POC Conf. Call 9-27-11

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POC meeting, Webex Conference Call; Date: Tuesday Sept 27th, 2011 10am (PDT)

In attendance:

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

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

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_9-20-11? no additions, deletions, or changes


Tech Issues for the Upcoming Release

Adding Dbx Refs

JP, JE and LC met with Chris and Seth on 9-26-11

It appears that our version of AmiGO has a built-in set of db xrefs and it is not reading the current GO file.

We got the details on how to add dbxref to AmiGO. The code that needs to be changed is not in svn, so will have to be done manually by JE (or JP). Just need to know what the url syntax is to be used for each, such as OBO_SF_PO.

Since we are using the old version of SVN, the DBxrefs reside in Perl file as part of AmiGO. In order to update these, this file has to be edited. We will use the PO_DBXref.txt file to store the updated dbxrefs stanzas. It is on the SVN already. The new Amigo will read the syntax of this file.

The OB_SF_PO (used to link to SF trackers) link is currently in the PO_DBXref.txt file on SVN. Will correct text for broken Gramene links and fix MaizeGDB abbreviation.

LC: after the meeting: Do we really need to have this file PO_DBXref.txt on our website, since it is just for our internal use?

Other Issues discussed:

  • Column 6: DB:Reference

Also, with the current version of the code, it is impossible to have multiple references for a single association. Whichever one is last in column 6 in the assoc file will be displayed. A workaround would be to split on multiple lines, but this is less than ideal.

We should add a note to this effect on the page for the curators. We would prefer this to be the pubmed id if possible, but in cases, such as with the MaizeGDB annotations, using the MaizeGDB:9021432 provides links to the tissue pages and the PubMed link as well.

  • "Associated to" column in our browser display:

This is not part of the original AmiGO coding and was presumably added by Shuly in order to link to the GO associations.

Links back to GO, may look at hosting the GO data. The Justins are working tracing down the code responsible for this linking.

See resolution at: "Associated_to"_links

for MaizeGDB

See notes from the Follow_up_meeting_re:_Association_files_for_the_Kaeppler_data_set_Sept_15,_2011

We can use one database abbreviation to access all MaizeGDB pages. It uses their url for anything with a MaizeGDB id, but also works for gene model names.

File format (modified from http://www.geneontology.org/cgi-bin/xrefs.cgi - changed object to include gene model name):

abbreviation: MaizeGDB

database: Maize Genetics and Genomics Database

object: MaizeGDB Object ID Number or Gene Model Name

example_id: MaizeGDB:881225

generic_url: http://www.maizegdb.org/

url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id]

url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225


Mary will update all of the xrefs in MaizeGDB's old association files to use this abbreviation when she does her next update. Until then, we should keep the other MaizeGDB abbreviation in the dbxref file, so the links will still work.

Existing MaizeGDB stanzas are incorrectly formatted. We cannot add the new stanza to http://plantontology.org/docs/dbxref/PO_DBXref.txt without removing at least one of the old ones. Not sure what repercussions this will have.


We have the correct MaizeGDB links in the PO_DBXref.txt, as well as others. Should we get rid of the other ones?. MaizeGDB fixed it on their end so this is working. The other MaizeGDB files should be updated this week.

GO associations to the maize gene models- These will come to MS through their collaboration and the Gramene update. Should be the ID in column 2. We can help MS access this info. For the future we should consider getting rid of this column and hosting the GO data in our database directly.

Gramene

Two of the Gramene dbxrefs in PO_DBXref.txt are not working:

GR: http://www.gramene.org/perl/protein_search?acc=P93436

GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198

Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.

JP sent the correct links, and RW fixed them in Dbxref.txt. They will need to be fixed in the AmiGO code

Others

We are also working on adding new annotation files for Physcomitrella, grape and strawberry. We will need to add DBXrefs for these sources as well.

strawberry- will link to the Roseacea database- need link, pankaj will send it to us.

grape - The original contributor, Nicola sent an additional file with the evidence code IEA (Inferred from Electronic Annotation) - thus these are based on homology to Arabidopsis, not actual assays in the grape leaf. Not a strong evidence to create annotations based on.

The current file we are working on should be combined with the new one, put onto the SVN, but not loaded into the database. Gene or coding region may match, but without promoter analysis, it is too weak. PJ will talk to PlexDB to get the microarray expression data- PlexDB has ~17 grape experiments, so we could link to m/a probe ids mapped to the genes. Julie Dickerson may be able to send us a dump for the database.


We will not try to include these in this release, but will continue building it. Column 1. DB reference should be to CRIBI (sp?) link?. Column

non-standard definition dbxrefs

We have a few definition dbxrefs that don't have an isbn or pmid number. We need to create a dbxref library for these, similar to what GO uses (GO reference collection). RW can add this to the OE file. Need to look into how AmiGO interfaces with this.

RW Created a PO_references page on the wiki and added a few of the PO_REF definition dbxrefs to the ontology file now so we can test out how they work. For example see thallus, PO:0030027.

From RW by email: "I could also make it so all references are on one page, instead of a separate page for each one. The separate pages seem a bit excessive now, but I think they will allow us greater flexibility if we start having more complex references (like for unpublished datasets)."

Inclusion of synonyms

The Spanish synonyms are now working fine, have the descriptor "(Spanish)" following them.

  • Japanese synonyms?

Will have Japanese synonyms in obo file, but JE will strip them out before the file gets loaded on AmiGO

Japanese synonyms are not currently in the editors' file. Should be added. What is the status on this?

For the release, we will highlight this new feature as we are the first ontology to offer spanish (and possibly Japanese) translations. Will send out the announcements in Spanish as well.

JE- the code is written and needs to be tested. RW will send in the list of new terms to Yukiko to get them translated. New Spanish synonyms have been added to the Obo file.

Eliminating_Zea/Poaceae_terms_from_PO

This is complete for both PAO and PGDSO, although some names and definitions in the PGDSO may change as we go forward.

Status of New Annotation Files:

MaizeGDB Annotations

The MaizeGDB anatomy and development annotations are in the SVN already, may need some minor fixing on Weds, when MS gets back from vacation.

Things to fix: pubmed id, links, duplicate lines

Physcomitrella Annotations

From 9-20-11 meeting: PJ will reply to SR about the Physco annotations- re: they should be using the actual gene ids rather than the microarray probe ids

What link do we need to use for these and how do we get AmiGO to recognize it?

Need to set up SVN access for SR or whoever will be sending the files.

PJ will contact SR about the files

Gramene Annotations

Regarding the following tech section from today's mtg agenda:

Two of the Gramene dbxrefs in PO_DBXref.txt are not working:

GR: http://www.gramene.org/perl/protein_search?acc=P93436

GR_MUT: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198

Don’t know if it is because the urls are wrong, or if it is because the ids are bad. If someone from Gramene can provide the correct urls, we can write new stanzas for the dbxref file.


JP hunted down the correct link templates and confirmed them with Ken:

http://www.gramene.org/db/protein/protein_search?acc=# (e.g. P93436)

http://www.gramene.org/db/genes/search_gene?acc=GR:# (e.g. GR:0060198 ...yes, Ken says mutant searches should be processed via the gene search)

JP and JE and I will work to get these implemented in the AmiGO codebase. RW will update the xref file.

New annotations should be coming from Gramene in the next 1-2 weeks

Grape and Strawberry

  • LC working on grape file, see sample

What links do we need to use for these and how do we get AmiGO to recognize them?

See notes above

Potato Annotations

LC has been in contact with the group who published the potato genome paper and they are interested in collaborating with us to assign ontology terms to the annotations.

From Dr. Richard Finker (Wageningen, The Netherlands):

"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."

This will go in the next release, do they have expression data- RNA Seq?

Comments from PJ about Annotation Guidelines

Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR

-This will also be helpful when applying for new grants

-it would be helpful to have a detailed guide on our wiki for collaborators

Edits to complete before release: PAO

All the edits from last weeks agenda have been completed.

Legume terms

phyllode

At an earlier meeting, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.

Background:

The main reference people cite for phyllodes is: D.R. Kaplan 1980, Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.

Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."

Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets.

Some more contemporary uses of the term phyllode:

Gardner et al. 2005 (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):


Leroy and Heuret 2007 (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by a type of foliar organ called a phyllode." and "...the different transitional forms range from pinnate leaves to phyllodes..."

See fig. 1 in this paper. They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.


Yang et al. 2008 (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.


Forster and Bonser 2009, Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."


RW did not find any contemporary papers that said that a phyllode is a petiole.

Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.

Proposed terms and definitions:

vascular leaf

>unifacial leaf

>>terete leaf (round in cross section)

>>ensiform leaf (flat in cross section)

>>>phyllode

>>>transition phyllode

Should use names unifacial vascular leaf, terete vascular leaf, and ensiform vascular leaf.

unifacial leaf: A vascular leaf that has increased activity of either the adaxial or abaxial meristem early in development, leading to absence of the opposite surface on the leaf. (ref: Lawrence (ISBN:9780023681905), Kaplan 1970 fig. 1 (PO_REF:00006), Sajo and Rudall 1999 (PO_REF:00005))

Comment: A unifacial leaf may be round in cross-section (terete) or it may be laminar (ensiform), in which case lamina development is in a median plane (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Unifacial leaves may be bifacial at the leaf base. Many unifacial leaves develop by reduced (or absent) activity of the marginal meristems and increased activity of the adaxial meristem early in development, leading to mature leaves with only an adaxial surface (e.g., Acacia, most monocots?). However, some develop by increased activity of the abaxial meristem early in development, leading to mature leaves with only an abaxial surface.


terete leaf: A unifacial leaf that is round in cross section throughout all of part of the length of the leaf. (ref.: Lawrence (ISBN:9780023681905))

Comment: The surface of a terete leaf corresponds to either the adaxial or abaxial surface of a normal leaf.


ensiform leaf: A unifacial leaf that is flat in cross section due to a lamina that develops in a median plane (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout all of part of the length of the leaf.(ref: Lawrence, Sajo and Rudall 1999)

Comment: Common in many monocots and some dicots. Both surfaces of an ensiform leaf correspond to only one of either the adaxial or abaxial surface of a normal leaf. In some leaves, the petiole may twist, giving the appearance that the lamina is ensiform, but it is not.


proposed def'n: phyllode: An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in develop. (Ref.: Kaplan 1970 (PO_REF:00006) and Boke 1940 (PO_REF:00007))

Comment: Common in legumes of the genus Acacia. Similar development occurs in other ensiform leaves in some monocots, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:xxxxxxx, transition phyllode). Phyllodes are generally xeromorphic.

Note: dual parentage: is_a ensiform leaf, is_a adult leaf


proposed def'n:transition phyllode: A transition vascular leaf in which the basal portion of the leaf has unifacial lamina development in a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf. (Ref.: Kaplan 1970 (PO_REF:00006) and Boke 1940 (PO_REF:00007))

Comment: Common in seedlings of legumes of the genus Acacia. May also occur later, after the plant has begun to produce phyllodes.

Note: dual parentage: is_a transition leaf, is_a ensiform leaf

will call it "phyllode leaf" and have synonyms "phyllode" and "adult phyllode leaf" and will call the transition phyllode: "transition phyllode leaf"

leaf spine (PO:0025173) and stipule spine (PO:0025174)

Note: spines are really unifacial leaves -- Should we make leaf spine is_a unifacial leaf?

We decide that we won't change leaf spine to unifacial leaf for now, because maybe not all of them are. Should change name to 'spine leaf' and 'spine stipule'.

bristle

(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)

We have the term stipule spine. Could also add the term stipule bristle: A stipule that has a brush-like appearance.

Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.


A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).

We will leave bristle for now and deal with it in the next release.


PJ: We need to start developing our own Plant Phenotype Ontology

cone

This is a request from Traitnet. Since the term cone is so widely used, it would be good to get this in ASAP.

Current definition of strobilus (PO:0025083): A reproductive shoot system consisting of a number of modified leaves (sporophylls) or ovule-bearing scales grouped terminally on a stem.

Suggest adding cone as a synonym of strobilus. The two terms are often used interchangeably. Later, we should add terms for simple strobilus and compound strobilus.

We should also add ovulate cone and pollen cone as synonyms, for now

Possible new Collaborator Group:e-monocot

RW met with the director (name?) of the project at IBC in Melbourne. He was interested in PO.

DWS knows Paul Wilkin at the Kew Garden and will be visiting there in a few weeks

PJ: We need to know what type of data sets they have, probably more trait-related as a systematics community, but they probably have entities that we could annotate to. (similar to the cycads). We should start developing a collaboration and look at mappings to the terms they are using. Start with GrassBase. Need to get them engaged and keep it going. LC will create a collaborator page.

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

  • Pricing

Academic Package $1055

Graduate/PhD Student Package $880

Corporate Package $1340

Academic/Student No-Housing Package $720


RW could attend, but DWS will be away,

May still be able to submit abstract. Must be registered to submit abstract.

See: Instructions

"After the meeting: RW will register for the CSHL meeting through the OSU

PAG 2012

January 14-18, 2012, San Diego, California

Registration and Abstract submissions open on Sept 22nd

LC is presenting in the Plant Phenotypes workshop on Sunday Morning, 15 January 2012 -- 8:00 am - 10:10 am.

The PO will take part in an Outreach booth organized by MaizeGDB

Other activities?


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:

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

Instructions

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.

RW could attend, but DWS will be away,

PJ: we should ask MS, and possibly SR, to contribute to the abstract and the annotation guide. See notes above

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.

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.

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 sction or systematists.


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.

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