Incorporate jats2spar.xsl

Klortho commented 10 years ago

I imported it into the repo: https://github.com/Klortho/eutilsrdf/blob/master/jats2spar.xsl. It is from From Markup to Linked Data: Mapping NISO JATS v1.0 to RDF using the SPAR (Semantic Publishing and Referencing) Ontologies, by David Shotton, Silvio Peroni, and Debbie Lapeyre. I'd like to get it working with esummary and efetch from PMC, inasmuch as possible.

Klortho commented 10 years ago

Maybe also esummary and efetch from PubMed -- that might require a new XSLT, but the data output should jibe.

See also what PubChem is doing (Gang, feel free to elaborate). See, for example, http://pubchem.ncbi.nlm.nih.gov/rest/rdf/reference/PMID10395478.

flamingofugang commented 10 years ago

Hi Chris,

I suggest to work on esummary first. I have looked through JATS2RDF mappings and found they currently just mapped article and journal metadata into RDF: "The JATS Journal Publishing Tag Library Version 1.0 specification is large, containing 246 elements and 134 attributes. We chose to map the JATS metadata entities that describe an article (e.g. for metadata about the journal in which the article was published, such as the name of the journal), and to leave aside (possibly for a later mapping exercise using DoCO, the Document Components Ontology) those entities describing the textual and graphical structure and content of the article (e.g. , <body>, <fig>, <table>)."</p> <p>I am wondering whether the document components (e.g. abstract text ) and MeSH headlines in efetch can be well mapped...</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/Klortho"><img src="https://avatars.githubusercontent.com/u/77226?v=4" />Klortho</a> commented <strong> 10 years ago</strong> </div> <div class="markdown-body"> <p>Hi, Gang, I've been working on #12 for the last couple of days. I decided to try to port to a new platform first, because:</p> <ul> <li>jats2spar.xsl is written in XSLT 2.0, which the existing Perl CGI can't handle,</li> <li>I am not sure I should be serving this thing from my NCBI staff account, and</li> <li>MarkLogic Server is a much better fit for this kind of app, anyway.</li> </ul> <p>So far, I have just got the MLS instance up and running. When it comes time to porting the code itself, I will work in a separate git branch.</p> <p>I agree that we should start applying jats2spar to the esummary outputs first (both pubmed and pmc).</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/Klortho"><img src="https://avatars.githubusercontent.com/u/77226?v=4" />Klortho</a> commented <strong> 10 years ago</strong> </div> <div class="markdown-body"> <p>The initial work here has been done.</p> </div> </div> <div class="page-bar-simple"> </div> <div class="footer"> <ul class="body"> <li>© <script> document.write(new Date().getFullYear()) </script> Githubissues.</li> <li>Githubissues is a development platform for aggregating issues.</li> </ul> </div> <script src="https://cdn.jsdelivr.net/npm/jquery@3.5.1/dist/jquery.min.js"></script> <script src="/githubissues/assets/js.js"></script> <script src="/githubissues/assets/markdown.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/highlight.min.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/languages/go.min.js"></script> <script> hljs.highlightAll(); </script> </body> </html>

Klortho / eutils-org

Incorporate jats2spar.xsl #6