Plant Ontology Web Site Update: 2013

Note: To access the page on Plant Ontology web site technical issues, go back to the POC_Technical_Issues_Page. For changes to site content and the site design "refresh", read on...

Site "Refresh"

We are refreshing the look-and-feel of the Plant Ontology web site. Due to everyone's project load and timeline, we want to keep the redesign as low-key and trim as we can. We're aiming for big impact on the visuals, low impact on the current functionality.

The redesign will focus on two areas: 1) Changing the aesthetics of the non-AmiGO portion of the site, and 2) Updating static content.

   * Aesthetics: Colors, imagery (inc. logos), fonts, table and content layout, stylesheet-driven features
   * Static content: Generally speaking, HTML pages currently maintained in SVN under 
   "/plantontology/html/docs/otherdocs" (mostly by Laurel, Ramona, and Justin Elser)

We would love your input to help us reach both of these goals. At the moment, we're focusing on aesthetics first, static content after that. If we may be so bold as to suggest how you can help, here are two ways:

  1. If you have a favorite research web site whose design and layout you just love, please add the link
  to the "Example sites" section (below) so we can check it out.
  2. Start thinking about the static pages on the site (the home page, documentation, etc.), whether or not
  their contents need to be changed, and how. Ponder these things in your heart, and we'll start asking
  you for specific thoughts soon. 

This sort of "redesign" often falls victim to the slippery slope of expectations, so let's be as clear as possible about what we want to focus on (unless the PI's and project coordinator say otherwise):

   * Our focus: The aesthetic and static items mentioned above, including the header and navigational elements
   * Not our focus (at this time): AmiGO functionality, behavior of search bars and web forms, email
   notification features, the "site map" (that is, the location and organization of static pages)

We would love to address everything you want to see changed on the site, but we're attempting to lay down boundaries that make our short-term goals achievable. Ultimately, Pankaj, Lol, and our major collaborators will set direction and have the final say on this redesign. We are here to act as facilitators and technical implementers.

After some initial information gathering, we will produce a couple of page mock-ups proposing new designs, so everyone can see them and give their feedback. Thanks in advance for your help! We hope the result is a site we can all be proud of showing to the research community. :)

Current PO Site Map

Screenshots of site content (circa Spring 2012) have been collected, mapped to URLs, and tagged with summary descriptions. You can download the site map here. This is a clickable PDF: the screenshots are linked to the actual site.

Or, if you would rather just look at the pretty picture...

This document is intended to capture the state of affairs on the site as they are, not necessarily as we wish them to be. The grouping and categorization of pages is arbitrary and meant to be a discussion starter about how you would like the site content to be organized going forward. If corrections are needed, just let us know.

For the moment, please feel free to leave your comments and suggestions about site content organization here. If that discussion becomes substantial, we can move it to its own page.

Example sites whose design and layout we like

We welcome more suggestions...

• On the Solanaceae Genomics site, I like their "Image of the week" feature. This would be a way to feature the images we are developing, with PO terms. LC

• GARNet has a clean, fresh look- I like it: GARNet LC

• MosDB: http://mips.helmholtz-muenchen.de/plant/rice/index.jsp

Drupal Suggestion

We are kicking around the idea of taking this "site refresh" opportunity to port our non-AmiGO content to Drupal 6, a community and Oregon State University standard web framework. The Jaiswal Lab site has almost been converted to Drupal 6, and handling the Plant Ontology site in a similar manner would bring new capabilities to our site. This would, of course, broaden the scope of our redesign efforts a bit...but the payoff comes in the form of increased design sophistication and a new method of content management for contributors to the site (no more SVN for HTML pages). We are merely exploring the idea (and it's technical feasibility); any decision to use Drupal 6 will belong to the deciders. Let's have a meeting about this once we have tested running a default Drupal 6 site and AmiGO in parallel on our Palea web server (currently in progress).

Requests for Content Change

A list of requested content corrections...

See also the items listed on the POC_Technical_Issues_Page- some of which are AmiGO specific

High priority fixes

RW has marked these as high priority to fix before the Botany meeting (by mid-June).

Link on Homepage to Source Forge tracker

submitted 9-28-11- LC Now that people need to log in to SF to submit a request, this link needs to be fixed. Currently take you to a dead-end if you are not already logged in. Current link: [1]. I suggest we create an intermediary wiki page with some explanation

RW (4/2012): Maybe this has been fixed? Seems to work. I have created a wiki page for How_to_use_the_SourceForge_tracker.

This could be made into a web page, as part of the browser, rather than leaving it on the wiki.

(7/3/12) The "Request term" tab now links to the wiki help page, instead of directly to Source Forge. The wiki help page should be converted to a web page. Need to check PO web site for other places that link to SourceForge, and see if they should stay as direct links or go to the help page first.

Plant Ontology Browser Users Guide

http://plantontology.org/amigo_user_guide/index.html#intro fixed

- No images show up. Text not displaying correctly (missing spaces).

-This page would be very useful for the PO workshop.

JE (6/5/12) -- Fixed missing images in svn revision 247. Spacing fixed in revision 248.

RW (6/6/12) -- Thanks Justin! A few of the images reference "gametophyte", which is now obsolete. I will try to update those before July.

RW (6/28/12) -- Updated this file and added new images as needed. Committed to SVN in revision 249.

Web pages that are out of date - high priority

• publications Needs updated

• links to mailing lists and archives Needs updated

• http://plantontology.org/docs/otherdocs/principles_rationales.html - Out of date. This page is labeled, and starts out as, an overview of the PO, but the second part of this page cover only plant anatomical entities. I (RW) will keep this page as an overview of the PO, since that seems to be its main content, and create a separate page for anatomical entities, to correspond to the growth and development pages.
• http://plantontology.org/docs/growth/growth_stages.html - Out of date. This page should be changed to reflect whole plant development stages.
• http://plantontology.org/docs/faq/growth_faq.html - Out of date. fixed with commit #251
• http://plantontology.org/docs/development/developmental_stages.html - Out of date. This page should be changed to reflect plant structure development stages, other than whole plant stages.

• http://plantontology.org/docs/otherdocs/ontology_doc.html Developers' guide. Content is not too bad, but this should be only on the wiki, and not on the web page since it is only for developers -- most users never need to see this.

Changes:

• Updated growth_faq.html (6/28/12), principles_rationales.html (6/29/12), developmental_stages.htm (6/29/12), growth_stages.html (6/29/12), docs.html (6/20/12)
• Created a new doc for anatomical entities, but have not updated the content or committed the file yet. This page could be updated to parallel the development stage pages.

Tutorials and Demos out-of-date

Presentations/tutorials that need to be updated:

• Introduction to the project - Slide show. There are links to this from both the web page and the wiki. Much of it is still valid, so it could be updated, rater than replaced. link to svn folder

(7/3/12) Fixed and loaded onto beta and dev browsers.

Tutorials:

http://wiki.plantontology.org/index.php/Plant_Ontology_Tutorials is the wiki equivalent of http://plantontology.org/docs/otherdocs/tutorials.html

• Introduction to ontologies: http://plantontology.org/docs/presentations/tutorials/poc_intro.mov, http://plantontology.org/docs/presentations/tutorials/poc_intro.ppt Powerpoint slides
• Development of ontologies: http://plantontology.org/docs/presentations/tutorials/ontology.mov, http://plantontology.org/docs/presentations/tutorials/ontology.ppt
• Annotations: http://plantontology.org/docs/presentations/tutorials/annotation.mov, http://plantontology.org/docs/presentations/tutorials/annotation.ppt
• Plant ontology browser and POC web site: http://plantontology.org/docs/presentations/tutorials/website.mov, http://plantontology.org/docs/presentations/tutorials/website.ppt

Out of date wiki pages

Principles, Rationales and Key Organizing Rules of the PO (These correspond to the out of date web pages):

• Plant Structure Ontology Rationale for high nodes in the ontology, examples and explanation of three "patterns" of the ontology structure.
• Growth Stages Ontology and frequently asked questions
• Developmental Stages Ontology

RW: Rather than maintain duplicate pages, this links form the wiki should go to the corresponding web pages, once they are updated.

• Wiki home page: under Formats of the Ontology Files, needs info on OWL (provide link).

RW: Added comment about OWL and link to Protege home page. (7/1/12)

Developers guide -Download SVN Page

submitted: 1-11-12

Need to correct spelling mistake and remove DagEdit, put in links to OBOEdit

http://www.plantontology.org/download/svn_doc.html Developers guide

RW: Thanks for adding instructions for Mac users!

RW: Fixed grammer and punctuation issues, removed section on DAG Edit and replaced with sections on OBO-Edit and Protege. Fixed with commit #250 on 6/28/12.

New images needed for browser

JE: I noticed in the server logs that errors are being created because we are missing images for participates_in and adjacent_to. Can someone create these for me to add to the browser?

We have now an images for all these relations.

RW: Minor point, but perhaps the list of icons could be have is_a first (as it is now) and then list the rest of them in alphabetical order.

Medium priority fixes

These fixes are important, but can wait until after June.

Web pages that are out of date - medium priority

• http://plantontology.org/docs/otherdocs/poc_project.html - Was updated in the past year, but needs new updates. Still refers to "Plant Growth and Developmental Stages". Could use more detail on the project.
• http://plantontology.org/docs/otherdocs/charter.html POC charter is out of date.
• http://plantontology.org/docs/otherdocs/resources.html out of date
• http://plantontology.org/docs/references/pub.html out of date

Feature requests

Link to PO curators page

We have this page: http://wiki.plantontology.org/index.php/Plant_Ontology_curators

Barry has requested that we put this material on the main PO page.

Also requested that we add a prominent link from the main PO page to the wiki.

(7/3/12) A link to this page has been added from the "Documentation" page of the PO website.

Color coding the Anatomy and Development terms differently?

This was a suggestion raised by PJ a the NYBG meeting Sept 2011 Saturday_Sept_10th,_2011 during the discussion of the cross-ontology relations.

add more details....

filter translation

Date: 9-13-11

This was sent as a feedback response on the web page- went to Po-internal. refer_to_url: http://www.plantontology.org/index.html

subject: filter translation

comments: It would help to have a link to what the filters mean from all pages where one can set the filters. A click on the help box seemed to missing this information, or require reading pages of stuff to find out it wasn't there. For example - most folks will not know that MGCSC refers to the maize mutant stock collection at Illinois.

name: Mary Schaeffer email: schaefferm@missouri.edu organization: MaizeGDB

Download annotations from the PO website

-Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML.

-Could we also have the ability to download as csv or txt, so it could be imported into excel? That would be of use to many users. or tab delimited!

for example: embryo axis

RW: Yes! This would be really great.