POC Conf. Call 4-9-13

POC meeting, Webex Conference Call; Date: Tuesday April 9th, 2013 10am PST/1pm EST

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

Absent: none

tapetum cells follow-up

Needed for cross-product with GO terms: [GO tracker for tapetum cell and tapetum terms].

tapetal cell differentiation, GO:0048657

tapetal cell fate specification, GO:0010234

These are being renamed as we discussed and also the tapetal layer terms.

• New term: tapetum cell (PO:0025543): A plant cell (PO:0009002) that is part of the tapetum (PO:0025313).

exact synonym: tapetal cell; part_of tapetum, comment: The tapetum is the inner-most layer of a sporangium wall (PO:0025306).

• New term: microsporangium tapetum cell (PO:0025544): A tapetum cell (PO:0025543) that is part of a microsporangium tapetum (PO:0025314). part_of a microsporangium tapetum, exact synonym: tapetal cell

• New term: anther wall tapetum cell (PO:0025545): A microsporangium tapetum cell (PO:0025544) that is part of the anther wall tapetum (PO:0009071). part_of the anther wall tapetum; exact synonym: anther wall tapetal cell

We should we also add a term for the cells of the megasporangium tapetum; PO:0025315

• proposed new term: megasporangium tapetum cell (new PO:id): A tapetum cell (PO:0025543) that is part of a megasporangium tapetum (PO:0025315).

part_of the megasporangium tapetum; exact synonym: megasporangium tapetal cell

• tapetum (PO:0025313): A portion of ground tissue that is the inner-most layer of a sporangium wall
  • microsporangium tapetum (PO:0025314):
    • • anther wall tapetum; (PO:0009071): A microsporangium tapetum that is part of an anther wall.

Comment from BS: It is fine to use the 'X is a part of Y' phrase in the def'n as long as there are no other structures that are also part of it. In this case, we can define the tapetum cell as "A plant cell (PO:0009002) that is part of the tapetum (PO:0025313).", because there is only one type of cell in the tapetum, unlike a leaf."

Comment from DWS: two types of tapetum: ameboid and secretory/glandular:

link to book

Probably need to look at the corresponding stage terms:

• E tapetum degeneration initiated stage (PO:0001032): Stage during which degeneration of the tapetum is initiated, as the deposition on the surface of the microspore primexine proceeds.

This might be a good example to illustrate in Buffalo, but TB will not be there.

LC will put together a short write/slides "PO_GO Interoperability Use Cases" and send to BS, Judy Blake (Lomax?) etc

References:

• Regulation of Arabidopsis tapetum development and function by DYSFUNCTIONAL TAPETUM1 (DYT1) encoding a putative bHLH transcription factor.

Zhang etal, 2006 PMID:16831835

• The Arabidopsis U-box/ARM repeat E3 ligase AtPUB4 influences growth and degeneration of tapetal cells, and its mutation leads to conditional male sterility.

Wang et al, 2013 PMID:23398263

• The excess microsporocytes1 gene encodes a putative leucine-rich repeat receptor protein kinase that controls somatic and reproductive cell fates in the Arabidopsis anther.

Zhao et al, 2002 PMID:12154130

Niu N, Liang W, Yang X, Jin W, Wilson ZA, Hu J, Zhang D. 2013. EAT1 promotes tapetal cell death by regulating aspartic proteases during male reproductive development in rice. abstract Nat Commun 4, 1445.

xylem sap

Suggested Definition: The mixture of water and solutes existing in a xylem vessel

Parent/relationship: part_of xylem (PO:0005352)

proposed new parent term and def'n:

• plant sap (new PO:00255380): A portion of plant substance (PO:0025161) that is an aqueous solution which may contain sugars, hormones, mineral elements and/or other nutrients.

Comment: plant sap should not be confused with latex or resins.

Alternatives:

A portion of plant substance (PO:0025161) that is an aqueous solution, that can be transported through the apoplast or symplast. Use GO terms for the process terms

A portion of plant substance (PO:0025161) that is an aqueous solution, that participate in apoplastic transport (new GO term) or symplastic transport (new GO term).

Existing terms in GO:

apoplast (GO:0048046): The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.

This definition needs to be modified to be similar to the one for symplast. Lots of this should go in the comment.

symplast (GO:0055044): The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.

- all the plasma connected, through plasmodesmata, transport through the cytoplasm

See: Link to diagram Apoplast_and_symplast_pathways

See: Apoplastic versus Symplastic Pathways in roots

• Suggest revised GO definitions for apoplast and symplast and add transport terms

Parent term:

• transport (GO:0006810): The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.

• apoplastic transport (new GO term): A transport process (GO:id) that occurs in the apoplast (GO:0048046)

• symplastic transport (new GO term): A transport process (GO:id) that occurs in the symplast (GO:0055044)

comments: symplastic transport is a diffusion process

Comments: PJ:

• Sap is not just nutrition. It carries RNA, proteins and I am sure microbes as well. Much of the content is also used to maintain turgor and the pressure flow in xylem and phloem as well.

Capture that in a comment:

Suggested child terms:

• We will need to have a root xylem sap and shoot xylem sap as they are different. Please add 4 more terms to be more specific

The reason xylem/phloem sap contents from root and shoot may differ.

New term: xylem sap (new PO:0025539): A plant sap (PO:0025538) that is an aqueous solution which may contain mineral elements, nutrients, and plant hormones, and is transported from the root system (PO:0025025) toward the leaves through the tracheary elements (PO:0000290) of the xylem.

Transport of sap in xylem is characterized by movement from the roots toward the leaves.

New term: phloem sap (new PO:0025539): A plant sap (new PO:0025538) that is an aqueous solution which may contain sugars, mineral elements, and plant hormones, and is transported through the phloem sieve elements (PO:0025406).

• xylem sap (new PO:0025539)
  • shoot system xylem sap
  • shoot axis xylem add later if needed

• • root system xylem sap

• phloem sap (new PO:0025539):
  • shoot system phloem sap

• • root system phloem sap

Add reference to the sap in the definition or comment on sapwood

Upcoming meetings and Presentations 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.

Phenotype RCN Plant Group Meeting- Ames, Iowa April 30th-May 3rd

We will be meeting to work on the Plant Phenotype Pilot Project, LC is going

PR-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.

• 1. To inform members of the Protein, Plant, Gene Ontology communities of developments in each of these ontologies, and in related ontologies such as the CL (Cell), TO (Plant Trait), ENVO (Environment), PATO (Phenotype) and IDO-Plant (Plant Infectious Disease) ontologies. Specifically:

a. To enhance the PO treatment of plant-related proteins

b. To address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages

• 2. To contribute to the cROP (Common Reference Ontologies for Plants) initiative
• 3. To contribute to the ontological understanding of phenotype and disease in all model organisms.
• 4. To identify potentially fruitful applications which enhanced ontology coordination might bring.

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)

Need to share the PO with representatives from the ontologies and resources such as PRO, PIR (Claire O'Donovan), Uniprot. Annotations to newly sequenced plant genomes are going into Plant Ensemble, Uniprot etc. Want to build early relationship with them to develop quality measures for plant-based ontology annotations. Section on annotations is needed.

JB wanted to explore genotype and phenotype connections, can only stay for part of the day on Thursday

Need to know who will speak about what. Looking for volunteers.

Separate the sessions on disease and phenotype, include TO discussion to there?

RW presentation on Plant-IDO?, interest in new Plant DO, existing DO is no good (?), Split phenotype and diseases into separate sessions.

Reference ontologies need to know how to deal with terms that are used by both plants and animals, e.g. senesence.

Alert attendees to bring applications for the users, biological examples

Notices could be posted in advance of the meeting, send out on PO-announce, will do IBC article later. Idea for future meeting- plants, human nutrition, toxicity, to include more NIH type people

Travel to Amherst: Need to book our rooms, plan to fly out Thursday afternoon.

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)

Workshop on Semantic Systems Biology 2013 (SSB2013) will be held as part of the International Conference on Biomedical Ontologies (ICBO2013) at Concordia University, Montreal, Quebec, on July 7th, 2013. The event is part of the Semantic Trilogy 2013 (above)

Topics of interest include, but are not limited to:

• ontologies & terminologies for modeling computational biology
• ontologies & terminologies for simulation (and result data) in computational biology/medicine/neuroscience
• semantic web technologies for description, integration, query and discovery of models, simulations and result data
• semantic web technologies for biological data and analysis
• semantic annotations of bio-models
• applications of ontologies in computational systems biology/medicine/neuroscience
• semantic platforms for undertaking and visualizing simulation results

We welcome four types of submissions:

• short papers, up to 4 pages.
• long papers, up to 7 pages.
• position papers, up to 1 page.
• late breaking reports, up to 1 page.

See the ICBO website for further information on the submission types.

All submission are due on Monday, April 15 2013. Notification of acceptance: May 6th, 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