Difference between revisions of "POC-MorphoBank Webex meeting 07-05-2011"

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In attendance:
 
In attendance:
  
−
POC members: Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Ramona Walls (NYBG)
+
POC members: Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Ramona Walls (NYBG); Barry Smith (University at Buffalo, NY), Justin Preece (OSU)
  
−
Collaborators:  
+
Collaborators: Maureen O'Leary
  
  
Line 9: Line 9:
  
  
−
=Background=
+
=Background Information @ Morphobank=
−
==Morphobank==
 
  
−
===Current utility, goals, etc.===
+
==Current utility and goals.==
  
−
MorphoBank is a web application for conducting phylogenetics or cladistics research on morphology that enables teams of scientists to work over the web - in real time - and to do research they could not easily do using desktop programs alone.  
+
From the MorphoBank website:
 +
 
 +
MorphoBank (MB) is a web application for conducting phylogenetics or cladistics research on morphology that enables teams of scientists to work over the web - in real time - and to do research they could not easily do using desktop programs alone.  
  
 
MorphoBank displays dynamic phylogenetic matrices of morphological characters with labeled images demonstrating homology statements, and implements the data editing functions of widely used desktop programs (e.g., Mesquite, Nexus Data Editor) over the web in a password protected environment. It is an environment for virtual collaboration by teams of researchers building phylogenetic matrices with affiliated image data.  
 
MorphoBank displays dynamic phylogenetic matrices of morphological characters with labeled images demonstrating homology statements, and implements the data editing functions of widely used desktop programs (e.g., Mesquite, Nexus Data Editor) over the web in a password protected environment. It is an environment for virtual collaboration by teams of researchers building phylogenetic matrices with affiliated image data.  
Line 20: Line 21:
 
MorphoBank can also draw on images in existing 2D and 3D digital libraries. If a scientist has images that are not deposited in other digital libraries, MorphoBank uses its database to store images (including films and CT scans) submitted by scientists, and allows contributors to label anatomical structures on the images. MorphoBank records metadata for the images.  
 
MorphoBank can also draw on images in existing 2D and 3D digital libraries. If a scientist has images that are not deposited in other digital libraries, MorphoBank uses its database to store images (including films and CT scans) submitted by scientists, and allows contributors to label anatomical structures on the images. MorphoBank records metadata for the images.  
  
−
===Future directions===
 
  
−
??
+
''MOL gave us a introduction to her site and some additional background. Started about 10 years ago to keep track of projects, media and be a way to work interactively.  She commented that it would be extremely useful for have an example matrix, using the PO, in order to demonstrate its utility to users.  Showed us an example of a character (x axis) by taxon (y axis) matrix. One idea would be converting an existing plant matrix to a Morphobank example.  Focus on interactive nature, web based''
  
−
==PO==
+
''Challenges exist in getting users to adopt ontologies, even have resistance to sharing matrices''
  
−
===Current utility, goals, etc.===
+
''The character states being used are basically free text, can be anything you want, not necessarily consistent across projects.  Some has been done in ATOL groups, virtual, interactive nature of MB promotes this.  Used for the generation of phylogenetic trees, using TNT and PAUP software. ''
 +
 
 +
''Currently, continuous characters have to be converted to discrete characters to display, but they are working on algorithms to deal with them.  See references in Journal "Cladistics".  '' 
 +
 
 +
 
 +
Here is a link to a FAQ on the site with more info: [http://www.morphobank.org/index.php?g=faq&s=new Morphobank FAQ]
 +
 
 +
=Plant Ontology=
 +
 
 +
==Current utility and goals==
  
 
'''Goals (from current grant):'''  
 
'''Goals (from current grant):'''  
Line 53: Line 62:
 
Used in genomic analysis tools (e.g., [http://virtualplant.org VirtualPlant], [http://bar.utoronto.ca/welcome.htm eFP Browser]) to aggregate data according to ontological rules.
 
Used in genomic analysis tools (e.g., [http://virtualplant.org VirtualPlant], [http://bar.utoronto.ca/welcome.htm eFP Browser]) to aggregate data according to ontological rules.
  
−
=Ideas and question re. collaboration between PO and Morphobank=
+
=Ideas and Questions re. collaboration between PO and Morphobank=
  
 
==Graphical interface for entering systematic data using ontologies==
 
==Graphical interface for entering systematic data using ontologies==
Line 61: Line 70:
 
PO could provides EQ (entity-quality) data for plants.
 
PO could provides EQ (entity-quality) data for plants.
  
−
From MO: "If you were to describe what would be an ideal tool or link, can you say what that would be? In other words, we are familiar and comfortable working in the matrix environment, if we were to open that matrix or character list, what tool or function would be ideal to link to PATO (and PO or other anatomy ontologies)?"
+
From MOL: "If you were to describe what would be an ideal tool or link, can you say what that would be? In other words, we are familiar and comfortable working in the matrix environment, if we were to open that matrix or character list, what tool or function would be ideal to link to PATO (and PO or other anatomy ontologies)?"
  
  
 
''PO would like to develop a species-neutral upper-level matrix, with characters on Y axis and states on X axis. Then people could use this to annotate characters. The whole matrix would not be exposed to users. Data would be stored in a multi-dimensional matrix, but users would interact with something more like a series of cascading drop-down menus.''
 
''PO would like to develop a species-neutral upper-level matrix, with characters on Y axis and states on X axis. Then people could use this to annotate characters. The whole matrix would not be exposed to users. Data would be stored in a multi-dimensional matrix, but users would interact with something more like a series of cascading drop-down menus.''
 +
 +
 +
==Ideas/Plans from PO: two prong approach:==
 +
 +
Top-down Approach: Large character matrix, plant-based, species-independent, all anatomical entities (~500) from PO, assayed for different characters
 +
for example: leaf shape, thickness, size, color; parts of leaf e.g. tip, lobes,
 +
 +
''Some of these matrices are already available in textbooks, etc.  This could be used by the individual projects and they could request terms that are missing, or create something on their own. Encourage communication between the two levels, and between projects to find common reference points''
 +
 +
bottom-up approaches: project-wide, e.g. Monocot or Gymnosperm tree of life projects
 +
 +
Three sides (dimensions) of a cube:  taxonomy + anatomical entities + state;
 +
 +
''The MB window: 'Matrix Character Viewer' would be the local place to put in ontology terms, best to put in as drop-down menus''
 +
 +
''Ontology button: place to put rules; relate traits to each other, for e.g. if this structure is absent, these traits are not relevant''
 +
 +
 +
Exemplar project would be very helpful- e.g. Gymnosperm TOL, pre-made matrix would save a lot time and effort.  Create a project and invite everyone, select a few matrices from the literature, mash them together and build a super-matrix;  Species/taxa identifiers; need to enrich the PO/TO list of phenotypic descriptors ''
 +
 +
 +
What would the ontologists like to be able to do? wish list should be developed to help guide the programming
  
 
''We need a data set to test the concept. Can DWS or MAG provide one?''
 
''We need a data set to test the concept. Can DWS or MAG provide one?''
 +
 +
''DWS can provide a matrix from: NSF: EF-0629817  Gymnosperms on the Tree of Life: Resolving the Phylogeny of Seed Plants or NSF: DEB-082762  From Acorus to Zingiber - Assembling the Phylogeny of the Monocots''
  
 
==Links to images==
 
==Links to images==
  
−
Adding links to images for PO terms is a priority of the PO now. Morphobank has an image data base. Can we set up links between PO terms and Morphobank images?  
+
Adding links to images for PO terms is a priority of the PO now. MorphoBank has an image data base. Can we set up links between PO terms and MorphoBank images?  
  
 
Need a stable url for individual images, in standard format, to set up as dbxref in GO database file.
 
Need a stable url for individual images, in standard format, to set up as dbxref in GO database file.
Line 90: Line 123:
 
example: http://www.gramene.org/perl/pub_search?ref_id=659
 
example: http://www.gramene.org/perl/pub_search?ref_id=659
  
 +
==Other==
 +
Comments about PATO vs PO and MB''
 +
 +
''BS: PATO annotates phenotypes identified in experiments, real instances of taxonomic groups, while MB is interested in the general representation of a taxonomic group.'' 
 +
 +
''MOL: there may be subsequent addition of polymorphism, with discussion''
 +
 +
''BS, PJ: The PO describes the typical or canonical (representative units), but those terms may be used to describe non-typical plants.  The PO tries to be species neutral eg. inflorescence is PO term representing the general state, with synonyms such as spike, panicle, ear,  ''
 +
 +
Cross-ref back to species neutral PO term and synonyms for the more specific bottoms up projects. 
 +
 +
MAG: Most matrices are for a specific clade using the canonical form,
 +
 +
DWS: This is useful as then we can search for the term "wood" and get back all the taxa.
 +
 +
Need to work with PATO to develop terms and definitions, interoperability between projects.
 +
 +
PATO terms could go into the states field, and maybe the names field (quality) as well, cross refs to ref ontologies.
  
−
abbreviation: GR_MUT
+
RW: Ideally, nice to have the association between the character state and species/taxon, similar to gene annotations in the PO
  
−
database: Gramene: A Comparative Mapping Resource for Grains.
+
Published projects are available publicly
  
−
object: Mutants
+
After the meeting PJ suggested we should use the book: Botany by AC Dutta as a reference for plant characters.
  
−
example: GR_MUT:GR:0060198
+
==Future directions==
  
−
generic_url: http://www.gramene.org/
+
MOL is preparing a grant submission for the [http://www.nsf.gov/pubs/2010/nsf10567/nsf10567.htm ABI program] (Due July 11th)
  
−
url_syntax: <nowiki>http://www.gramene.org/perl/mutant/search_mutant?id=ID number</nowiki>
+
Needs a paragraph describing the best what are the key projects to 'ontologize'. RW will prepare one and send it to the po-internal group.
  
−
example: http://www.gramene.org/perl/mutant/search_mutant?id=GR:0060198
+
What will the exemplar project be? ''For bottom-up approach, could use matrix from NSF: EF-0629817  Gymnosperms on the Tree of Life: Resolving the Phylogeny of Seed Plants or NSF: DEB-082762  From Acorus to Zingiber - Assembling the Phylogeny of the Monocots.''
  
−
==Other==
+
Note of support from PO for the proposal? See above
 +
DWS is preparing one for MB based on the TOL project and the Cladistics journal.
  
 
=References and Links=
 
=References and Links=
 +
 +
MOL sent this paper for further info: [[File:O'Leary and Kaufman 2011.pdf]]
 +
  
 
[http://kb.phenoscape.org/ Phenoscape]
 
[http://kb.phenoscape.org/ Phenoscape]

Latest revision as of 15:26, 7 July 2011

In attendance:

POC members: Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Ramona Walls (NYBG); Barry Smith (University at Buffalo, NY), Justin Preece (OSU)

Collaborators: Maureen O'Leary


The purpose of this meeting is to discuss potential collaboration between the Plant Ontology and Morphobank.org.


Background Information @ Morphobank

Current utility and goals.

From the MorphoBank website:

MorphoBank (MB) is a web application for conducting phylogenetics or cladistics research on morphology that enables teams of scientists to work over the web - in real time - and to do research they could not easily do using desktop programs alone.

MorphoBank displays dynamic phylogenetic matrices of morphological characters with labeled images demonstrating homology statements, and implements the data editing functions of widely used desktop programs (e.g., Mesquite, Nexus Data Editor) over the web in a password protected environment. It is an environment for virtual collaboration by teams of researchers building phylogenetic matrices with affiliated image data.

MorphoBank can also draw on images in existing 2D and 3D digital libraries. If a scientist has images that are not deposited in other digital libraries, MorphoBank uses its database to store images (including films and CT scans) submitted by scientists, and allows contributors to label anatomical structures on the images. MorphoBank records metadata for the images.


MOL gave us a introduction to her site and some additional background. Started about 10 years ago to keep track of projects, media and be a way to work interactively. She commented that it would be extremely useful for have an example matrix, using the PO, in order to demonstrate its utility to users. Showed us an example of a character (x axis) by taxon (y axis) matrix. One idea would be converting an existing plant matrix to a Morphobank example. Focus on interactive nature, web based

Challenges exist in getting users to adopt ontologies, even have resistance to sharing matrices

The character states being used are basically free text, can be anything you want, not necessarily consistent across projects. Some has been done in ATOL groups, virtual, interactive nature of MB promotes this. Used for the generation of phylogenetic trees, using TNT and PAUP software.

Currently, continuous characters have to be converted to discrete characters to display, but they are working on algorithms to deal with them. See references in Journal "Cladistics".


Here is a link to a FAQ on the site with more info: Morphobank FAQ

Plant Ontology

Current utility and goals

Goals (from current grant):

  • Develop and enrich the PO to describe plant anatomy and developmental stages of all plants including bryophyte, pteridophytes, and gymnosperms, as well as angiosperms
  • Develop the PO as reference ontology of plant structures and growth stages by developing mappings to similar vocabularies in use by plant databases
  • Outreach and education activities to extend the PO usage and awareness about Plant Biology research
  • Provide the vocabulary needed for phenotypic descriptors (qualities, as well as entities), by enriching the PO or PATO with quality terms. This is needed for:

-description of mutant phenotypes or natural variation for genetic or genomic research, or for large-scale phenomic screenings

-description of systematic/phylogenetic characters

  • Provide user-friendly tools for online data curation using ontologies such as the PO.
  • Provide links to images for terms to aid in understanding definition.


Current uses:

Primarily used by model organism databases to associate gene expression and phenotypic variation to plant anatomical entities or plant growth and development stages.

Used in genomic analysis tools (e.g., VirtualPlant, eFP Browser) to aggregate data according to ontological rules.

Ideas and Questions re. collaboration between PO and Morphobank

Graphical interface for entering systematic data using ontologies

Morphobank could provide software to store data (specimen data, images, etc.) and create character matrices based on ontology terms.

PO could provides EQ (entity-quality) data for plants.

From MOL: "If you were to describe what would be an ideal tool or link, can you say what that would be? In other words, we are familiar and comfortable working in the matrix environment, if we were to open that matrix or character list, what tool or function would be ideal to link to PATO (and PO or other anatomy ontologies)?"


PO would like to develop a species-neutral upper-level matrix, with characters on Y axis and states on X axis. Then people could use this to annotate characters. The whole matrix would not be exposed to users. Data would be stored in a multi-dimensional matrix, but users would interact with something more like a series of cascading drop-down menus.


Ideas/Plans from PO: two prong approach:

Top-down Approach: Large character matrix, plant-based, species-independent, all anatomical entities (~500) from PO, assayed for different characters for example: leaf shape, thickness, size, color; parts of leaf e.g. tip, lobes,

Some of these matrices are already available in textbooks, etc. This could be used by the individual projects and they could request terms that are missing, or create something on their own. Encourage communication between the two levels, and between projects to find common reference points

bottom-up approaches: project-wide, e.g. Monocot or Gymnosperm tree of life projects

Three sides (dimensions) of a cube: taxonomy + anatomical entities + state;

The MB window: 'Matrix Character Viewer' would be the local place to put in ontology terms, best to put in as drop-down menus

Ontology button: place to put rules; relate traits to each other, for e.g. if this structure is absent, these traits are not relevant


Exemplar project would be very helpful- e.g. Gymnosperm TOL, pre-made matrix would save a lot time and effort. Create a project and invite everyone, select a few matrices from the literature, mash them together and build a super-matrix; Species/taxa identifiers; need to enrich the PO/TO list of phenotypic descriptors


What would the ontologists like to be able to do? wish list should be developed to help guide the programming

We need a data set to test the concept. Can DWS or MAG provide one?

DWS can provide a matrix from: NSF: EF-0629817 Gymnosperms on the Tree of Life: Resolving the Phylogeny of Seed Plants or NSF: DEB-082762 From Acorus to Zingiber - Assembling the Phylogeny of the Monocots

Links to images

Adding links to images for PO terms is a priority of the PO now. MorphoBank has an image data base. Can we set up links between PO terms and MorphoBank images?

Need a stable url for individual images, in standard format, to set up as dbxref in GO database file.


Examples:

abbreviation: GR_REF

database: Gramene: A Comparative Mapping Resource for Grains.

object: Reference example: GR_REF:659

generic_url: http://www.gramene.org/

url_syntax: http://www.gramene.org/perl/pub_search?ref_id=ID number

example: http://www.gramene.org/perl/pub_search?ref_id=659

Other

Comments about PATO vs PO and MB

BS: PATO annotates phenotypes identified in experiments, real instances of taxonomic groups, while MB is interested in the general representation of a taxonomic group.

MOL: there may be subsequent addition of polymorphism, with discussion

BS, PJ: The PO describes the typical or canonical (representative units), but those terms may be used to describe non-typical plants. The PO tries to be species neutral eg. inflorescence is PO term representing the general state, with synonyms such as spike, panicle, ear,

Cross-ref back to species neutral PO term and synonyms for the more specific bottoms up projects.

MAG: Most matrices are for a specific clade using the canonical form,

DWS: This is useful as then we can search for the term "wood" and get back all the taxa.

Need to work with PATO to develop terms and definitions, interoperability between projects.

PATO terms could go into the states field, and maybe the names field (quality) as well, cross refs to ref ontologies.

RW: Ideally, nice to have the association between the character state and species/taxon, similar to gene annotations in the PO

Published projects are available publicly

After the meeting PJ suggested we should use the book: Botany by AC Dutta as a reference for plant characters.

Future directions

MOL is preparing a grant submission for the ABI program (Due July 11th)

Needs a paragraph describing the best what are the key projects to 'ontologize'. RW will prepare one and send it to the po-internal group.

What will the exemplar project be? For bottom-up approach, could use matrix from NSF: EF-0629817 Gymnosperms on the Tree of Life: Resolving the Phylogeny of Seed Plants or NSF: DEB-082762 From Acorus to Zingiber - Assembling the Phylogeny of the Monocots.

Note of support from PO for the proposal? See above DWS is preparing one for MB based on the TOL project and the Cladistics journal.

References and Links

MOL sent this paper for further info: File:O'Leary and Kaufman 2011.pdf


Phenoscape

Dahdul et al. 2010 - Paper on using EQ statements to describe legacy data set of morphological characters for fish.

NeXML

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