Thursday March 5th, 2015: Difference between revisions

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(Created page with "Who: PJ, EA, LC, JE, JP Not available: BS, JD == A. General Comments and Updates:== * Schedule for Monthly All-Hands meetings ''- do we need to do a new doodle poll or is t...")
 
 
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Who: PJ, EA, LC, JE, JP  Not available:  BS, JD
Who: EA, LC, JE, JP  Not available:  PJ, BS, GG, EZ, ST
 
* Link to recording- Video:  [[File:AllHands 3-5-15.mp4|thumbnail|AllHands 3-5-15.mp4]]
* Link to recording- Audio: [[File:AllHands Audio 3-5-15.m4a|thumbnail|AllHands Audio 3-5-15.m4a]]


== A. General Comments and Updates:==
== A. General Comments and Updates:==
* Schedule for Monthly All-Hands meetings
* Schedule for Monthly All-Hands meetings
''- do we need to do a new doodle poll or is this time good?''
''- We will do a new doodle poll- LC''
 
* Planteome Wiki page has been set up with password protection (if you are reading this, it must be working :-))


From last meeting...
From last meeting...
''* PJ will circulate final version of the proposal in a cleaned-up format''
* PJ will circulate final version of the proposal in a cleaned-up format


* Planteome Wiki page has been set up with password protection (if you are reading this, it must be working :-))
''- EA- It would be very useful to have a copy of the 'official abstract' to share with partners or colleagues.  See link to award on NSF site: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1340112''
*
 
''- LC will send EA the NSF logos to use with the announcement on the Crop Ontology page'' Done!


Progress on opening new Planteome-related positions in the Jaiswal Lab (software developer, curator)
* Progress on opening new Planteome-related positions in the Jaiswal Lab (software developer, curator)-
''- position is open, being advertised on various sites: [http://planteome.org/blog Planteome blog], [http://aspb.site-ym.com/networking/apply_now.aspx?view=2&id=276580 ASPB Careers]
''


== C. Update from IT group- Data Store, AmiGO2, Justin Elser:==
== C. Update from IT group- Data Store, AmiGO2, Justin Elser:==


* A test version of the AmiGO 2.2.3 browser is up and running at [http://dev.planteome.org/amigo Amigo 2.0 on Planteome.dev]. 
- It currently just has a standard set of ontologies and a small subset of annotations.
- To navigate: go to http://dev.planteome.org/amigo/search/ontology


== D. Update from AISO/BisQue group- Justin Preece:==
* Note: I was unable to get it to load with the ncbi taxon ontology like GO has because the loading program ran out of memory.  
* Lead by Sinisa, with two graduate students, [[Image_Annotation_Working_Group_Meetings]]
''Possibly amy be better to just load a branch of the NCBI taxonomy, for the plants- we do not really need the whole thing.''


* Next steps are to work on the theming and to clean up the list of the ontologies:


* Generation of Sample Images - DWS
''Currently, this is the list of ontologies that are loaded:''
** Need to generate the labeled images- initially using AISO
* Priorities would be images of leaf types, flowers, root and stem sections
* DWS has a large number of images from the plant anatomy textbook - will send us the link
* DWS owns them so it is not a problem, part of the laboratory exercises on a CD for the book
* Will go along with the glossary of anatomy terms based on the PO


* Recent AVATOL grant  meeting: http://avatol.org/; http://currents.plos.org/treeoflife/avatol/;  http://currents.plos.org/treeoflife/article/next-generation-phenomics-for-the-tree-of-life/
[[File:AmiGO2 Planteome dev.png|thumbnail|AmiGO2 Planteome dev.png]]
** Sinisa and Thomas G Dietterich are involved, machine learning direction is planned for later developemnts
* Their goal is automatically filling cells in data matrices for phylogenetic analysis, based on the images
* Our goal is integrating the ontologies, anatomy first, then the qualities, ultimately connect to the GO
* New AISO-BisQue tool will be online and version controlled,


== E. Update from Ontologies Working group:==
Links:
Who is involved: EA, BS, DWS, LC, PJ, others TBA
* http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
* [http://purl.obolibrary.org/obo/ncbitaxon.owl%20\ NCBI Taxonomy ]
* http://purl.obolibrary.org/obo/cl/cl-basic.owl \
* [http://purl.obolibrary.org/obo/eco.owl%20\ Evidence Code Ontology]
* http://purl.obolibrary.org/obo/go/extensions/gorel.owl \
* http://purl.obolibrary.org/obo/ma.owl \
* http://purl.obolibrary.org/obo/pato.owl \
* http://purl.obolibrary.org/obo/po.owl \
* http://purl.obolibrary.org/obo/emap.owl \
* http://purl.obolibrary.org/obo/chebi.owl \
* http://purl.obolibrary.org/obo/uberon/basic.owl \
* http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl


* We have had three meetings so far, including a face-to-face meeting with many of the CO curators at PAG.
* Priority for us will be refining the list of the ontologies: Do not need the following:
* Next meeting is Tuesday Mar 10th, 2015 8:30am PST (GMT-8)
** Mouse_ontology
**adult_mouse_anatomy
* Need to include the Trait Ontology


EA: Ad for postdoc position has been advertised, as of Friday Jan 30th, and open till end of February.  Anticipate having the person in place by Mid-March.
*Also need to check on the versions of the ontologies being loaded from the purls above- may be able to modify to use our verisons.
[https://hr4u.bioversity.cgiar.org/recruitment/Attachments%5CVA_Post%20Doc_CropOntology_NSF_MPL_Final.pdf VA_PostDoc_CropOntology_NSF_MPL_Final.pdf]


* PJ: We can help advertise the position advertisement- by posting on Planteome.org and the PO Facebook page.
* Load time for the ontologies is about 2 hours and the test set of annotations loaded in a few minutes.  
** EA: Bioversity HR does not want to advertise too widely in order to avoid too many Cvs to be screened between now and end of February as they are quite busy at the moment for the Bioversity programme restructuring, due end of March, so please just advertise on your web site and specialized ones.
* JE is working with Chris Sullivan to figure out a way to be able to do the load from one of the compute nodes in the cluster as they have much more RAM.
* For more information, please see the notes at: [[Data_storage_and_AmiGO2_Working_Group]]


* First steps for Ontologies WG is to decide on which of the species-specific Crop Ontologies we will focus on initially.  Previously we had discussed wheat, rice and maize as the initial targets.
== D. Update from AISO/BisQue group- Justin Preece:==
* The Plant Ontology should be fairly mature as a source of the entity terms, for the plant parts and stages, but need to assess what needs to be done from the CO side for the species specific trait ontologies.
* Bisque (http://bioimage.ucsb.edu/bisque) is the Image Annotation (IA) of iPlant, and is the platform we will be using for the Planteome
* Additional terms can be added to the PO as needed
* Last group meeting was Feb 12th, [[Image_Annotation_Working_Group_Meetings]]
* Setting up development environment for the two graduate students who work with Sinisa
* Starting to work on the IA modules with in Bisque
* Bisque has some aspects of segmentation, but it is limited, compared to the AISO desktop tool
* Initial focus is to build a basic user interface that allows single segmentation input- it sends it out to the Bisque server and returns a segmented image. Not interactive- done over the network
* Bisque lacks the software architecture to do interactive segmentation, over the network.
* Bisque developers are working on a more synchronous interactive mode (independent of our project)
* [https://docs.google.com/document/d/14i3ED8cAX6-qwdpko8eV8aQrwplLRfLHZ93dZYpjZu8/edit Draft doc of the specs] is linked to the wiki page.


* BS can look over the TO and provide guidance as to the structure-
===Continuing the discussion about the Generation of Sample Images from last month - DWS===
** Need to generate the labeled images- initially using AISO
* Priorities would be images of leaf types, flowers, root and stem sections
* Will go along with the glossary of anatomy terms based on the PO
* Recent AVATOL grant  meeting: http://avatol.org/; http://currents.plos.org/treeoflife/avatol/;  http://currents.plos.org/treeoflife/article/next-generation-phenomics-for-the-tree-of-life/
** Generating leaf clearance images
* DWS has a large number of images from the plant anatomy textbook - will send us the link or the CD, working on the 2nd edition now
* DWS owns them so it is not a problem, part of the laboratory exercises on a CD for the book
* Will need to make sure it is ok with the publisher- Wiley
* Machine learning will happen in Phase 3- can develop the needed images


* EA met with Ruaraidh Sackville-Hamilton (Head of Genetic Resources, IRRI)- They are working on updating the rice trait dictionary and they are interested in making sure the terms are cross-referenced with the TO terms.
== E. Update from Ontologies Working group:==
** Need to make sure they have access to the latest version of the TO, and may need some assistance to ensure the links are done correctly.  
* Updates from recent weekly meetings: [http://wiki.planteome.org/index.php?title=Ontology_Working_Group_Meetings-_Feb_2015#3._Panzea_Project:_Curating_Maize_Diversity_with_MaizeGDB Panzea project], [http://wiki.planteome.org/index.php?title=Ontology_Working_Group_Meetings-_Feb_2015#1._Review_of_the_Crop_Ontology_Structure Crop Ontology]
''- LC will follow up with EA to coordinate it''
* Barry presented the Planteome to the United Nations
* Initial efforts will need to be focused on maturing the Trait Ontology and filling in the gaps.
* [https://rd-alliance.org/groups/wheat-data-interoperability-wg.html Wheat Data Interoperability Working Group] at the RDA Plenary in San Diego next week. Presenting the Recommended data standards (ie: cookbook) and results of the ontology survey.
* Next meeting is Friday Mar 6th, 2015 8:30am PST (GMT-8)- Rosemary Shrestha - Data manager at CIMMYT, curator of the Maize trait Ontology
* New team member Leo Valette is joining the IBP and CO in Montpellier.


Links: http://www.cropontology.org/
===Update on Position advertisements:===
* Crop Ontology position is closed, interviews are March 19-20th


== F. Position Paper or "White Paper" ==
* Oregon State University Advertisement: posted on various sites: http://aspb.site-ym.com/networking/apply_now.aspx?view=2&id=276580
* In order to state our plans and cultivate our ideas, we should move quickly to produce a Position Paper or "White Paper".
* We do not want to lose out on ideas and concepts that we have proposed- others may take the credit and publish it first
* We should put forward our plans and stance, and what we expect to produce, rather than discussing it later in the project
* Possible places: Plant Methods, Nature Plants, Nature Methods, New Phytologist
* Will help us crystallize our ideas, goals and plans


Goals:  
==Other Comments==
* Build a community consensus on widespread acceptance and availability, invite discussions
DWS: Comments from colleagues at NYU, on the GO and how it does not really tell you too much in reality. Ideally the Planteome will link the genes and functions and processes, to the final outcome of the plant development and plant structures.
* Define the vocabularies and terms such as phenotypes, etc
* Suggestion is to do more links between the GO and PO- knowledge is there, but has not been exploited.  Moving into plant development and the traits
* What level of phenotypes are we looking at: molecular aspects, function, processes, location, etc
* Example shown by PJ- network graph, that shows the link genes, functions and processes, to the final outcome of the plant development and plant structures.
* Any evaluated characteristic of an entity can considered a phenotype
* Sun gear type diagrams

Latest revision as of 23:42, 15 April 2015

Who: EA, LC, JE, JP Not available: PJ, BS, GG, EZ, ST

A. General Comments and Updates:

  • Schedule for Monthly All-Hands meetings

- We will do a new doodle poll- LC

  • Planteome Wiki page has been set up with password protection (if you are reading this, it must be working :-))

From last meeting...

  • PJ will circulate final version of the proposal in a cleaned-up format

- EA- It would be very useful to have a copy of the 'official abstract' to share with partners or colleagues. See link to award on NSF site: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1340112

- LC will send EA the NSF logos to use with the announcement on the Crop Ontology page Done!

  • Progress on opening new Planteome-related positions in the Jaiswal Lab (software developer, curator)-

- position is open, being advertised on various sites: Planteome blog, ASPB Careers

C. Update from IT group- Data Store, AmiGO2, Justin Elser:

- It currently just has a standard set of ontologies and a small subset of annotations.

- To navigate: go to http://dev.planteome.org/amigo/search/ontology

  • Note: I was unable to get it to load with the ncbi taxon ontology like GO has because the loading program ran out of memory.

Possibly amy be better to just load a branch of the NCBI taxonomy, for the plants- we do not really need the whole thing.

  • Next steps are to work on the theming and to clean up the list of the ontologies:

Currently, this is the list of ontologies that are loaded:

AmiGO2 Planteome dev.png

Links:

  • Priority for us will be refining the list of the ontologies: Do not need the following:
    • Mouse_ontology
    • adult_mouse_anatomy
  • Need to include the Trait Ontology
  • Also need to check on the versions of the ontologies being loaded from the purls above- may be able to modify to use our verisons.
  • Load time for the ontologies is about 2 hours and the test set of annotations loaded in a few minutes.
  • JE is working with Chris Sullivan to figure out a way to be able to do the load from one of the compute nodes in the cluster as they have much more RAM.
  • For more information, please see the notes at: Data_storage_and_AmiGO2_Working_Group

D. Update from AISO/BisQue group- Justin Preece:

  • Bisque (http://bioimage.ucsb.edu/bisque) is the Image Annotation (IA) of iPlant, and is the platform we will be using for the Planteome
  • Last group meeting was Feb 12th, Image_Annotation_Working_Group_Meetings
  • Setting up development environment for the two graduate students who work with Sinisa
  • Starting to work on the IA modules with in Bisque
  • Bisque has some aspects of segmentation, but it is limited, compared to the AISO desktop tool
  • Initial focus is to build a basic user interface that allows single segmentation input- it sends it out to the Bisque server and returns a segmented image. Not interactive- done over the network
  • Bisque lacks the software architecture to do interactive segmentation, over the network.
  • Bisque developers are working on a more synchronous interactive mode (independent of our project)
  • Draft doc of the specs is linked to the wiki page.

Continuing the discussion about the Generation of Sample Images from last month - DWS

    • Need to generate the labeled images- initially using AISO
  • Priorities would be images of leaf types, flowers, root and stem sections
  • Will go along with the glossary of anatomy terms based on the PO
  • Recent AVATOL grant meeting: http://avatol.org/; http://currents.plos.org/treeoflife/avatol/; http://currents.plos.org/treeoflife/article/next-generation-phenomics-for-the-tree-of-life/
    • Generating leaf clearance images
  • DWS has a large number of images from the plant anatomy textbook - will send us the link or the CD, working on the 2nd edition now
  • DWS owns them so it is not a problem, part of the laboratory exercises on a CD for the book
  • Will need to make sure it is ok with the publisher- Wiley
  • Machine learning will happen in Phase 3- can develop the needed images

E. Update from Ontologies Working group:

  • Updates from recent weekly meetings: Panzea project, Crop Ontology
  • Barry presented the Planteome to the United Nations
  • Wheat Data Interoperability Working Group at the RDA Plenary in San Diego next week. Presenting the Recommended data standards (ie: cookbook) and results of the ontology survey.
  • Next meeting is Friday Mar 6th, 2015 8:30am PST (GMT-8)- Rosemary Shrestha - Data manager at CIMMYT, curator of the Maize trait Ontology
  • New team member Leo Valette is joining the IBP and CO in Montpellier.

Update on Position advertisements:

  • Crop Ontology position is closed, interviews are March 19-20th

Other Comments

DWS: Comments from colleagues at NYU, on the GO and how it does not really tell you too much in reality. Ideally the Planteome will link the genes and functions and processes, to the final outcome of the plant development and plant structures.

  • Suggestion is to do more links between the GO and PO- knowledge is there, but has not been exploited. Moving into plant development and the traits
  • Example shown by PJ- network graph, that shows the link genes, functions and processes, to the final outcome of the plant development and plant structures.
  • Sun gear type diagrams
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