Difference between revisions of "Plant Ontology Web Site Update: 2013"
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| − | Plant Ontology | + | 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... |
| − | |||
| − | =Developers guide -Download SVN Page= | + | =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. | ||
| + | |||
| + | Our next step is to 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 [http://solgenomics.net/ 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 | ||
| + | |||
| + | |||
| + | |||
| + | =Requests for Content Change= | ||
| + | |||
| + | A list of requested content corrections... | ||
| + | |||
| + | ===Developers guide -Download SVN Page=== | ||
submitted: 1-11-12 | submitted: 1-11-12 | ||
| Line 10: | Line 44: | ||
[http://www.plantontology.org/download/svn_doc.html Developers guide] | [http://www.plantontology.org/download/svn_doc.html Developers guide] | ||
| − | = | + | ===Link on Homepage to Source Forge tracker=== |
| − | |||
| − | |||
| − | |||
| − | =Link on Homepage to Source Forge tracker= | ||
submitted 9-28-11- LC | 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. | 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: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation | Current link: [http://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555]. I suggest we create an intermediary wiki page with some explanation | ||
| − | =Color coding the Anatomy and Development terms differently?= | + | ===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. | 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.... | add more details.... | ||
| − | =filter translation= | + | ===filter translation=== |
Date: 9-13-11 | Date: 9-13-11 | ||
| Line 36: | Line 66: | ||
name: Mary Schaeffer | name: Mary Schaeffer | ||
| − | |||
email: schaefferm@missouri.edu | email: schaefferm@missouri.edu | ||
| − | |||
organization: MaizeGDB | organization: MaizeGDB | ||
| − | =Download annotations from the PO website= | + | ===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. | -Currently, when you are on the PO page and want to save the list of associations, the only format available is RDF-XML. | ||
| Line 48: | Line 76: | ||
for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis] | for example: [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0019018&session_id=8191b1311111248&show_associations=list embryo axis] | ||
| − | =Tutorials and Demos out-of-date= | + | ===Tutorials and Demos out-of-date=== |
[http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials] | [http://www.plantontology.org/docs/otherdocs/tutorials.html Tutorials] | ||
The ppt tutorials on this page are severely outdated! | The ppt tutorials on this page are severely outdated! | ||
| Line 54: | Line 82: | ||
and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo] | and this one is as well: [http://www.plantontology.org/docs/presentations/demo/poc-demo-1.html POC Demo] | ||
| − | =New images needed for browser= | + | ===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? | 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.'' | ''We have now an image for participates_in, still need one for adjacent_to and also has_participant.'' | ||
Revision as of 00:51, 3 February 2012
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.
Our next step is to 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
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
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.
