Changes between Version 77 and Version 78 of ImplementationBootcamp

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2010/02/16 11:07:17 (13 years ago)
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  • ImplementationBootcamp

    v77 v78  
    5454For ontology integration, our work has led us to conclude that: 
    5555 * instance data should be fully ontologized. For example, our phenoscape use case could not be completed because phenoscape uses XML literals to express trait post-composition. These traits were consequently inaccessible for the purpose of data integration. 
    56  * ontologies should be designed as reusable modules rather than monolithic artifacts. Aligning [http://www.evolutionaryontology.org/ CDAO] with [http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome DarwinCore] was relatively easy because DarwinCore doesn't have a lot of structure (which is a good thing from the perspective of re-use). (although DarwinCore still needs to be ontologized). 
     56 * ontologies should be designed as reusable modules rather than monolithic artifacts. Aligning [http://www.evolutionaryontology.org/ CDAO] with [http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome DarwinCore] was relatively easy because !DarwinCore doesn't have a lot of structure (which is a good thing from the perspective of re-use). (although !DarwinCore still needs to be ontologized). 
    5757 * data integration is most easily achieved by developing small adaptor ontologies rather than merging of large (and potentially well-established and "stable") artifacts. Merging large ontologies has a greater potential to have irreconcilable incongruities. Adapting smaller ontologies requires immediate reconciliation, but insulates the practitioner from irrelevant inconsistencies. Implementations are likely to be more efficient and scalable. Nevertheless, if two domains have significant overlap, it is probably better to merge them, reconcile the inconsistencies and thereby decrease the overall noise subsequent use of the domain.  
    5858 * URIs (URLs) for terms should be carefully constructed, predictable and stabilized, perhaps using PURLs. For example, several queries failed to produce expected results due to omission of `www` prefixes or `#` suffixes in URLs. 
     
    6161===  What are the similarities and differences between the various shared names proposals?  === 
    6262 
    63 Shared names proposals such as LSRN? UniProt? 
     63Shared names proposals such as LSRN? !UniProt? 
    6464 
    6565> MDW:  See above, and ask specific questions that I can try to answer myself, or invite the representatives from the other proposals to answer.  (Get well soon, Alan!!!!) 
     
    7474 * URI documentation must be open so that it can be replicated and reused. 
    7575 
    76 === UniProt PURLS === 
    77  
    78 UniProt uses its own purls not only for their own data but also for all the cross references that we link to. 
     76=== !UniProt PURLS === 
     77 
     78!UniProt uses its own purls not only for their own data but also for all the cross references that we link to. 
    7979 * For example purl.uniprot.org/HGNC/37122 is redirected to http://www.genenames.org/data/hgnc_data.php?hgnc_id=37122 
    8080 * We do this because we have to maintain and keep stable links into the future. Meaning that when one of our cross reference databases changes their urls. We change the redirection. One maintenance location. 
    8181 * When merging datasets people have to collapse these different URL's into one. Using either a regexp or owl:sameAs statements. 
    82  * Benefit to using UniProt purls when available is that there is an ongoing maintenance effort. 
     82 * Benefit to using !UniProt purls when available is that there is an ongoing maintenance effort. 
    8383 * They are documented in [http://www.uniprot.org/docs/dbxref dbxref] for the external datasets. 
    8484 ** And there is work being done to make this available in owl/rdf including the internal datasets. 
     
    9090===  I have an analysis tool, how do I expose it as a semantic web resource? === 
    9191 
    92 SADI provides one solution.  Luke !McCarthy gave a Java tutorial Thursday 11 February 2010, and Mark Wilkinson gave the Perl tutorial on the same day.  Edward Kawas from the Wilkinson lab has produced movies detailing how to create services in Perl for SADI, and Mark will be doing the voice-over for these movies and putting them up on YouTube in the second week of February 2010.  Mark will add a link here.  The same will be done for the Java side once we have the extra-cool Java functionalities coded and ~stable.  In particular, Luke !McCarthy and Paul !Gordon have been working together at the Hackathon finding simple ways to put SADI Java services into the Google Cloud... so you might not even have to consume your own compute resources to achieve this! 
     92SADI provides one solution.  Luke !McCarthy gave a Java tutorial Thursday 11 February 2010, and Mark Wilkinson gave the Perl tutorial on the same day.  Edward Kawas from the Wilkinson lab has produced movies detailing how to create services in Perl for SADI, and Mark will be doing the voice-over for these movies and putting them up on !YouTube in the second week of February 2010.  Mark will add a link here.  The same will be done for the Java side once we have the extra-cool Java functionalities coded and ~stable.  In particular, Luke !McCarthy and Paul !Gordon have been working together at the Hackathon finding simple ways to put SADI Java services into the Google Cloud... so you might not even have to consume your own compute resources to achieve this! 
    9393 
    9494===  When someone calls GET on my URLs, what should I return in order to be semantic webby? === 
     
    289289select ?p where (?p a :HumanKinase) 
    290290}}} 
    291 is much more readable to a human/biologist. This :HumanKinase type can be generated on the fly using owl inference. 
     291is much more readable to a human/biologist. This :!HumanKinase type can be generated on the fly using owl inference. 
    292292 
    293293