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  • Bill Flanagan ( at MIT) 12:35, 15 April 2009 (EDT)Check out what we're up to regarding making the OWW Materials section more useful. Jakob Suckale brought this to my attention a while back. I've been working on a number of related enhancements to OWW to make upgrades to the way we enter and categorize information about them. The Protocols page does a better job at aggregating content. But it also is in need of improvements. Rather than presuppose tools, I'm interested in seeing how we can make them up as we move forward to get the most out of the members of OWW.


This is a proposed restyling of the materials page. I thought I would put it here to see what people thought before making it go live on the real page. Comments welcome. I just thought the page could be made more compact and easy to view. Feel free to retweak if you have a better idea. A similar thing could be done to the protocols page. My only concern is whether it makes it more difficult/intimidating for those new to wikis to edit? Which is definitely not what I want. -- RS

  • Jennyn 16:58, 26 February 2006 (EST): The page has been restylized. Please feel free to edit as you feel necessary.

Proposed Changes to Materials Page

Bill Flanagan ( at MIT) 11:40, 6 April 2009 (EDT)This is a good idea. We've discussed redoing the protocols page for a long time but to date it's still 'the same as it ever were'. I'll be glad to participate (i.e., provide technical assistance as needed) in the work if someone can help work on the requirements:

  • What are the existing pages in OWW that would be related to materials?
  • What would the best way to view and search these pages?
  • How can we identify requests for information on materials that currently are not present in OWW pages?
  • How can we provide a structure that encourages OWW members to participate in actively evolving this over time?

I would hope that what we would do for Materials could be applied to make protocols more user accessible as well.

Also, it's great to see someone using Talk pages; they're a pretty useful resource that we don't see a lot of people taking advantage of!. I'm still researching Southern blots to get back in the game after Jacob's last post to my talk page! Thanks for the comments, Jakob.

Bill Flanagan ( at MIT) 09:39, 15 April 2009 (EDT)

Material Category Tree Browser

This is a proposed mechanism for modifying categories and adding general taxonomy editing ==

This is a category tree of the current contents of the categories used in the Materials page. If anyone has suggestions about how this process can be streamlined, please add to the section at the end for process comments.

To start with, I think we could do some pruning to get the tree in better shape. That doesn't involve removing categories in my book. It does mean doing a better job connecting them together.

What I would suggest is to see if anyone can contribute their comments about how the existing set of categories can be changed. To do this, start by looking at the list and put entries below regarding what you would suggest needs to be changed. I'll come up with a more tructured way of doing this if I start to get input. I don't think it should take a lot of time to make this assessment. If it does, then I'm doing something wrong.


"Uncategorized" Material Categories

Please make suggestions about how the MANY materials listed below under the "Materials" category can be handled.

When possible, for now do this by either adding appropriate category tags to make them show up in the right place in the existing tree or make suggestions using the templates below to create or change the existing tree to better reflect them.

Material Search Suggestions

Currently there is no formal search for materials other than the one we use based upon the Dynamic Page List (DPL) extension. This has proved to be a valuable tool in the past but it may be time to look at a better way to do the searching. For one thing, it's a bit cpu-cycle consuming to search via the DPL. It's a very complicated extension that seems to have issues with the most recent versions of MediaWiki. I think we need to address this. But first we need to scope out the data that is to be searched and see if we can better collect requirements for search.

Keep in mind. We also will get a LOT of mileage out of better documenting the categories for OWW Materials. The richness of the content of these pages can be used to make suggestions of material. But we need an accurate and meaningful set of material pages and categories that we all buy into.

Moving Toward Standard Biological a Standard Ontology for Materials

If we were doing this as ignorant outsiders (like me, for instance!), this would be considered a 'folksonomy'. But this is not a group of IT people masquerading as biologists. You people can make a meaningful contribution by helping to structure a taxonomy that can eventually become a part of a formal ontology. If you have pointers to existing ontologies that would be helpful, please mention them and provide links to appropriate references as well. I'm not interested in reinventing the wheel and will jump at the opportunity to refactor the existing categories with biological standards used outside of OWW where applicable.

Suggested Ontology List (Please add Here!)

Category Information Template Page: Input required!

If someone wants to take a crack at editing the template for a material category page for all categories we have or may change or add, dig in.

We're using the material template page created by Reshma Shetty as a starting point.

Here's a pointer to a Category Template that we can star with. This won't be used until we reach consensus on the format.

Material Category Page Template

Like article pages, Categories are represented as pages that can accompany each category label. Although we have not used them extensively, they would be just as useful to many members as the 'leaf-node' pages describing the material.

Suggested protocol for submitting Changes to the Existing Materials Category Tree

If anyone contributes proposed, please think of using the following formats. Just copy and past them to the bottom of this page. Please DO NOT DELETE or CHANGE these templates. We will make the changes to the tree after people think they understand and like changes.

Copy the text between the START and END labels for each proposed change and paste it at the bottom of this page, THEN add your text.

Category Name Change

  • Label for this suggestion:
  • Related to Label:
  • Author:
  • Existing Material Category Name:
  • Proposed New Material Category Name:
  • Description:
  • Comments:
  • End of Change



Category Add

  • Label for this suggestion:
  • Related to Label:
  • Author:
  • Proposed New Material Category Name:
  • Descending-from Existing Parent Category Name:
  • Description:
  • Comments:
  • End of Add



Category Delete

  • Label for this suggestion:
  • Related to Label:
  • Author:
  • Proposed Material Category Name to be Deleted:
  • Description:
  • Comments:
  • End of Delete


Current Material Category Tree.

Use the +/- labels to expand and collapse the categories.

<categorytree mode="pages">Material</categorytree>

Suggested changes initially will not be reflected in this tree. These are the actual working categories. If there is demand, we can add more interactive tree editing but let's use our imagination for now!

Proposed Changes to the Category Tree.

Please use the above entries to suggest changes to the category tree.

If we start getting a lot of traffic, I'll replace the current manual method with a more automatic version.

For the author field, just enter four tilde characters (~~~~) and your name and a timestamp will be inserted.


Category Add

  • Label for this suggestion: Add subcategory of Restiction Enzymes
  • Related to Label:
  • Author: Bill Flanagan ( at MIT) 09:23, 15 April 2009 (EDT)
  • Proposed New Material Category Name: Custom
  • Descending-from Existing Parent Category Name:Restriction Enzymes
  • Description: These enzymes are not part of catalogs but have been created by vendors on a one-off basis.
  • Comments: Many more are now available. It may be useful to reference vendor in some cases.
  • End of Add

Material Page Maintenance Process Suggestions/Comments

Please make any suggestions here for changing the process we're proposing/crafting. If we use standard formats during this process, we can both handle suggestions about process as specific changes are made in the hierarchy.

automatic link collection

The materials page unlike the protocols page still does not collect pages according to their tag. I think this is a very useful feature, since new materials pages would then appear here without an additional edit to the materials page. This should be set up for this page as well.

Best, Jakob Suckale 11:18, 6 April 2009 (EDT)

Bill Flanagan ( at MIT) 14:55, 16 April 2009 (EDT) Jakob, Protocols and materials do work differently but new materials do get added to the Materials page automatically. The difference is the content of the Material page relies upon using Categories. These are the tags at the bottom of the page. Any page that has a 'Material' category will be listed here. The tag is located in the page text generally on the last line. It looks like this:


Just to make sure people know that the categories are there, I added a sidebar box that shows the list of documents contained in documents. You can follow the category link to a page where all the docs that are part of that category are shown sorted alphabetically.

Per your comments, we need to show more people how they work. Materials is at least consistent in the way the links are created. But if people don't use the Category tags in the document, they will not show up.

Thanks for pointing this out. The box on the sidebar is a crude but hopefully useful first step in making a generally more useful set of tools.

I'm using the email message you sent today as a basis for continuing this effort.

More Search Information

Bill Flanagan ( at MIT) 19:02, 23 April 2009 (EDT)Still at it. I've now created a sort of generalized extension that will allow us to add searches like the Google Suggest search for any namespace. I've removed it from the core MediaWiki code I hacked it together with originally and now rolled it into a parser tag extension.

I'm now doing the same (generalizing) a way to allow adding new categories to any page without opening the page for editing. You do need to be logged in but it's still a lot more convenient. If you do choose to add category tags, they will still work but this clearly will be the way to do it.

I'm also thinking about introducing a way to view protocol and material information as a formal namespace. That would mean you will be able to apply the protocol: and material: tag to a search. This will allow us to organize the display of this information as it relates to those terms. It's a sort of shortcut but it may be useful. To make it work we need to apply a more rigorous rating function to the OWW content than a simple full text search. I'm investigating how to do this now. A good bet is to follow what academics and some companies are doing to organize the content of Wikipedia. What's good for the goose...

I should have the new linking in place within the next week. I'm also going to contribute the extension to MediaWiki: it's a good solution to a lot of sites problems using search within MediaWiki.

I'm also adding support to allow people to subscribe to Material and Protocol categories. Any page including those categories will be added to their watch list. This is a good time to also roll out work I did with Jason Kelly to define a way to include a list of someone else's watchlist pages and now some categories to their own watchlist.

I'll expand upon this list as I deploy the mods in a set of Community blog entries.


More Information

Bill Flanagan ( at MIT) 08:56, 28 April 2009 (EDT) I'm deploying the new category tools in test today and in production over the next few days. I held off until I completed a blog entry to describe it and (hopefully) to provide info to members on how to use it. My goal is to make this sufficiently transparent to allow uses with good lab and research experience but limited wiki markup experience to make entries. One issue I'm looking for help here and elsewhere in is a way to maintain the category trees themselves. When you make a new category, how does it relate to an existing one? In particular, there's no clear-cut way of handling aliases or even recognizing they exist. One way is to merge two categories into one by making one category a redirect to a more well accepted term. As to which of two terms is the primary one and which is an alias is a matter that will probably be determined by context or the member who puts more into providing the information. The category pages can be uses to show their place in a hierarchy. The category tree extension also does a great job at this. I know there are better ways but for now I'm trying to get something moving then make it perfect later.


I'm also interested in creating a new top-level page for equipment. I'm starting to collect the existing info in OWW that can be used as the basis for such a taxonomy. I don't want to go crazy defining a large empty set of categories; in fact, a goal would be to make sure than any new category contains at least one member or is a branch leading to a member. OWW seems to be much more about the 'what is' of the lab and not a format definition of what a lab could or should be. In that regard, using an external set of categories for something like equipment could be a good idea as long as only the items in the taxonomy that are in use are elevated to formal OWW categories. This implies a virtual taxonomy that 'will exist' as well as a real taxonomy that 'current does exist' within OWW.

I'm very much in favour of another top level page for equipment. We should probably shouldn't put it into the menu frame on the left until the content is mature. Together with consumables (=material) and protocols, it should be the 3rd major category of information on OWW. Jakob Suckale 12:58, 29 April 2009 (EDT)

Bill Flanagan ( at MIT) 13:58, 29 April 2009 (EDT)**100% agreement. I'm not proceeding to even revisit protocols until material is in better shape.


If anyone has an interest in assisting, either by providing input to the equipment category definitions or with requirements related to them, please contact me via external email(bill at openwetware dot org) or via OWW email. You can also leave comments either here or on my talk page.