Talk:OBO-Edit: OBO-Edit 2.0 Feature Request Prioritization

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How To Use This Page

Please list the features you are most interested in adding to OBO-Edit 2.0 here. To add your list, click the Edit link in the Features section, and add a new entry to the wiki using the following template:

Wiki Template Example Code Example Results

=== Your name ===
# SourceforgeID
# SourceforgeID
#* Optional comment about item above
# SourceforgeID

=== John Boy ===
# 1762418 (Reasoner)
# 1762416 (OWL)
#* We need OWL Adapters if we want the DL community to take us seriously
# 1761395 (New Filter interface)

John Boy
  1. 1762418 (Reasoner)
  2. 1762416 (OWL)
    • We need OWL Adapters if we want the DL community to take us seriously
  3. 1761395 (New Filter Interface)

Please add items in order of preference. Feel free to add any additional comments you want after your list. If you're a wiki master, feel free to hyperlink your sourceforge ids to the sourceforge feature request page (see John Day-Richter for wiki syntax examples).


John Day-Richter

  1. 1761395 (New Filter interface)
  2. 1762416 (OWL)
  3. 1762418 (Reasoner)
  4. 1613629 (Database Adapter)

Of course, my vote probably shouldn't count...

Erika Feltrin

  1. 1613629JDBC database adaptor (Database Adapter)
    • I think that have the GO in a Chado shema could be very useful for having a standard GO shema. Chado is a relational schema and it is a modular schema, designed in such a way as to allow the addition of new modules for new data types. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny.
  2. 1664572 Browsing ontologies other than those being edited (Other)
    • I am very interested in this feature since I often load two or more ontologies in the same session and I need to save just one of them.
  3. 1671379 batch queries (Filtering)
  4. 1533914 search by number range (Filtering)
  5. 1604421 part_of parent filter (Filtering)
  6. 1699359 search and replace (Filtering)
  7. 1660882 Tabular displays and data entry (Interface)
  8. 1756995 additional info in ontology editor panel (Interface)
  9. 1593531 Set default relationship to something other than is_a (Interface)
  10. 1612882 NCBO: reasoning over instances (Reasoner)
  11. 1762416 OWL data adapter (Database Adapter)
  12. 1604638 quick save (Interface)
  13. 1710747 better labelling of search tabs (Filtering)
  14. 1570687 graphviewer select (Interface)
  15. 1756733 newlines in def (Verification)
  16. 1698351 namespace (Verification)
  17. 1576900 warn against saving XX:<newdbxref>s (Verification)

Jennifer Deegan

It seems to me that OBO-Edit 2 can't be released until the features already added have been made useable and have been fully tested. Therefore anything that is required to get the graph editor up and running would be my priority, before other features are added:

  1. 1753339 - graph editor

Real time-savers:

  1. 1761436 - Dialog box for approving reasoner results en-masse
  2. 1633306 - 'Remove all redundant relations' option
  3. 1604638 - quick save
  4. 1694190 - human-friendly history output
  5. 1680238 - Extended definitions
  6. 1542525 - Duplicate ids
  7. 1755435 - verification plugin synonym options
  8. 1756733 - newlines in def
  9. 1698351 - namespace
  10. 1576900 - Warn against saving XX:<newdbxref>s
  11. 1570549 - jump to top of page

Nice to have:

  1. 1699359 - search and replace (We have a script that can do this.)
  2. 1526122 - create a subset by ID list (We have a script that can do this.)
  3. 1533914 - search by number range
  4. 1655443 - Plugin for applying 'rules' to new terms?
  5. 1654414 - lock view not quite locked
  6. 1593531 - Set default relationship to something other than is_a

Interesting to develop:

  1. 1660882 - Tabular displays and data entry
    • I am currently developing terms in a spreadsheet and adding them in to the file with a script so having a sort of intergrated spreadsheet might be useful.
  2. 1604641 - mid level clone


  1. 1594409 - Unclear choices under Add root] (I could do this one if you would like volunteer labour)

Midori Harris

Features I would certainly use:

  1. 1655443 (applying rules)
  2. 1604421 (part_of parent filter)
  3. 1633306 (remove redundant relations)
    • It would also be cool to have a quick-fix option to remove an individual redundant relation at the press of a button.
  4. 1576785 (scroll down)
    • If this is implemented, several of the other verification requests will be easier for us to deploy ourselves.

Features I can envision myself using:

  1. 1762418 (Reasoner)
  2. 1761395 (New Filter interface)
    • Might as well do this, since I'm voting for some of the specific things that "come free" with it.
  3. 1761436 (en masse reasoner approval)
  4. 1756995 (additional info)
  5. 1745864 (anonymous term bin)
  6. 1604641 (clone)
    • I would also like to be able to clone just all text fields and parent in currently selected path (as opposed to all parents and children).
  7. 1535974 (extra search category)
  8. 1660882 (tabular things)
  9. 1694190 (history output)
  10. 1605593 (property values)
  11. 1604638 (quick save)
  12. 1537199 (rendering)

Features that I think ought to be developed, whether I use them myself or not:

  1. 1762416 (OWL)
  2. 1613629 (Database Adapter)
  3. 1567962 (extended characters)
  4. 1612882 (Reasoning over instances)

Random other comments:

  • Of the ones I haven't listed, I'm neutral on most of them. There are one or two that I would actually vote against (1748284, 1730961).
  • A comment on 1570549 (page up/down etc.) - it already does this for me, with the OS page up, page down, home and end keys.

Karen Christie

Things I would personally like, from the point of view of a regular but rather simplistic user/editor:

  1. 1761395 Rebuild filtering interface
    • This one would be really important to me. I don't need complex filtering often, so I don't remember how to do it. Thus, I find a case where it would be useful, I just can't use the existing filtering easily enough or quickly enough to ever bother. When others at SGD ask me about complex queries, I've showed them where the help is, but generally by the time I mention link vs term filtering, they glaze over if they hadn't already, so I think improving this would be really helpful for making OBO-Edit a little less intimidating.
  2. 1710747 better labelling of search tabs
    • I would love this one, since much of what I use OBO-Edit for is to find terms for annotation, so I often do lots of searches in a row and it becomes difficult to quickly identify the correct search.
  3. 1766461 - clear tabs without search settings reset
    • This would also be really helpful when I'm searching for terms and have a bunch of tabs open.
  4. 1753339 - graph editor
    • I think I would prefer this behaviour too to have more flexibility on what part I'm viewing when I'm editing.

Comments on items where I might want them, or something related:

  1. 1756995 - additional info in ontology editor panel
    • I don't necessarily care where it gets shown, but I would love to have a view where I can see other info more easily. For example, I can't see the def and the comment at the same time and sometimes it would be really useful to be able to see them both without having to keep clicking to change which tab you are viewing.
  2. 1580619 - improving searching
    • I think I might like the ability to have keyword searches of names or 'names and synonyms', but I wouldn't want to lose the ability to do exact searches, so if we do this, I'd want to have a way to toggle it on or off.
  3. 1604635 - center panel problem
    • What I'd really like here is more flexibility in moving the boundaries between various components, so that I can resize on the fly as desired. There are some boundaries that don't seem to have adjustable boundaries. Scroll bars might be useful too when the window gets below a minimum size, but I'm not sure I'd want to seem them all the time.

Comments against:

  1. 1730961 - adding obsolete as static synonym category
    • I agree with Midori. At the last GO meeting, it was suggested that we should remove some of these bizarre synonyms that used to be term names, especially if they were obsoleted because they just don't belong in the ontology as terms at all.
  2. 1620285 - Versioning
    • GO is already versioned via CVS, which was designed specifically for data versioning. It seems that it is better to leave the official versioning to existing software which is specifically designed for that purpose. I wouldn't mind if OBO-Edit read that comment and displayed it somewhere, but I don't think we should duplicate the versioning control which can already be done by CVS or a number of other similar softwares.
  3. 1576785 - Bring back scroll down
    • I found the scrolling behaviour really hard to use when the terms were more than a little bit apart. In contrast, I find it very simple to split the screen into two panels so that I can see both my source and my target terms. Thus if this is implemented, I would vote against it being done in a way that affects the behaviour when you drag from one panel into the other.

Question on:

  1. 1754279 - Webcollaboration
    • I'm not sure it's really necessary to do anything via OBO-Edit here. After all, when GO began it had exactly the same issue, a number of different editors working in different locations around the world. We addressed that issue by using CVS for versioning control. More recently, we have been doing Webex content meetings so that a number of people can work together with one person running OBO-Edit, but everyone can see the same screen. This worked really well for the three of us who worked on rRNA processing content development.

I haven't commented on, and have no strong opinion on, the majority of items relating to data adaptors or reasoning.

  1. The reasoning, I don't use and probably don't completely understand. The one thing that really bugged me during cross-product testing is that is seems really silly for the reasoner to infer a link that is already there; if it was already there then it IS a link and is NOT inferred. I did like Chris's comment in the item about mass approval of reasoner results that once they were approved they would just become normal is-a links. It makes a lot of sense to me that once they were approved as being valid that they would just be normal links.
  2. For the data adaptors, it just seems like some of that may be a higher level of decision making about where GO needs to be going that may be more appropriate with input from the GO managers group. I don't feel like I have enough of a sense to really comment on these issues.

Jane Lomax

  1. 1664572 Browsing ontologies other than those being edited
  2. 1761395 Rebuild filtering interface
  3. 1655443 Plugin for applying 'rules' to new terms?
  4. 1660882 Tabular displays and data entry
    • Should also be useful for generating mappings files
  5. 1699359 search and replace
  6. 1604421 part_of parent filter
  7. 1671379 batch queries
    • I added this last one because I THINK it's the same infrastructure as 'Plugin for applying 'rules' to new terms?', and if so we may as well have both