Semtools: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-04-08T20:18:51ZEcoinformatics Redmine
Redmine Bug #5376 (New): Create JUnit tests for semantic query capabilitieshttps://projects.ecoinformatics.org/ecoinfo/issues/53762011-04-08T20:18:51Zben leinfelderleinfelder@nceas.ucsb.edu
<p>With a given test corpus (EML+annotations) we should be able to replicate query results to make sure reasoning and query processing does not break once we determine exactly how it should work.</p> Bug #5374 (New): Use 'semquery' within Morphohttps://projects.ecoinformatics.org/ecoinfo/issues/53742011-04-04T22:26:31Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Instead of loading all remote annotations from Metacat into Morpho before performing the semantic query, Morpho should just generate a semquery and submit it to Metacat and process those results. As a prototype it was fine to load all the remote annotations, but as the number of annotations increases, it will not be feasible to load them all on every client.</p> Bug #5373 (New): OntologyManager: registration and archivinghttps://projects.ecoinformatics.org/ecoinfo/issues/53732011-04-04T21:47:39Zben leinfelderleinfelder@nceas.ucsb.edu
<p>I think we all agree that when an annotation references an ontology we should import the referenced ontology and any ontology that it imports and run the reasoner over it so that it can be used for querying (and data integration in the future).</p>
<p>Some options for making sure we always have this ontology in the future:<br />-Save the ontology in Bioportal with a specific versioning policy. This might also require grabbing and versioning each imported ontology.<br />-Save ontology and imported ontologies in Metacat.</p> Bug #5371 (New): AnnotationManager: query performancehttps://projects.ecoinformatics.org/ecoinfo/issues/53712011-04-04T21:30:41Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Identify long-running aspects of semquery. First glance indicates that returning the metadata/annotation content to be displayed in Metacat is the biggest bottleneck. This is good and bad. It means using the DB for managing annotations is pretty efficient, but it also means that returning large results sets will not be so efficient.<br />Probable solution: include only a subset of annotation information in the resultset rather than the entire annotation xml content.</p> Bug #5368 (New): Compound query conditionshttps://projects.ecoinformatics.org/ecoinfo/issues/53682011-04-04T21:05:18Zben leinfelderleinfelder@nceas.ucsb.edu
<p>We allow grouping of semantic query conditions, but not in the web UI. Adding grouping makes the UI much more complicated, but allows exact query authoring. We've taken a simpler approach that is largely based on browsing and drilling down iteratively after applying a set of conditions (thereby making an implicit intersection of the criteria and their results).<br />This is a place-holder bug to track whether we need to support super-expressive compound grouping.</p> Bug #5367 (New): Verify "same observation as" query criteriahttps://projects.ecoinformatics.org/ecoinfo/issues/53672011-04-04T21:02:40Zben leinfelderleinfelder@nceas.ucsb.edu
<p>The "strict=true" query condition mode indicates that the criteria in that group must come from the same observation in order to be considered true. During testing, we should make sure that the query results reflect the desired distinction is being made.</p> Bug #5366 (New): Integrate semantic query with keyword and spatial queryhttps://projects.ecoinformatics.org/ecoinfo/issues/53662011-04-04T20:53:23Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Combining semantic, keyword and spatial criteria will allow a smoother transition from non-semantic metadata to semantically annotated data. It will also allow us to refine query results further by limiting to specific organizations, locations, people, etc.</p>
<p>Metacat should support combining "squery", "semquery" and "spatialquery" actions in an extensible way that lets future query mechanisms contribute conditions to the query so that additional (or fewer) matches are returned.</p>
<p>This may require additional or wrapper syntax for specifying a compound, multi-faceted query.</p> Bug #5365 (New): Context-based semantic queryhttps://projects.ecoinformatics.org/ecoinfo/issues/53652011-04-04T20:48:07Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Include interace for expressing context criteria for a semantic query. The query syntax allows context criteria, but there is no GUI for it. The criteria assume a basic context template rather than any specific entity (because of the general nature of the query there is not a concrete observation before submitting the query). Context is defined as <Entity> <Relationship> <Entity> and can be combined to further expand/refine context conditions. The classes are expanded using the ontology as you would expect.</p> Bug #5135 (New): Loading ontology from local file does not seem functionalhttps://projects.ecoinformatics.org/ecoinfo/issues/51352010-08-09T23:32:14Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Tried to use the logical/physical mapping of managed ontologies in Morpho, but the ontology did not load. Perhaps it needs to be prefixed with file:\\ or some such. Will investigate.</p> Bug #5078 (New): Measurement templateshttps://projects.ecoinformatics.org/ecoinfo/issues/50782010-07-06T23:44:02Zben leinfelderleinfelder@nceas.ucsb.edu
<p>Currently you can select a subclass of [oboe-core] Measurement and have the other fields populate with a valid class for that field (the Entity, say). But there are cases where there are many valid Entities for a given Measurement and we would only be selecting the first (seems to be alphabetical at this point). What should probably happen is that the selection widget further constrains the ontology browser for that field so that only valid classes (and subclasses) can be selected.</p> Bug #5004 (New): oboe: create an oboe-examples ontology for documenting "best practices"https://projects.ecoinformatics.org/ecoinfo/issues/50042010-05-12T17:44:52ZShawn Bowersbowers@gonzaga.edu
<p>Should be comprised of a set of examples from the oboe "getting started" guide. These examples should also encode "best practices" with respect to using oboe.</p> Bug #5003 (New): oboe: develop a high-level "getting started" guide / documentationhttps://projects.ecoinformatics.org/ecoinfo/issues/50032010-05-12T17:41:51ZShawn Bowersbowers@gonzaga.edu
<p>This should also include a set of simple examples and a corresponding ontology oboe-examples simply for the sake of the guide.</p> Bug #5002 (New): oboe-unit: create new oboe-unit for oboe-corehttps://projects.ecoinformatics.org/ecoinfo/issues/50022010-05-12T17:38:51ZShawn Bowersbowers@gonzaga.edu
<p>Modify the current oboe-unit to conform to the new oboe-core structure. Primarily requires modifying the characteristic hierarchy (simplify).</p> Bug #5001 (New): oboe-core: ensure new characteristic structure still supports unit conversionhttps://projects.ecoinformatics.org/ecoinfo/issues/50012010-05-12T16:12:58ZShawn Bowersbowers@gonzaga.edu
<p>This needs to be done using some examples ... maybe a "unit-test" ontology (not sure what this would be)?</p> Bug #4946 (New): Look-ahead search freezeshttps://projects.ecoinformatics.org/ecoinfo/issues/49462010-04-19T20:18:43Zben leinfelderleinfelder@nceas.ucsb.edu
<p>In the ontology browser, quick typing will render the popup useless.<br />My hunch is that it will go away when we stop searching the class descriptions.</p>