POC Conf. Call 1-31-12 - Revision history

Cooperl: /* xylem */

2012-02-24T18:46:24Z

xylem

Cooperl: /* Adding PO Ids to terms in comments and definitions: */

2012-02-06T10:56:56Z

Adding PO Ids to terms in comments and definitions:

Rwalls: /* From POC_Conf._Call_1-17-12: */

2012-02-01T17:07:00Z

From POC_Conf._Call_1-17-12:

Rwalls: /* From POC_Conf._Call_1-24-12: */

2012-02-01T16:43:04Z

From POC_Conf._Call_1-24-12:

Rwalls at 13:11, 1 February 2012

2012-02-01T13:11:38Z

Rwalls: /* 5th International Biocuration Conference */

2012-02-01T13:10:08Z

5th International Biocuration Conference

Cooperl: /* The following items were postponed until next week's discussion */

2012-01-31T23:36:10Z

The following items were postponed until next week's discussion

Cooperl: /* PO terms for lateral meristems */

2012-01-31T23:35:06Z

PO terms for lateral meristems

Cooperl: /* leaf vein, primary vein, midvein */

2012-01-31T23:31:11Z

leaf vein, primary vein, midvein

Cooperl: /* xylem */

2012-01-31T23:27:16Z

xylem

@@ Line 178: / Line 178: @@
 '''secondary xylem (PO:0005848) current def.:''' A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators]
-Existing definition is okay.
+Existing definition is okay: A portion of xylem (PO:0005352) tissue that develops from a vascular cambium (PO:0005598).
 New comment: Secondary xylem develops as part of GO:0080117 secondary growth. Found in gymnosperms and most dicots. Secondary xylem is the "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas. May be organized into axial and ray systems. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth and may produce lignified tissue that appears woody, but is not composed of secondary xylem.

← Older revision		Revision as of 10:56, 6 February 2012
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	''This also makes it more likely that the name we used in the comments or definitions matches the PO term name.''		''This also makes it more likely that the name we used in the comments or definitions matches the PO term name.''
		+
		+	==Links to sources==
		+	* Need to create a POC:curators, po-ref page with a list of who the curators are
		+	* Link to list of ISBN #s with the references

	=New relations=		=New relations=

@@ Line 103: / Line 103: @@
 ''comment: A spore is usually single-celled in homosporous plants but may be multicellular in heterosporous plants. May have a spore wall (GO:0031160) made of sporopollenin.''
-''Keep this term as is, and add specific terms for uni- and multicellular spores, since most spores are a single cell. Add single celled mega and microspores now, since that covers the majority of plants.''
+''Keep this term as is, and add specific terms for uni- and multicellular spores, since most spores are a single cell. Maybe add single celled mega and microspores now, since that covers the majority of plants.''
 ==From [[POC_Conf._Call_1-24-12]]:==

← Older revision		Revision as of 16:43, 1 February 2012
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	Comment: Metaphloem develops after the vascular tissue has stopped elongating, in the same location as the primary phloem, replacing the protophloem. Sieve elements in the metaphloem are larger than in the protophloem. Differentiates before the secondary phloem, if any is formed.		Comment: Metaphloem develops after the vascular tissue has stopped elongating, in the same location as the primary phloem, replacing the protophloem. Sieve elements in the metaphloem are larger than in the protophloem. Differentiates before the secondary phloem, if any is formed.

−	''Revised definition: A portion of primary phloem that has as parts companion cells (in angiosperms) or albuminous cells (in gymnosperms) associated with the sieve cells that develops after the protophloem.	+	''Revised definition: A portion of primary phloem that has as parts companion cells (in angiosperms) or albuminous cells (in gymnosperms) associated with the sieve cells and that develops after the protophloem.

← Older revision		Revision as of 13:11, 1 February 2012
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	Back to [[POC Meetings Minutes]]		Back to [[POC Meetings Minutes]]
−
−	~~Streaming recording link:~~
−
−	~~https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=61902932&rKey=eca857eefea40919~~
−	~~Download recording link:~~
−
−	~~https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=61902932&rKey=b4449adc3cd01a81~~

	=Miscellaneous=		=Miscellaneous=

@@ Line 246: / Line 246: @@
 • Notification date: February 3, 2012
-''PJ is planning to attend may doing a talk.  LC is planning to attend.''
+''PJ is planning to attend may do a talk.  LC is planning to attend.''
 ==[http://peabody.yale.edu/collections/spnhc2012/home SPNHC 2012]==

@@ Line 199: / Line 199: @@
 part_of seed; adjacent_to hilum
-=The following items were postponed until next week's discussion=
+=The following items were postponed until next week's discussion:=
 Details moved to [[Items for future meetings]]''
-* [https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, primary vein, midvein]
+==[https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, primary vein, midvein]==
 =Upcoming meetings and Presentations 2012:=

← Older revision		Revision as of 23:35, 31 January 2012
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	* [https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, primary vein, midvein]		* [https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, primary vein, midvein]
−
−	~~==[https://sourceforge.net/tracker/?func=detail&aid=3481640&group_id=76834&atid=835555 PO terms for lateral meristems]==~~
−	~~See [[Items_for_future_meetings#Primary_and_secondary_growth.2C_etc.]] for more details on terms that will be requested in GO.~~
−
−	~~The PO has a general term for lateral meristem, of which cambium is a subtype:~~
−
−	~~[[File:lateral_meristem1.jpg]]~~
−
−	~~'''lateral meristem (PO:0020145)'''~~
−
−	~~'''revised def'n:''' A meristem located parallel to the circumference of a plant organ.~~
−
−	~~comment: Participates in lateral growth (GO:xxxx) of a plant organ, primarily shoot axes and roots. Contrast with apical meristem (PO:0020144).~~
−
−
−	~~'''root lateral meristem (PO:0006308)'''~~
−
−	~~This is just a cambium in the root, which also has vascular cambium and phellogen.~~
−
−	~~'''proposed new name and def'n: root cambium:''' A cambium that is part of a root.~~
−
−	~~This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.~~
−
−	~~If we are going to have this term, maybe we should have root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium?~~
−
−
−	~~'''cambium (PO:0005597)'''~~
−
−	~~'''revised def'n:''' A lateral meristem that has a part a single layer of cambial initial cells and their derivatives, arranged orderly in radial files. (Ref.: Esau)~~
−
−	~~comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).~~
−
−
−	~~'''vascular cambium (PO:0005598)'''~~
−
−	~~'''revised def'n:''' A cambium that gives rise to secondary xylem and secondary phloem.~~
−
−	~~comment: Vascular cambium is located between the secondary xylem and secondary phloem and gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis.~~
−
−
−	~~'''cork cambium/phellogen (PO:0005599)'''~~
−
−	~~'''revised def'n:''' A cambium that is part of a periderm and produces phellem (cork) and phelloderm.~~
−
−	~~comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.~~
−
−
−	~~'''primary thickening meristem (PO:0005039)'''~~
−
−	~~Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.~~
−
−	~~'''revised def'n:''' A lateral meristem that has a parts multiple layers of cells located near the shoot apical meristem.~~
−
−	comment: Contributes to primary thickening of the stem, adventitious root formation, and formation of linkages between the stem, leaf, and root vasculature. Contiguous with the shoot apical meristem in some species, but not all. Produces more or less distinct vascular bundles surrounded by ground tissue, as opposed to the more or less continuous xylem and phloem produced by a vascular cambium. A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.
−
−
−	~~'''secondary thickening meristem (new term)'''~~
−
−	~~'''proposed def'n:''' A lateral meristem that is part of a shoot axis not contiguous with the shoot apical meristem and has a parts multiple layers of cells.~~
−
−	comment: Contributes mainly to formation of the body of a stem, but may also produce adventitious roots. May be continuous or discontinuous with the primary thickening meristem. Found in some monocot species of the Liliales and Asperigales.
−
−
−
−	~~'''Other types of lateral meristems'''~~
−
−	~~PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel meristem (PO:0009107), plus their subtypes.~~
−
−	~~Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches develop from apical meristems, not a lateral meristem.~~
−
−	~~There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.~~
−
−	~~'''inflorescence lateral meristem (PO:0009105)'''~~
−
−	~~'''current def'n:''' The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.~~
−
−	~~This should be called '''inflorescence branch meristem''', and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.~~
−
−
−	~~'''ear lateral meristem (PO:0009110)'''~~
−
−	This should be called '''ear inflorescence branch meristem''', and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).
−
−	~~'''revised def'n:''' An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.~~

	=Upcoming meetings and Presentations 2012:=		=Upcoming meetings and Presentations 2012:=

← Older revision		Revision as of 23:27, 31 January 2012
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	part_of seed; adjacent_to hilum		part_of seed; adjacent_to hilum
		+
		+	=The following items were postponed until next week's discussion=
		+	Details moved to [[Items for future meetings]]''

	==[https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, primary vein, midvein]==		==[https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, primary vein, midvein]==