ppy/OntologySummit2013_hc-07-integration_chat-transcript_unedited_20130413a.txt ------ Chat transcript from room: hc-07-integration 2013-04-13 GMT-08:00 [PDT] ------ [1:07] TillMossakowski: == Project: HC-07. Ontohub-OOR-OOPS! Integration == Project homepage: http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2013_Hackathon_Clinics_Ontohub_OOR_OOPS_Integration [1:08] TillMossakowski: Hi Maria [1:08] MariaPovedaVillalon: Hi Till [1:08] TillMossakowski: we are still setting up things here... [1:09] MariaPovedaVillalon: good [1:10] MariaPovedaVillalon: I was making sure our servers are up [1:11] TillMossakowski: good [1:16] julian: good morning everyone [1:17] MariaPovedaVillalon: good morning from Paris :-) [1:19] TillMossakowski: Maria, could you dial in on Sykpe? [1:19] TillMossakowski: Dial-in: Phone (US): +1 (206) 402-0100 ... Conference ID: 141184# ; or Skype: joinconference ... Conference ID: 141184# [1:19] MariaPovedaVillalon: ok [1:21] TillMossakowski: We are looking at http://oops-ws.oeg-upm.net/ [1:24] MariaPovedaVillalon: http://ontohub.org/ontologies/11/versions/1 [1:24] julian: http://staging.ontohub.org/ [1:27] MariaPovedaVillalon: http://sweet.jpl.nasa.gov/1.1/material_thing.owl [2:20] TillMossakowski: Hi Maria, for http://www.mygrid.org.uk/ontology OOPS! outputs (among other things): A cycle between two classes in the hierarchy is included in the ontology, although it is not intended to have such classes as equivalent. That is, some class A has a subclass B and at the same time B is a superclass of A. An example of this type of pitfall is represented by the class ěProfessorî as subclass of ěPersonî, and the class ěPersonî as subclass of ěProfessorî. This pitfall appears in the following elements: http://www.mygrid.org.uk/ontology#ENZYME_Record -- But how can a cycle consist of just one element??? [2:21] MariaPovedaVillalon: let me check [2:22] MariaPovedaVillalon3: I think it is the element appearing twice in the hierarchy [2:23] MariaPovedaVillalon6: in this cases is not exactly the same one (same uri) it is an ID appearing twice [2:23] TillMossakowski: aha, I see [2:23] MariaPovedaVillalon6: I was thinking about changing this detection and make it flag up only when it is exactly the same URI [2:24] MariaPovedaVillalon6: in this case there would be people saying they could be different concepts even though they have the same identifier, logically it will not create a set of "equivalent class" among all the clases involved in the cycle, but still "weird" modelling for me [2:25] MariaPovedaVillalon6: I can note that to change the detection method in OOPS!, would you change it? [2:25] TillMossakowski: at least the description could be modified so that it becomes clear why only one element is displayed as part of a cycle [2:25] MariaPovedaVillalon6: ok, thank you [2:25] TillMossakowski: change what? [2:27] MariaPovedaVillalon6: the detection method, now it says it is a cycle if 2 classes in a hierarchy have the same identifier (2 differente URIs), but it might be better to detect only when it is one class (only one URI) appearing twice in the hierarchy [2:27] MariaPovedaVillalon6: or I could make 2 different outputs, one for each case [2:29] TillMossakowski: this sounds good! [2:29] TillMossakowski: I mean, the latter suggestion [2:29] TillMossakowski: Again for http://www.mygrid.org.uk/ontology, there is one pitfall P22. The HTML output gives: Ontology elements are not named using the same convention within the whole ontology. It is considered a good practice that the rules and style of lexical encoding for naming the different ontology elements is homogeneous within the ontology. One possibility for rules is that concept names start with capital letters and property names start with non-capital letters. In the case of style, there are different options such as camel case, hyphen style, underscore style, and the combinations. Some notions about naming conventions are provided in [2]. There are elements following different naming conventions as for example: http://www.mygrid.org.uk/ontology#Prints_accession and http://www.mygrid.org.uk/ontology#HGVbaseID. Note that some of the namespaces involved in this pitfall may be out of your control so you can't correct it. In that case, you should check whether this pitfall also appear in the namespaces under your control or ignore it if it only affects elements that you can't modify. *This pitfall applies to the ontology in general instead of specific elements. And the XML output is: P22Using different naming criteria in the ontology Ontology elements are not named using the same convention within the whole ontology. It is considered a good practice that the rules and style of lexical encoding for naming the different ontology elements is homogeneous within the ontology. One possibility for rules is that concept names start with capital letters and property names start with non-capital letters. In the case of style, there are different options such as camel case, hyphen style, underscore style, and the combinations. Some notions about naming conventions are provided in [2]. Shouldn't the XML also contain the two sample elements? At least for Ontohub users, this would be helpful. [2:31] MariaPovedaVillalon6: the thing is that the examples are random as the pitfall affect to the whole ontology [2:31] MariaPovedaVillalon6: so I can not point to the particular examples [2:32] MariaPovedaVillalon6: and in addition if there are some entities named like Entity_Name and others as EntityName I can not say which naming rule is the good one [2:33] MariaPovedaVillalon6: the example just pick two element following different naming convention but if you make groups and classify them... at the end it is the whole ontology [2:33] MariaPovedaVillalon6: am I clear? [2:33] MariaPovedaVillalon6: also pitfall 10 does not give example, because it is other case of when it affects to the ontology as a whole [2:34] TillMossakowski: yes, but still the HTML contains two randomly selected examples for P22 [2:34] MariaPovedaVillalon6: yes [2:34] TillMossakowski: I assume that this is the case because you want to display this to the user [2:34] MariaPovedaVillalon6: you mean that 2 ramdom example could be in the output too [2:34] TillMossakowski: yes, in the XML output [2:34] MariaPovedaVillalon6: right [2:34] TillMossakowski: because we also want to present this to the user [2:35] MariaPovedaVillalon6: yes, now I get it [2:35] MariaPovedaVillalon6: ummm [2:35] TillMossakowski: would it be difficult? [2:35] MariaPovedaVillalon6: I need to extend the outuput then [2:35] MariaPovedaVillalon6: no [2:35] TillMossakowski: good [2:35] MariaPovedaVillalon6: it would be easy but it can not be updated now in the server [2:35] TillMossakowski: no hurry [2:35] MariaPovedaVillalon6: would it be a problem if you see that on monday/tuesday? [2:36] MariaPovedaVillalon: (I lost connection from this chat from time to time :s ) [2:37] MariaPovedaVillalon: (*lose) [2:37] MariaPovedaVillalon: would it be a problem if you see that on monday/tuesday? [2:37] TillMossakowski: yes, that's fine, no hurry [2:37] MariaPovedaVillalon: cool! [2:38] TillMossakowski: Another question: can oops:MightBeEquivalentProperty, oops:MightBeEquivalentAttribute and oops:MightNotBeInversedOf all appear simultaneously within one pitfall? Or only in different pitfalls? [2:39] MariaPovedaVillalon: oops:MightBeEquivalentProperty, oops:MightBeEquivalentAttribute appear together [2:39] MariaPovedaVillalon: in P12. Missing equivalent properties [2:40] TillMossakowski: do you have an example ontology where they appear together? [2:40] MariaPovedaVillalon: oops:MightNotBeInversedOf appears in P5. Defining wrong inverse relationships [2:40] MariaPovedaVillalon: let me check [2:41] MariaPovedaVillalon: http://data.semanticweb.org/ns/swc/swc_2009-05-09.rdf in this ontology [2:43] TillMossakowski: thanks! [2:43] MariaPovedaVillalon: :-) welcome [2:47] TillMossakowski: my suggestion is that (for the reason to keep the database structure simple) in Ontohub we split a P12 into a lot of small P12's, each with only one of oops:MightBeEquivalentProperty and oops:MightBeEquivalentAttribute, and two affected elements. Does this makes sense to you? [2:50] MariaPovedaVillalon: yes, like the original output from oops were a "refactorization" of that, but note that oops:MightBeEquivalentProperty and oops:MightBeEquivalentAttribute could involve more than 2 elements [2:50] MariaPovedaVillalon: it is difficult to find a case but it could happen [2:51] MariaPovedaVillalon: like the relationships "hasPart" defined in 3 or 4 different namespaces and all of them gathered in the ontology being analyzed [2:54] TillMossakowski: OK, this is no problem [3:04] TillMossakowski: Here is the data model that we will use in ruby on rails: [3:05] TillMossakowski: create_table :oops_responses do |t| t.references :oops_request, null: false t.integer :code t.string :name, null: false t.string :description t.string :type, null: false [3:05] TillMossakowski: create_table :oops_responses_entities do |t| t.references :oops_response, null: false t.references :entity, null: false [3:05] TillMossakowski: create_table :oops_requests do |t| t.references :ontology_version, null: false t.references :oops_response t.string :state, default: 'pending', null: false t.string :last_error [3:06] TillMossakowski: That is, we store a request to OOPS! in the table oops_requests. A dara element in this table will refer to an ontology version and an OOPS! repsonse. [3:08] TillMossakowski: oops, I just see that this does not make sense: we have to delete the reference to the OOPS! repsonse... [3:08] MariaPovedaVillalon: but the oops response do not refer to the oops_responses_entities? sorry if I'm saying non sense, first time reading this notation [3:08] TillMossakowski: So we get: create_table :oops_requests do |t| t.references :ontology_version, null: false t.string :state, default: 'pending', null: false t.string :last_error [3:09] TillMossakowski: oops_responses_entities is a join table, linking oops_responses with entities (the latter are classes, object properties or data properties) [3:10] TillMossakowski: Since one response can refer to many entities, there is no direct reference from oops_responses to entities (and conversely) [3:10] MariaPovedaVillalon: ok [3:10] TillMossakowski: Moreover, we intend to store each pitfall, suggestion and warning in a separate repsonse [3:11] MariaPovedaVillalon: so 1 request have several responses? [3:12] TillMossakowski: exactly [3:13] TillMossakowski: (therefore, it did not make sense to let a request point to a response - there can be many of them) [3:13] TillMossakowski: and in case of a P12 response, this is even split further in sub-responses (as said above) [3:14] MariaPovedaVillalon: yes, I remember [3:14] MariaPovedaVillalon: by the way I had a little problem with staging ontohub [3:14] TillMossakowski: what kind of problem? [3:15] MariaPovedaVillalon: when looking for ontologies in owl and showing 500 per page I only got ontologies in the first page http://staging.ontohub.org/ontologies?page=2&per_page=500 [3:16] MariaPovedaVillalon: but 3 pages where there should be results [3:16] TillMossakowski: you are right, I will file a ticket [3:18] TillMossakowski: https://github.com/ontohub/ontohub/issues/139 [3:20] TillMossakowski: we will concentrate on the OOPS! integration now and take care of this ticket later, OK? [3:20] MariaPovedaVillalon: good, I just wanted to inform you [3:21] MariaPovedaVillalon: Indeed I was looking for ontologies that could be used to test the integration and I think this ones are ok http://staging.ontohub.org/ontologies/1184/entities http://www.cs.man.ac.uk/%7Ehorrocks/OWL/Ontologies/ka.owl http://www.mindswap.org/ontologies/family.owl [3:22] TillMossakowski: thanks! [3:22] MariaPovedaVillalon: not too big, and they give results [3:43] julian: Maria, are your currently improving your webservice? [3:43] MariaPovedaVillalon: no [3:43] MariaPovedaVillalon: what do you mean? [3:43] MariaPovedaVillalon: I can not change the online version until monday [3:44] MariaPovedaVillalon: so if there is a problem it is not me right now [3:44] julian: mhh .. I have just got a internal server error after I submittet a invalid hostname. But now I get another 200. [3:44] julian: ok, no problem [3:44] julian: it works with a valid URL :) [3:45] MariaPovedaVillalon: :-) [3:45] MariaPovedaVillalon: good to hear that, I have no access to the server :( [3:46] julian: I have to correct myself - I only get a 500 if the request body is missing. [3:47] MariaPovedaVillalon: is that what had to happen? if you find any error with the responses or behavior please let me know [3:49] PeterYim: Hi everyone! [3:50] MariaPovedaVillalon: hi! [3:52] PeterYim: Attn: ALL .. the HC-07 Ontohub-OOR-OOPS! Integration "open webcast segment" featuring the "API Development" work will be starting in about 7 minutes [3:57] PeterYim: @Till - Ken and I seem to be the only people on the voice conference bridge now [3:58] PeterYim: Dial-in: Phone (US): +1 (206) 402-0100 ... Conference ID: 141184# ; or Skype: joinconference ... Conference ID: 141184# . [3:58] MariaPovedaVillalon: I'll be in one second [5:12] List of members: Christian, Daniel Couto Vale, FrancescaQuattri, henning, julian1, KenBaclawski, MariaPovedaVillalon, PeterYim, TillMossakowski [5:12] Sent transcript to: ppy@cim.us [9:54] MariaPovedaVillalon: Hi, I will need to drop off soon, is there anything else you would need from my side? [10:01] TillMossakowski1: we are going to deploy a first version in about 5 minutes. Maybe you can have a first look? [10:03] MariaPovedaVillalon: sure! [10:21] TillMossakowski1: sorry, it is deployed but there are still some bugs... working intensively on it [10:23] MariaPovedaVillalon: no sorries [10:23] MariaPovedaVillalon: how long do you reckon it could take? [10:24] MariaPovedaVillalon: more than 20 min? I can do my house stuff and check the chat from time to time :) [10:26] MariaPovedaVillalon: is it ok? 20 mins? [10:26] MariaPovedaVillalon: shall I wait instead? [10:27] TillMossakowski1: OK, it should work now [10:28] TillMossakowski1: http://staging.ontohub.org [10:29] MariaPovedaVillalon: I see [10:30] MariaPovedaVillalon: how do you represent P10. Missing disjointness? [10:30] TillMossakowski1: the status is "pending" a for while. Unfortunately, you have to reload the page from time to time [10:30] MariaPovedaVillalon: yeah, i realized [10:30] TillMossakowski1: do you have an ontology with P10? [10:30] MariaPovedaVillalon: :-( [10:31] MariaPovedaVillalon: not in ontohub [10:31] TillMossakowski1: elsewhere? [10:31] MariaPovedaVillalon: it is just how would you represent it [10:31] MariaPovedaVillalon: let me check [10:31] TillMossakowski1: we just output what is in your XML [10:32] MariaPovedaVillalon: something happens with the layout for this one http://staging.ontohub.org/ontologies/1378/entities [10:32] MariaPovedaVillalon: or is it just in my browser? [10:33] TillMossakowski1: you mean that the class and property names jump a bit once you expand a pitfall? [10:34] MariaPovedaVillalon: without expandind the pitfall I think [10:34] MariaPovedaVillalon: I'll check again [10:34] MariaPovedaVillalon: this one has the P10 : http://purl.org/ontology/af/ [10:35] TillMossakowski1: do you have an OWL file for it? [10:35] TillMossakowski1: "something happens with the layout" - what exactly does happen? [10:36] MariaPovedaVillalon: http://lov.okfn.org/dataset/lov/agg/down/file_af.n3 is ok in .n3? [10:37] MariaPovedaVillalon: the elements appear each time I click in one position, like first a lot more to the right than in the previous ontology I tried [10:37] MariaPovedaVillalon: but then, I click in "classes" for example and they change positions [10:37] MariaPovedaVillalon: some times they go more to the left and others more to the right [10:39] TillMossakowski1: yes, we know that. It is caused by HTML table layout [10:39] TillMossakowski1: I cannot read in http://lov.okfn.org/dataset/lov/agg/down/file_af.n3 , neither with Protégé nor with Ontohub [10:39] MariaPovedaVillalon: http://d-nb.info/standards/elementset/agrelon.owl# another exampel of the P10 [10:40] TillMossakowski1: but again I need an owl file [10:41] MariaPovedaVillalon: what does it mean OOPS State: done (7 Responses) ? [10:42] MariaPovedaVillalon: sorry, I thought it was an owl because of the url [10:42] TillMossakowski1: It means that OOPS has sent 7 pitfalls (or warnings or suggestions) in the XML [10:42] TillMossakowski1: However, since we display it symbol wise, you will see more [10:43] MariaPovedaVillalon: ah ok [10:43] TillMossakowski1: But we also will have a more compact display on the page of the ontology [10:43] MariaPovedaVillalon: I'm looking for other owl [10:43] MariaPovedaVillalon: I can't trust url file extensions :( [10:43] TillMossakowski1: indeed [10:44] MariaPovedaVillalon: http://www.aktors.org/ontology/support# [10:44] MariaPovedaVillalon: that one redirects to an owl file for me [10:44] MariaPovedaVillalon: can you use it? [10:48] TillMossakowski1: yes: http://staging.ontohub.org/ontologies/1397 [10:49] MariaPovedaVillalon: I can't see where the P10 is shown [10:49] MariaPovedaVillalon: as it is not associated to any particular element [10:50] TillMossakowski1: sorry, these global pitfalls are not displayed yet. Julian will implement this soon [10:50] MariaPovedaVillalon: in addition it could be nice if you include in the "X responses" a way to now at a glance which responses are, maybe just the title of the pitfalls involved [10:50] TillMossakowski1: Good point. [10:51] MariaPovedaVillalon: and I would be so happy if you link to OOPS website with a link from OOPS status.. for example [10:51] TillMossakowski1: OK [10:53] TillMossakowski1: I suggest that we close the session now, and implement your feedback later [10:53] MariaPovedaVillalon1: just a idea of how to do it: http://twitter.github.io/bootstrap/javascript.html#popovers [10:53] MariaPovedaVillalon1: just a suggestion :-) [10:54] MariaPovedaVillalon1: ok, thank you very much let me know if you need anything else, I'll let you know when I get the changes we speak about this morning done [10:54] MariaPovedaVillalon1: and updated in the server [10:54] TillMossakowski1: Good. Many thanks for your feedback and the discussion [10:54] MariaPovedaVillalon1: thanks you for the interest :) [10:54] TillMossakowski1: For now, we will close the session, and resume next week [10:54] MariaPovedaVillalon1: have a good weekend, the rest of it [10:55] TillMossakowski1: we will keep in contact [10:55] MariaPovedaVillalon1: :) [10:55] TillMossakowski1: also have a nice wwekend [10:55] TillMossakowski1: weekend [11:04] PeterYim: -- session ended: 11:01am PDT -- [11:05] List of attendees: Christian, Daniel Couto Vale, FrancescaQuattri, KenBaclawski, MariaPovedaVillalon, PeterYim, TillMossakowski, anonymous, hburg1234, henning, julian, ------