POC Conf. Call 5-11-10

POC meeting, Webex Conference Call; Date: May 11th, 2010 10am (PDT)

Acceptance of the minutes from last weeks meeting? All in favor?

Agenda:

1. Discussion of the Cell Type Ontology and our plant cell terms in preparation for the workshop in Bar Harbor.

(Cell Type Ontology Workshop on May 18th and 19th, 2010. Jackson Laboratory, Bar Harbor, ME)

Questions to Consider/Discuss:

• Introduction to the Cell Type Ontology- what is it and what are their goals?

Browse Cell Type Ontology on BioPortal

Based on the 2005 Genome Biology paper Cell Type Ontology, Genome Biology, 2005, the goals of the Cell Type Ontology are to:

• Describes the cell types of the major model organisms, both animal and plant
• Facilitate cross-organism queries in a single database

It is designed to be useful in the sense that a researcher should be able to find, in a rapid and intuitive way, any cell type in any of the major model organisms and, having found it, learn a considerable amount about that cell type and its relationships to other biological objects.

• explicitly sets out to include cell types from all the major model organisms within a common framework
• incorporate a great deal of phenotypic information about these cell types and is thus far more comprehensive in its cellular detail than these other resources. The intention is that the new cell-type ontology should provide organism-independent knowledge as well as cell-type unique identifiers (ID) that can be incorporated into any database holding cell-type-associated knowledge.
• expected short-term use of the ontology will thus be in cataloging phenotypes and gene expression patterns

Cell Type Ontology Workshop

• Laurel and Ramona will attend and will give a 10-15 minute presentation

Points: Basic goals of PO

Current goalsto encompass all plants

is_a completeness

machine-readable definitions

Organization of the plant cell terms:

• separation of in vitro and in vivo plant cell terms

• Plant cell child terms: organization, completeness, definitions. Are we happy with them, or do we plan on a major overhaul?

-- current PO browser with all cell types expanded

-- dev PO browser with possible new organization for plant cell types

• Should we aim for complete redundancy between cells in PO and plant cells in CL?

- If CL is going to use PO terms, definitions, and structures, should they use our numbers and should we set up live links between the CL and PO browsers?

- From OBO foundry wiki:

Reuse Entries that are re-used in a second, derivative ontology should NOT make copies and give the copied entities new IDs. Connection to the original term via an xref is firmly discouraged. One primary reason is that xrefs are used for many purposes, and do not imply that the terms are equivalent. The original ids must be used directly in the derivative ontology.'

• List of PO plant cell types that are not in the Cell.obo file (thanks Rex!). Do we want to request that these terms be included in the CL?

• Need to think about tissues and organs that we and CL might want to use for cross-product definitions.

From last week:

• Laurel, Ramona and Rex had a brief discussion about plant cells at the end of the meeting. Rex said he made the list of terms that were in the PO but not the CL by going through the two ontologies term by term. Ramona said there do not appear to be any terms that are in the CL but not the PO, but we need to check systematically.

• The two ontologies have similar structure, with a few differences, probably changes that were made after terms were imported into the CL. It might be better to have a more hierarchical structure so there are not so many direct children of plant cell.

• In addition to cell by organism, the CL also lists cells by type. Right now, it gamete is the only haploid plant cell, but this leaves out all the cells in gametophytes. May also want to add triploid cells of endosperm under polyploid cell.

Items carried over from last week's agenda:

1. fruit (See SF Tracker: fruit)

Current def'n: The seed-bearing structure in angiosperms, formed from the ovary after flowering.

Proposed new def'n: A collective plant structure that contains a post-fertilization stage gynoecium and any other structures of the flower that mature with it. (Comment: Exceptions are cases of parthenocarpy, apomixis or other hormone-induced conditions.

Note that we may need to define parthenocarpy at some point (or put in a dbx ref for it). Dbx ref to parthenogenesis: Medical subject heading Ontology D010312

2. Embryo (See SF Tracker: embryo)

Current def'n: A young sporophyte contained within a seed. [source: APWeb:Glossary, GR:pj]

Proposed def'n: A sporophyte in the early stages of growth and differentiation, consisting of precursor tissues for the leaves, stem (see epicotyl/hypocotyl) and root (see radicle).

We could mention the cotyledons in a comment- specific to flowering plants

(2) See Cultured embryo PO:0000010 for definition of in vitro plant embryo

(3) Adventitious embryos do not arise from zygotes -add a comment?

Relationships:

(1) has no is_a parent, is_a sporophyte, which makes it a whole plant through transitivity (2) develops_from zygote (see comment above) Usually (3) embryo contained_in archegonium (works for land plants, not charophytes (doi: 10.1111/j.1469-8137.2009.03054.x)

4. Upcoming Conferences and Meetings: Updates'

* POC meeting/Annotation workshop to be held in Corvallis on June 29th/30th.

Pankaj suggested we plan on meeting for two days. Dennis can make June 30th, but has to be back in NYC early on July 1st, so we will try to meet June 29th and 30th.

Alejandra cannot travel that day -- can attend via conference call.

Ramona will be in Portland June 26-29, will request that her talk be scheduled for the 27th or 28th. Ramona has sent a request to schedule her talk on the 27th or 28th. Barry will be in France this week and can't attend. What about Chris?

Pankaj would like to also include Aaron Liston (OSU), Richard Halsey (OSU) and Quentin Cronk (UBC; http://cronklab.wikidot.com/quentin-cronk).

* Bio-Ontologies 2010: Semantic Applications in Life Sciences. July 9th and 10th, 2010, Boston, Mass. Satellite Interest Group (SIG) meeting preceding the International Society for Computational Biology (ISCB). Laurel, Ramona are registered.

-Flash updates, up to 1 page: (short talks (5 min) giving the salient new developments on existing public ontologies) -Poster abstracts, up to 1 page (posters will be up for 2 days, with at least 1 poster session) Poster authors can also do a flash update.

Laurel submitted the 1 pager on Friday April 16th to Bio-Ontologies meeting for a poster presentation and possibly a short flash update talk. We will be notified by May 7th if we are doing a flash update.

* American Society of Plant Biology (ASPB) July 31-Aug 4th 2010, Montreal, Quebec, Canada. Laurel, Pankaj going, PO Poster presentation and Annotation Workshop with Gramene.

Laurel is looking into the possibility of hosting a booth with other database groups. SGN and maizeGDB are interested and she will check with TAIR and Gramene. The estimated costs are $1600 for the plain booth (no carpet, electricity or tables). This could be shared or PJ said POC could host it.

We should prepare a brochure to distribute, similar to the one Gramene has.

Annotation workshop with Gramene is scheduled for Saturday July 31, 8am-12pm. more details TBA

* International Botanical Congress (IBC2011). July 23rd-30th 2011, Melbourne, Australia. Important dates (http://www.ibc2011.com/Dates.htm):

Dennis and Alejandra are already planning to attend IBC2011 and speak in other symposia.

Ramona circulated a proposal that was submitted on Thursday April 29th and contacted the organizers about whether or not it is possible to get a room with internet for outreach activities.

Pankaj will be co-organizer with Ramona. Laurel and Ramona are interested in going and speaking if funds are available.

Ramona has contacted Angelica Cibrian (Harvard) from the Genomics of Seed Plants project and she is interested in being a potential speaker, will contact other possible speakers in Australia if the proposal is accepted.

• Latin American Congress of Botany (http://www.botanica-alb.org/X_Congreso/index.php). La Serena, Chile, October 4-10; MAG: "I am not sure about due dates for this one due to the earthquake".

from 3-23-10: Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.

• Annotation workshops to be held at NYBG in fall 2010. Date TBD. Will invite outside experts, scientists, students and postdocs.

8. Next meeting scheduled for Tuesday May 25th at 10am PDT.