bio-ontology-research-group / aberowl-orepo Goto Github PK

Autocompletion should work for terms that contain a space, such as 'pancreas development'.

In Manchester OWL syntax, single quotes must be used to specify a label which contains a space. They are not currently added by Aber-OWL, leading to invalid syntax.

Make it possible to autocomplete based on multiple fields. E.g., when typing "apopto go" I would like to have matches that match both "apopto" (apoptotic process, label field) and "go" (from the ontology field).

Add the tags to the ontology overview (Browse)

Change "reasoned" to "classified" in the tag name.

The autocomplete should not only list the matched name, but also its ontology and its class URI in smaller font (there is some cool JQuery UI widget for this kind of autocompletion).

The autocomplete should have an option to show all matches, not only the top 10.

Please define a new and working email address for owning ontologies, preferably your's (or the mailinglist, or a new mailinglist).

Add sample queries to the frontpage (same ones as on old AberOWL page, 'ventricular septal defect', etc.)

Alternatively, show the obsolete classes in grayish shade at the bottom.

Also, hide them from visualize, if possible.

For comparison, have a look at FYPO in BioPortal; it hides all the obsolete classes (they have an annotation property marking them as 'obsolete', or 'deprecated' in OWL). Normally, these classes appear directly under owl:Thing, which messes up the treeview and visualization.

It's sufficient to have a date for the versions, a special name field is not necessary.

Some ontologies don't use labels, e.g., APATREATMENT. The autocomplete does not work at all for these ontologies, so you cannot query. Solution would be to add the URI to the autocomplete, or at least the string after the last occurrence of "#" or "/" (preference for "#").

Add a simple text-based class search to the front page. The results should list matching ontologies, classes, and - if only one class matches or if one of many matching classes is selected - the complete information on this class.

Would it be possible to add a simple class search, with autocomplete, just above the treeview, which allows jumping straight to the class in the treeview browser?

There should be, for each ontology, an "Inconsistent" (red) or "Consistent" (green) tag, and also a "Incoherent" (red, if contains classes equivalent to owl:Nothing) or "Coherent" (green) tag.

The annotation properties used to refer to definitions, and sometimes labels, and basically most of the other annotations we would like to display, may be different for each ontology. BioPortal makes this information available for each ontology; if available, this information should be used.

Furthermore, this information should be captured (with reasonable defaults, like rdfs:label for label, etc.) in the upload form.

To follow bio-ontology-research-group/AberOWL#1

If the "Query" tab is empty, PubMed and SPARQL queries should default to a simple subclass/equiv search for the class that is currently selected in the Treeview Browser.

There seems to be a slightly hard to reproduce bug in the treeview. To try to reproduce:
Unfold 1 class with many subclasses.
Then unfold three classes on the same level.
Unfold some classes below and close again.

What happens is that if you open and close a subclass of the last one, sometimes the last unfolded class above disappears.

A possibly related bug: if you quickly open and close subclasses, the treeview breaks entirely in that it does not respond any longer to queries.

Probably configured prefix

Add the object property hierarchy (and possible datatype and annotation properties).

Replace QueryParser by manually created BooleanQuery (so that things like "-" and "+" and "(" won't have semantics.

Sort matches by length; exact matches should be listed at the top.

Add possibility to download ontologies, their versions, and all ontologies to API.

Add all the versions (with properly formatted date) to the Overview page, including the Download option of each version. Perhaps only list the three most recent versions, adding a link to retrieve all the versions that are stored.

There should be a visualization/browsing option for ontologies included.

Add documentation on the new API

Like on front page, just make available for each ontology, in a tab.

If possible, merge query and overview pages, so that one less click is required to query the ontology. Alternatively, use anchors (#) to structure the menu for individual ontologies.

this will make orepo sad

Make older versions of an ontology available to the AberOWL API on request so that they can be queried. Keep the classified version of the ontology for a certain duration (or the duration of a session) so that it will not have to be reclassified, but make sure that the classified version is discarded after a while.

Numbers should be separated by commas after 3 digits for better readability.

Use all annotation properties (and their labels) to show all the information about a class.

The search button should be on the left, not on the right.

Set fields of ontology name/overview to uneditable when not having the admin rights.

To reproduce the bug, just select a completion with a "," in the label and then type Backspace.

Enable browsing of hierarchical properties, like part-of, develops-from, etc. For this, axioms patterns need to be queries, e.g., ?X SubClassOf: part-of some ?Y for part-of.

I think "visualize" can be removed, as the functionality is (will be) entirely supported by "browse".

Keep track of answers to queries; in particular, track often did classes in an ontology appear in a query. Use this as "accesses" to an ontology.

There should be an "ontology" of metadata associated with the ontologies, that would allow us to show all the necessary information.

Add the same kind of selectors as on the frontpage to each ontology, so that you can query within an ontology for superclasses, for example.

Also 'show' button on autocomplete and query results.

Sort ontology list alphabetically

Rename to "Remove ontology from AberOWL repository"

Set up a release pipeline, including basic tests (basic queries, load tests, etc.).