POC Conf. Call 2-26-13

POC meeting, Webex Conference Call; Date: Tuesday Feb 26th, 2013 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Dennis W Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU).

Absent: Pankaj Jaiswal (OSU)

Shoot system development stage and child terms

See the POC Conf call (2-19-13) for notes on the revision to shoot system

Current def'n:

shoot system development stage (PO:0025527): A plant structure development stage (PO:0009012) that begins with the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.

shoot system development stage has_participant shoot system (PO:0009006)

Revised def'n: A collective plant organ structure development stage (PO:0025338) that begins with the onset of the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (PO:0007017) or death.

Added "begins with the onset of" and corrected the parent name in the definition. Should this also be "ends with 'the onset of' either..."?

We had a fairly extensive discussion about the two collective plant structure terms:

BS: It would be good to add a comment to clarify the meaning of the two collective plant structure terms. e.g. "A CPOS is a collection of plant organs (a multi-organ structure). Could also add this as a synonym.

LC: I suggested we could add clarity by dropping the word "structure" from the names and it would not change the meanings. Also we would avoid adding a new, undefined word to the ontology. I am not sure that 'multi-organ structure' adds clarity to the meaning.

* collective plant organ structure (PO:0025007): A collective plant structure (PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacent plant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).

Propose revising the comment by adding this at the beginning: A CPOS is a collection of two or more plant organs (a multi-organ structure).

* collective organ part structure (PO:0025269): A collective plant structure (PO:0025497) composed of two or more cardinal organ parts (PO:0025001) that are part of adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007)

Propose revising the comment by adding this at the beginning: A COPS is a collection of two or more cardinal organ parts (PO:0025001) that are part of adjacent plant organs (PO:0009008). But this is basically just restating the def'n, not sure it helps much.

plant organ development stage (PO:0025339)

• plant organ development stage (PO:0025339)- made part_of shoot system development stage, cannot be is_a as it also covers root development.

Current def'n: plant organ development stage (PO:0025339): A plant structure development stage that has as participant a plant organ.

Comment: Includes development stages for leaves and roots.

Propose revised def'n: plant organ development stage (PO:0025339): A multi-tissue plant structure development stage (new PO:id) that begins when the shoot apical meristem initiates plant organ primordia.

Comments- first stage in the development of all the types of shoot systems and bud development. The SAM meristem transitions to a developing shoot system by forming organ primordia.

Tsiantis, M. and Hay, A., (2003) Comparative plant development: the time of the leaf? Nat Rev Genet, 4(3), 169–180. Available at: http://dx.doi.org/10.1038/nrg1002. See link to article

bud development stage and child terms

• bud development stage (new PO:0025528): A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006).

added relations: bud (PO:0009006) participates_in bud development stage (PO:0025528).

Propose revised def'n: A shoot system development stage (PO:0025527) that begins with the onset of the organ development stage (PO:0025339) and ends with the beginning of bud burst stage (PO:id).

develops_from a portion of meristem tissue, more specific types of buds

-moved to new tracker

• bud dormancy stage (new PO:0025529):

proposed def'n: A bud development stage (PO:0025528) during which a bud (PO:0009006) participates in a bud dormancy process (GO:0097207)

bud dormancy process GO:0097207

Definition: A dormancy process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a bud. Bud dormancy is a suspension of most physiological activity and growth that can be reactivated. It may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. The exit from bud dormancy is marked by the resumed growth of the bud.

Source: GOC:PO_curators, PO_REF:00009 Comment: Bud dormancy may precede dormancy of the whole plant.

Then we added:

• bud swell stage (new PO:0025531)

Definition: A bud development stage (PO:0025528) during which a bud (PO:0009006) enlarges due to growth of the shoot system (PO:0009006).

Synonyms: exact: E-L 2

• bud burst stage (new PO:0025532):

A shoot system development stage (PO:0025527) during which a shoot system (PO:0009006) emerges from the bud (PO:0009006). Synonyms: exact: E-L 4

Agreement that the bud burst stage is_a shoot system development stage, even though it is much shorter than the two stages. In fact, it could almost be considered as a landmark of the transition from bud to shoot, but we have gene expression data annotated to it, so we will keep it as a separate stage.

The covering of the bud is the bud scale leaf (PO:0020054).

reproductive shoot system development stage (new PO:0025530)

Proposed def'n: A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).

add relation: reproductive shoot system (PO:0025082) participates_in reproductive shoot system development stage (PO:0025530).

flower development stage (PO:0007615)

flower development stage (PO:0007615): A reproductive shoot system development stage (PO:0025530) that has as primary participant a flower (PO:0009046).

already has a cross product flower is participant, needs to be revised for the new parent term.

A reproductive shoot system development stage (PO:0025530) that begins when the SAM transitions from vegetative to becoming a floral primordium. This is part of the reproductive bud development stages, generally determinate.

add p/i relations from repro SAM to repro ss dev stage

inflorescence development stage (PO:0001083)

inflorescence development stage (PO:0001083) current def'n: A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).

added relation: inflorescence (PO:0009049) participates_in reproductive shoot system development stage (PO:0025530)

All have DbxRef to OBO_SF_PO: 3595703

Should add the relation inflorescence development stage has_part flower development stage

Upcoming meetings and Presentations 2013:

Biocuration 2013 conference, Cambridge, 7-10th April 2013

submission deadline for abstracts for posters is Jan 31st.

website and registration are now open: Biocuration 2013

NCBO Hackathon April 29-30, 2013

The NCBO Hackathon will take place at Stanford University on April 29-30, 2013. This event will focus on projects in biomedical or clinical informatics that can benefit from use of ontology-based technology.

The entire NCBO Team will be available to brainstorm application ideas and to answer development questions. We will also have separate sessions to provide training on the NCBO Web services, the BioPortal SPARQL endpoint, and other topics of interest requested by participants.

If you are thinking of incorporating semantics into your software application, the Hackathon will provide a great opportunity to get a head start on your project.

Register soon at the link below to hold your spot!

PRO-PO-GO meeting, May 15-16th 2013

Please see this page for more information: PRO-PO-GO_Meeting

Location: Buffalo, NY

Dates: May 15-16th, 2013.

Goals:

1. To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
2. To identify potentially fruitful applications which such enhanced coordination might bring
3. To enhance the Protein Ontology treatment of plant-related proteins
4. To address coordination issues between the GO and PO, for example as concerns treatment of development stages
5. To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]

Tentative participant list:

PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?

GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?

PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)

1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013

S4BIODIV

Registration Information ESWC 2013

Early Registration deadline March 17th

Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.

Held in parallel with the 10th Extended Semantic Web Conference (ESWC 2013)

Workshop date: May 27, 2013

IMPORTANT DATES:

• Pre-submission inquiry deadline: February 24, 2013 (Abstract up to 500 words)
• Submission Deadline: March 4, 2013
• Notification: April 1, 2013
• Camera ready: April 15, 2013

Note: May be able to send abstract on March 11th and then the final paper by April 15th

TOPICS:

Scientific themes of interest (include but are not limited to):

• sustainable agriculture
• plant
• health and habitat
• relationship between plant-pests/pathogens
• usages of plants by community
• biodiversity conservation
• ecosystems services
• quality of biodiversity data

Informatics technologies of interest (include but are not limited to):

• ontology applications
• knowledge engineering
• linked biodiversity data
• remote sensors
• mobile devices
• vizualization tools
• data mining

MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)

The New York Botanical Garden & Fordham University

ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013

4th International Conference on Biomedical Ontologies 2013 (ICBO2013)

Concordia University, Montreal, Quebec, July 7th - 9th 2013 call for papers

The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.

The event is part of the Semantic Trilogy 2013 featuring:

• International Conference on Biomedical Ontologies (ICBO 2013)
• Canadian Semantic Web Symposium (CSWS 2013)
• Data Integration in the Life Sciences (DILS 2013)

Botanical Society Meeting July 27-31st New Orleans

BSA 2013

- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract