiGO read the common file.''
  
is_a ensiform leaf, is_a adult leaf
+
''LC will send PJ the broken Gramene links, need new ones for the new files. JP will set up meeting with JE and CM to work on this''
 
 
 
 
'''phyllode-type transition leaf:''' A transitional vascular leaf in which the basal portion of the leaf has unifacial lamina development in a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.
 
 
 
Comment: Common in seedlings of legumes of the genus Acacia. May also occur later, after the plant has begun to produce phyllodes.
 
 
 
is_a transitional leaf, is_a ensiform leaf
 
 
 
===[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle]===
 
 
 
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
 
 
 
At the meeting of RW, MAG and DWS on 8/29/11, we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.
 
  
 +
=Edits to complete before release: PAO=
 
==New children of [https://sourceforge.net/tracker/index.php?func=detail&aid=3241802&group_id=76834&atid=835555 calyptra perianth]==
 
==New children of [https://sourceforge.net/tracker/index.php?func=detail&aid=3241802&group_id=76834&atid=835555 calyptra perianth]==
 
This was raised at the POC meeting [[POC_Conf._Call_8-23-11]]
 
This was raised at the POC meeting [[POC_Conf._Call_8-23-11]]
Line 150: Line 148:
 
In Eucalyptus, there may be one or two calyptras: an inner operculum or calyptra composed of fused petals and an outer operculum or calyptra composed of fused sepals. In many species, the sepals to do not fuse, and there is no outer operculum.  
 
In Eucalyptus, there may be one or two calyptras: an inner operculum or calyptra composed of fused petals and an outer operculum or calyptra composed of fused sepals. In many species, the sepals to do not fuse, and there is no outer operculum.  
  
Our current definition of calyptra perianth includes fused tepals, which would encompass the existing term "fused collective tepal structure" (PO:0025138), but to my knowledge, tepals are not present in Eucalyptus. (The ANBG provides [http://www.anbg.gov.au/cpbr/cd-keys/euclid3/euclidsample/html/learn.htm EUCLID], an excellent resource for description of Eucatypus morphology.)
+
Our current definition of calyptra perianth includes fused tepals, which would encompass the existing term "fused collective tepal structure" (PO:0025138), but to my knowledge, tepals are not present in Eucalyptus. (The ANBG provides [http://www.anbg.gov.au/cpbr/cd-keys/euclid3/euclidsample/html/learn.htm EUCLID], an excellent resource for description of Eucalyptus morphology.)
  
 
Suggest adding a new term "'''fused perianth'''", that is consistent with our other terms such as "fused collective tepal structure". This would be a more general term, and could include perianths that are partially fused.
 
Suggest adding a new term "'''fused perianth'''", that is consistent with our other terms such as "fused collective tepal structure". This would be a more general term, and could include perianths that are partially fused.
Line 170: Line 168:
  
 
===terms and definitions===
 
===terms and definitions===
 +
''These changes are in the editor's file''
  
 
*'''fused perianth:''' A perianth that is composed of two or more fused perianth parts (sepals, petals or tepals).
 
*'''fused perianth:''' A perianth that is composed of two or more fused perianth parts (sepals, petals or tepals).
Line 177: Line 176:
 
*'''calyptra perianth''' (PO:0025299): A fused perianth that is composed of fused sepals or petals and located on top of a gynoecium that contains an inferior ovary.
 
*'''calyptra perianth''' (PO:0025299): A fused perianth that is composed of fused sepals or petals and located on top of a gynoecium that contains an inferior ovary.
  
Comment: Found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra or fruit operculum. Use the more specific term (calytra corolla or calytra calyx) if possible. Species of the subgenus Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development.
+
Comment: Found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra or fruit operculum. Use the more specific term (calyptra corolla or calyptra calyx) if possible. Species of the subgenus Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development.
  
Synonyms: flower operculum, floral operculum, floral calyptra; angiosperm calyptra
+
Synonyms: flower operculum, floral operculum, floral calyptra, flower calyptra, angiosperm calyptra
  
 
*'''calyptra calyx''': A calyptra perianth composed of fused sepals.
 
*'''calyptra calyx''': A calyptra perianth composed of fused sepals.
Line 185: Line 184:
 
Comment: Sometimes found in Eucalyptus and other Myrtaceae, covering an inner operculum or calyptra corolla. The sepals are generally completely fused.  
 
Comment: Sometimes found in Eucalyptus and other Myrtaceae, covering an inner operculum or calyptra corolla. The sepals are generally completely fused.  
  
Synonyms: outer operculum, calyx operculum
+
Synonyms: outer operculum, operculum calyx
  
 
*'''calyptra corolla''': A calyptra perianth composed of fused petals.
 
*'''calyptra corolla''': A calyptra perianth composed of fused petals.
Line 191: Line 190:
 
Comment: Often found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. If an outer operculum (calyptra calyx) is present, it covers the inner operculum (calyptra corolla).  
 
Comment: Often found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. If an outer operculum (calyptra calyx) is present, it covers the inner operculum (calyptra corolla).  
  
Synonyms: inner operculum, corolla operculum
+
Synonyms: inner operculum, operculum corolla
  
 
* fused collective tepal structure (PO:0025138), calyptra calyx and calyptra corolla all have dual parentage (is_a fused perianth and is_a collective tepal structure, calyx, or corolla. If we were to import PATO:0000642 (fused with), we could make cross product definitions and infer one of the relations.
 
* fused collective tepal structure (PO:0025138), calyptra calyx and calyptra corolla all have dual parentage (is_a fused perianth and is_a collective tepal structure, calyx, or corolla. If we were to import PATO:0000642 (fused with), we could make cross product definitions and infer one of the relations.
  
==PGDSO==
+
''These edits will be fixed in the editors file for the release.''
 +
 
 +
''If there is a case where things may change from being fused to unfused (or visa versa), then we should use a cross ref to the PATO Id#, and make it an inferred class rather than an asserted class.  This is what was done for fused collective tepal structure (FCTS).''
 +
 
 +
''Suggestion: Get rid of fused perianth and make calyptra perianth is_a perianth (as it was before). So FCTS is_a collective tepal structure.  Makes it more general than having the specific term calyptra. Calyptra is specific to certain species''
 +
 
 +
''MAG: Tubiliform (tube-shaped)corolla is also a case.  You cannot tell where the petals start and end.  Calyptra is a specific case, ansd in some cases they are not completely fused.''
 +
 
 +
''Suggestion: get rid of calyptra perianth, avoid dual parentage, keep calyptra calyx (is_a calyx) and calyptra corolla (is_a corolla).  Make calyptra perianth a broad (''RW: should be narrow'') synonym of perianth.  Will also add the synonyms from MAG: calyptra calyx: calycine operculum; outer operculum and for calyptra corolla: corolline operculum; inner operculum''
 +
 
 +
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3397632&group_id=76834&atid=835555 floret]==
 +
 
 +
floret is currently a synonym of flower (as decided at the [[POC_Conf._Call_8-30-11]]).
 +
 
 +
''Background Comment: In the live version, we had the term floret (PO:0009082). Def'n: Small flowers, especially of the spikelets of Poaceae and Cyperaceae. After the 8-30-11 POC meeting, it was been renamed 'spikelet floret' (see below) and we added "ray flower", "disk flower" as narrow synonyms of flower and "disk floret", "ray floret" and floret as related synonyms.
 +
 
 +
 
 +
Since then there was a suggestion that we needed a general term 'floret':
 +
 
 +
proposed def'n: A small flower that is part of an inflorescence. Inheritance: is_a flower, part_of inflorescence.
 +
 
 +
Spikelet floret would then be a child of floret.
 +
 
 +
 
 +
 
 +
'''''In the dev file:''''', ''note: We should make these def'ns consistent and in the g-d format.''
 +
 
 +
*'''spikelet floret (PO:0009082)''': Def'n: A small flower that is part of a spikelet. [source: APWeb:Glossary, PMID:20197291]
 +
Comment: Found in Poaceae, Cyperaceae and other Poales. Lemma, palea and lodicule are associated with a spikelet floret, but since it is not clear what they correspond to in conventional flowers, no assumptions of homology are made at the present time. To describe a ray or disk floret of the Asteraceae, use flower (PO:0009046).
 +
 
 +
*'''ear floret (PO:0006354)''': def'n: Small flowers of the spikelets of maize ear. [source: GR:pj]
 +
 
 +
proposed def'n: A spikelet floret found specifically in the Zea mays ear.
 +
 
 +
''What about other grasses.  Some references to ears in the grains.''
 +
 
 +
new proposed def: A spikelet floret that is part of an ear spikelet (this way it is not specific to Zea mays, but any species that has an ear).
 +
 
 +
 
 +
*'''tassel floret (PO:0006310)''': def"n: Flowers of the spikelets of maize tassel. [source: GR:pj]
 +
 
 +
proposed def'n: A spikelet floret found specifically in the Zea mays tassel.
 +
 
 +
new proposed def: A spikelet floret that is part of a tassel spikelet.
 +
 
 +
* Will update definitions of all children of ear and tassel floret as well.
 +
 
 +
 
 +
''PJ: we need to have the terms 'ray flower' and 'disc flower', they would be is_a flower, do not need the specific term floret.  Synonyms are ray floret, disc floret.''
 +
 
 +
''We will need to change the comment for spikelet floret to match the above changes.
 +
 
 +
''This edit is not in the file, will be added for the release.''
 +
 
 +
=Edits for release: PGDSO=
 
Edits requested by MS for MaizeGDB
 
Edits requested by MS for MaizeGDB
  
===[http://wiki.plantontology.org:8080/index.php/Items_for_future_meetings#coleoptile_emergence_--_definition coleoptile emergence]===
+
We don't need to fix the definitions of [http://sourceforge.net/tracker/?func=detail&aid=3324056&group_id=76834&atid=835555 coleoptile emergence PO:0007045] before this release, because Mary decided she should use "radicle emergence" (PO:0007015) instead.
  
From MS (MaizeGDB): It would be more useful for maize if the definition for '''coleoptile emergence PO:0007045''' were altered to be: Emergence of coleoptile from the seed. (rather than above ground)
+
===[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3374186&group_id=76834 5 fruit formation; FF.00 fruit size 10%]===
  
This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.
+
Initial Comment from MS:
  
At the POC meeting on [[Sunday_Sept_11th,_2011]], we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.''
+
"There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view.  Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size.  For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory."
  
Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.
+
[[File:fruitsize.jpg]]
 +
 
 +
current def'n:'''FF.00 fruit size 10% (PO:0007032):''' The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]
 +
 
 +
Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green
 +
 
 +
All the other sizes are defined similarly.
 +
 
 +
proposed def'n.: (based on Mary's suggestion): A fruit formation stage that begins with the formation of a fruit and ends when the fruit has reached 10% of its final size.
 +
 
 +
Comment: This stage can only be used when the final size of the fruit is known.
 +
 
 +
At the POC meeting on 9-11-11, we agreed that these stages could be up to and including the % size for now. Should rename terms "fruit size up to 10%", etc.''
 +
 
 +
'''proposed def'n: FF.00 fruit size up to 10% (PO:0007032):'''  A fruit formation stage that begins with fertilization of an ovary and ends when the fruit has reached 10% of its final size.
 +
 
 +
 
 +
'''''new proposed def'n: FF.00 fruit size up to 10% (PO:0007032):'''  A fruit formation stage that begins the formation of the zygote and ends when the fruit has reached 10% of its final size.''
 +
 
 +
''We will put the old term names as synonyms.''
 +
 
 +
Comment: A fruit development stage may begin without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions.
 +
 
 +
'''Problem with staging reproductive development across different species is there is no consistency.  Hard to find landmarks.''
 +
 
 +
''Proposed new names were rejected. The stages will be up to 10%, then 10%-30%, etc:''
 +
 
 +
[[File:fruit_formation.jpg]]
 +
 
 +
 
 +
''These edits will be fixed in the file for the release.''
 +
 
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3306250&group_id=76834&atid=835555 PGDSO terms without is_a parents]==
 +
 
 +
As discussed at the NYBG meeting, we can fix the three remaining PO terms without is_a parents: shoot emergence, seedling growth and imbibition.
 +
 
 +
Shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.
  
 
'''current structure:'''
 
'''current structure:'''
Line 216: Line 305:
 
Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.
 
Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.
  
====current and proposed terms and definitions====
+
===current and proposed terms and definitions===
'''0 germination (PO:0007057):''' rename "germination stage".
+
*'''germination (PO:0007057):''' rename "(0) germination stage". (Tested the parentheses around the zero, and they display fine in the dev browser. Will remove them before release until we are ready to change them all).
 +
''This was discussed at the NYBG meeting''
  
'''imbibition (PO:0007022):''' rename "imbibition stage" and make is_a child of "germination stage".
+
*'''imbibition (PO:0007022):''' rename "imbibition stage" and make is_a child of "germination stage".
  
 +
''We will rename these:"seed germination stage" and "seed imbibition stage"''
  
'''current: seedling growth (PO:0007131):''' Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination
 
  
Seedling growth stage should begin after germination, not after imbibition. Imbibition is part of germination, and a seedling does not exist until after germination.
+
*'''current: seedling growth (PO:0007131):''' Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination  
  
'''new proposed  name and def.: '''seedling development stage:''' A vegetative growth stage that has as a participant a whole plant during the interval between germination and development of the first adult leaves.''
+
'''proposed  name and def.: seedling development stage:''' A vegetative growth stage that has as a participant a whole plant during the interval between germination and development of the first adult leaves.''
  
 
Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.
 
Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.
  
'''Note:''' After the PGDSO is revised, the parent of this term will be sporophyte vegetative development stage, so definition will change slightly. Also, the numbering of the children of vegetative growth stage is messed up now. '''Should we renumber the stages?'''
+
'''Note:''' After the PGDSO is revised, the parent of seedling growth stage will be sporophyte vegetative development stage, so definition will change slightly. Also, the numbering of the children of vegetative growth stage is messed up now. '''Should we renumber the stages?'''
 
 
 
 
'''All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.'''
 
  
'''current: shoot emergence (PO:0007030):''' Shoot or leaf breaks through the soil surface.
+
''this was not discussed at the meeting- should leave till after the release is out''
  
'''proposed: shoot emergence from growth medium development stage (PO:0007030):''' A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.
 
  
Comment: This terms is used only for seed plants.
+
*'''shoot emergence (PO:0007030):''' Shoot or leaf breaks through the soil surface.
  
'''proposed: shoot emergence from seed coat development stage (new number):''' A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.
+
Propose that we rename '''shoot emergence stage''' and make it is_a seedling growth stage, instead of part of seedling growth stage. Can work on definition when we revise the PGDSO.
  
Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.
 
  
 +
''We will rename thie term "seedling shoot emergence stage".  We will check to make sure GO Biol processes has seed imbibition.  Definitions need further reworking for the next release.''
  
'''current: coleoptile emergence (PO:0007045):''' Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]
 
  
'''proposed: coleoptile emergence from growth medium development stage (PO:0007045):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???
 
  
Comment: This terms is used only for seed plants.
+
''These edits will be made in the file for upcoming release.''
  
'''proposed: coleoptile emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???
+
=Upcoming meetings and Presentations 2011/2012:=
 +
'''* [http://conference.cgrb.oregonstate.edu/ 2011 CGRB Fall Conference]'''  
 +
Oregon State University, on Sunday-Monday, September 18-19, 2011.
  
Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.
+
Two posters related to the Plant Ontology will be presented.
  
 +
JP will present a poster at the  regarding the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service, and includes an initial data set built from PO GAF (.assoc) files for ''Oryza sativa''.
  
'''current: cotyledon emergence (PO:0007049):''' Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]
+
Additionally, he and PJ will host a web presentation for Syngenta employees on the same topic on Sept 26.
  
'''proposed: cotyledon emergence from growth medium development stage (PO:0007049):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???
+
LC will present the poster: Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa.
  
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.
+
==[http://meetings.cshl.edu/meetings/plants11.shtml Plant Genomes & Biotechnology: From Genes to Networks], CSHL==
  
'''proposed: cotyledon emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???
+
Dates: November 30 - December 3, 2011
 +
Abstract Deadline: September 9, 2011
  
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.
+
*Pricing
 +
Academic Package $1055
  
 +
Graduate/PhD Student Package $880
  
 +
Corporate Package $1340
  
'''current: epicotyl emergence (PO:0007054):''' Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]
+
Academic/Student No-Housing Package $720
  
'''proposed: epicotyl emergence from growth medium development stage (PO:0007054):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???
+
Corporate No-Housing Package $905
  
Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.
 
  
'''proposed: epicotyl emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???
+
''DWS will be away, but RW could attend''
  
Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.
+
==[http://www.intl-pag.org/ PAG 2012]==
 +
 
 +
January 14-18, 2012, San Diego, California
  
 +
Registration and Abstract submissions open on Sept 22nd
  
'''current: hypocotyl emergence (PO:0007043):''' Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]
+
LC is presenting in the [http://www.intl-pag.org/20/20-plant-pheno.html Plant Phenotypes] workshop on Sunday Morning, 15 January 2012 -- 8:00 am - 10:10 am.
  
'''proposed: hypocotyl emergence from growth medium development stage (PO:0007043):''' A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???
+
The PO will take part in an Outreach booth organized by MaizeGDB
  
Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.
+
Other activities?
  
'''proposed: hypocotyl emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???
+
==[http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]==
  
Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.
+
April 2-4, 2012, Washington DC
  
 +
Call for abstracts is now open: Need to clarify the deadlines
  
 +
There are three submission categories for abstracts:
  
Could also add terms for feeder emergence for some gymnosperms.
+
1.    Talk or Poster (with consideration for oral presentation)
  
For all of the above terms, need to check existing synonyms and move or copy them as needed.
+
2.   Poster only
  
===[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3374186&group_id=76834 5 fruit formation; FF.00 fruit size 10%]===
+
3.   Workshop only
  
Initial Comment from MS:
+
•    Submission deadline November 30, 2011
  
"There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view.  Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size.  For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory."
+
•    Notification of acceptance February 3, 2012
 
 
[[File:fruitsize.jpg]]
 
  
current def'n:'''FF.00 fruit size 10% (PO:0007032):''' The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]  
+
[http://pir.georgetown.edu/biocuration2012.html/instructions.html Instructions]  
  
Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green
+
There are seven topic sessions from which submitters are invited to select:
  
All the other sizes are defined similarly.
+
  1. Ontologies, standards and best practices, including gold standard datasets.
 +
  2. Protein annotation; sequences, structures and pathways.
 +
  3. Community annotation and Wikis.
 +
  4. Genomics and metagenomics data curation.
 +
  5. High throughput proteomics data (focus on NGS and MS data) curation and presentation.
 +
  6. Literature collection, text mining and curation.
 +
  7. Tools to assist curation, including automated pipelines.  
  
proposed def'n.: (based on Mary's suggestion):''' A fruit formation stage that begins with the formation of a fruit and ends when the fruit has reached 10% of its final size.
+
There are four submission tracks:
  
Comment: This stage can only be used when the final size of the fruit is known.
+
  1. Paper, with consideration for oral presentation
 +
  2. Talk
 +
  3. Workshop
 +
  4. Poster
  
At the POC meeting on 9-11-11, we agreed that these stages could be up to and including the % size for now. Should rename terms "fruit size up to 10%", etc.''
+
From the Instructions page: For authors wishing to submit to DATABASE for the 2012 BIOCURATION VIRTUAL ISSUE:
 +
* Submission deadline: October 15, 2011
 +
* First decisions: November 15, 2011
 +
* Revisions deadline: December 15, 2011
 +
* Final decisions: January 10, 2012
 +
* Conference: April 2-4 2012
  
RW: When does formation of a fruit occur? Should we say fertilization of an ovary instead?
+
''PJ planning to attend, LC and RW can go.  Check with Pascal to confirm dates''
  
'''new proposed: FF.00 fruit size up to 10% (PO:0007032):  A fruit formation stage that begins with fertilization of an ovary and ends when the fruit has reached 10% of its final size.
+
==[http://www.2011.botanyconference.org/info/Botany2012.php Botany 2012]==
  
Comment: A fruit may begin development without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions.
+
July 7 - 11, 2012 - Columbus, Ohio
  
=Upcoming meetings and Presntations 2011:=
+
Call for Symposia, Colloquia and Workshops:
  
LC and JP will present a poster at the 2011 CGRB Fall Conference regarding the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service, and includes an initial data set built from PO GAF (.assoc) files for Oryza sativa.
+
Submission site now open
  
Additionally, he and Pankaj will host a web presentation for Syngenta employees on the same topic on Sept 26.
+
''RW and DWS will look at putting in a proposal for a half day workshop.''
  
=Next Tues meeting scheduled for Tuesday,  Sept. 27th, 2011 at 10am PDT/1pm EDT=
+
=Next meeting scheduled for Tuesday,  Sept. 27th, 2011 at 10am PDT/1pm EDT=

Latest revision as of 19:40, 8 March 2012

POC meeting, Webex Conference Call; Date: Tuesday Sept 20th, 2011 10am (PDT)

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),Justin Preece (OSU), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University), Barry Smith (University at Buffalo, NY).

POC members: Chris Mungall (Lawrence Berkeley National Lab), Justin Elsner (OSU)

Absent: no additions, deletions, or changes

Collaborators: none

Acceptance of the minutes from the POC Meeting at NYBG; Sept 10th-11th, 2011? no additions, deletions, or changes


Summary of Discussions at NYBG; Sept 10th-11th, 2011

  • Main topics of discussion was the revision of the PGDSO and the upcoming release.
  • We made some significant steps on the PGDSO- see complete details: here Saturday_Sept_10th,_2011
  • The revision of the PGDSO will be the focus of the next major release later this fall.

Upcoming Release

Major changes for this release are:

1. Inclusion of Spanish synonyms.

They seem to be working fine, except that we still should have the descriptor "(Spanish:)" preceding them. 9-21-11: this has been fixed

Not clear if this is a problem with just the dev browser.

For the release, we will highlight this new feature as we are the first ontology to offer spanish (and possibly Japanese) translations. Will send out the announcements in Spanish as well.

2. Eliminating_Zea/Poaceae_terms_from_PO

This is more or less complete. PGDSO may change as we go forward, but we can use as is for now.

3. New annotation files:

We are working on getting the new set of MaizeGDB annotations in.

Addition of new annotations for grape (LC working on) and strawberry

What is the status of the Physcomitrella annotations? PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids


We will move ahead with the release with the maizeGDB anatomy annotations (in SVN already), may need some minor fixing

There is increasing interest in the OBOEdit community to be able to include non-standard characters. JP will bring it up ont he next AmiGO development meeting


4. Other changes

  • Japanese synonyms?

Will have Japanese synonyms in obo file, but JE will strip them out before the file gets loaded on AmiGO.

Japanese synonyms are not currently in the editors' file. Should be added. What is the status on this?


5. For more details see: Summary_of_Changes_to_PO_September_2011

Target dates:

We discussed having a release in September, 2011

  • Finish all edits: By Monday 9/26/2011 Or weds 9/28/11, after our meeting next week
  • Update annotation files and test on beta browser: Grape annotation file is almost done, will ask JE to load on beta to test.
  • Other tasks?
  • Final release: First week of Oct, by Friday, October 7th.

Note: Need to make sure all the Ontology QCs are run first, loading the annotations will be a big job

Tech issues:

these have been posted on the POC_Technical_Issues_Page

Adding Dbx Refs

for MaizeGDB

See notes from the Follow_up_meeting_re:_Association_files_for_the_Kaeppler_data_set_Sept_15,_2011

We can use one database abbreviation to access all MaizeGDB pages. It uses their url for anything with a MaizeGDB id, but also works for gene model names.

File format (modified from http://www.geneontology.org/cgi-bin/xrefs.cgi - changed object to include gene model name):

abbreviation: MaizeGDB

database: Maize Genetics and Genomics Database

object: MaizeGDB Object ID Number or Gene Model Name

example_id: MaizeGDB:881225

generic_url: http://www.maizegdb.org/

url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id]

url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225


Mary will update all of the xrefs in MaizeGDB's old association files to use this abbreviation when she does her next update. Until then, we should keep the other MaizeGDB abbreviation in the dbxref file, so the links will still work.

Existing MaizeGDB stanzas are incorrectly formatted. We cannot add the new stanza to http://plantontology.org/docs/dbxref/PO_DBXref.txt without removing at least one of the old ones. Not sure what repurcussions this will have.

Gramene

Two of the Gramene dbxrefs in PO_DBXref.txt are not working:

GR: http://www.gramene.org/perl/protein_search?acc=P93436

GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198

Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.

Others

We are also working on adding new annotation files for Physcomitrella, grape and strawberry. We will need to add DBXrefs for these sources as well.

dbxref file

Does PO's version of AmiGO read from http://plantontology.org/docs/dbxref/PO_DBXref.txt? This file seems very out of date and appears to have incorrect formatting in a number of places.


PJ will work with the JE/JP to get the Dbxrefs working.

PJ: The local file is not used. The major library of Dbxrefs is coming from GO, as part of AmiGO. For JP: when you are working with CM on the new AmiGO, need to make sure that the local installations, can amend the library of cross refs from GO with the ones from the local databse.

RW: The problem we are having is that even if we request new DBxrefs to be added to the GO file, they are not showing up in our browser. It appears that our version of AmiGO has a built-in set of refs and it is not reading the current GO file. Go is using an updated version of AmiGO, we are using a customized version of the older version. Suggestion is to have the new AmiGO read the common file.

LC will send PJ the broken Gramene links, need new ones for the new files. JP will set up meeting with JE and CM to work on this

Edits to complete before release: PAO

New children of calyptra perianth

This was raised at the POC meeting POC_Conf._Call_8-23-11

Existing terms:

  • fruit operculum (PO:0025298): A collective organ part structure that is the apical part of a circumsessile capsular fruit that separates from the rest of the capsule during dehiscence. [source: POC:curators]

Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.

and

  • calyptra perianth (PO:0025299): A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary. [source: POC:curators]

Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra.

Synonyms: related: floral operculum; exact: angiosperm calyptra; exact: floral calyptra (suggest we add flower operculum as related and flower calyptra as exact)

Proposed changes: More specific terms for calyptra

At the 8/23/11 meeting, there was a request for more specific terms for calyptras formed of fused petals or fused sepals.

In Eucalyptus, there may be one or two calyptras: an inner operculum or calyptra composed of fused petals and an outer operculum or calyptra composed of fused sepals. In many species, the sepals to do not fuse, and there is no outer operculum.

Our current definition of calyptra perianth includes fused tepals, which would encompass the existing term "fused collective tepal structure" (PO:0025138), but to my knowledge, tepals are not present in Eucalyptus. (The ANBG provides EUCLID, an excellent resource for description of Eucalyptus morphology.)

Suggest adding a new term "fused perianth", that is consistent with our other terms such as "fused collective tepal structure". This would be a more general term, and could include perianths that are partially fused.

Proposed new terms and ontology structure:

perianth

> fused perianth (new)

>> fused collective tepal structure (PO:0025138)

>> calyptra perianth (flower operculum) (PO:0025299)

>>> calyptra calyx (outer operculum) (new)

>>> calyptra corolla (inner operculum) (new)

  • Should we also add terms for fused petal and fused sepal (already have fused tepal)?

terms and definitions

These changes are in the editor's file

  • fused perianth: A perianth that is composed of two or more fused perianth parts (sepals, petals or tepals).

Comment: Perianth parts may be partially or wholly fused.

  • calyptra perianth (PO:0025299): A fused perianth that is composed of fused sepals or petals and located on top of a gynoecium that contains an inferior ovary.

Comment: Found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra or fruit operculum. Use the more specific term (calyptra corolla or calyptra calyx) if possible. Species of the subgenus Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development.

Synonyms: flower operculum, floral operculum, floral calyptra, flower calyptra, angiosperm calyptra

  • calyptra calyx: A calyptra perianth composed of fused sepals.

Comment: Sometimes found in Eucalyptus and other Myrtaceae, covering an inner operculum or calyptra corolla. The sepals are generally completely fused.

Synonyms: outer operculum, operculum calyx

  • calyptra corolla: A calyptra perianth composed of fused petals.

Comment: Often found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. If an outer operculum (calyptra calyx) is present, it covers the inner operculum (calyptra corolla).

Synonyms: inner operculum, operculum corolla

  • fused collective tepal structure (PO:0025138), calyptra calyx and calyptra corolla all have dual parentage (is_a fused perianth and is_a collective tepal structure, calyx, or corolla. If we were to import PATO:0000642 (fused with), we could make cross product definitions and infer one of the relations.

These edits will be fixed in the editors file for the release.

If there is a case where things may change from being fused to unfused (or visa versa), then we should use a cross ref to the PATO Id#, and make it an inferred class rather than an asserted class. This is what was done for fused collective tepal structure (FCTS).

Suggestion: Get rid of fused perianth and make calyptra perianth is_a perianth (as it was before). So FCTS is_a collective tepal structure. Makes it more general than having the specific term calyptra. Calyptra is specific to certain species

MAG: Tubiliform (tube-shaped)corolla is also a case. You cannot tell where the petals start and end. Calyptra is a specific case, ansd in some cases they are not completely fused.

Suggestion: get rid of calyptra perianth, avoid dual parentage, keep calyptra calyx (is_a calyx) and calyptra corolla (is_a corolla). Make calyptra perianth a broad (RW: should be narrow) synonym of perianth. Will also add the synonyms from MAG: calyptra calyx: calycine operculum; outer operculum and for calyptra corolla: corolline operculum; inner operculum

floret

floret is currently a synonym of flower (as decided at the POC_Conf._Call_8-30-11).

Background Comment: In the live version, we had the term floret (PO:0009082). Def'n: Small flowers, especially of the spikelets of Poaceae and Cyperaceae. After the 8-30-11 POC meeting, it was been renamed 'spikelet floret' (see below) and we added "ray flower", "disk flower" as narrow synonyms of flower and "disk floret", "ray floret" and floret as related synonyms.


Since then there was a suggestion that we needed a general term 'floret':

proposed def'n: A small flower that is part of an inflorescence. Inheritance: is_a flower, part_of inflorescence.

Spikelet floret would then be a child of floret.


In the dev file:, note: We should make these def'ns consistent and in the g-d format.

  • spikelet floret (PO:0009082): Def'n: A small flower that is part of a spikelet. [source: APWeb:Glossary, PMID:20197291]

Comment: Found in Poaceae, Cyperaceae and other Poales. Lemma, palea and lodicule are associated with a spikelet floret, but since it is not clear what they correspond to in conventional flowers, no assumptions of homology are made at the present time. To describe a ray or disk floret of the Asteraceae, use flower (PO:0009046).

  • ear floret (PO:0006354): def'n: Small flowers of the spikelets of maize ear. [source: GR:pj]

proposed def'n: A spikelet floret found specifically in the Zea mays ear.

What about other grasses. Some references to ears in the grains.

new proposed def: A spikelet floret that is part of an ear spikelet (this way it is not specific to Zea mays, but any species that has an ear).


  • tassel floret (PO:0006310): def"n: Flowers of the spikelets of maize tassel. [source: GR:pj]

proposed def'n: A spikelet floret found specifically in the Zea mays tassel.

new proposed def: A spikelet floret that is part of a tassel spikelet.

  • Will update definitions of all children of ear and tassel floret as well.


PJ: we need to have the terms 'ray flower' and 'disc flower', they would be is_a flower, do not need the specific term floret. Synonyms are ray floret, disc floret.

We will need to change the comment for spikelet floret to match the above changes.

This edit is not in the file, will be added for the release.

Edits for release: PGDSO

Edits requested by MS for MaizeGDB

We don't need to fix the definitions of coleoptile emergence PO:0007045 before this release, because Mary decided she should use "radicle emergence" (PO:0007015) instead.

5 fruit formation; FF.00 fruit size 10%

Initial Comment from MS:

"There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view. Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size. For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory."

Fruitsize.jpg

current def'n:FF.00 fruit size 10% (PO:0007032): The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]

Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green

All the other sizes are defined similarly.

proposed def'n.: (based on Mary's suggestion): A fruit formation stage that begins with the formation of a fruit and ends when the fruit has reached 10% of its final size.

Comment: This stage can only be used when the final size of the fruit is known.

At the POC meeting on 9-11-11, we agreed that these stages could be up to and including the % size for now. Should rename terms "fruit size up to 10%", etc.

proposed def'n: FF.00 fruit size up to 10% (PO:0007032): A fruit formation stage that begins with fertilization of an ovary and ends when the fruit has reached 10% of its final size.


new proposed def'n: FF.00 fruit size up to 10% (PO:0007032): A fruit formation stage that begins the formation of the zygote and ends when the fruit has reached 10% of its final size.

We will put the old term names as synonyms.

Comment: A fruit development stage may begin without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions.

'Problem with staging reproductive development across different species is there is no consistency. Hard to find landmarks.

Proposed new names were rejected. The stages will be up to 10%, then 10%-30%, etc:

Fruit formation.jpg


These edits will be fixed in the file for the release.

PGDSO terms without is_a parents

As discussed at the NYBG meeting, we can fix the three remaining PO terms without is_a parents: shoot emergence, seedling growth and imbibition.

Shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.

current structure:

Germination stages.jpg

Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.

Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.

current and proposed terms and definitions

  • germination (PO:0007057): rename "(0) germination stage". (Tested the parentheses around the zero, and they display fine in the dev browser. Will remove them before release until we are ready to change them all).

This was discussed at the NYBG meeting

  • imbibition (PO:0007022): rename "imbibition stage" and make is_a child of "germination stage".

We will rename these:"seed germination stage" and "seed imbibition stage"


  • current: seedling growth (PO:0007131): Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination

proposed name and def.: seedling development stage: A vegetative growth stage that has as a participant a whole plant during the interval between germination and development of the first adult leaves.

Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.

Note: After the PGDSO is revised, the parent of seedling growth stage will be sporophyte vegetative development stage, so definition will change slightly. Also, the numbering of the children of vegetative growth stage is messed up now. Should we renumber the stages?

this was not discussed at the meeting- should leave till after the release is out


  • shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

Propose that we rename shoot emergence stage and make it is_a seedling growth stage, instead of part of seedling growth stage. Can work on definition when we revise the PGDSO.


We will rename thie term "seedling shoot emergence stage". We will check to make sure GO Biol processes has seed imbibition. Definitions need further reworking for the next release.


These edits will be made in the file for upcoming release.

Upcoming meetings and Presentations 2011/2012:

* 2011 CGRB Fall Conference Oregon State University, on Sunday-Monday, September 18-19, 2011.

Two posters related to the Plant Ontology will be presented.

JP will present a poster at the regarding the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service, and includes an initial data set built from PO GAF (.assoc) files for Oryza sativa.

Additionally, he and PJ will host a web presentation for Syngenta employees on the same topic on Sept 26.

LC will present the poster: Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa.

Plant Genomes & Biotechnology: From Genes to Networks, CSHL

Dates: November 30 - December 3, 2011 Abstract Deadline: September 9, 2011

  • Pricing

Academic Package $1055

Graduate/PhD Student Package $880

Corporate Package $1340

Academic/Student No-Housing Package $720

Corporate No-Housing Package $905


DWS will be away, but RW could attend

PAG 2012

January 14-18, 2012, San Diego, California

Registration and Abstract submissions open on Sept 22nd

LC is presenting in the Plant Phenotypes workshop on Sunday Morning, 15 January 2012 -- 8:00 am - 10:10 am.

The PO will take part in an Outreach booth organized by MaizeGDB

Other activities?

5th International Biocuration Conference

April 2-4, 2012, Washington DC

Call for abstracts is now open: Need to clarify the deadlines

There are three submission categories for abstracts:

1. Talk or Poster (with consideration for oral presentation)

2. Poster only

3. Workshop only

• Submission deadline November 30, 2011

• Notification of acceptance February 3, 2012

Instructions

There are seven topic sessions from which submitters are invited to select:

  1. Ontologies, standards and best practices, including gold standard datasets.
  2. Protein annotation; sequences, structures and pathways.
  3. Community annotation and Wikis.
  4. Genomics and metagenomics data curation.
  5. High throughput proteomics data (focus on NGS and MS data) curation and presentation.
  6. Literature collection, text mining and curation.
  7. Tools to assist curation, including automated pipelines. 

There are four submission tracks:

  1. Paper, with consideration for oral presentation
  2. Talk
  3. Workshop
  4. Poster 

From the Instructions page: For authors wishing to submit to DATABASE for the 2012 BIOCURATION VIRTUAL ISSUE:

  • Submission deadline: October 15, 2011
  • First decisions: November 15, 2011
  • Revisions deadline: December 15, 2011
  • Final decisions: January 10, 2012
  • Conference: April 2-4 2012

PJ planning to attend, LC and RW can go. Check with Pascal to confirm dates

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

Submission site now open

RW and DWS will look at putting in a proposal for a half day workshop.

Next meeting scheduled for Tuesday, Sept. 27th, 2011 at 10am PDT/1pm EDT