Difference between revisions of "PO/CL Conference call 08-30-11"
| Line 12: | Line 12: | ||
CL will provide bridge files as part of the CL release process. | 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== | ==New subset for CL== | ||
| Line 20: | Line 23: | ||
This subset will need to be updated whenever we add new cell types. | 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= | =Problematic xrefs to CL terms from PO= | ||
Revision as of 21:04, 30 August 2011
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".
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.
CL should probably use PO:0009002 as the primary number, and either obsolete CL:0000610 or merge it into PO:0009002.
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.
This is okay.
epidermal cells
POC agreed to the suggestions below, but need to confirm with CL that or interpretation of their terms is correct.
- 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.
- 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.
- 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.
We should remove the xref to CL:0000034 and keep the xref to CL:0000266. See below on treating xrefs as equivalent terms.
PO cell types that should reference cell types in CL
A few types of cells are equivalent to remaining CL terms. If so, then they should have a general xref, then assert the general xrefs as equivalent using the header "treat-xrefs-as-equivalent: CL" (see obo format guidelines).
PO:0009002 plant cell > CL:0000610 plant cell (but maybe CL will use PO id)
PO:0000423 zygote > CL:0000365 zygote
PO:0004011/PO:0000070 intial cell/meristemoid > CL:0000266 meristemoid
This is okay for zygote and meristemoid. Maybe CL should get rid of CL:0000610.
PO:0004010 meristem > CL:0000034
Treat xrefs as g-d
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.
