OBO-Edit: OBO-Edit 2.0 Feature Request Prioritization

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Possible Items

Reasoner

  • 1762418 - Reasoner improvements
    • Summary - Improve the reasoner to take advantage of all the reasoning capabilities in the OBO spec
    • Estimated Time - 1 - 2 weeks
  • 1612882 - NCBO: reasoning over instances
    • Summary - Improve the reasoner by adding the ability to reason about instances (right now the reasoner ignores them)
    • Estimated Time - 1 week
    • Note - This would be very useful for any annotation tool (like Phenote), and could be used for a lot of annotation-related software, like search engines and annotation validators

Filtering

  • 1671379 - batch queries
    • Summary - Given a batch of ids or term names, display all the associated terms and their details in a table
    • Estimated Time - 3 - 5 days
  • 1604421 - part_of parent filter
    • Summary - Make it possible to do a search that says "find part_of ancestors with the following properties...".
    • Estimated Time - 1 week (infrastructure)
    • Special Issues - I've been working on a general proposal for an OBO query language that can handle this kind of thing. You'd specify a link filter to use when searching ancestors and descendants. Only links that match the link filter are traversed when finding ancestors (or descendants). This time estimate only includes the time required to modify the underlying infrastructure. The interface modifications would come free as part of the "rebuild filtering interface" feature request.
  • 1580619 - improving searching
    • Summary - Really an addendum to "rebuild search interface". This item contains a few sub-requests:
      • Allow keyword search dynamics for all searches - By default, automatically break search requests into tokens unless they are quoted
      • Automatically follow consider and replaced_by tags - If an obsolete term is returned, provide a mode to automatically follow consider and replaced_by tags and return *those* results.
    • Estimated Time - 4 - 7 days (as part of "rebuild filter interface" item)

Interface

  • - 1761449 - colored namespaces
    • Summary - Make terms from different namespaces appear in different colors. These would be configurable, but a set of colors would be assigned by default
    • Estimated Time - 3 - 5 days
  • 1756995 - additional info in ontology editor panel
    • Summary : Suggestion that we add a way to show additional term information, such as synonyms, definition, etc. right in the ontology editor panel. This would probably be implemented as a general system where the summary info can be manipulated with the scripting language (with some easy presets for people who don't want to mess with that).
    • Estimated Time : 1 - 3 weeks
  • 1753339 - graph editor
    • Summary : Jen wants to disable automatic centering of the focused term in "no animations" mode
    • Estimated Time : < 1 day
  • 1745864 - binning of anonymous terms in display
    • Summary : Remove anonymous terms from the display and add an "anonymous" grouping to the term editor panel where anonymous terms are displayed (similar to the "Obsolete" grouping for obsolete terms)
    • Estimated Time : 2 - 4 days
    • Note : This is essential for many cross-product projects
  • 1660882 - Tabular displays and data entry
    • Summary - Support fast spreadsheet-like ways of entering various sorts of mappings (term to term, term to dbxref, term to annotation?)
    • Estimated Time - 2 - 8 weeks (depending on the implementation we choose)
    • Special Issues - This one deserves a lot of conversation. I could create special-purpose tools for each scenario Chris proposes, or we can develop a general-purpose mapping solution. Chris's suggestion that we reuse components from Phenote is probably unworkable, given recent research I've done into how to accomplish an OBO-Edit/Phenote integration. If we constrain the problem a little and only try to solve the term maps to term problem, I think I can have a quite flexible solution in under 2 weeks. (Maybe we solve the term/dbxref mapping problem with the batch editing feature above)
  • 1655443 - Plugin for applying 'rules' to new terms?
    • Summary - Allow curators to specify rules to allow the automated addition of new synonyms (or other metadata?) based on the contents of a term. The example given is the automatic addition of a "downregulation" synonym when a "negative regulation of" term is added.
    • Estimated Time - 3 weeks / 3 days (see notes)
    • Notes - This feature request requires almost exactly the same infrastructure as "batch editing" above. If we have batch editing, this feature is just a tiny, minor extension.
    • Special Issues - We need to talk about how these are triggered. Do they get added as soon as you type in the term name, or as soon as you commit the term, or not until you save?
  • 1654414 - lock view not quite locked
    • Summary - Change the lock view behavior so that locked views cannot respond to new selections at all. This will prevent new selections from changing the expansion state of the tree and causing the terms of interest to scroll off the screen.
    • Estimated Time - 1 day
  • 1633306 - 'Remove all redundant relations' option
    • Summary - Have a menu option that deletes all links that are redundant because of transitivity
    • Estimated Time - 3 - 5 days
    • Notes - Sometimes we want to introduce redundancy too, by realizing links created by intersection implications. I suggest that I add the "realize this link" option as part of this feature, since they both require very similar implementations.
  • 1605593 - Make term property_values visible
    • Summary - OBO format allows users to add their own extensions to the format. Right now, OBO-Edit round-trips these values, but they aren't editable. This is a request to make these attributes visible and editable
    • Estimated Time - 2 - 4 days (no undo) / 1 week (undo)
  • 1604641 - mid level clone
    • Summary - Allow "deep" cloning
    • Estimated Time - 1 week
    • Special Issues - We need to talk about exactly what this means. Since "clone" reproduces parents and children, a truly "deep" clone would clone all the descendants and ancestors of the selected term. We probably want something a little smaller.
  • 1604638 - quick save
    • Summary - Provide a "Save" menu item with a hot key, so that you don't have to use the "save as" dialog all the time
    • Estimated Time - 1 - 3 days
  • 1604635 - center panel problem
    • Summary - Put a scrollbar on the text editor panel
    • Estimated Time - 1 - 3 days
    • Notes - This sounds easy, but it would be a nightmare to get this to look good in both squished and unsquished mode. This feature request probably isn't necessary anymore, because of the new maximize buttons on the screen components.
  • 1594409 Unclear choices under Add root]
    • Summary - Change the "Add root" and "Add type root" menu item names to "Add root class" and "Add root relation"
    • Estimated Time - 5 minutes
  • 1593531 - Set default relationship to something other than is_a
    • Summary - Add the ability to specify a different default relationship than is_a when a new term is added. This could probably be done by changing the existing menu item to read "Add new is_a child" and adding a new sub menu named "Add new child of type..."
    • Estimated Time - 1 - 2 days
  • 1576785 - Bring back scroll down
    • Summary - Reinstate auto-scrolling when a term is dragged near the edge of a term editor panel (or graph editor, I suppose)
    • Estimated Time - 2 days
  • 1570687 - graphviewer select
    • Summary - Provide a way to indicate which ontology editor panel or graph viewer will be used to display a selected term. I think the best way to do this is to change the ontology editor panel so that if a term is dropped on empty space, the term is displayed and selected (or a popup menu appears with that option)
    • Estimated Time - 1 - 2 days
  • 1570549 - jump to top of page
    • Summary - Add page up/page down key bindings to ontology editor panel (and probably shift+page up to jump to top and shift+page down to jump to bottom)
    • Estimated Time - 1 day
  • 1555463 - ability to add multiple terms at once
    • Summary - Add the ability to add multiple terms (I assume to a single parent) at once
    • Estimated Time - 2 - 3 days
    • Notes - This might be redundant with the "batch editing" request, but this one's a lot easier to do
  • 1550703 - remove disjoint_from etc from display
    • Summary - Remove the built-in relationships (disjoint_from, inverse_of) from the Relations section of the ontology editor panel
    • Estimated Time - 1 day
    • Notes - I don't think this is a great idea. I'd like to hear people's thoughts
  • 1537199 - Rendering options
    • Summary - Allow renderers to change the term background color, and use renderers when showing search results
    • Estimated Time - 3 - 5 days

Data Adapters

  • 1748284 - adding information about number of terms
    • Summary : Add some summary fields at the top of an OBO file to show how many terms are in each category
    • Estimated Time : < 1 day, but...
    • Special Issues : This just won't work. In general, an OBO ontology isn't contained within a single file. A user might decide to load 10 files, 3 of which have terms defined in a certain category, and this header information is useless. We need to know more about why this feature is being requested; maybe there is some way to give this users what he/she wants in a non-broken way.
  • 1680238 - Extended definitions
    • Summary - Add a way to see the definitions for all the is_a parents of the currently selected term
    • Estimated Time - 1 - 5 days (see Issues)
    • Special Issues - The estimate above is for building a stand-alone component to do this. But if we do [1] we get this request for free, because we can show definitions (and anything else we want) in the DAG Viewer or the Graph DAG Viewer.
  • - 1660775 dangling parents & non-advanced interface
    • Summary - Put the "allow dangling references" checkbox on the regular, non-advanced file loading interface.
    • Estimated Time - 1 day (or < 10 minutes, see below)
    • Notes - I think we should just go ahead and make "allow dangling" the default. Now that ontologies are being broken into more and more independent pieces, I think the current defaults are overly conservative.
  • 1581394 - Save separate OBO xml files
    • Summary - Provide an OBO XML adapter (that can at least save files) in OBO-Edit, and the ability to save every term in an ontology to a separate file.
    • Estimated Time - 1 - 2 days (write)/4 - 8 days (read/write)
  • 1567962 - ASCII Character Issue
    • Summary - Allow extended ASCII characters in OBO files
    • Estimated Time - 1 day ( + 2 - 4 days to add a verification check for people who DON'T want extended characters)
  • 1542525 - Duplicate ids
    • Summary - Warn if two terms with the same id appear in an OBO file
    • Estimated Time - 1 - 3 days
    • Special Issues - This can be done for duplicate ids within the same file, but it cannot be done for duplicate ids across multiple files. Duplicate ids across multiple files is an important part of the OBO spec.
  • 1540835 - clobber policy with flat ID spaces
    • Summary - Implement a mechanism to allow unqualified relationship type names to be automatically prefixed with a special, file-specific prefix
    • Estimated Time - 2 - 4 days
    • Special Issues - This would mean that part_of in GO would be a different relationship type than part_of in SO.

Verification

  • 1755435 - verification plugin synonym options
    • Summary : Add various quick fixes for the synonym text verification check
    • Estimated Time: 1 week
    • Special Issues : This feature request suggests that one of the fixes include the ability to change synonym scope, which in turn suggests that Jane thinks that the synonym check is taking synonym scope into account. Which it is not. To implement the expected behavior, I may need to change the basic functionality of the synonym check.
  • 1698351 - namespace
    • Summary - Add a quick-fix for missing namespaces
    • Estimated Time - 1 - 3 days
  • 1576900 - Warn against saving XX:<newdbxref>s
    • Summary - Add a validation check and auto-fix for empty dbxrefs. (While we're add it, we might as well check for empty synonyms and term names too)
    • Estimated Time - 1 - 3 days (just dbxrefs)/3 - 5 days (everything)

Other

  • 1754279 - Webcollaboration
    • Summary : Asking for some kind of (built-in?) web collaboration from OBO-Edit
    • Estimated Time : < 1 day - 3 years
    • Special Issues : We need to figure out what this user needs, and what we think is reasonable for us to pursue. This could be done just by educating this users about the existing collaboration possibilities via the history file mechanism (and maybe improving that mechanism to make it easier to use). On the other hand, we could implement an entire web-based OBO-Edit. A larger discussion is needed.


  • 1730961 - adding obsolete as static synonym category
    • Summary : Add a special synonym category that's present in every ontology called "Obsolete". When a synonym is added to a "consider" or "replaced_by" term as the result of obsoletion, mark that that synonym with the "Obsolete" category
    • Estimated Time : 1 - 3 days
    • Special Issues : Many people (like Midori) hate this idea because of the possibility that it provides redundant functionality to the consider/replaced_by mechanism massive confusion caused by using obsolete term names as synonyms at all
  • 1672096 - importing ontologies and caching
    • Summary - Add a mechanism for locally caching ontologies imported from a URL
    • Estimated Time - 1 week
    • Notes - This is essential for cross product projects and is needed by Phenote
  • 1664572 - Browsing ontologies other than those being edited
    • Summary - Original idea: Provide a way to do a read-only import of an ontology that can be browsed alongside the current ontology without saved out. Discussion evolved this idea into a general list of issues with OBO-Edit's multi-file save behavior.
    • Estimated Time - 2 - 4 weeks
    • Special Issues - I think this feature request is best taken as a list of problems to solve. The best solution to this problem would include several new features:
      • On the fly ontology imports - OBO-Edit can integrate new ontologies into the currently loaded ontology set [~ < 2 weeks]
      • Read only namespaces - Allow a namespace to be marked "read only", so that no edits may occur on any term in that namespace [1 week]
      • Smarter default save behavior - This would involve adding metadata to OBO-Edit so that it can try to save terms back into the same place from which they were loaded. [1 week]
  • 1663117 - automatic use of alt_id
    • Summary - Develop a general solution where OBO-Edit can update links that point to obsolete terms or alt_ids.
    • Estimated Time - 1 - 3 weeks
    • Notes - Chris claims that this is low priority in the feature request, but it actually is essential for Phenote and is essential for implementing a truly general import mechanism
  • 1620285 - Versioning
    • Summary - Provide a means for OBO-Edit to auto-increment version numbers
    • Estimated Time - 3 days - 2 weeks
    • Special Issues - This isn't as easy as it sounds, especially when many users may be editing the file concurrently. It may require some kind of server side versioning mechanism, which is a lot more work.
  • 1606072 - graphviz included
    • Summary - Include GraphViz with OBO-Edit, or provide some kind of auto-download mechanism
    • Estimated Time - 1 - 2 weeks
    • Notes - This may not be necessary any more, now that the graph editor is included
  • 1537197 - Term labels
    • Summary - Allow the creation of temporary categories that are discarded at the end of an editing session (or maybe are saved to a local file outside of the current ontology)
    • Estimated Time - 2 - 4 days (discard at end of session), 5 - 8 days (if categories can be saved)