POC Conf. Call 6-11-13

POC meeting, Webex Conference Call; Date: Tuesday June 11th, 2013 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell), Laura Moore (OSU)

Absent: Barry Smith

New Look to the SourceForge Tracker

• Differences we have noticed so far:
  • Emails that come to your mailbox appear to be coming directly from the submitter, with a SF address and contain the original post below, but not all the other comments. You may have to adjust your filter settings: e.g. lauramooray@users.sf.net

• • On the tracker site, topics in the trackers are now oldest to newest at the bottom. Scroll down to see the most recent and add a comment.

• • No easy way to get back to the main page now, (that we have found)

• • New feature- sort by last updated, (but not sure if this is working correctly)

• • For the average users, it should not be too different

• • If you are opening new trackers the groups are now called "milestones"

• • You can now reply to (and follow) specific comments

• • We are sorting out a few administrative details such as how to reopen or close and assign trackers. It appears that the user permissions have changed. Currently LC is a developer- probably should be an admin in order to manage trackers. Need to add Brian as developer.

• • Currently, we cannot make links to new SF trackers in the browser, JE and LC are working on how to do it

• • It looks like all trackers can be commented on, even if they are closed. (no longer has "close for comments" check box)

• • If cROP goes forward, we may want to move all our trackers to a common platform that we have more control over?

Request from GO: make protoxylem and metaxylem part_of xylem rather than is_a xylem?

Text from TB on SF:

"While trying to align the GO terms for xylem/metaxylem/protoxylem development with the PO, we encountered a difference which we hope to clarify."

(copying Chris M's summary of the situation)

When GO talks of xylem development, it means development of the 4D entirety, meaning a developmental partonomy for the parts of the xylem:

• GO:0010089 ! xylem development: The formation of the principal water-conducting tissue of a vascular plant.

<-- part_of GO:0090058 ! metaxylem development: The process whose specific outcome is the progression of the metaxylem over time, from its formation to the mature structure. The metaxylem is the part of the primary xylem that differentiates after the protoxylem and before the secondary xylem, if any of the latter is formed.

<--- part_of GO:0090059 ! protoxylem development [DEF: "The process whose specific outcome is the progression of the protoxylem over time, from its formation to the mature structure. The protoxylem comprises the first formed elements of the primary xylem.

In PO, represents these structures in a subclass hierarchy:

PO:0009007 ! portion of plant tissue: A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types.

<-- is_a PO:0009015 ! portion of vascular tissue: "A portion of plant tissue (PO:0009007) that has as parts tracheary elements (PO:0000290) or sieve elements (PO:0025406).

<-- is_a PO:0005352 ! xylem: "A portion of vascular tissue (PO:0009015) that has as parts tracheary elements (PO:0000290).

<-- is_a PO:0005849 ! primary xylem: "A portion of xylem (PO:0005352) tissue that develops from the procambium (PO:0025275).

<-- is_a PO:0000272 ! protoxylem: A portion of primary xylem (PO:0005849) tissue that has as parts tracheary elements (PO:0000290) with only annular or helical secondary wall thickening that are the first formed tracheary elements (PO:0000290) at a particular location."

<-- is_a PO:0000372 ! metaxylem: A portion of primary xylem (PO:0005849) tissue that develops after the vascular tissue (PO:0009015) has stopped elongating and after the protoxylem (PO:0000272).

This gives us an inferred subclass hierarchy for development.

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Summary: GO = inferred part_of relationship between protoxylem/metaxylem and xylem, PO = is_a relationship between protoxylem/metaxylem and (primary) xylem

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Could the relationship between (protoxylem and metaxylem) and primary xylem be part_of instead of is_a?

Keeping the is_a relationship between primary xylem and metaxylem/protoxylem. Revising the definition for both terms to encompass the new metaxylem/protozylem tracheary element terms. We will have to ask GO to charge their hierarchy to match the PO.

Proposed Solution:

• Made protoxylem and metaxylem children of portion of vascular tissue and part_of primary xylem- this was rejected
• Could not make primary xylem tracheary element part of the protoxylem and metaxylem, created a cycle, so we created two new terms to describe the tracheary elements in the primary xylem this is ok, accepted
• Revised the definitions of protoxylem and metaxylem- incorporating the reference to the new terms this is ok, accepted

Link to tracker: primary xylem tracheary element terms:

Revised primary Xylem heirarchy

We decided to change the part_of relationship between protoxylem/metaxylem and primary xylem back to is_a and delete the is_a relation between protoxylem/metaxylem and portion of vascular tissue to avoid a loop.

Revised definition of metaxylem and protoxylem:

• metaxylem (PO:0000372): A primary xylem (PO:0005849) tissue that has as part metaxylem tracheary elements (PO:0025576) embedded in parenchyma (PO:0005421) tissue, may contain xylem fiber cells (PO:0000274) and develops after elongation has completed.

Comment: Metaxylem develops after the protoxylem (PO:0000272) and has larger elements than the protoxylem.

• protoxylem (PO:0000272): A primary xylem (PO:0000272) tissue that has as part protoxylem tracheary elements (PO:0025575) embedded in parenchyma (PO:0005421) tissue.

Comment: Develops while the vascular tissue (PO:0009015) is still elongating. When protoxylem tracheary elements (PO:0025575) are destroyed they may become obliterated by surrounding parenchyma cells (PO:0000074). Protoxylem has smaller elements than the metaxylem (PO:0000372).

• primary xylem tracheary element (PO:0025444): A tracheary element (PO:0000290) that is part of a primary xylem tissue (PO:0005849).

• • protoxylem tracheary element (new PO:0025575): A primary xylem tracheary element (PO:0025444) with predominately annular or helical secondary wall thickening that are the first formed tracheary elements (PO:0000290) at a particular location.

Comment: In a given portion of primary xylem (PO:0005849), protoxylem tracheary elements are generally smaller in size, fewer in number and have less secondary wall material than metaxylem tracheary elements (PO:0025576).

• • metaxylem tracheary element (new PO:0025576): A primary xylem tracheary element (PO:0025444) that may have helical, scalariform, reticulate and/or pitted secondary wall thickening.

Comment:In a given portion of primary xylem (PO:0005849), metaxylem tracheary elements are generally larger in size, greater in number and have more secondary wall material than protoxylem tracheary elements (PO:0025575).

Created new metaxylem/protoxylem tracheary element terms (see above) as children of primary xylem tracheary element. Made part_of relations between protoxylem tracheary element (PO:0025575) and protoxylem (PO:0000272); and between metaxylem tracheary element (PO:0025576) and metaxylem (PO:0000372).

See also notes on POC_Conf._Call_4-23-13, additional children of protoxylem added recently. These are not affected

Issues: * xylem vessel PO:0025417: A portion of xylem (PO:0005352) tissue that has as parts a tube-like series of vessel members (PO:0002003), the common walls of which have perforations.

This sound probably be handled in a similar way- make it a portion of vascular tissue, part of xylem.

We decided that this term can stay where it is, since the protoxylem and metaxylem are remaining

Other Items for discussion

- please see the Items_for_future_meetings page, will be moved here before the meeting

Upcoming meetings and Presentations 2013:

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