POC Conf. Call 2-21-12

POC meeting, Webex Conference Call; Date: Tuesday Feb 21st, 2012 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Pankaj Jaiswal (OSU)

Absent: Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_2-14-12?

Back to POC Meetings Minutes

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=62529057&rKey=d65262dbec210e7b

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=62529057&rKey=e11a869c8a99a04e

Follow up from the Wood Ontology Meeting:

• Link to the Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda#10:40AM-11:20PM_Wrap_up

This was discussed briefly on the POC_Conf._Call_2-14-12

* Question: How do we want to approach the TO terms, since this is a complex area and officially outside the mandate of the PO?

Where does this fit into our list of top priorities??

PJ: The TO will be moving into the domain of the PO, so it is important to continue developing this for the wood community. LC will take the lead on organizing and directing this effort.

LC has updated the notes on the TO and PATO discussion: Goal_3._Wood_qualities_and_phenotypes, adding links to references and and list of questions and tasks to proceed with.

* RW will assist adding the needed terms discussed at the meeting to GO - should be referenced to the PO

* Question: How do we want to proceed with the IAWA short publication and more extensive paper later.

At the Workshop, we decided FL would take the lead in sending a short announcement of the Wood Ontology Meeting for IAWA Journal. Pieter Baas, editor-in-chief of IAWA Journal, was 'really excited' about the content of this short text and suggested that with minor adjustments (e.g., maybe adding few sentences, some key references and a general scheme), this short text could be published as a mini paper. This should still be a meeting report, rather than an short paper. Want to be able a cite it. Needs a paragraph describing the Plant (and Trait) Ontology, what was discussed at the meeting, what is available for the wood science community, focus on trees in general, feedstock for biofuels, cite the PO papers.

We will remove the reference to the plant cell- GO example, and replace it with a more wood-oriented example. eg sieve tube elements, part of phloem

People will be directed to the feedback link on the website to make inquiries.

Suggested title: "Plant Ontology Embraces Tree Species"'

For the future renewal: "Ontologies for Plant Biology": all hosted under our umbrella: PO, TO, GO, Plant PATO and Plant Disease Ontology

- may be able to use web services, but limited by AmiGO at this time

• Need to look at "tension wood, immature xylem, immature phloem"- is this an anatomical structure or a trait?

Tension wood is the reaction wood of angiosperms, develops on the upper side of leaning trunks or limbs. (Raven et al., 5th edition)

Eucalyptus annotations are being developed and they measured the tensile strength of the wood. This is definitely a trait

PJ will get more information regarding how the gene expression analysis was done and send it out so we can assist with the mapping to the PO terms.

~24 minutes

Revisions of existing terms:

Summary of changes to lateral meristems from last week

lateral meristem (PO:0020145)

revised def.: A portion of meristem (PO:0009013) tissue located parallel to the sides of a plant axis (PO:0025004), the cells of which undergo periclinal and anticlinal division as part of lateral growth.

New comment: Participates in lateral growth (request has been made for lateral growth in GO) of a shoot axis (PO:0025029) or root (PO:0009005), leading to an increase in the cross-sectional area. Contrast with apical meristem (PO:0020144) or intercalary meristem (PO:0006073).

intercalary meristem (PO:0006073)

Current def.: A shoot meristem separated from the apical meristem in the primary body by more or less mature tissues.

Current definition is okay, but we nee to distinguish it from lateral meristem.

Proposed def.: A shoot meristem (PO:0006079) that is separated from an apical meristem (PO:0020144) by more or less mature tissues, the cells of which undergo (longitudinal?) division as part of primary growth.

cambium (PO:0005597)

Definition was okay with minor changes.

vascular cambium (PO:0005598)

Definition was okay.

New comment: A vascular cambium produces cells in both directions by periclinal division, leading to an increase in the cross-sectional area of a plant axis (PO:0025004).

cork cambium/phellogen (PO:0005599)

Definition was okay. Phellogen was changed from related synonym to exact synonym.

primary thickening meristem (PO:0005039)

Definition was okay. Added synonyms: PTM, meristematic cap, and collar meristem.

secondary thickening meristem (new term)

revised def. A lateral meristem (PO:0020145) that is not contiguous with the shoot apical meristem (PO:0020148) and has a parts multiple layers of meristematic cells (PO:0004010).

comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042) and may also be found in the roots (PO:0009005) of some species. May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.

Added Cheadle 1937, JSTOR:2471543 as definition dbxref.

root lateral meristem (PO:0006308)

revised def.: A lateral meristem (PO:0020145) that is part of a root (PO:0009005).

Comment: Not to be confused with lateral root apical meristem (PO:0006020), which is an apical meristem (PO:0020144) of a lateral root (PO:0020121).

Set up root lateral meristem as XP, so we don't have multiple inheritance.

This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.

shoot lateral meristem (PO:0006344)

revised def.: A lateral meristem (PO:0020145) that is part of a shoot axis (PO:0025029).

Set up shoot lateral meristem as an xp, so subtypes and be inferred, just like root lateral meristem.

There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.

new terms

shoot axis cork cambium (PO:0025435): A cork cambium (PO:0005599) that is part of a shoot axis (PO:0025029).

root cork cambium (PO:0025436): A cork cambium (PO:0005599) that is part of a root (PO:0009005).

shoot axis vascular cambium (PO:0025437): A vascular cambium (PO:0005598) that is part of a shoot axis (PO:0025029).

root vascular cambium (PO:0025438): A cork cambium (PO:0005599) that is part of a root (PO:0009005).

cambial zone, proposed def.: A cardinal organ part that is part of a shoot axis and has as parts a cambium and adjacent cells.

Comment: This term is used for the cambium and surrounding area, especially the borders of the cambium are not clear.

inflorescence meristems

inflorescence branch meristem (PO:0009105)

Was inflorescence lateral meristem.

revised def: An inflorescence meristem (PO:0009108) that gives rise to an inflorescence branch (PO:0009081).

ear inflorescence branch meristem (PO:0009110)

Was ear lateral meristem.

revised def.: An inflorescence branch meristem (PO:0009105) that gives rise to a branch of an ear inflorescence (PO:0020136).

tassel branch meristem (PO:0009107)

Was tassel lateral meristem.

revised def.: An inflorescence branch meristem (PO:0009105) that gives rise to the long lateral tassel branch (PO:0009101), short tassel branch (PO:0009102), and tassel spikelets (PO:0006309) in a tassel inflorescence (PO:0020126).

There are a lot of other changes needed to inflorescence meristems. Rife with multiple inheritance, which could be fixed with cross products.

vascular and related cell types

Current parent: axial cell

axial cell

axial cell (PO:0000081): A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208] Comment: These cells make up the axial system, also known as vertical or longitudinal system.

The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).

Suggest that we obsolete this term, replace with new terms for axial system and radial system (see Items for future meetings#other wood terms)

New proposed hierarchy (children of plant cell):

plant cell

>sieve element (new term)

>>sieve tube member (syn.: sieve tube element)

>>sieve cell (new term)

>tracheary element

>>tracheid

>>vessel member

>ground tissue cell (PO:0025030)

>>sclerenchyma cell (PO:0000077)

>>>sclerid (new term)

>>>fiber cell (new term)

>>>>phloem fiber cell

>>>>xylem fiber cell

New definitions - sieve elements

Definitions from Esau's Anatomy of Seed Plants

sieve element (new term)

proposed def.: A plant cell that is part of a portion of phloem tissue, has sieve areas in its walls, and lacks a nucleus in its mature protoplast.

Comment: Sieve cells function mainly in longitudinal conduction of organic solutes. Classified into sieve cells and sieve tube members based on the presence of sieve plates and specialization of sieve areas in different parts of the cell. Develops from either a cambial initial or a cell of the procambium.

part_of phloem, participates_in sporophyte stage

sieve cell (new term)

proposed def.: A sieve element in which the sieve areas are not aggregated into sieve plates.

Comment: Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants. Differ from sieve tube members, which have sieve plates and more pronounced specialization of sieve areas.

sieve tube member (PO:0000289)

proposed def.: A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.

Comment: Sieve tube members have sieve areas that are specialized into those with wide pores in sieve plates and those with with narrow pores in lateral sieve areas. Sieve tube members may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells, which have less pronounced specialization of sieve areas and no sieve plates.

syn.: sieve tube element, sieve tube segment

part_of sieve tube (new term)

See below for companion cells and other parenchyma cells found in vascular tissue.

New term for sieve tube

sieve tube, proposed definition: A portion of phloem tissue that has as parts a series of sieve tube members arranged end to end and interconnected through sieve plates.

Comment: A sieve plate (GO:0097218) is part of a sieve tube member.

New terms for GO

These subcellular components have been added to GO:

• GO:0097217 sieve area
• GO:0097218 sieve plate
• GO:0097219 compound sieve plate
• GO:0097220 simple sieve plate

New definitions - tracheary elements

These edits are done in the obo file.

xylem element (PO:0000273): A cell making up xylem tissue.

Currently, this is parent of tracheary element and xylem fiber. I suggest we obsolete it and make xylem fiber cell a child of fiber cell. Xylem element could be a broad synonym of tracheary element and xylem fiber. (still need to add this)

tracheary element (PO:0000290)

Currently is part_of primary xylem and part_of secondary xylem. Changed to part_of xylem.

proposed def.: A plant cell (PO:0009002O) that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.

comment: More or less elongated and with pits of various types in the cell wall. Tracheary elements function in the conduction of water and dissolved substances such as mineral nutrients from the roots to the shoot system. Tracheary elements can be distinguished from fiber cells (PO:0025407) by the presence of bordered pits, although there are intermediate forms called fiber tracheids (PO:0000355).

participates_in sporophyte stage, part_of xylem, disjoint from hydroid

tracheid (PO:0000301)

proposed def.: A tracheary element (PO:0000290) that has no perforations in its cell wall.

comment: May have any of the kinds of secondary wall thickenings found in tracheary elements. The area of contact between two tracheids has only bordered pits, whereas in vessel members (PO:0002003) it has openings in the cell wall called perforations, organized into perforation plates (term has been requested in GO).

vessel member (PO:0002003)

proposed def.: A tracheary element (PO:0000290) that is part of a vessel (PO:0025417) and has as parts perforation plates.

Comment: The cell wall of a vessel member has openings called perforations, which are organized into perforation plates (term has been requested in GO). These are usually on the end walls of a cell, but may also be on the side walls. A perforation plate may be simple, with one perforation, or multiperforate, with more than one perforation.

syn.: vessel element, vessel segment

part_of vessel (new term)

vessel (PO:0025417)

proposed def.: 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.

perforation plate (for GO)

proposed def.: A cell wall part that is the part of a wall of a vessel member and bears one or more openings (perforations).

comment: Part of a vessel member (PO:0002003). May be simple, with one perforation, or multiperforate, with more than one perforation. Perforation plates are usually on the end walls of a cell, but may also be on the side walls.

Reference ISBN:0471245194 (Esau's Anatomy of Seed Plants).

New definitions - ground tissue cells

sclerenchyma cells

These edits are done in the obo file.

sclerenchyma cell (PO:0000077)

proposed def.: A ground tissue cell (PO:0025030) with thickened secondary cell walls that are lignified.

comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from tracheary elements (PO:0000290) or sclerified parenchyma cells (PO:0000074). Distinguishable from collenchyma cells (PO:0000075) because collenchyma cells are alive at maturity. Collenchyma cells provides flexibility while sclerenchyma cells provide hardness.

Currently, sclerenchyma cell part_of sclerenchyma, but this is not always true. There can be isolated sclerenchyma cells.

sclerid (PO:0025418)

proposed def.: A sclerenchyma cell (PO:0000077) that has thick secondary walls with many pits.

comment: Usually not very elongated.

parenchyma cells in phloem tissue

These edits are done in the obo file.

companion cell (PO:0000071)

proposed definition: A parenchyma cell (PO:0000074) that is adjacent to a sieve-tube member (PO:0000289) and arises from the same initial cell (PO:0004011) as the sieve-tube member.

comment: Found in angiosperms. Compare to albuminous cells (PO:0025412), which are found in gymnosperms.

Maybe add comment that it is connected to a sieve element through numerous plasmodesmata and aids in phloem loading.

Currently part_of primary phloem and part_of secondary phloem, which can't be true. Changed to part_of phloem.

Added relation companion cell adjacent_to sieve tube member.

Need to look at definition of phloem mother cell. Does it only differentiate into secondary phloem, or can it be for primary phloem too?

Do we want to add a separate term for "intermediary cell", the type of companion cell found in apoplastic loaders? See, for example Amiard et al..

albuminous cell (new term)

proposed def.: A parenchyma cell (PO:0000074) that is morphologically and physiologically associated with a sieve cell (PO:0025415) but does is not derived from the same initial cell (PO:0004011) as the sieve cell.

comment: May be found in the ray system (PO:0025411) and sometimes the axial system (PO:0025410) of gymnosperms. Compare to companion cells (PO:0000071), which are found in angiosperms.

is_a parenchyma cell, part_of phloem, adjacent_to sieve cell.

fiber cells

These edits are done in the obo file.

Need to add exact synonyms to all of these that don't have the word "cell", e.g., fiber for fiber cell.

fiber cell (new term, PO:0025407)

proposed def.: An elongated, tapering schlerenchyma cell (PO:0000077) with a more or less thick secondary cell wall.

comment: May or may not have lignin in the secondary wall or a living protoplast at maturity. It may be difficult to distinguish fiber cells from tracheary elements (PO:0000290).

phloem fiber cell (PO:0004519) (was called phloem fiber)

proposed def.: A fiber cell (PO:0025407) that is part of a portion of phloem (PO:0005417) tissue.

Made part_of phloem, instead of part_of secondary phloem.

xylem fiber cell (PO:0000274) (was called xylem fiber)

proposed def.: A fiber cell (PO:0025407) that is part of a portion of xylem (PO:0005352) tissue.

comment: It may be difficult to distinguish xylem fiber cells from tracheary elements (PO:0000290).

Made part_of xylem, instead of part_of secondary xylem.

libriform fiber cell (PO:0004520)

proposed def.: A xylem fiber cell (PO:0000274) with simple pits.

Comment: Libriform fiber cells have unbordered pits while fiber tracheids (PO:0000355) have bordered pits. Many intermediate forms exists and are generally classified as fiber tracheids. If both libriform fiber cells and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Libriform fiber cells have a slit-like aperture toward the cell lumen, but no pit cavity.

fiber tracheid (PO:0000355)

proposed definition: A xylem fiber cell (PO:0000274) with bordered pits with pit cavities.

comment: Commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures. If both libriform fiber cells (PO:0004520) and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessel members (PO:0002003) or tracheids (PO:0000301) of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.

septate fiber (PO:0004521)

current def.: A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.

Septate fibers can be found in both the xylem and the phloem. PO:0004521 is_a xylem fiber, but both tracheid-type and libriform-type xylem fibers can be septate. There are no annotations on this term, so I suggest we obsolete it, and replace it with two new terms: septate fiber tracheid and septate libriform fiber. Could also add septate phloem fiber, is_a phloem fiber.

proposed definition, septate fiber tracheid: A fiber tracheid (PO:0000355) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

proposed definition, septate libriform fiber cell: A libriform fiber cell (PO:0004520) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

proposed definition, septate phloem fiber cell: A phloem fiber cell (PO:0004519) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

other kinds of fiber cells

gelatinous fiber cell (new term, PO:0025422): A xylem fiber cell (PO:0000274) in which the inner-most layer of the secondary wall contains abundant alpha-cellulose and is poor in lignin.

comment: Commonly found in reaction wood in dicots. The inner layer of the cell wall, or G-layer, can absorb much water and swell and is relatively porous and less compact than the outer layers of the cell wall.

ref: Fahn

synonym: mucilaginous fiber cell

Next PO Release:

In October, we had planned the next release for Feb 2012:

POC_Conf._Call_10-18-11#Next_PO_Release

We will aim for the second week of March- would be great to have it done for the presentation at the Maize Genetics Meeting, March 16th.

Goals and Priorities:

• First major Revisions of PSDS (formerly PGDSO):

Status to 1-30-11: This needs to be updated...

-22 new terms added, many existing terms have been modified, eg changed all the 'phase' names to 'stage'

All terms PSDS terms names are now singular. Some still need to have "stage" appended.

-most of the recent work has been on the whole plant development stage (PO:0007033) and its children

-Wood development stages were started at the NYBG Workshop

• Complete old user requests/SF tracker items:

- This is an ongoing process, we have added about 50 new PAE terms recently

• New association files: Physcomitrella (released Jan 2012), small set of cotton annotations (TBA Feb 2012)

• Glossary of PO terms (see PO Glossary on dev)

This was discussed at the RCN meetings 2011, plan is to eventually replace APWeb Glossary. 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.

what is the status of this?

Other Items

• from POC_Conf._Call_10-18-11

• 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 - Update?

Wood development stages

See: SF tracker

Translations

Will need to update translations for PAE terms before release. Can JE generate a file (after we stop editing) that includes all terms without Spanish or Japanese translations?

Collaborative projects:

• Mapping of Flora of North America Glossary to PO terms:

We now have id's for FNA terms. Can finish adding synonyms before this release. Still need to add new terms from the FNA list and create mapping file.

Are we okay with using these FNA ids? They are UUID and are very long and contain dashes (e.g., 40b5fa5d-a75b-49d8-8328-b4c28d54ea66). See antheridium (PO:0025125) on dev browser for an example of how it will look.

Where did this synonym go?

RW is working on modifying a perl script from JE to insert FNA synonyms into the PO file. May needs some help from JE.

-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):

• Linking ontology terms to character matrices using Morphobank.

Upcoming meetings and Presentations 2012:

Phenotype RCN meeting, February 23rd-25th, 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).

This meeting will focus on bringing in new people and training them on how to develop and use anatomy ontologies. RW offered to help with the training.

The projects of the Plant Working Group that we started in CO will be worked on during the next meeting, in the fall.

RW will attend. Planning to talk with George Gkoutos re. plant quality terms and with Bruce Kirchoff re. images in ontologies.

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link

LC will present a short talk abstract Friday march 16th, 5:45pm

No PO-Gramene workshop is planned

Katherine Esau Research Symposium

Integrating Plant Structure with Function, Development and Evolution

Hosted by the Katherine Esau Fellowship Program,

Date and location: Thursday, March 29, 2012, 1002 Giedt Hall, UC Davis

Space is limited and registration will close at 5 pm on March 10th.

LC contacted the organizer; Neelima Sinha (Sinha@ucdavis.edu) and she said a short presentation was a possibility and would be pleased if a couple of PO people could attend.

LC may be interested in attending if we can get a slot. Could also combine the visit with a follow up meeting with Jill Wegrzyn and Andrew Groover about the wood terms and data for the PO.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted and has been selected for a poster presentation.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• PJ is planning to attend, may do a talk. LC is planning to attend

The early bird registration ends this Friday, February 25.

SPNHC 2012

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:

RW, DWS and MAG 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.

Proposal was submitted, waiting for news.

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.

exhibitor's booth

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 may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

Three types of submissions.

- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page

Successful papers will be presented at the Bio-Ontologies SIG.

Poster abstracts: time will be allocated during the 2 days for at least one poster session.

Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Link to meeting page: ASPB2012

Abstract submission for minisymposia consideration ends March 2!

Joint workshop is planned with PO, Gramene and TAIR

Registration scheduled is open

Early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology.

Relevant dates

• Feb. 28th, 2012: Notification of paper acceptance
• March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
• June 30th 2012: Deadline for all camera-ready copies for the proceedings

RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts