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allow to manually specify version of submitted ontology (internal)

From [email protected] on November 12, 2008 16:38:20

What capability do you want added or improved? Allow to manually specify the version in ontmd (instead of having that
version be automatically assigned with the current date/time) Where do you want this capability to be accessible? In the ontmd tool when called directly (not from the main front-end) and
with a special parameter as this is a capabality for internal usage.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=46

Handle non-UTF8 and UTF8 inputs

From [email protected] on November 12, 2008 10:41:56

What steps will reproduce the problem? Voc2RDF case:

  1. Use non UTF-8 contents
  2. Conversion completes OK.
  3. Proceed with registration
  4. Ontmd fails to load the generated ontology What is the expected output? Either 1) better error report that the input is not in UTF-8 even the
    conversion to RDF if performed;
    or 2) Do the conversion to UTF-8 automatically and continue successfully in
    ontmd. What do you see instead? Ontmd fails with a message like this:

Cannot read RDF model:
/Users/Shared/mmiregistry/ontmd/preuploads/voc2rdf/1226497416068 :
com.hp.hpl.jena.shared.JenaException : rethrew:
org.xml.sax.SAXParseException: Invalid byte 2 of 2-byte UTF-8 sequence." Please use labels and text to provide additional information.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=43

visualizations don't show instances

From [email protected] on November 10, 2008 10:27:08

What steps will reproduce the problem? 1. Go to the ontology browser and select an ontology
2. Click on the Examine link, then on the Visualize tab What is the expected output? What do you see instead? I expect the visualization that comes up to show instances, in addition to classes. As far as I can tell
it only shows classes. So none of the terms from our ontologies are visible.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=35

don't reversion terms with every revision of ontology

From [email protected] on November 11, 2008 13:13:40

What steps will reproduce the problem? 1. Create new version of existing ontology.
2. Look at ontology output in HTML. What is the expected output? What do you see instead? We want the terms to maintain their older URIs if they are not changed. Right now all the terms
get new URIs, corresponding to the new version of the ontology. Please use labels and text to provide additional information. This has been discussed on [email protected] and internally. While we can't be
absolutely sure, this is probably (>95%) the right approach.
To do this, you'll have to parse all the concepts in the ontology, determine which ones have
changed, and only generate new URIs with new revisions for the changed ones. All the other
URIs will stay the same.
I wanted to give this a milestone "UrgentAfterWorkshop", but couldn't figure out how.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=39

URIs have # signs instead of / before terms

From [email protected] on November 04, 2008 21:33:53

What steps will reproduce the problem? 1. create voc2rdf vocabulary (may also happen with regular ontology, not sure)
2. go through process to submit to repository
3. go to HTML presentation of URI, e.g., http://mmisw.org/ont/mmitest/20081105T041952/Discipline.html What is the expected output? What do you see instead? Expect to see URIs with / before term, instead they have # before term What version of the product are you using? On what operating system? Latest release Please provide any additional information below.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=27

double-click on visualization component goes to bioportal

From [email protected] on November 12, 2008 20:57:29

What steps will reproduce the problem? 1. Go to browse, click on Explore for an ontology
2. Click on Visualize tab
3. Double-click on a displayed component What is the expected output? Something that works. What do you see instead? It redirects to Bioportal site. What version of the product are you using? Beta

Please provide any additional information below (particular ontology/ies, text contents of
vocabulary (voc2rdf), operating system, browser/version (Firefox, Safari, IE, etc.), screenshot,
etc.)

Original issue: http://code.google.com/p/mmisw/issues/detail?id=47

Why need to re-login to edit own ontology file?

From [email protected] on November 05, 2008 13:19:25

What steps will reproduce the problem? 1. Load new ontology to repository
2. Try to edit ontology using "edit ontology" button 3. What is the expected output? What do you see instead? Expect to see the ontology metadata and have the ability to edit it.
Instead, I'm asked to log in again (despite already being logged in). Once,
I re-login, the view is of the ontology and its metadata is blank. What version of the product are you using? On what operating system? test version. Mac OS 10.4.10 Please provide any additional information below. Generated this ontology file using Voc2RDF web service and then used the
submit to repository button.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=30

mapping from versioned to unversioned terms and vice-versa

From [email protected] on November 12, 2008 22:27:56

What capability do you want added or improved? (1) When each term is put in an ontology, it should include a mapping that explicitly points to
the unversioned term as well; and (2) when an unversioned output is delivered, the unversioned
terms should have a mapping to the versioned terms. Where do you want this capability to be accessible? In ontology relationships: (1) in the original ontology (2) in the unversioned output What sort of input/command mechanism do you want? Should happen automatically. What is the desired output (content, format, location)? In addition to having the relations in the ontologies, we should modify the HTML to show them. Other details of your desired capability? Probably need to build the relations concepts (inverse):
isUnversioned
isVersioned What version of the product are you using? Please provide any additional information below (particular ontology/ies, text contents of
vocabulary (voc2rdf), operating system, browser/version (Firefox, Safari, IE, etc.), screenshot,
etc.)

Original issue: http://code.google.com/p/mmisw/issues/detail?id=49

sparql response is empty

From [email protected] on October 16, 2008 21:43:00

What steps will reproduce the problem? 1. Open http://mmisw.org/ont_tests/sparql.html and write the query:

PREFIX rdfs: < http://www.w3.org/2000/01/rdf-schema# >
CONSTRUCT { ?s ?p ?o } where{?s rdfs:label ?o. } LIMIT 20

  1. Summit query
  2. Response is:
    <rdf:RDF
    xmlns:rdf=" http://www.w3.org/1999/02/22-rdf-syntax-ns# "
    xmlns:rdfs=" http://www.w3.org/2000/01/rdf-schema# " >
    </rdf:RDF> What is the expected output? What do you see instead? Expected output should be non-empty.

Note that the query:
CONSTRUCT { ?s ?p ?o } where{?s ?p ?o. } LIMIT 20
works ok. So, the problems seems related with URIs being included in the query.

I already confirmed that there is no encoding/decoding problems: the server
gets exactly what is submitted.

So, the problem should be in the way the query is processed. But I'm
following the same logic as with the grails-based registry (which
presumably works ok).

Here is the main source: https://code.google.com/p/mmisw/source/browse/trunk/org.mmisw.ont/src/org/mmisw/ont/OntGraph.java See the getRDF(String sparqlQuery) method, which is the java version
of the same groovy method in: https://code.google.com/p/remembermyid/source/browse/trunk/Registry/grails-app/services/SparqlService.groovy

Original issue: http://code.google.com/p/mmisw/issues/detail?id=1

make more room for ontmd in aquaportal front-end

From [email protected] on November 10, 2008 14:07:11

What steps will reproduce the problem? 1. pick an ontology in the browse list in the front-end
2. click "submit new version" or "edit ontology metadata" What is the expected output? What do you see instead? The metadata editor should be fully visible in the area.
It is not. In concrete, the Contributor(s) field is half visible. Besides,
if I click the tooltip icon, the popup is almost entirely hidden so the
user won't be able to read read anything.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=37

want sorting of columns in Browse view

From [email protected] on November 12, 2008 15:38:27

What capability do you want added or improved? I so want the columns to be sortable. Particularly timestamp. Where do you want this capability to be accessible? In the Browse view of the front end. What sort of input/command mechanism do you want? Click on the column to sort. What is the desired output (content, format, location)? Sorted display. Other details of your desired capability? Multiple sorts should maintain previous order (i.e., in-place sorting, so you get the effect of
multi-level sorting). What version of the product are you using? Please provide any additional information below (particular ontology/ies, text contents of
vocabulary (voc2rdf), operating system, browser/version (Firefox, Safari, IE, etc.), screenshot,
etc.)

Original issue: http://code.google.com/p/mmisw/issues/detail?id=44

show the "owl" and "html" links

From [email protected] on November 10, 2008 14:11:12

What steps will reproduce the problem? 1. click any of the entries in the browse list in the front-end What is the expected output? What do you see instead? The read-only view of the metadata should include hot links to the ontology
itself and the HTML version (as it's the case when the ontology was just
uploaded). What I see is just the URI but not any hot link associated.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=38

Resolve latest version

From [email protected] on November 01, 2008 21:11:31

A request to: http://mmisw.org/ont/mmi/parameter returned a 404 error even though that the following versions were available: http://mmisw.org/ont/mmi/20081031T011613/parameter http://mmisw.org/ont/mmi/20081101T215945/parameter Note: in general, ONLY versioned URIs are to be stored in the database. Ont
need to check the available version for a given "un-versioned" ontology URI
query and return the latest ontology available.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=23

single-click access from Browse to rdf and html versions

From [email protected] on November 13, 2008 13:44:37

What capability do you want added or improved? The browse interface to have single-click access to both RDF and HTML forms of each vocabulary Where do you want this capability to be accessible? The Browse interface of the front end -- not sure exactly where to put it What sort of input/command mechanism do you want? Named links, as in 'RDF' and 'HTML' What is the desired output (content, format, location)? If HTML is clicked, browser window is replaced by HTML information. If RDF is clicked, RDF file is
downloaded. Other details of your desired capability? latest and unversioned would both be desirable. Of course, so would other features, like
_versions or whatever. Hmm, I'm beginning to appreciate why replacing the front end might be
necessary. What version of the product are you using? Please provide any additional information below (particular ontology/ies, text contents of
vocabulary (voc2rdf), operating system, browser/version (Firefox, Safari, IE, etc.), screenshot,
etc.)

Original issue: http://code.google.com/p/mmisw/issues/detail?id=50

Ontology Registry home page credits

From [email protected] on November 04, 2008 21:43:00

What steps will reproduce the problem? 1. Go to mmisw.org/or What is the expected output? What do you see instead? Expect to see material crediting bioportal, but no What version of the product are you using? On what operating system? Please provide any additional information below. I can't remember if we discussed text. How about something like "This portal was made possible
thanks to resources from National Institute of Health's BioPortal project. We thank the BioPortal
team for their collaboration." Your improvements welcome.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=28

URIs in voc2rdf owl files still have _tmp_ in them

From [email protected] on November 04, 2008 21:31:25

What steps will reproduce the problem? 1. create default voc2rdf vocabulary
2. go to submit to registry
3. both after metadata is entered, and after submission, look at property names What is the expected output? What do you see instead? The URIs should have the authority in them; instead I see tmp What version of the product are you using? On what operating system? Umm...today's? Please provide any additional information below.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=26

Republish externally managed ontologies

From [email protected] on November 11, 2008 16:32:12

What capability do you want added or improved? The ability to accept a URL of a remote ontology, read in that ontology, and provide MMI
ontology services that correspond to the ones provided for local ontologies. I think these
services include:

  • look up a URI for a term in the ontology, and find the term and its metadata
  • keep track of versions of the ontology, and changes to each version
  • find terms and definitions in the ontology using our search capabilities
  • present browsable descriptions of the ontology, its metadata, and its terms
  • provide a mappable resource in the form of a URI; this may be one of the following
    • a URI specified within the original ontology, in its namespace
    • a URI that builds on the original ontology's namespace (adding /term or #term)
    • a URI in mmisw's namespace that represents the term itself (dicey)
    • a URI in mmisw's namespace that represents an alias to the term (dicey)
    • a URI in mmisw's namespace that represents a new resource, call it a 'term reference' (dicey)
      See last section for more discussion of this. Where do you want this capability to be accessible? Ideally, seamlessly wherever our internally managed ontologies are kept. What sort of input/command mechanism do you want? The same as when people currently submit an ontology they have edited/created with Protege: a
      web interface that has a button for uploading locally or from the web What is the desired output (content, format, location)? As seamless as is reasonable with the existing MMI internal ontologies. Other details of your desired capability? Next step will be to configure the polling of the address, so that changes are automatically
      picked up and versioned. What version of the product are you using? Please provide any additional information below (particular ontology/ies, text contents of
      vocabulary (voc2rdf), operating system, browser/version (Firefox, Safari, IE, etc.), screenshot,
      etc.)

If an ontology provider does not version its own ontology, than none of the ontology releases will
have any versioned resource URIs. So if we provide versioned URIs (in our namespace) for their
ontology, that are additional to the unversioned URIs in the ontology, we are not creating a
duplicated resource space. In that scenario, the unversioned URI in our name space will not be a
resource URI; it can both provide the services we provide for the ontology (description, html,
metadata, visualization) and offer the redirect to their page (if any) and the actual resource they
define for their ontology.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=42

Support URIs other than the autogenerated one

From [email protected] on November 11, 2008 13:39:21

What steps will reproduce the problem? 1a. User specifies an alternate URI (e.g., a URN,or remote URL) for their term (in vocab or
ontology) or whole ontology OR
1b. User specifies they want a URN, not a URI
2. User submits vocab or ontology

What is the expected output?
A. URI for term is set appropriately, instead of to the default (a: to their value; b: to appropriate
URN)
B. Service to resolve all known URIs knows how to get metadata and data (RDF) for this URI,
whether term or ontology
C. Various other features of the registry have to be modified accordingly. Please use labels and text to provide additional information. a. I think we resolve the default URL, but indicate it is not the resource URI
b. If the URI is a resolvable URL, point to it using some button (?)
...

Original issue: http://code.google.com/p/mmisw/issues/detail?id=40

include URIs for Topic in the ontmd Topic URI field

From [email protected] on November 12, 2008 16:30:57

What capability do you want added or improved? When the user selects a topic in OntMD, auto-fill the Topic URI. Where do you want this capability to be accessible? In OntMD's first metadata page. If easy, also in voc2rdf, but there the RDF metadata must be
filled. What sort of input/command mechanism do you want? Existing 'choose' mechanism. What is the desired output (content, format, location)? Whatever URI corresponds to the topic selection in that vocabulary. Other details of your desired capability? What version of the product are you using? Please provide any additional information below (particular ontology/ies, text contents of
vocabulary (voc2rdf), operating system, browser/version (Firefox, Safari, IE, etc.), screenshot,
etc.)

Original issue: http://code.google.com/p/mmisw/issues/detail?id=45

select main theme from a number of vocabularies

From [email protected] on November 01, 2008 21:04:44

j: Eventually we'll want the main theme to be a selection from a number of
vocabularies. Not sure if we'll want every term in each vocabulary though,
or if we'll want the name to match the vocabulary's term. Probably "all of
the above", knowing how these things work. For now, we just need to
populate this from an easily edited table that has 'menu selection', 'term
name', 'uri', and 'description'. The third and fourth make up the tool tip
for each selection. The URI goes into the URI field, and the menu selection
and description go into the drop down). Or something along those lines.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=21

Error should be more friendly when user tries to register and usename already exists

From [email protected] on November 05, 2008 05:10:29

What steps will reproduce the problem? 1. try to register a new user with existing username What is the expected output? What do you see instead? The username [username] already exists, please use another one... or
recommend one [username1]...

Error produced:

Hibernate operation: could not insert:
[org.ncbo.stanford.domain.generated.NcboUser]; SQL [insert into
bioportal.ncbo_user (username, password, email, firstname, lastname, phone,
date_created) values (?, ?, ?, ?, ?, ?, ?)]; Duplicate entry 'bermud' for
key 2; nested exception is
com.mysql.jdbc.exceptions.MySQLIntegrityConstraintViolationException:
Duplicate entry 'bermud' for key 2

Original issue: http://code.google.com/p/mmisw/issues/detail?id=29

unversioned and latest-version requests

From [email protected] on November 03, 2008 19:54:04

(1) request: http://mmisw.org/ont/someAuth/-/someVoc response: the most recent version available of the ontology.

Should this be handled with a redirect?

(2) request: http://mmisw.org/ont/someAuth/someVoc response: the most recent version of the ontology but with
omv:version="unversioned" and some other attribute used to determine which
version was actually retrieved.

Original issue: http://code.google.com/p/mmisw/issues/detail?id=24

correctly relate new term versions to old

From [email protected] on November 12, 2008 22:20:14

What capability do you want added or improved? When a new version of a term is generated, some ontology magic should relate it to the previous
term, and the previous term should be related forward. Where do you want this capability to be accessible? In inferencing engines, and in metadata for the term. What sort of input/command mechanism do you want? Should happen automatically, no user input required. What is the desired output (content, format, location)? Ontology relationships that carry the relationships; not sure where they should live. Other details of your desired capability? You could create all these relationships (at least the forward-mapping ones) in a second
ontology, that manages all the versioning. It will essentially contain a version history for all term
changes, expressed as newOne IsNewVersionOf oldOne, or whatever the appropriate relationship
is; and vice-versa. (Well, vice-versa is the inverse, so it is a free inference.)

Hmm, as I think about it more, probably better if that statement can be made in the original
ontology.

I have no idea what the right relationship is, though. Don't think SKOS has one. What version of the product are you using? Please provide any additional information below (particular ontology/ies, text contents of
vocabulary (voc2rdf), operating system, browser/version (Firefox, Safari, IE, etc.), screenshot,
etc.)

Original issue: http://code.google.com/p/mmisw/issues/detail?id=48

Front-end doesn't inform users that their search contained no results

From [email protected] on November 05, 2008 22:37:45

(from Sara Haines' email today)

(big bug?) http://mmisw.org/or/search Chose "cf" vocab and search term "temperature"
Typed in a search term and it did absolutely nothing.

If only "temperature" search and no vocab chosen got this:

"There is no data to support this query at this time or you've encountered
an error. If you have questions, please contact us at
[email protected] (snip the rest)"

Where's the beef?

Original issue: http://code.google.com/p/mmisw/issues/detail?id=32

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