PO/CL Conference call 08-30-11

In attendence:

from POC: Ramona Walls (NYBG), Laurel Cooper (OSU)

from CL: Terry Meehan (Jackson Labs), Alex Diehl (University at Buffalo)

Syncing PO and CL

CL plans to obsolete most of its plant cell types, and keep xrefs to those for PO terms.

CL will provide bridge files as part of the CL release process.

Terry has already obsoleted the necessary terms from CL.

CM: For future CL releases, the standard release will be a metazoan CL, without specific cell types form organisms like Drosophila or zebra fish. Will probably also want other versions, like standard CL plus plants (for use by GO, etc) and possibly an in depth eukaryotic CL, with anatomy terms from PO, flybase, ZFIN, and others.

New subset for CL

RW has created a new subset for plant cells. It contains all of the is_a descendents of plant cell. CL can use this to create their bridge file.

This subset will need to be updated whenever we add new cell types.

In the future OORT will be able to generate subsets like this automatically. For now, PO can maintain it mannually, since it is already done.

Problematic xrefs to CL terms from PO

PO has xrefs to 46 CL terms.

• Most are accurate and reference CL plant cell types. Suggest that we delete these xrefs, because CL is going to obsolete those terms.

• Nine of the xrefs are not under CL's category for plant cells, and require special attention (see below).

• Here is what CM said about the xrefs to CL: "Hmm, have to figure out what to do about the CL xrefs. I think all the ones that have been obsoleted should be translated to alt_ids. If we have one remaining, PO:0009002, keep the xref and add a header: treat-xrefs-as-equivalent: CL".

Links to repository urls for current versions of PO and CL are in the Skype chat window.

plant cell

PO:0009002 (plant cell) xref to CL:0000610 (plant cell).

CL defines plant cell as "A cell found in seeded plants." This is outdated.

Suggest that CL adopt PO's definition of plant cell. We should keep this xref. See below on treating xrefs as equivalent terms.

From PO meeting: CL should probably use PO:0009002 as the primary number, and either obsolete CL:0000610 or merge it into PO:0009002.

For now, CL will keep CL:0000610 (but use PO's definition, instead of the current one) and add an xref to PO:0009002. CL will add header to treat PO xrefs as equivalent.

If CL were to use PO:0009002 as the primary id (by Mireoting it or other mechanism), it would not show up in CL basic.

PO will remove xref to CL:0000610.

Note: as of 2013, CL:0000610 has been obsoleted

zygote

PO:0000423 (zygote) xref to CL:0000365 (zygote).

CL:0000365 is_a cell by lineage, is_a early embryonic cell. This is probably fine.

We should keep this xref. See below on treating xrefs as equivalent terms.

We don't need to name this "plant zygote" because it is really the same thing across organisms.

CL zygote currently is a descendent of animal cell. PO will remove xref to CL:0000365. May put it back in later if CL makes zygote more general. Text definitions are already compatable. CL already removed xref to PO term.

epidermal cells

CL has already obsoleted socket cell, pavement cell, and trichome. PO will remove all of the xrefs listed below.

• PO:0004013 (epidermal cell) xref to CL:0000362 (epidermal cell)

CL:0000362 is_a squamose epithelial cell, is_a general ecto-epithelial cell

At an earlier meeting and via email exchanges, we decided that the CL definition of epidermal cell is not appropriate for plants.

PO:0004013 will be renamed plant epidermal cell. Remove xref to CL terms. PO:0004013 will be imported into CL with other plant cell types.

• PO:0000332 (epidermal pavement cell) xref to CL:0000400 (pavement cell)

CL:0000400 is_a epidermal cell. CL should obsolete this term, and PO should remove xref. PO:0000332 will be imported into CL with other plant cell types.

• PO:0000115 (socket cell) xref to CL:0000297 (socket cell)

CL:0000297 is_a epidermal cell, is_a supportive cell. CL should obsolete this term, and PO should remove xref. PO:0000115 will be imported into CL with other plant cell types.

• PO:0000282 (trichome) xref to CL:0000282 (trichome)

CL:0000282 is_a epidermal cell.

The xref from PO:0000282 to CL:0000282 should be on removed, because CL:0000282 really corresponds to PO:0008030 (trichome cell).

It is not clear from the CL definition if CL:0000282 refers to a hair in any organism or only to plant trichomes. If it refers to plant trichome cells only, then CL should obsolete CL:0000282 along with the other plant cell types. Should look at how GO treats trichome cells.

others

We agreed to the suggestions below, but will set up a call with CL to go over them. For example, need to make sure that sheath cell really was supposed to refer to a type of plant cell and that this is not some kind of animal cell called a sheath cell.

note: there is a sheath cell in C. elegans

• PO:0004531 (sheath cell) xref to CL:0000618 (sheath cell).

CL:0000618 has no definition, but is_a columnar/cuboidal epithelial cell. Suggest we remove this xref and the CL obsolete the term.

There are various types of sheath cells in animals, but they are not all the same type of entity, and they are not comparable to plant sheath cells. PO will remove xref to CL:0000618. CL may obsolete general term sheath cell, but keep specific types.

• PO:0000263 (atrichoblast) xref to CL:0000332 (atrichoblast).

CL:0000332 is_a epidermal initial, is_a non-terminally differentiated cell (second is_a relation is redundant).

PO definition of atrichblast is: A root epidermal cell that is formed after asymmetric division of an epidermal initial and does not give rise to a root hair.

Suggest that CL obsolete CL:0000332, because it is a plant cell, and their definition is not up to date. We will remove xref. PO:0000263 will be imported into CL when they bridge to plant cell types.

CL has already obsoleted this. PO will remove xref.

• PO:0004011/PO:0000070 (initial cell) xref to CL:0000034 (stem cell) and CL:0000266 (meristemoid)

definition of PO:0004011/PO:0000070: A meristematic cell that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body. Comment: Initial cells are often part of a portion of tissue that is composed mostly of somewhat older, differentiating cells. The division of an initial cell is often uneven, with the smaller daughter cell remaining meristematic.

definition of CL:0000034: A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.

definition of CL:0000266: A cell constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells.

Based on these definitions, PO:0004011/PO:0000070 is a better match to CL:0000266. Furthermore, meristemoid is an exact synonym of initial cell.

PO should not reference CL:0000266, because it is an animal cell. Will remove xrefs. See below about xref for meristematic cell.

Equivalent cell types in PO and CL

Based on the decisions above, the only equivalent terms in PO and CL are for plant cell (PO:0009002 and CL:0000610). CL will add PO:0009002 as xref, and use "treat-xrefs-as-equivalent: PO"

PO:0004010 meristem is a subtype of CL:0000034 stem cell.

PO will add CL:0000034 as a general xref to PO:0004010, then assert the general xrefs as genus-differentia, using the header "treat-xrefs-as-genus-differntia: CL part_of NCBITaxon:3193 (Embryophyta)"

See obo format guidelines.

New terms for CL

There are four terms in CL for which PO does not have equivalent terms, because it was set up for only angiosperms. Suggest we add terms like these when we work on the revisions of conducting tissue and cells. For now, Terry has removed the problematic xrefs from CL, will update them if we add new terms.

See conducting cells for non-vascular plants.