vascular bundle

Mon Aug 30 14:57:01 EDT 2004

Hi all,

Mea culpa! I admit, it was my mistake saying that vascular bundle was
obsoleted. Reason for that was that we obsoleted some other 'vascular
terms' and not all obsoleted terms are in the 'obsoleted' node (some terms
were just deleted). As a result, we have fewer terms in the obsolete node.
I looked into all the older revisions in cvs and didn't find this term, so
Pankaj rightly stated, VB was never in the PO. We did discuss it and opted
not to have term vascular bundle in PO, since it is not a tissue type, but
a kind of 'grouping term' and we already had several terms in PO that
seemed sufficient at the time (back in the May).

However, it really doesn't change much my point (and Toby's elaboration of
problems that we are going to face if we introduce VB the way Pankaj
suggested). To summarize, 1) we can use terms that are already in the PO,
and/or 2) annotation can be made to a more granular term, 3) having
vascular bundle everywhere under sporophyte node will cause large-scale
term proliferation, resulting in a dozens of terms like 'xylem of the
vascular bundle of the stamen'. This is the case of 'full instantiation'
or structure 3 in the POC Documentation. Now, we had discussion about the
full instantiation and problems associated with it, and decided to go with
this option ONLY when absolutely needed for annotation purposes. I have
hard time believing that we need VB everywhere under sporophyte for
annotation purposes (and I would like to believe that question about
gametophyte was a joke). I want to remind you of a similar situation with
sensu terms (I can't let go), where we ended up with 74 sensu terms only
to find out later that less than 50% of those were indeed required for
maize annotation in near future (if I recall correctly Mary's
information). And we also said for sensu terms 'only when absolutely
required'.

So my suggestion is to look in the Gramene and TAIR and see how many gene
annotations are currently associated to term 'vascular bundle'. Term
'vascular bundle' is also present in TAIR:
Term: vascular bundle (TAIR:0000362)
Def: A strandline part of the vascular system composed of xylem and
phloem.

However, I have not finished my list of unmapped terms for TAIR, so this
one is still not on my list. Mapping on one-to-one basis (meaning
term-to-term) is just a first round. There are terms that have different
names but they refer to the same structure, and this is determined by a
curator on case-to-case basis. We need to look into definitions, synonyms
and other info provided for each term, in some cases even looking into
annotations and original papers (if required). This is the most time
consuming part of the mapping process, and the most important one too.

In most cases, (I am still going through details) annotations in TAIR are
referring to the leaf vascular bundle, although the term definition itself
is very general.

At the end, just to remind you that we have following PO terms: vascular
cambium, vascular tissue, root stele, leaf vein, midvein, secondary vein,
lateral vein.

As I said earlier, we are going in circles with this issue of
instantiation and term proliferation, and it is one of the issues that
will come up over and over again. In nature, it is similar to problem with
sensu terms. Toby described it nicely in the documentation she sent to
Lincoln, and I hope we can discuss this next week.
GO folks are aware of this problem and are currently thinking of solutions
as well. One of the possible solutions is to change the way the
annotations are done. Again, I hope we can discuss it soon.

Katica

On Mon, 30 Aug 2004, Pankaj Jaiswal wrote:

> BTW, the term "vascular bundle" was never introduced to the POC anatomy
> files, despite Gramene having it. So no question of obsolete or
> un-obsolete. This is a new term request based on our mapping and new
> annotation requirements. I was the one who was doing tissue node and did
> not introduce the term at that time because, VB is not a tissue type.
>
>
> One another note, we have a term called bundle sheath which is
> suggesting there is a plant structure called VB.
>
> bundle sheath
>
>      * Accession: PO:0006023
>      * Aspect: plant structure
>      * Synonyms: None
>      * Definition:
>             A layer or layers of cells surrounding the vascular bundles
> of leaves. It may consist of parenchyma or sclerenchyma.
>
> -Pankaj
>
>
> Pankaj Jaiswal wrote:
> >
> >
> > Kellogg, Elizabeth A. wrote:
> >
> >> Isn't "vascular bundle" simply the term applied to a vein when viewed
> >> in cross section?
> >
> >
> >  > I agree with Katica's earlier message that the term vascular bundle
> > should remain obsolete.
> >
> >> The gene in question can be annotated to vein or vascular tissue if it
> >> can't be
> >
> >  > annotated to one of the parts of the vein.  I haven't checked the
> > publication myself, but I'd be pretty
> >  > surpirsed if it were actually expressed in every cell of the vein.
> >
> >>
> > I don't think so. As a curator I would be very cautious on making such a
> > statement and extrapolating the information provided by the author. In
> > the first instance, I would go by the authors suggestions. This is also
> > a sort of leverage given to the curator since he/she may not be an
> > expert in plant anatomy and by having a term like this the curator still
> > has an option of doing the correct annotation as well as the user
> > finding the right query term. Another argument is that from the top,
> > (intact tissue) and not the section, it is hard to tell whether the
> > location of the expressed gene as we are suggesting to annotate to vein
> > (only for leaf) is actually expressed in bundle sheath/surrounding
> > bundle sheath extensions or anywhere inside the leaf VB.
> >
> > This was just a case of leaf VB/vein, but in other parts, I doubt if
> > people call it veins. Its either Vascular bundle/tissue/strand.
> >
> >
> >> If the group decides to un-obsolete (great verb!) the term, then the
> >> ontology would
> >
> >  > have to be considerably more complex than Pankaj outlined earlier.  I
> > think it would be more like:
> >
> >>
> >> Sporophyte
> >> --p--vascular bundle
> >> -----i--leaf VB
> >> -----i--stem VB
> >> -----i--root VB
> >> -----i--stamen VB
> >> -----i--petal VB
> >> -----i--sepal VB
> >> -----i---etc., one each for every organ
> >
> >
> > I agree on this, the example I gave was just a simple representation.
> >
> >> -----p--xylem
> >> -----p--phloem
> >> -----p--cambium
> >> -----p--bundle sheath
> >> ---------i--mestome sheath
> >> ---------i--parenchyma sheath
> >> -----p--parenchyma
> >> -----p--schlerenchyma
> >> --p--shoot
> >> -----p--stem
> >> --------p--stem VB
> >> -----p--leaf
> >> --------p--root VB
> >> --p--root
> >> -----p--root VB
> >>
> >> Finally, to respond to an earlier message in this thread - veins
> >> (vascular bundles) are present in all plants, not just C4s.   Toby
> >>
> >>
> >> -----Original Message-----
> >> From:    owner-po-dev at brie4.cshl.org on behalf of Pankaj Jaiswal
> >> Sent:    Fri 8/27/2004 9:55 AM
> >> To:    po-dev at plantontology.org
> >> Cc:
> >> Subject:    Re: vascular bundle
> >>
> >> The purpose for asking this term was, that they are present in all
> >> kinds of organs and not just limited to the leaves.
> >>
> >> In leaves mid veins are representing the vasculature and the leaf VB
> >> is a part of that network of vasculature and as Dave pointed out there
> >> are many other parts as well.
> >>
> >> My suggestion is to include this term. If agreed, the other question
> >> would be, where should we place it, it's not just a tissue, but
> >> contains a lot of tissue types. Thus it is an organized structure or a
> >> region in an organ.
> >>
> >> The proposed structure is
> >> i = instance of
> >> p = part of
> >>
> >>
> >> Sporophyte
> >> --p--vascular bundle
> >> -----i--leaf VB
> >> -----i--stem VB
> >> -----i--root VB
> >> -----i--stamen VB
> >> -----p--xylem
> >> -----p--phloem
> >> -----p--cambium
> >> --p--shoot
> >> -----p--stem
> >> --------p--stem VB
> >> -----p--leaf
> >> --------p--root VB
> >> --p--root
> >> -----p--root VB
> >>
> >> I am not sure....
> >>
> >> #1
> >> Its true that that the three terms xylem, phloem and cambium are not
> >> always part of VB.
> >>
> >> But as we know the PART of relationship we have suggests that, a child
> >> is a partof but not always a partof parent term. Thus this lineage
> >> seems correct.
> >>
> >> #2
> >> Do gametophytes also have VB?
> >>
> >>
> >>
> >> Suggested definitions for VB are
> >>
> >> by Fahn: A strand of conducting tissue
> >>
> >> By Essau: A strand like part of the vascular system composed of xylem
> >> and phloem. occurs in stem, leaf and flower.
> >>
> >> By Dickison: A strand like association of primary xylem and phloem
> >> that extends throughout the plant body.
> >>
> >> http://www.cogsci.princeton.edu/cgi-bin/webwn?stage=1&word=vascular+bundle
> >>
> >> a unit strand of the vascular system in stems and leaves of higher
> >> plants consisting essentially of xylem and phloem
> >>
> >>
> >>
> >> If that is an accepted structure then we may need a further
> >> instantiation of the terms xylem, phloem and cambium, because as of
> >> now these are the generic terms. But that is a topic for another
> >> request to be sent on the mailing list.
> >>
> >>
> >> Thanks
> >> Pankaj
>

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