{"action":"created","issue":{"url":"https://api.github.com/repos/ontoden/ontobee/issues/43","labels_url":"https://api.github.com/repos/ontoden/ontobee/issues/43/labels{/name}","comments_url":"https://api.github.com/repos/ontoden/ontobee/issues/43/comments","events_url":"https://api.github.com/repos/ontoden/ontobee/issues/43/events","html_url":"https://github.com/ontoden/ontobee/issues/43","id":99051119,"number":43,"title":"Obsolete ENVO classes retrieved ","user":{"login":"pbuttigieg","id":2276146,"avatar_url":"https://avatars.githubusercontent.com/u/2276146?v=3","gravatar_id":"","url":"https://api.github.com/users/pbuttigieg","html_url":"https://github.com/pbuttigieg","followers_url":"https://api.github.com/users/pbuttigieg/followers","following_url":"https://api.github.com/users/pbuttigieg/following{/other_user}","gists_url":"https://api.github.com/users/pbuttigieg/gists{/gist_id}","starred_url":"https://api.github.com/users/pbuttigieg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pbuttigieg/subscriptions","organizations_url":"https://api.github.com/users/pbuttigieg/orgs","repos_url":"https://api.github.com/users/pbuttigieg/repos","events_url":"https://api.github.com/users/pbuttigieg/events{/privacy}","received_events_url":"https://api.github.com/users/pbuttigieg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-08-04T20:09:06Z","updated_at":"2015-08-05T18:07:47Z","closed_at":null,"body":"Dear OntoBee team,\r\n\r\nSome of ENVO's obsolete classes are retrieved in the general search, but it's not really made clear that they are obsolete. \r\n\r\nFor example:\r\n\r\n `\r\n  <!-- http://purl.obolibrary.org/obo/ENVO_00002993 -->\r\n\r\n    <owl:Class rdf:about=\"http://purl.obolibrary.org/obo/ENVO_00002993\">\r\n        <rdfs:label rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">Tropical humid forests</rdfs:label>\r\n        <oboInOwl:hasOBONamespace rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">ENVO</oboInOwl:hasOBONamespace>\r\n        <oboInOwl:id rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">ENVO:00002993</oboInOwl:id>\r\n        <oboInOwl:consider rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">ENVO:01000228</oboInOwl:consider>\r\n        <owl:deprecated rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\">true</owl:deprecated>\r\n    </owl:Class>\r\n    `\r\nPerhaps checking for <owl:deprecated> boolean = true or the presence of consider or replaced by annotation properties may be a good way to filter these.\r\n    "},"comment":{"url":"https://api.github.com/repos/ontoden/ontobee/issues/comments/128094528","html_url":"https://github.com/ontoden/ontobee/issues/43#issuecomment-128094528","issue_url":"https://api.github.com/repos/ontoden/ontobee/issues/43","id":128094528,"user":{"login":"ontoden","id":6226073,"avatar_url":"https://avatars.githubusercontent.com/u/6226073?v=3","gravatar_id":"","url":"https://api.github.com/users/ontoden","html_url":"https://github.com/ontoden","followers_url":"https://api.github.com/users/ontoden/followers","following_url":"https://api.github.com/users/ontoden/following{/other_user}","gists_url":"https://api.github.com/users/ontoden/gists{/gist_id}","starred_url":"https://api.github.com/users/ontoden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ontoden/subscriptions","organizations_url":"https://api.github.com/users/ontoden/orgs","repos_url":"https://api.github.com/users/ontoden/repos","events_url":"https://api.github.com/users/ontoden/events{/privacy}","received_events_url":"https://api.github.com/users/ontoden/received_events","type":"User","site_admin":false},"created_at":"2015-08-05T18:07:47Z","updated_at":"2015-08-05T18:07:47Z","body":"OK. Edison just finished another update. The new update works as shown below:\r\n\r\nFor example, if we search for “forest” in the Ontobee general search (shown on the cover page), we get:\r\nhttp://www.ontobee.org/browser/search.php?ontology=ENVO&keywords=forest&Submit2=Search+terms\r\n\r\nThe deprecated (or obsolete) terms are listed at the bottom of the page like this:\r\n[cid:image001.jpg@01D0CF88.01A692A0]\r\n\r\nIf we click on the “Show Deprecated Terms”, we can see:\r\n[cid:image002.jpg@01D0CF88.01A692A0]\r\n\r\nHere all the deprecated terms are crossed with a strikethrough line.\r\n\r\nWe can click on one deprecated term IRI:\r\nhttp://www.ontobee.org/browser/rdf.php?o=ENVO&iri=http://purl.obolibrary.org/obo/ENVO_00000875\r\nIt also shows the term is deprecated in the annotation section:\r\n[cid:image003.jpg@01D0CF88.01A692A0]\r\n\r\nPlease check them out and let us know if you have more comments and suggestions.\r\n\r\nThanks!\r\n\r\nEdison and Oliver\r\n\r\n\r\n\r\nFrom: Melanie Courtot [mailto:notifications@github.com]\r\nSent: Wednesday, August 05, 2015 5:41 AM\r\nTo: ontoden/ontobee\r\nCc: ontoden\r\nSubject: Re: [ontobee] Obsolete ENVO classes retrieved (#43)\r\n\r\nCould the obsolete classes also be pushed to the bottom of the list when\r\ndoing a general search?\r\n\r\nOn Tue, Aug 4, 2015 at 11:10 PM, Chris Mungall <notifications@github.com<mailto:notifications@github.com>>\r\nwrote:\r\n\r\n> owl:deprecated is standard\r\n>\r\n> On 4 Aug 2015, at 14:35, ontoden wrote:\r\n>\r\n> > There are several issues related to Pier’s ENVO example:\r\n> >\r\n> > <!-- http://purl.obolibrary.org/obo/ENVO_00002993 -->\r\n> >\r\n> > <owl:Class rdf:about=\"http://purl.obolibrary.org/obo/ENVO_00002993\">\r\n> >\r\n> > <rdfs:label\r\n> > rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\">Tropical humid\r\n> > forests</rdfs:label>\r\n> >\r\n> > <oboInOwl:hasOBONamespace\r\n> > rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\r\n> <http://www.w3.org/2001/XMLSchema#string\u000B>> \">ENVO</oboInOwl:hasOBONamespace>\r\n> >\r\n> > <oboInOwl:id\r\n> > rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\r\n> <http://www.w3.org/2001/XMLSchema#string\u000B>> \">ENVO:00002993</oboInOwl:id>\r\n> >\r\n> > <oboInOwl:consider\r\n> > rdf:datatype=\"http://www.w3.org/2001/XMLSchema#string\r\n> <http://www.w3.org/2001/XMLSchema#string\u000B>> \">ENVO:01000228</oboInOwl:consider>\r\n> >\r\n> > <owl:deprecated\r\n> > rdf:datatype=\"http://www.w3.org/2001/XMLSchema#boolean\r\n> <http://www.w3.org/2001/XMLSchema#boolean\u000B>> \">true</owl:deprecated>\r\n> >\r\n> > </owl:Class>\r\n> >\r\n> > Here the classification of the term as deprecated is different from\r\n> > classifying it as a subclass of an “obsolete” class. It provides\r\n> > an Boolean value. Ontobee has not handled this issue yet.\r\n> >\r\n> > Another issue is how to clearly show it’s an obsolete or deprecated\r\n> > class, such as using the strikethrough sign.\r\n> >\r\n> > I have discussed with Edison. He will be working on it soon. Once an\r\n> > outcome is available, we will inform it and ask for feedback.\r\n> >\r\n> > Oliver\r\n> >\r\n> >\r\n> > From: Alan Ruttenberg [mailto:notifications@github.com]\r\n> > Sent: Tuesday, August 04, 2015 5:11 PM\r\n> > To: ontoden/ontobee\r\n> > Subject: Re: [ontobee] Obsolete ENVO classes retrieved (#43)\r\n> >\r\n> >\r\n> > I would suggest not filtering by default but instead a) show a clearly\r\n> > visible visual indicator with the term(eg strike through and badge on\r\n> > page) and b) have any obsolete terms sorted to the end of results.\r\n> > Perhaps have a cookie-remembered checkbox asking for them not to be\r\n> > shown, not checked by default.\r\n> >\r\n> > The principle is to ensure that the principle that terms don't just\r\n> > disappear I reinforced. In addition obsolete terms may have useful\r\n> > information such as deprecation reason or suggested alternatives.\r\n> >\r\n> > The suggested checkbox is for people who are familiar enough that they\r\n> > understand what they will be missing. Remember the state by cookie is\r\n> > to avoid irritating users that choose this option.\r\n> >\r\n> > —\r\n> > Reply to this email directly or view it on\r\n> > GitHub<\r\n> https://github.com/ontoden/ontobee/issues/43#issuecomment-127762942>.\r\n> > **********************************************************\r\n> > Electronic Mail is not secure, may not be read every day, and should\r\n> > not be used for urgent or sensitive issues\r\n> >\r\n> >\r\n> > ---\r\n> > Reply to this email directly or view it on GitHub:\r\n> > https://github.com/ontoden/ontobee/issues/43#issuecomment-127769354\r\n>\r\n> —\r\n> Reply to this email directly or view it on GitHub\r\n> <https://github.com/ontoden/ontobee/issues/43#issuecomment-127776844>.\r\n>\r\n\r\n\r\n—\r\nReply to this email directly or view it on GitHub<https://github.com/ontoden/ontobee/issues/43#issuecomment-127935763>.\r\n**********************************************************\nElectronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues \n"}}