ljgarcia
commented
10 years ago This is the Biotea schema, which is based on Bio2RDF
- BASE_URL: dataset URL, it this case it would be http://rdf.ncbi.nlm.nih.gov/
- Anything between <> is replaced depending on the data coming from the XML
- Main article, the one being RDFized BASE_URL + "pmcdoc/pmc/" +
- Main article resources: authors, lists, etc.
- General pattern: BASE_URL + “
/pmcdoc_resource/” + + “/ /” + - Entity ids are usually derived from the original data in the XML, spaces and other not URL-friendly characters are replaced by “-”
- Person (author, editor, translators): BASE_URL + "person/pmcdoc_resource/" +
+ "/name/“ + - → we do not have ambiguity here as person URLs have the pmcID … BUT … we then need some sameAs mechanism to consolidate the person URLs that are actually the same … ORCID, VIVO? - Organization (some times authors are organizations rather than persons): BASE_URL + "organization/pmcdoc_resource/" +
+ "/name/“ + - Groups (if we have the group a person belongs to): BASE_URL + "group/pmcdoc_resource/" +
+ "/id/” + - - References without a PubMed or DOI: BASE_URL + "reference/pmcdoc_resource/" +
+ "/“ + - Lists for the main article: BASE_URL + “
- /pmcdoc_resource/" +
+ "/list “ - Lists for references: BASE_URL + “
/pmcdoc_resource/" + + "/ :list “ - Proceedings: BASE_URL + "proceedings/pmcdoc_resource/" +
+ "/title/“ + </li> <li>Conference: BASE_URL + "conference/pmcdoc_resource/" + <pmcID> + "/name/“ + <name></li> <li>Sections: BASE_URL + "section/pmcdoc_resource/" + <pmcID> + "/“ + <section_title></li> <li>Paragraph: BASE_URL + "paragraph/pmcdoc_resource/" + <pmcID> + "/<section_title>:para_<consecutive></li> <li>Appendix: BASE_URL + "appendix/pmcdoc_resource/" + <pmcID >+ "/“ + <appendix_title></li> <li>Annotations: BASE<em>URL + "annotation</em><annotator_id>/pmc_resource/“ + <pmcID >+ "/“ + <annotated_text_md5></li> </ul></li> <li>Other resources across articles: <ul> <li>PubMed document (come from references with a PubMed id): BASE_URL + "pubmeddoc/pubmed/ + <pmid></li> <li>DOI document (come from references with a PubMed id): BASE_URL + “doidoc/doi/ + <doi></li> <li>✓Journal with issn/isbn: BASE_URL + "journal/issn/ + <issn></li> <li>✓Journal with out any id: BASE_URL + "journal/name/“ + <name></li> <li>Journal issue: BASE_URL + "issue/journal<em>resource/<either “issn” or “name”>:<issn or name as in the journal>/issue</em>“ + <issue number></li> <li>Publisher with ID: BASE_URL + "publisher/pmc_internal_id/“ + <id></li> <li>Publisher with name: BASE_URL + "publisher/name/“ + <name></li> </ul></li> <li>Resources for references with PubMed or DOI: Follow the same idea as those for the main PMC RDFized article <ul> <li>Person: author, editor, translators): BASE_URL + "person/pubmeddoc_resource/" + <pmid> + "/name/“ + <lastName>-<firstName> (similar for DOI)</li> <li>Organization: BASE_URL + "organization/pubmeddoc_resource/" + <pmid> + "/name/“ + <organization_name> (similar for DOI)</li> <li>Lists</li> <li>Proceedings</li> <li>Conferences</li> </ul></li> </ul> </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>I'm starting trying to work on this, in the git branch <code>issue-16-blank-node-uris</code>, and documenting on <a href="https://github.com/Klortho/eutils-org/wiki/JATS2RDF">the wiki</a>. I will try to follow this scheme, and let you know if I have questions.</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>Leyla, I fixed up your comment so that it is in Markdown format. All angle-bracket tags, like "<pmcid>", have to be preceded with a backslash, otherwise they don't show up.</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/ljgarcia"><img src="https://avatars.githubusercontent.com/u/5427252?v=4" />ljgarcia</a> commented <strong> 10 years ago</strong> </div> <div class="markdown-body"> <p>Thanks!</p> <p>On Sun, Feb 16, 2014 at 8:05 PM, Chris Maloney notifications@github.comwrote:</p> <blockquote> <p>Leyla, I fixed up your comment so that it is in Markdown format. All angle-bracket tags, like "<pmcid>", have to be preceded with a backslash, otherwise they don't show up.</p> <h2></h2> <p>Reply to this email directly or view it on GitHubhttps://github.com/Klortho/eutils-org/issues/16#issuecomment-35208984 .</p> </blockquote> </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>I got some work started on this, including the journal URI. Documenting the final patterns I come up with on the wiki, <a href="https://github.com/Klortho/eutils-org/wiki/JATS2RDF#wiki-uri-patterns">here</a>. It's a bit tedious!</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>As mentioned by Leyla: "For authors: whenever possible we will use ORCID for the URI. If not available we will combine last name-first name to create a URI. We will follow in this case the URI proposed by Chris "<a href="http://rdf.ncbi.nlm.nih.gov/pmc/PMC123456/contrib/john-doe">http://rdf.ncbi.nlm.nih.gov/pmc/PMC123456/contrib/john-doe</a>"'</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>
- General pattern: BASE_URL + “
Use this scheme from bio2rdf