Plant Ontology Web Site Update: 2013

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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. :)

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

Current PO Site Map

Screenshots of current content have been catalogued and URLs have been mapped. Diagram of PO's current site map will be posted shortly...

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...

Developers guide -Download SVN Page

submitted: 1-11-12

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

Developers guide

Link on Homepage to Source Forge tracker

submitted 9-28-11- LC Now that people need to login 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

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

Tutorials and Demos out-of-date

Tutorials The ppt tutorials on this page are severely outdated!

and this one is as well: POC Demo

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 image for participates_in, still need one for adjacent_to and also has_participant.