POC Conf. Call 9-27-11

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POC meeting, Webex Conference Call; Date: Tuesday Sept 27th, 2011 10am (PDT)

In attendance:

POC members:

Absent:


Collaborators: none


Any changes or corrections(additions/deletions, etc) needed in the minutes from the POC_Conf._Call_9-20-11?

Tech Issues for the Upcoming Release


Status of New Annotation Files:

MaizeGDB Annotations

The MaizeGDB anatomy and development annotations are in the SVN already, may need some minor fixing on Weds, when MS gets back from vacation.

Physcomitrella Annotations

From 9-20-11 meeting: PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids

What link do we need to use for these and how do we get AmiGO to recognize it?

Need to set up SVN access for SR or whoever will be sending the files.

Grape and Strawberry

  • LC working on grape file, see sample

What links do we need to use for these and how do we get AmiGO to recognize them?

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

It appears that our version of AmiGO has a built-in set of db xrefs and it is not reading the current GO file. JP, JE are meeting CM to work on this on Monday Set 26th

Add new details...

non-standard definition dbxrefs

We have a few definition dbxrefs that don't have an isbn or pmid number. We need to create a dbxref library for these, similar to what GO uses (GO reference collection). RW can add this to the OE file. Need to look into how AmiGO interfaces with this.

Inclusion of synonyms

The Spanish synonyms are now working fine, have the descriptor "(Spanish:)" preceding them.

  • 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?

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.


Eliminating_Zea/Poaceae_terms_from_PO

This is complete for both PAO and PGDSO, although some names and definitions in the PGDSO may change as we go forward.

Edits to complete before release: PAO

All the edits from last weeks agenda have been completed.

Legume terms

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.

Background:

Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:

"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."


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.

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."


Some more contemporary uses of the term phyllode:

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:

"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.

"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)."


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.


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.


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."


RW did not find any contemporary papers that said that a phyllode is a petiole.

Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.

Unifacial leaf as synonym? No- not exactly the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311).

Proposed terms and definitions:

vascular leaf

>unifacial leaf

>>terete leaf (round in cross section)

>>ensiform leaf (flat in cross section)

>>>phyllode


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)

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.


RW: need to check and add references for all of these

terete leaf: A unifacial leaf that is round in cross section throughout all of part of the length of the leaf. (ref.: xxx)

Comment: The surface of a terete leaf corresponds to either the adaxial or abaxial surface of a normal leaf.


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)

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?

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.

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, transition phyllode). Phyllodes are generally xeromorphic.

is_a ensiform leaf, is_a adult leaf


transition phyllode: A transition 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 transition leaf, is_a ensiform leaf


Note: spines are really unifacial leaves -- Make leaf spine is_a unifacial leaf

Also, add terms for root spine (adventitious root on palms and on climbers), abscised petiole spine (in Foukiaria)

bristle

(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)

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.

We have the term stipule spine. Could also add the term stipule bristle: A stipule that has a brush-like appearance.

A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).

There are two meanings for bristled:

1. Stiff and sharp (e.g., a bristled trichome)

2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)


Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):

1. bristle-like:

This is a combination of two PATO descriptors:

Something describing the shape:

PATO:0001954 (subulate, awl-shaped, needle-shaped): A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base.

or

PATO:0001873 (cylindrical): A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.

and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.


and something describing a quality of a substance:

PATO has:

PATO:0001544 (flexible): A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. (bendy)

PATO:0001545 (inflexibile): A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. (stiff)

A bristle is stiff but also bendy! I think in addition to flexible/inflexible, PATO needs terms for stiff or rigid/flacid, and that stiff should be a related synonym of inflexible, rather than exact.

PATO:

quality of a substance (existing)

>flexibility (existing)

>>flexible (existing)

>>inflexible (existing)

>rigidity (new)

>>rigid (new)

>>flacid (new)


2. bristle-bearing: A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.

is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)

Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).


To describe legume stipules, we may also need a term brush-like: A shape quality inhering in a bearer by virtue of the bearer's having a shape that is a cluster of bristle-like structures.

Then if we want to, we could add terms like brush-like stipule (is_a stipule) or bristle-like stipule (is_a stipule) or bristle-bearing stipule, or users could post-compose these terms on their own.

Possible new Collaborator Group:e-monocot

Fill in some details:...

RW met with the director of the project at IBC in Melbourne. He was interested in PO.

Upcoming meetings and Presentations 2011/2012:

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?


Phenotype RCN meeting, 23-25 February 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

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.

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