Fw: [protege-discussion] Re: XSLT for XML-Instance Import into protege

[cognizor@cognizor.com]

This takeup of Medline data into [ontological form] is relevant 
to some of the work committee members are doing.

SC

Begin forwarded message:

Date: Fri, 31 Oct 2003 07:42:16 -0800
From: Daniel Rubin <rubin@SMI.Stanford.EDU>
To: protege-discussion@SMI.Stanford.EDU
Subject: [protege-discussion] Re: XSLT for XML-Instance Import into  protege



If you are comfortable writing out the .pins format (be careful though--if 
there are any syntactical mistakes, your project will generate errors when 
you open it), then this could work. The instance ID's you can create 
yourself, and can be any unique string--the only requirement is that they 
be unique to each instance, since they represent the frame handle for the 
instance. The instance ID is also the default slot that is displayed for 
the instance in Protege (but you can change this in the Forms tab--you may 
want to choose, for example, to display the PMID in Protege). One person in 
our lab imported the Gene Ontology into Protege using this approach.

Another possibility would be to use the XML plugin, though I personally 
haven't tried using it in this situation.

Daniel

At 03:20 PM 10/31/2003 +0100, you wrote:

>I would like to import Instances from a (Medline) XML-File into a
>Protege-class with slots equal some Medline XML-Elements.
>Is writing an XSLT for extracting the needed elements and converting
>them into a pins File the right way to insert Instances?
>If so, where do I know possible & correct "Instance-IDs" (like the
>[DCOMedlInstance_01278] below)?
>Or should I use the XML Import Plugin and "block" undesired Elements?
>Has anybody written such XSLT`s?
>
>XML-Example:
>
><?xml version="1.0"?>
><!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st
>November 2002//EN"
>"http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_021101.dtd";>
><PubmedArticleSet>
><PubmedArticle>
><MedlineCitation Owner="NLM" Status="In-Process">
><MedlineID>22590267</MedlineID>
><PMID>12704145</PMID>
><DateCreated>
><Year>2003</Year>
><Month>04</Month>
><Day>21</Day>
></DateCreated>
><Article>
><Journal>
><ISSN>0019-9567</ISSN>
><JournalIssue>
><Volume>71</Volume>
><Issue>5</Issue>
><PubDate>
><Year>2003</Year>
><Month>May</Month>
></PubDate>
></JournalIssue>
></Journal>
><ArticleTitle>Amastigote load and cell surface phenotype of infected
>cells from lesions and lymph nodes of susceptible and resistant mice
>infected with Leishmania major.</ArticleTitle>
><Pagination>
><MedlinePgn>2704-15</MedlinePgn>
></Pagination>
><Abstract>
><AbstractText>Cells of the dendritic cell (DC) lineage, by their unique
>ability to stimulate naive T cells, may be of crucial importance in the
>development of protective immune responses to Leishmania parasites. Our
>results suggest that infected CD11c(+) DC-like cells might constitute a
>reservoir of parasites in lymph nodes.</AbstractText>
></Abstract>
><Affiliation>Laboratory of Parasitology, Université Libre de Bruxelles,
>Erasme, Brussels, Belgium.</Affiliation>
><AuthorList CompleteYN="Y">
>
>
>
>pins-Example:
>
>; Fri Oct 31 13:17:58 CET 2003
>;
>;+ (version "1.9")
>;+ (build "Build 1120")
>
>([DCOMedlInstance_01278] of Medline_Reference
>         (article_title "Amastigote load and cell surface phenotype of 
> infected
>cells from lesions and lymph nodes of susceptible and resistant mice
>infected with Leishmania major.")
>         (medline_ID "22590267")
>         (abstract_text "Cells of the dendritic cell (DC) lineage, by their
>unique ability to stimulate naive T cells, may be of crucial importance
>in the development of protective immune responses to Leishmania
>parasites. Our results suggest that infected CD11c(+) DC-like cells
>might constitute a reservoir of parasites in lymph nodes.")
>         (descriptor_name "Animal")
>         (name_of_substance "antigens, CD")
>         (qualifier_name "analysis"))
>
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 ;););) blessed are the geeks -- for they shall inherit the source code :):):)