POC Conf. Call 10-18-11
POC meeting, Webex Conference Call; Date: Tuesday Oct 18th, 2011 10am (PDT)
In attendance:
POC members: Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Justin Elsner (OSU), Justin Preece (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY)
Absent: Chris Mungall (Lawrence Berkeley National Lab), Laurel Cooper (OSU), Marie Alejandra Gandolfo (Cornell University)
Collaborators: none
Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_10-11-11? None
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PO Releases
Current release
Release 16 should occur on or around Oct. 19, 2011.
Any issue to deal with arising from the release?
Test files are loading on beta browser. Release will proceed, unless there is a problem with final test on beta. JE will make release notes and other pages; he is in contact with LC.
derives_from relation: At the POC_Conf._Call_7-19-11 we decided to rename “derives_from” to “derives_by_manipulation_from”, but it has not bee updated in the obo-file.
Since it does not have an icon, AmiGO displays the text as “derives_from”.
We can add an icon 
to AmiGO. Should we keep the relation as "derives_from" for this release, then update if for the next release? This would give users more warning about the change in the relation.
We will add icon to both live and dev browsers. Will use derives_from in live brower, but switch to derives_by_manipulation_from for next release, and use latter on dev.
Next PO Release
Goals and Priorities:
- First major revision of PSDSO (formerly PGDSO) this is top priority
- Complete old user requests/SF tracker items this is top priority
- New association files: Physcomitrella, grape, potato (?)
- Fix dbxrefs for Fragaria annotations
- ABRC annotations to PO and TO terms These are descriptions of mutant phenotypes from Arabidopsis stock center, based on free text descriptions
- Links to images on PlantSystematics.org - Skype meeting with KN scheduled for 2:00/11:00 on Friday, October 21 PJ will confirm that he can make it on Friday. JE and JP can attend.
Collaborative projects:
- Mapping of Flora of North America Glossary to PO terms:
-What are the plans after this?
Once mappings are done, want to see how PO shows up in their data base. Show utility of PO for recovering descriptors from free text.
FNA is using natural language processing to map their descriptions to PO. We are starting with plant structures and later will add phenotype descriptors. We will start with leaf characters.
Will use PATO as it has terms available, and add PO terms as needed. Will also help show utility of PO to systematists.
-Others (These may be longer term than the next release):
- Leaf character ontology for Phenotype RCN? see notes above
- Linking ontology terms to character matrices using Morphobank?
Also need to work on providing PO in glossary form, to eventually replace APWeb Glossary. PJ has hired new grad student who will be working on this. This will be useful for users of APWeb Glossary who need a glossary, but don't want to use AmiGO browser. We could eventually incorporate other terms from APweb into PO if needed.
Timeline
We will have an interim release in December to add new data (data release). Have new data sets ready by December 15, so release can happen before holidays and is out in year 2011.
- Target date for finishing edits: late January
- Target date for release: February 15
PSDSO Revisions - Review
Review of changes discussed at NYBG meeting in on Saturday_Sept_10th,_2011.
PGDSO was renamed PSDSO (See below).
General changes
We agreed to make the following changes:
- Use only stage, instead of phase. Can add phase as synonym, where appropriate. ok
- Keep numbers in term names for now (so they line up properly), but put them in parentheses. ok
- Change any names that suggest that they are not stages into stage names, e.g., vegetative growth to vegetative growth stage. ok
- Make any plural names singular. e.g., leaf development stages to leaf development stage
- Convert definitions to genus-differentia form, as we are doing with PAO. ok
- Define stages as occurring between some landmarks (beginning and end points), rather than starting and ending at some landmarks. In this way, stages that are sub-parts of a larger stage will have is_a relations to the larger stage, rather than part_of. For example, protonema stage is_a gametophyte stage. ok
- The landmarks used to define the beginnings and ends of stages will general fall within the domain of GO biological process, not be part of PO. Will request new terms in GO as needed. ok
We will start making these changes in the developers' file (plant_ontology.obo) and document changes on SourceForge.
Changes to upper level hierarchy and definitions
New root term: Plant Structure Development Stage
It was decided that whole plant development stage should be is_a plant structure development stage, because a whole plant is a plant structure. This left plant structure development stage as the only sub-type of plant growth and development stage. It was decided to merge these two terms into one new root term: plant structure development stage.
proposed def. of plant structure development stage: A stage in the life of a plant structure during which the plant structure undergoes developmental processes.(POC:curators).
comment: Refers to GO:0032502 (developmental process), including growth, differentiation, and senescence.
BS: How does aging relate? In animals, they use delopement, growth and aging? We need to make it clear that we include these post-developmental (by which he means post-juvenile) stages.
PJ: Every organ goes through stages (e.g., embryonic or juvenile, reproductive or ripening, senscent, as well as the whole plant
DS: There is a parallel between whole plants (embryos, seedling, juvenile plants, reproductively mature, senescent plants) and a leaf (embryonic leaf, expanding leaf, functional leaf, senescent leaf). Unlike mammals, each organ goes through the same thing as the whole organsim.
PJ: but there are e.g., individual cells within an animal that are short lived
BS: We need to make clear in definition and gloss on ontology that the word development has a different meaning in plants, because organs have development, growth and aging as well as the whole plant, so development is going on all the time.
PJ: should start thinking about having GO process terms for the different types of senescence or aging -- cell aging or organ aging or whole organism aging.
RW: We will come back to our discussion of senescence from our NYBG meeting at a future meeting.
We will add something to the comment of PSDS about this.
New top-level structure for PSDSO:
whole plant development stage
proposed def. of whole plant development stage: A plant structure development stage that has as participant a whole plant. ok
Added a new term - life of whole plant - child of whole plant development stage:
proposed def. of life of whole plant: A maximal whole plant development stage.
Comment: There are only two types of life of whole plant: every life of a whole plant is either a maximal gametophyte stage or a maximal sporophyte stage.
ok
However, gametophyte stage and sporophyte stage are part_of children of life of whole plant, because not every gametophyte or sporophyte stage is_a life of whole plant (e.g., protonema phase is_a gametophyte phase, is not a life of whole plant).
In order for the definition of life of whole plant to work (and for other reasons), we decided that seed (PO:0009010) should no longer be a subtype of whole plant. It will be is_a plant structure.
Will need to come back to definition of seed at some point.
We will not have a term plant life cycle as a child of plant structure development stage, because there is not single plant structure that participates in an entire life cycle.
gametophyte and sporophyte development stages
Gametophyte development stage and sporophyte development stage (formerly gametophyte phase and sporophyte phase) are direct children of whole plant development stage. These are defined as any interval between their beginning and end, so other whole plant growth stages are subtypes of gametophyte and sporophyte stages.
proposed definition, gametophyte development stage: A whole plant development stage that has as a participant a whole plant during the interval between meiosis or apospory and its death or fertilization.
comment: During the gametophytic phase, a plant may produce gametes by mitosis. In bryophytes and pteridophytes, a gametophytic phase may begin without meiosis by apospory. This usually occurs when damage to a plant in the sporophytic phase leads directly to the growth of a plant that is in the gametophytic phase but bears the chromosome complement that would normally be found in the sporophytic phase. A whole plant in the gametophytic phase usually has half the chromosome complement of a plant in the sporophytic phase, but not in the case of apospory.
ok
proposed definition, sporophyte development stage: A whole plant development stage that has as a participant a whole plant during the interval between fertilization or apogamy and its death.
comment: During the sporophytic phase, a plant may produce meiospores by meiosis. A whole plant in the sporophytic phase usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy. Examples of apogamy include both naturally occurring instances (such as sporophytes arising form haploid cells as in bryophytes or ferns) as well as in vitro instances (such as haploid embryo culture or in vitro fusion of non-gamete cells or protoplasts).
ok
Upcoming meetings and Presentations 2011/2012:
Plant Genomes & Biotechnology: From Genes to Networks, CSHL
Dates: November 30 - December 3, 2011 Abstract Deadline: September 9, 2011...
Academic/Student No-Housing Package $720
RW registered and submitted abstract (Media:PO_abstract_PGBatCSHL2011.pdf). Will need to present a preliminary data analysis for the talk/poster.
No word yet on talk vs poster. Data analysis for presentation; This presentation should involve the larger analysis for the PO paper with the data from Physco and grape etc.
PAG 2012
January 14-18, 2012, San Diego, California
PO will host an Ontology workshop for PAG on Saturday January 14th from 10:20am-12:30pm
Use of Ontologies for Organizing Plant and Animal Genomics Data
Please see the PAG 2012 Ontology workshop wiki page.
LC is working on inviting speakers. Additional suggestions are welcome.
Important Dates:
- Registration and Abstract submissions: open on Sept 22
- Early Pre-Registration Deadline: October 31
- Travel Grants Deadline: November 1
- Abstract Submission Deadline: November 11
PJ may be tied up on Sat am, so we will not plan on him giving a talk. LC will also do a computer demo.
LC is also presenting in the Plant Phenotypes workshop on Sunday Morning, 15 January 2012 -- 8:00am - 10:10am.
We need to discuss what the PO approach and strategy to phenotypes is. Abstract deadline is November 11
See additional notes under FNA and ABRC work above.
Besides annotations, could also talk about Phenolog (from CM). Also use data sets for corn and Arabidopsis; corn classic genes identified using phenotypes, query annotations and orthology data JE has created; are there comparable phenotypes in Arabidopsis?
The PO will take part in an Outreach booth organized by MaizeGDB and host a computer demo.
Stefan Rensing has asked us to present a talk on expanding the PO to include bryophytes, as part of a non-seed plant workshop (Saturday, Jan 14, 3:50-6PM). LC will give this presentation.
Who is attending: LC, PJ (weekend), maybe JP, JE?
Phenotype RCN meeting, 23-25 February 2012
The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.
It will be held again at NESCent (Durham, NC).
RW has a friend there she can stay with and is interested in going.
5th International Biocuration Conference
April 2-4, 2012, Washington DC
Call for abstracts is now open: Need to clarify the deadlines
There are three submission categories for abstracts:
1. Talk or Poster (with consideration for oral presentation)
2. Poster only
3. Workshop only
• Submission deadline November 30, 2011
• Notification of acceptance February 3, 2012
There are seven topic sessions from which submitters are invited to select:
1. Ontologies, standards and best practices, including gold standard datasets. 2. Protein annotation; sequences, structures and pathways. 3. Community annotation and Wikis. 4. Genomics and metagenomics data curation. 5. High throughput proteomics data (focus on NGS and MS data) curation and presentation. 6. Literature collection, text mining and curation. 7. Tools to assist curation, including automated pipelines.
There are four submission tracks:
1. Paper, with consideration for oral presentation 2. Talk 3. Workshop 4. Poster
PJ planning to attend and will be running a biocuration workshop, LC and RW can go, DWS will be away,
'From 9-27-11: PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide.
Annual meeting of the Society for the Preservation of Natural History Collections
Yale University New Haven Connecticut June 11-16, 2012
Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).
The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).
From PJ: If we can show progress in the FNA work or Morphobank yes we should
Botany 2012
July 7 - 11, 2012 - Columbus, Ohio
Call for Symposia, Colloquia and Workshops:
Submission site now open. Deadline for submissions is Saturday, October 15th, 2011 at 11:59 PM PST.
RW, DWS and MAG will put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes. RW will put the draft plant PATO on the SVN.
- We need to have a section sponsor for the workshop proposal, DWS suggested the structural section (Head: Bruce Kirchoff), paleo section or systematists. Development and structural, genetics, and teaching sections would also be appropriate co-sponsors.
From meeting website:
When you submit your proposal, you will be asked for the following information:
- What Societies and Sections will be sponsoring the session. Please provide contact information for any persons who have approved the sponsorship
- The societies participating in Botany 2012 of which you are a member
- The names, email and street addresses of the organizers, and which of them will lead the session
- A title and description of the session
- Keywords and web links that are relevant
- Requirements, such as room type, food, special equipment or transportation, depending on the type of proposal
- An estimate of anticipated attendance
- A list of invited speakers or leaders, if relevant.
Proposal was submitted last week.
We should also consider having JP present on the new annotation wiki at this meeting.
We should also consider hosting an outreach booth.
Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)
• 2 months of Rotating Banner Ads in the online American Journal of Botany
• A Rotating Banner Ad in one edition of the online Plant Science Bulletin
• A Rotating Banner Ad on the Botany 2012 abstract submission site
• A Rotating Banner Ad on the 2012 Conference Registration site.
PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.
Annotation wiki
JP can also present a talk (maybe genomics section)
Sematic web conference focused on life science
JP will attend this meeting in December. Folks such as TW from NCBO will be there.
Will put more notes on next meeting agenda.
ICBO 2012
International Conference on Biomedical Ontologies (ICBO 2012)
co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)
22-25 July 2012; Graz, Austria.
Conference Web site: http://purl.bioontology.org/ICBO/
We also have the opportunity to organize an anatomy workshop as well along with CM and MH- need to decide about this soon
BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts.
Could also consider organizing a phenotype ontology workshop.
Relevant dates
31 December 2011: Workshop and tutorial proposal submission deadline
25 January 2012: Notification of acceptance of workshops and tutorials
31 January 2012: Paper submission deadline
28 February 2012: Notification of paper acceptance
15 March 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
15 April 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
30 June 2012: Deadline for all camera-ready copies for the proceedings
We have until Jan. 31 to submit a paper. Do we want to try to prepare a manuscript for this?
Possible topics: finding commonality in development stages across the plant kingdom (revisions of PGDSO), plant phenotypes in ontologies, community driven annotation efforts (new application from JP and others), others?
BS would like to collaborate on a preliminary paper on Plant Disease Ontology if anyone is interested.
Next Reg Tues meeting scheduled for Tuesday, Nov. 1, 2011 at 10am PDT/1pm EDT
No meeting on 10/25/2011.
