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submit a new ontology page title is "undefined | undefined" it should have more meaningful title like "submit new ontology"

Need to add the usernames of the ontology administrator(s) to the admin report view.

On the current Properties tab for all ontologies in BioPortal, we only display the label, definition, and ID of each property in the Property Details pane.

Received a request on the support list to also display user defined properties. For example, the SCDO ontology has additional annotation properties attached to many of their properties:

Implement the synonym cloud view of CCV, as in:

After the recent integration of Bootstrap, the classes page for all ontologies has minor issues with alignment, e.g., poor text alignment in tables:

One example of such a page can be seen here.

Page should be refactored to lay out components in the Bootstrap grid system.

Implement the main view of CCV - the graph view:

Implement a view of ontologies using the search term, as in the screenshot below:

Implement the ontologies URLs view of CCV, as in:

Steps to reproduce:

1. Navigate to the account creation page in BioPortal.
2. Fill in the form fields and check the box to "Register for the BioPortal announcements email list".
3. Click the Create button, and notice that no confirmation email is ever sent to complete the subscription process.

I've confirmed that sending email isn't the problem (I can successfully receive an email for a password reminder). Also confirmed via the Mailman interface that email addresses don't get added to the list.

On a related note, the UI says that you are requesting a subscription to the announce list, but the production config file is actually pointing to the list address of bioontology-support. This should perhaps be bioportal-announce instead?

Steps to reproduce:

1. Navigate to Tools -> Ontology Browser page
2. Click the Submit New Ontology button
3. Select "private" from the viewing restrictions dropdown box. The select box that subsequently appears to allow users to select accounts for view permissions is clipped to a very small size - basically unusable.

Some ontologies that are present in the UMLS but are not imported in the NCBO BioPortal with the umls2rdf tool, contains CUI/STY information that are not parsed by BioPortal.

E.g.,
http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C3224

In that case the CUI information is in:
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P207
And the STY information is in:
"http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#P106

It's a pitty because without this, everyone using the Annotator and using the very useful feature t filter with STY cannot use for instance NCIt

For initial clarification, REST mappings are mappings that are created by end users, vs. the LOOM and SAME_URI mappings that are auto-generated by BioPortal at ontology parse time.

Steps to reproduce:

1. Navigate to any ontology in BioPortal and select the Classes link.
2. Select any class in the class hierarchy and click the Class Mappings tab.
3. Click the Create New Mapping button and fill out the dialog to create a new mapping.
4. After closing the Create New Mapping dialog, check the Delete checkbox for the mapping that was just created and click the Delete Selected Mappings button.

The "loading" spinner appears and nothing happens. Error message in the browser console window:

Uncaught ReferenceError: ontology_id is not defined
    at deleteMappings (bp_mappings.self-ba25ade….js?body=1:110)
    at HTMLAnchorElement.onclick (EFO?p=classes:699)
deleteMappings @ bp_mappings.self-ba25ade….js?body=1:110
onclick @ EFO?p=classes:699

Steps to reproduce:

1. Log into BioPortal and navigate to the Account Settings page.
2. Under the "Custom Ontology Set" section, click the "select ontologies" link.
3. Choose any one or two ontologies from the "Select Custom Ontologies" ontology picker.
4. Click the "Save Custom Ontologies" button.
5. Repeat steps 2 and 3. Notice that the list of ontologies in the ontology picker is limited to the ones that were initially selected in step 3. This makes it impossible for a user to modify the set if they are interested in making additions.

The root of the problem appears to be that this ontology picker widget is reused across many pages in the application. It is correct behavior on other pages to limit the options in the picker to the custom ontology set, but it's not correct to do this on the account page where the intention is to be able to see the full list of ontologies in order to modify the set.

We should probably use a one-off ontology picker on this page that always shows the full list of ontologies.

The BioPortal Virtual Appliance needs have a different header and footer than the production site hosted at Stanford.

URI do not get encoded properly (or validated) when users edit OWL ontology properties.
For example, users mistakenly put their names instead of URI into preferred name property. This data gets saved into triple store in the following manner:

<http://data.bioontology.org/ontologies/ACRONYM/submissions/1> <http://data.bioontology.org/metadata/authorProperty> <local:Firstname\u0020\Lastname> .
<http://data.bioontology.org/ontologies/ACRONYM/submissions/5> <http://data.bioontology.org/metadata/prefLabelProperty> <local:My Ontology Name> .

This creates problems for us when metadata graph is imported back into the triple store:

URI http://data.bioontology.org/metadata/OntologySubmission:8009 raptor error - Turtle URI error - illegal Unicode escape \u0020 in URI.

Steps to reproduce:

1. Navigate to the Annotator page
2. Click the "insert sample text" link
3. Click the "Get Annotations" button
4. In the resulting Annotations table, click any of the "filter" links in the table header row. Nothing happens...

Barry Smith notes the term References is not quite right in the search results label "Additional References from Other Ontologies". He suggests 'Reuses in', so, "Reuses in Other Ontologies".

Implement the definitions view for a search term (with counts) in CCV. Example:

After the recent Bootstrap integration, the styles for the badges on the Ontology Browse page have made the text difficult to read.

Go to e.g.,
http://bioportal.bioontology.org/ontologies/goslim_goa/
That is a view of
http://bioportal.bioontology.org/ontologies/GO

Pick up any class.
Try to create a manual mapping.
It is impossible to select the current ontology view in the pop-up. So once can not create a mapping from an ontology that is a view to some other ontologies (view or not).

The DataTables Formatted numbers plug-in is deprecated. DataTables 1.10+ has formatted number detection and sorting abilities built-in, so we should remove this plug-in and do any necessary code updates to use built-in functionality.

The changes we made to integrate Bootstrap resulted in overlapping UI components in the dialog that allows users to create new mappings. To view the dialog:

1. Navigate to any ontology in BioPortal
2. Click the Classes link
3. Select any class
4. Click the Class Mappings link
5. Click the "Create New Mapping" button

Should refactor the dialog to layout components in a Bootstrap grid.

stage.biootnology.org makes users load .js and .css scripts from bioportal.bioontology.org instead of from stage.bioontology.org. This is the case for NCBO Appliance as well.
http://bioportal.bioontology.org/javascripts/JqueryPlugins/autocomplete/jquery.autocomplete.css
http://bioportal.bioontology.org/javascripts/bp_crossdomain_autocomplete.js?_=1446073964103

setting BP_INTERNAL_SEARCH_SERVER variable in ioportal_config_env.rb doesn't do the trick

After the recent integration of Bootstrap, the Recommender page now has several presentation issues including poor component alignment and unreadable placeholder text.

There is a formatting problem with the Description field in the summary page for the IAO ontology -- lots of embedded HTML. {B Smith}

In the class tree, sometimes the lines with no classes show the bullet (arrow) icon, sometimes they don't (totally blank)

this problem pre-dated UI change

from https://jira.bmir.stanford.edu/browse/NCBO-1870

How to reproduce:
Log in with you user account.
Goes to "Custom Ontology Set" and add an ontology to your custom set that has a view in BioPortal e.g. MESH
Then go to browse (you will see only the set)
Click on the ontology in the set
=> Something went wrong.

@vemonet to complete with logs or other info we have observed locally.

As reported by a user: The "Recently viewed" list in the search box: I expected it to show me everything I recently viewed when logged in, but it seems to be limited to the ontologies I viewed on a particular browser. So my Firefox "recently viewed" is different from my Safari "recently viewed", even when logged in to the same account on both browsers.

The SCDO ontology has several properties, e.g. "modified", and "modified by" that are retrievable via the REST endpoint, but aren't showing up on the Properties tab.

After the recent integration of Bootstrap, the Annotator page has some minor issues with component alignment and placeholder text that isn't fully visible.

Occasionally it would be helpful to display sitewide notices, for example:

"Advanced ontology upload processing will be suspended until Sunday 2300 (GMT-8) for routine system maintenance."

... during periods when we have to turn off cron to reparse all ontologies after UMLS imports.

The link "Open concept homepage in tab" is broken. It points to:
http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C22187

The last part (conceptid=<>) should be URL-encoded but it isn't.

To reproduce:

1. http://bioportal.bioontology.org/ontologies/NCIT/?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25379#visualization
2. Right click on the term and click on "Open concept homepage in tab"

SNOMED ontology classes representation looks screwy. This issue is inconsistent but frequent; these issues also seen with other big ontologies (e.g., NCIT).

Specific issues Mark saw:

• classes table just runs right through the footer, and beyond
• right-hand section gets placed under tree widget
• sometimes class tree doesn't fill out visually, is mostly blank

Originally reported in JIRA: https://jira.bmir.stanford.edu/browse/NCBO-1870.

When someone submit a new ontology with the option “Metadata Only”, and fill all the information required, there is a message “something went wrong” after clicking on Add Submission.

If the NCBO Tree Widget (described here) is placed on a secure page, selecting any of the tree nodes results in mixed content errors from the browser.

There's a unadvertised test page for this widget on the BioPortal website. Changing the protocol to HTTPS and selecting any of the tree nodes will reproduce the mixed content errors (API key parameter removed from snippet below):

Mixed Content: 

The page at 'https://bioportal.bioontology.org/widgets/ncbo_tree.html' was loaded over HTTPS, 
but requested an insecure XMLHttpRequest endpoint 

'http://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.b…ntology%2FSNOMEDCT%2F123037004'. 

This request has been blocked; the content must be served over HTTPS.

Upgrade the DataTables plug-in to the latest version (1.10.13). We're currently on 1.10.7. DataTables is now available with a Bootstrap styling option. Should look at this since we recently refactored the UI to use Bootstrap.

Drop-down list of ontology groups is "totally screwy".

• AgroPortal ontologies should not be at the top.
• First should be UMLS, OBO, WHO, CTSA, caBIG, and then it doesn't matter.
• AgroPortal should go last

from https://jira.bmir.stanford.edu/browse/NCBO-1870

admin page doesn't list any ontologies when site is accessed via https protocol. It works fine when accessed via non-https protocol.

UI includes the following external script imports:
http://www.google.com/recaptcha/api/js/recaptcha_ajax.js
http://www.google-analytics.com/ga.js

These scripts are hosted on google servers which does 301 redirect to https. This causes user's web clients to handle this additional redirect.
It is more optimal to hard code https protocol for those URLS.

Create a custom Rails environment to support the ability to customize the appearance of the BioPortal UI when running as a virtual appliance. Should be able to use Rails.env.appliance? in the code.

Steps to reproduce:

1. Navigate to the Resource Index page.
2. Start typing anything in the "Search biomedical resources" text box at the top of the page.
3. Notice that autocomplete functionality doesn't work, and/or entering a term like "Heart" and pressing the "Search Resource Index" button results in no classes found.

Refactor the Projects page to take advantage of the fact that we recently integrated Boostrap. Layout components on this page in the Bootstrap grid.

I apologize if this is the wrong forum for this question. If this is the wrong forum, I would appreciate any assistance in pointing me to the correct support forum.

I recently installed version 2.4 of the NCBO BioPortal Appliance AMI on a m3.large aws ec2 instance. After uploading an ontology via an OWL file, I noticed that "Loading" messages would persist when accessing the Classes and Properties tabs of the ontology. This behavior was seen for both the standard default ontology packaged with the AMI and the ontology that I supplied. It would take a page refresh in order to load the content of these tabs. Is it known how to remedy this behavior.

In addition, I noticed that version 2.3 of the appliciance was available as an AMI on aws. I installed this version on the same instance type and was successfully able to access the Classes tab for both my provided ontology and the pre-packaged ontology that came with the appliance. However I did not see where Properties could be viewed. Are Properties unable to be viewed in version 2.3, or is there a setting that needs to be enabled in order to view them.

Thank you so much for any help provided and please let me know if any further information would help answer my inquiry.

Implement the number of BioPortal searches view (based on the Google Analytics data) of CCV. Example:

Implement the related images view of CCV, as in:

The UI implementation of CCV uses a number of graphical components that will need to be ported to existing BioPortal. These include:

Jssor (http://www.jssor.com/)
jQCloud (http://mistic100.github.io/jQCloud/)
D3 (http://d3js.org/)

Need to make Browse Ontologies link more visible [Mark]

from https://jira.bmir.stanford.edu/browse/NCBO-1870

Resizing a browser window down to a small size on either a desktop monitor or a laptop monitor causes the top navigation bar menus to properly collapse into a vertical mobile view (screen shot below). However, the same doesn't happen if you view BioPortal on a mobile device, i.e., the menu items are not collapsed into the vertical mobile-friendly view.

The "insert sample input" link on the Recommender page does nothing in Firefox (I'm currently using v 51.0.1). Works fine in Chrome and Safari browsers. Error message in developer console is:

ReferenceError: event is not defined

Thrown from this line in bp_recommender.js.