OBO-Edit: Documentation Week

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NOTE: This page is obsolete. Please visit OBO-Edit:_Help_document_OBO-Edit_2 instead.

The OBO-Edit Working Group has agreed to devote the week of June 30th, 2008, to testing OBO-Edit2 and writing user documentation. We appreciate your help!

Please let everyone know what you're concentrating on in your testing, and which help pages you're working on, so we don't duplicate each others' work. You can enter this information below.

Help pages

Below is the table of contents listing the current OBO-Edit2 help pages. If you are working on a page or section, please put your name after it, and commit your changes to svn (or send them to Nomi) as soon as you're done. If you've checked a page and it's up-to-date, please put "(ok)" after it. If you think we should add a new help page (or delete an existing one) please tell Nomi.

Midori has done a draft of a reorganized table of contents. Please comment!

Please note: the user guide pages linked here are not updated automatically--they are updated manually by Nomi. If you want to see your recent changes reflected here, please ask Nomi to update these pages.

OBO-Edit User's Guide (intro)

Viewing Ontologies

Filtering, Rendering & Searching

  • (midori: why don't you go ahead and reorganize these pages however you like. I trust your judgment. --Nomi) (Done! In fact, search docs pretty much done except for rendering. -midori)
  • Filters (Jen - ok)
  • Link Filters vs Term Filters (Jen - ok)(could be rolled into above section, both are small-melissa) (Done. --Nomi)
  • Building Filters (Not empty--was wrong page. Needs updating) This page is hopelessly out of date; the Attribute, Comparison, and Aspect sections should be folded into the Advanced Search (or just "Search") page; then this page should be deleted. I've changed my mind about this page; I'm now keeping it and using it as an overview of search parameters. -midori
    • Setting the Filter Mode (Jen - This page deleted) It still shows up in my svn checkout, but deleting it is the right thing to do. -midori (Oh, I see, it was deleted from svn but still on the wiki. Now it's gone. --Nomi)
    • Term Filters (Jen - part done - This documentation derails here because the filter button has not yet been added back and the ancestor/descendant menu has not been added back. I think it would make more sense to wait until this is complete to write the docs as screenshots will all soon be obsolete.) Actually, we could just lose this page. A lot of it duplicates the Building a Filter page, and both are superseded by the new search interface. -midori
    • Link Filters This could either be incorporated into Advanced Searching or kept separate; if we keep it separate, the screenshot and a few lines of text have to be updated. Let me know if you want me to do either. -midori
    • Compound Filtering Delete this page - it's completely, utterly, and happily superseded by the new search interface. It might be worth keeping the last section (move to the main search doc), on search speed, because I think that's still relevant. -midori (Done --Nomi)
    • Reusing Filters (ok -midori)
    • Searching Out of date. Copy the last section (Saving Search Results to a File) over to the main search doc, then delete this page. -midori
    • Filtering What does OE2 do about root picking algorithms (last section)? Rest of this page is out of date; I can update it, but need to know what to do with the root-picking bit. (midori)
    • Rendering Partially out of date; need decision about "render button" feature (SF 1958908) to update. -midori
    • Global Filters & Renderers (ok -midori)
    • Other Uses of Filters (ok -midori)
    • Custom Search Buttons It looks like this page is entirely out of date, because it depends on the old XML layout system. If so, delete it. -midori (Deleted --Nomi)
  • Advanced Searching (Nomi made a few changes) Because this search interface supersedes so much of the OE1 search documentation, this page could be renamed just 'Searching', or it could become the new 'Building a Filter' page. In any case, "advanced" no longer makes sense. Anyway, it looks nearly done, but would benefit from a bit more explanation of subqueries. I've added a couple of subheadings. Let me know if you want me to work on this any further. -midori
    • HTML Rendering (Jen - done: requires one more screenshot once ancestor/descendant menu is added to global filter interface.) This page should go under Rendering. -midori
    • Term Image Display Panel (Nomi - done) (Does this really belong under "Advanced Searching"? Is there a better place for it?) Hi Nomi, I wondered if it might make sense to have categories that mirror the categories under which the many components are grouped in the OBO-Edit menus. So, for example, Term Image Display Panel would be under the heading 'Viewers'. Does that seem good? (Jen) I think this should move to the "Tools" menu; it's neither an ontology viewer nor a search. (midori)


History (all ok)

Working with Data Adapters

The Reasoner (Amina)

Ontology Verification

Cross Products (Karen Eilbeck)



The Command Line

Frequently Asked Questions

  • How Do I Make a 'Slim' Ontology?
  • How Do I Find Terms Without an is_a Parent? (updated -midori)
  • How Do I Spell Check? (what is the current status of spell check? I know it's been disabled, but was there any plan to bring it back? No pressure; just useful to know for the docs -midori) (Not sure what you mean--it automatically does spell checking of the definition and name during the Verification Checks. What else do you want to spell-check? --Nomi) (I think I got confused because of the problem from a while back, where some spell checking thing was really slowing down load or save ... anyway, I can do this document based on current OE2 behavior and stop fretting. -midori)
  • How Do I Not Search Obsoletes? (midori; done)