POC Conf. Call 7-12-11

POC meeting, Webex Conference Call; Date: Tuesday July 12th, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Elsner (OSU), Justin Preece (OSU)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_7-05-11? There were no changes, additions, or deletions.

Plant Physiology Publication

RW and LC are working on a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PO in the past year, focusing on restructuring of PAO. Will focus on how PO is now applicable to a wider range of plant species.

BS commented that the manuscript is quite long. No need to provide extra explanations if it will have to be cut out later. The idea was to have everything in this manuscript, then cut as needed, and some of the background material could go into the AJB manuscript.

Discussion items arising from manuscript:

• Last week, we agreed to use "type" and "term" in the way BS suggested based on the Hill et al. 2008 gene annotation paper, rather than using "class"

Type = A universal, represents the entity or stage/phase in reality.

Term = the thing in the PO that corresponds to a PO id.

From BS: In the database computational world, the word type is used, but they don't distinguish between the type in reality and the thing in the ontology, because they only need to describe reality in the computer. In our circles, the name or term in the ontology is a linguistic representation of the type, which is present in reality.

Where confusion might arise, we can use the words "node" and "edge" to refer to the ontology, which is a graph. The node refers to a collection of term, name, synonym, definition, references, etc.

Use node when we are referring to that collection of things.

Use term to refer to the linguistic string that plant scientists use to describe different aspects of biology.

Use type and subtype to talk about that in reality that the linguistic strings refer to. Types have instances, which are the actual things (like leaves) that you observe.

Then when people talk about PO in OWL context, they can use class as used in OWL.

We will need to add a sentence or two to the introduction to explain that an ontology is a graph, and what nodes and edges are.

• How terms are represented in the text of the manuscript.

Need to be consistent with old papers.

Will use italics for both term names and relations.

Can use bold face to refer to instances (even though we don't have any in the manuscript now.

• Formal definition of develops_from

There was an extensive discussion of the difference between transformation and derivation

Transformation is always a one to one change, there is not division or fusion. So initial cell > epidermal cell > root hair cell is not a transformation.

The definition of develops_from was written so it could include instances of transformation or derivation. Sometimes, it is not know which is true, so develops_from can include either or both.

There are some examples of transformation in the PO, such as in vitro structures. There are also examples of derivation, like structures that arise from initial cells and transformation like structures transformed from meristems.

RW will make a list of where we use develops_from and derives_from for next week. Then we can examine each one to see if they represent derivation, transformation or unknown. If we know which one it is, it may be better to use specific relations, but then we may get backlash from evo-dev community, who want to see the word "develops".

• Prefixing some of the term names with "plant" (e.g. plant cell, plant embryo)

CM:"So I see you've decided to prefix many terms with "plant". I don't think this is necessary (we decided this at the JAX CL meeting), and no other ontology does anything similar. I guess if this is just for the upper level terms (which should be hidden from view in most applications) then the user-unfriendliness doesn't matter. It's also a little curious as the terms that have the potential to cause confusion in a pan-eukaryotic context (epidermis, cuticle) are _not_ prefixed. I would recommend omitting all "plant" prefixes. For details on automatic assignment of obo foundry unique labels, see our paper from WOMBO/ICBO this year."

Do we want to add "plant" as prefix to terms like epidermis, cuticle, vascular system? Probably should be consistent.

Do we want to remove other plant prefixes?

RW: I think they make sense for the upper level terms, because they are only defined in terms of plants (e.g., a plant anatomical entity is an AE that is in a plant).

Having "plant" in the name makes the PO more useful to non-plant biologists. For example, a plant cell is different than other cell (has a cell wall). If we don't add it, it will have to be added before terms can be imported to other ontologies.

We should try to be consistent with upper level terms, see if they all have plant in the prefix.

RW will make a list of terms that we may to add plant as a prefix to.

From CM (later via email): If plant is automatically prefixed to all PO terms before importing into another ontology, terms like "plant structure" will become "plant plant structure". (RW: but it could easily be scripted to make sure it is not added twice)

• Use of noun form in term names: Is it nb that it is consistent across the ontology? (We decided this at the POC conf call POC_Conf._Call_5-17-11#Items_arising_from_previous_meetings:.)

CM: "I would say "embryonic plant structure" rather than "embryo plant structure", the relational adjective form is far more common in other ontologies, but horses for courses.

Should we change this? It does sound better.

BS: There is no reason we can't use noun form in the names, as long as the whole name string is a noun. Suggests using the one that people (biologists) will be most happy with.

Noun form seems fine in the ontology, but sounds odd in the manuscript.

PJ: just say we are using noun form for consistent style, but the other form is present as a synonym. If reviewers or users complain, we can explain it. The other form is already present as an exact synonym.

Can explain the rationale in the paper and in the wiki as well.

• The defense of the "portion of" prefix doesn't sound very convincing.

Current text: "Although the phrase “portion of plant substance” is not part of everyday language, that name was chosen, rather than plant substance, to clearly express that this class can include any portion of a plant substance (such as xylem sap) found anywhere in the world, be it all of the xylem sap in the world, all of the xylem sap in any whole plant, or just the xylem sap found in one particular branch of one particular plant."

Suggestions for better wording?

BS will edit the mansuscript or add comments/suggestions for this.

• The reflexive part_of case is interesting (trichomes). What is in the manuscript is 100% correct. However, it is worthwhile bringing this up on the RO list.

RW will send an email to the RO list.

• Never say "children" or "parents" if you can be more specific (subtype, part_of)???

We can say "is_a child" or "part_of parent" or "is_a descendent" if we need to, so there is no confusion about the type of relation.

• Should PAO and PGDSO should be referred to as branches, rather or as sub ontologies

We will refer to them as branches of the PO. The most current version of the manuscript does this. BS will check it.

Should not refer to parts of the ontology as domains, because domain refers to reality. However, the domain of each branch of the PO is different. In the long term, PO may cover all aspects of the plant domain, either directly or indirectly.

• Use of "relation" versus "relationship": is there a rule about when to use these words?

They mean the same thing. We can continue to use relation.

See: http://groups.google.com/group/obo-relations/browse_thread/thread/29fc616eb570f7dc/fc0647f190b5f178

• participates_in relation

The [RO web page] has the most current version, not the paper.

RO has has_participant relation, but not participates_in. Eventually, we may want to use both relations. We may be able to resolve conflicts between different types of plants using it. But then we will have to find a structure that is present in every example of the phase we want to describe. We will have to be careful because it will cause problems like part_of/has_part. It might be useful for moving annotations from phase to structure.

From the RO page, there is a list to RO proposed, which includes the relations like participates_in. We can site that web site.

RO will eventually merge into BFO.

User requests, Plant Anatomy Ontology:

postponed until a future meeting

User requests: PGDSO:

postponed until a future meeting

Upcoming meetings 2011:

• Botany 2011 Meeting [Botany 2011] St. Louis, MO at the Chase Park Plaza, July 9-13.

Societies participating: Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).

DWS is attending, but will not present. Many people from the BSA will be at the IBC meeting in Melbourne.

• ICBO 2011 Second International Conference on Biomedical Ontology

July 26-30, 2011 Buffalo, New York ICBO

-LC will present the PO on Friday July 29th, 3:30pm in the session: "Parallel Sessions on Special Topics: The OBO Foundry, featuring discussions of the Infectious Disease Ontology, the Ontology for Biomedical Investigations, the Ontology for General Medical Sciences and the Plant Ontology"

Link to program: [1]

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Date: July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

• Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Gramene and Plant Ontology are hosting a [Data Curation Workshop] again, focusing on pathway curations.

LC and PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Plant_Biology_2011_Outreach_Booth and we are invited to take part. We are hosting the website.

• International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, will be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details

• POC Meeting at New York Botanic Garden Tentative dates, Sept 9th-11th, 2011

DWS will look into booking the apartments at the NYBG for accommodations

More details TBA....